[1] "ofn"        "-oTHNSC-TP"
[1] "opt"       "-OPMUTSIG"
[1] "tl" ""  
[1] "dx" ""  
[1] "opt"    "MUTSIG"
[1] "dx" ""  
[1] "cfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/HNSC-TP/22506490/HNSC-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/HNSC-TP/22508725/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 
               74               448 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               74               448 
[1] "1Q GAIN MUTATION ANALYSIS"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              124               398 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              124               398 
[1] "2P GAIN MUTATION ANALYSIS"
[1] 3
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               96               426 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               96               426 
[1] "2Q GAIN MUTATION ANALYSIS"
[1] 3
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               73               449 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               73               449 
[1] "3P GAIN MUTATION ANALYSIS"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               82               440 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               82               440 
[1] "3Q GAIN MUTATION ANALYSIS"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
              257               265 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
              257               265 
[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 
               75               447 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               75               447 
[1] "6P GAIN MUTATION ANALYSIS"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               85               437 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               85               437 
[1] "6Q GAIN MUTATION ANALYSIS"
[1] 3
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               64               458 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               64               458 
[1] "7P GAIN MUTATION ANALYSIS"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              184               338 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              184               338 
[1] "7Q GAIN MUTATION ANALYSIS"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              128               394 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              128               394 
[1] "8P GAIN MUTATION ANALYSIS"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
              158               364 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
              158               364 
[1] "8Q GAIN MUTATION ANALYSIS"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              318               204 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              318               204 
[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 
              145               377 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
              145               377 
[1] "10P GAIN MUTATION ANALYSIS"
[1] 3
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                42                480 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                42                480 
[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 
                68                454 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                68                454 
[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 
                92                430 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                92                430 
[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 
               153                369 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
               153                369 
[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 
               109                413 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
               109                413 
[1] "16Q GAIN MUTATION ANALYSIS"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
               105                417 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
               105                417 
[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 
                86                436 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                86                436 
[1] "18P GAIN MUTATION ANALYSIS"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
               124                398 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
               124                398 
[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 
                77                445 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                77                445 
[1] "20P GAIN MUTATION ANALYSIS"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               192                330 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               192                330 
[1] "20Q GAIN MUTATION ANALYSIS"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               204                318 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               204                318 
[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 
               51               471 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               51               471 
[1] "XQ GAIN MUTATION ANALYSIS"
[1] 3
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               96               426 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               96               426 
[1] "1P LOSS MUTATION ANALYSIS"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               56               466 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               56               466 
[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 
               32               490 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               32               490 
[1] "2Q LOSS MUTATION ANALYSIS"
[1] 3
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               44               478 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               44               478 
[1] "3P LOSS MUTATION ANALYSIS"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
              296               226 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
              296               226 
[1] "3Q LOSS MUTATION ANALYSIS"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               58               464 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               58               464 
[1] "4P LOSS MUTATION ANALYSIS"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
              193               329 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
              193               329 
[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 
              160               362 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
              160               362 
[1] "6P LOSS MUTATION ANALYSIS"
[1] 3
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               67               455 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               67               455 
[1] "6Q LOSS MUTATION ANALYSIS"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               70               452 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               70               452 
[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 
               41               481 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               41               481 
[1] "8P LOSS MUTATION ANALYSIS"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
              185               337 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
              185               337 
[1] "8Q LOSS MUTATION ANALYSIS"
[1] 3
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               25               497 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               25               497 
[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 
               83               439 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               83               439 
[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 
               114                408 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
               114                408 
[1] "11P LOSS MUTATION ANALYSIS"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
               137                385 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
               137                385 
[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 
                36                486 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                36                486 
[1] "12Q LOSS MUTATION ANALYSIS"
[1] 3
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                31                491 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                31                491 
[1] "13Q LOSS MUTATION ANALYSIS"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
               168                354 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
               168                354 
[1] "14Q LOSS MUTATION ANALYSIS"
[1] 3
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                56                466 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                56                466 
[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 
                62                460 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                62                460 
[1] "16Q LOSS MUTATION ANALYSIS"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                82                440 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                82                440 
[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 
                32                490 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                32                490 
[1] "18P LOSS MUTATION ANALYSIS"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
               103                419 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
               103                419 
[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 
               100                422 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
               100                422 
[1] "19Q LOSS MUTATION ANALYSIS"
[1] 3
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                88                434 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                88                434 
[1] "20P LOSS MUTATION ANALYSIS"
[1] 3
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                46                476 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                46                476 
[1] "20Q LOSS MUTATION ANALYSIS"
[1] 3
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                27                495 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                27                495 
[1] "21Q LOSS MUTATION ANALYSIS"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
               185                337 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
               185                337 
[1] "22Q LOSS MUTATION ANALYSIS"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                74                448 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                74                448 
[1] "XP LOSS MUTATION ANALYSIS"
[1] 3
  XP LOSS MUTATED XP LOSS WILD-TYPE 
              136               386 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
              136               386 
[1] "XQ LOSS MUTATION ANALYSIS"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               82               440 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               82               440 
[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=202,	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=286,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'TUMOR_TISSUE_SITE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "TUMOR_TISSUE_SITE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'PATHOLOGIC_STAGE':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY_T_STAGE':	nDistinctValues=8,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY_N_STAGE':	nDistinctValues=8,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY_M_STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=22,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 12:'DAYS_TO_LAST_KNOWN_ALIVE':	nDistinctValues=21,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 13:'RADIATION_THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'HISTOLOGICAL_TYPE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'NUMBER_PACK_YEARS_SMOKED':	nDistinctValues=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    33  41
  1P GAIN WILD-TYPE 268 178
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               74               446 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               41               178 
$`1P GAIN MUTATED`
TCGA-BB-A5HU TCGA-CN-4727 TCGA-CQ-7067 TCGA-CR-6472 TCGA-CR-6478 TCGA-CX-7082 
       25.71        51.29        16.73        34.52         6.02         0.36 
TCGA-DQ-5629 TCGA-DQ-7588 TCGA-BA-5149 TCGA-BA-5555 TCGA-BA-6870 TCGA-BA-6872 
       30.94        14.04        26.50        17.10        14.83        12.62 
TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A6DI TCGA-BB-8596 TCGA-BB-8601 TCGA-BB-A5HY 
        4.01        41.85        11.05        71.05        20.52        10.55 
TCGA-BB-A5HZ TCGA-C9-A47Z TCGA-CN-4739 TCGA-CN-4742 TCGA-CN-5359 TCGA-CN-6020 
       27.19         6.28        45.83        13.05        12.39         6.74 
TCGA-CN-6989 TCGA-CN-A49A TCGA-CN-A6V6 TCGA-CR-6482 TCGA-CR-7379 TCGA-CR-7388 
       32.22        17.29        20.88        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-7101 TCGA-CV-7102 TCGA-CV-7235 
       20.52       111.16        18.81         5.26         1.84        77.16 
TCGA-CV-7255 TCGA-CV-7263 TCGA-CV-7407 TCGA-CV-7415 TCGA-CV-7421 TCGA-CV-7422 
        2.10        18.41        35.54        22.85         0.07        34.09 
TCGA-CV-A45R TCGA-CV-A45X TCGA-CV-A461 TCGA-CV-A6JE TCGA-CV-A6JO TCGA-D6-A74Q 
      180.16         6.51        67.86        35.34         6.48        23.34 
TCGA-DQ-5625 TCGA-DQ-7596 TCGA-F7-8298 TCGA-H7-7774 TCGA-H7-A76A TCGA-IQ-A61K 
       37.25        41.59        32.71        13.38        20.94         5.29 
TCGA-IQ-A61O TCGA-IQ-A6SH TCGA-P3-A5Q5 TCGA-P3-A5Q6 TCGA-P3-A6SW TCGA-P3-A6SX 
       13.84        15.48        29.92        15.78        36.82        47.01 
TCGA-P3-A6T3 TCGA-QK-A8Z7 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-T2-A6WZ TCGA-UF-A719 
       18.97        12.89        14.76        12.20        15.91        54.67 
TCGA-UF-A7JH TCGA-KU-A66T 
       29.46        18.15 

$`1P GAIN WILD-TYPE`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4IG 
        9.30        37.28        20.48        68.48         3.55        28.11 
TCGA-BA-A4II TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6992 
       30.18         9.07         9.24        52.08        11.08        35.05 
TCGA-CN-6997 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-6221 TCGA-CQ-7063 
       32.48        19.82        24.39        48.20        32.88        70.13 
TCGA-CQ-7068 TCGA-CQ-A4C7 TCGA-CX-7219 TCGA-DQ-7589 TCGA-DQ-7593 TCGA-H7-A6C5 
       43.04        11.61        34.36        46.32        40.24        21.11 
TCGA-HD-8634 TCGA-HD-8635 TCGA-UF-A71D TCGA-UF-A7JV TCGA-4P-AA8J TCGA-BA-4074 
       12.66        22.85        48.03         2.96         3.35        15.19 
TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5556 
       13.64         9.07        23.74        42.35        57.93        23.84 
TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-A4IF TCGA-BA-A4IH TCGA-BA-A6D8 
       65.59        15.52        21.17        29.42        20.45        27.95 
TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG 
       11.54         7.10         5.69        14.47         7.82         2.27 
TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 
       13.38        20.48        16.41         6.15       105.90         9.14 
TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 
        4.80         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-A6UM 
       50.20        44.98        66.28        24.66        38.40        12.92 
TCGA-BB-A6UO TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 
        8.81        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-4735 
       56.68        12.89        26.86        32.81        52.14        57.11 
TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-5355 
       12.99        20.55        14.33        27.58        73.61        42.02 
TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 
       46.32         8.58        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-6988 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 
       19.07        34.13        10.45        38.89         3.68        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-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-A6V7 TCGA-CQ-5324 TCGA-CQ-5325 
       12.07         2.70        23.44        19.53        52.37        21.50 
TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 
        2.93        54.58        70.45        62.37        45.99        10.42 
TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6220 TCGA-CQ-6223 TCGA-CQ-6224 
       11.21         4.24        41.19        32.38        46.95        56.58 
TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7065 
       13.25         4.24        14.99        38.76        64.87        53.52 
TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CB 
       41.88        43.10        77.56        44.48        23.24        29.36 
TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 
       33.60        29.49        14.14        12.46        31.23        84.23 
TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 
       11.77        54.67        37.87        26.27        58.42        50.01 
TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6480 TCGA-CR-6481 
       39.52        36.99        18.54        16.90        11.90        10.22 
TCGA-CR-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-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 
       49.58        30.02        46.85        32.65        44.25        30.58 
TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 
       24.79         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-5439 
      139.43       129.21       108.95        76.24        19.20        17.95 
TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5443 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 
      107.51        94.88        91.53        17.92        13.35        23.05 
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-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6938 TCGA-CV-6939 
        9.60         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-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-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7103 TCGA-CV-7104 
      172.67        12.66         7.99         9.01        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        89.65 
TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7248 TCGA-CV-7250 
       36.00        31.36        26.20        18.97        17.13        95.34 
TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7409 
        4.96        11.87        47.97        49.71        57.47        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-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-A45T 
        6.38        22.19        27.98        21.01       169.38       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-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-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 
       29.79        28.01         3.62        21.24        23.47        19.92 
TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-A4AQ TCGA-D6-6515 
       22.52        10.42        10.55        18.84        51.12        13.25 
TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 
       25.41         9.60        23.05         2.53        16.14        11.44 
TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK 
       18.67        24.95        25.32        17.72        12.36        28.77 
TCGA-D6-A6EM TCGA-D6-A6EN TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES 
        7.63        22.59        24.95        13.94        12.10        12.79 
TCGA-DQ-5624 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 
       58.45        33.86        18.02        46.45        20.45        37.58 
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-HD-7229 TCGA-HD-7753 
       20.25        12.43        15.16        15.06        33.76        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-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-A61L TCGA-IQ-A6SG TCGA-KU-A6H7 TCGA-KU-A6H8 
        0.07        33.57        13.68        19.04        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-A5QA TCGA-P3-A5QE 
       15.42         7.13        16.08        17.98        71.74        51.25 
TCGA-P3-A5QF TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T6 
       10.85        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-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC 
       21.47         9.34        12.72        27.39        21.07        19.73 
TCGA-QK-A8Z8 TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-RS-A6TO TCGA-RS-A6TP 
        5.62        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-A71E 
       13.25        20.35        64.80         2.83        49.51        49.45 
TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JJ 
       44.65        74.47        17.95        24.30        55.43        18.05 
TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UP-A6WW TCGA-WA-A7GZ 
       13.94        20.75        22.36        32.65        17.03        20.55 
TCGA-WA-A7H4 TCGA-KU-A66S 
       14.56        13.35 

  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             21.21 
[1] "0.1 - 180.2 (20.5)" "0.1 - 211.0 (21.2)"
[1] "hr=" "1.4"
D1V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  1P GAIN MUTATED         3        7         9        37         2         0
  1P GAIN WILD-TYPE      24       69        73       215        10         1
D1V3, multiclass
           clus
vv          1P GAIN MUTATED 1P GAIN WILD-TYPE
  STAGE I                 3                24
  STAGE II                7                69
  STAGE III               9                73
  STAGE IVA              37               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
  1P GAIN MUTATED       3  19  15  23
  1P GAIN WILD-TYPE    47 118  85 150
D1V4, multiclass
       clus
vv      1P GAIN MUTATED 1P GAIN WILD-TYPE
  T0+T1               3                47
  T2                 19               118
  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
  1P GAIN MUTATED    15  12  28   1
  1P GAIN WILD-TYPE 164  56 140   7
D1V5, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  N0              15               164
  N1              12                56
  N2              28               140
  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    20   0
  1P GAIN WILD-TYPE 170   1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     20    0
  1P GAIN WILD-TYPE  170    1
   clus
vv  1P GAIN MUTATED 1P GAIN WILD-TYPE
  0              20               170
  1               0                 1
[1] 2 2
[1] FALSE
D1V7, binary
                   cls
clus                  0   1
  1P GAIN MUTATED    19  55
  1P GAIN WILD-TYPE 121 327
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     19   55
  1P GAIN WILD-TYPE  121  327
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  FEMALE              19               121
  MALE                55               327
[1] 2 2
[1] FALSE
D1V8, binary
                   cls
clus                  0   1
  1P GAIN MUTATED    17  50
  1P GAIN WILD-TYPE 145 251
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     17   50
  1P GAIN WILD-TYPE  145  251
     clus
vv    1P GAIN MUTATED 1P GAIN WILD-TYPE
  NO               17               145
  YES              50               251
[1] 2 2
[1] FALSE
                   vv
clus                HEAD & NECK SQUAMOUS CELL CARCINOMA
  1P GAIN MUTATED                                    70
  1P GAIN WILD-TYPE                                 441
                   vv
clus                HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  1P GAIN MUTATED                                                   3
  1P GAIN WILD-TYPE                                                 7
                   vv
clus                HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  1P GAIN MUTATED                                                           1
  1P GAIN WILD-TYPE                                                         0
D1V9, multiclass
                                                           clus
vv                                                          1P GAIN MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                    70
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       3
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT               1
                                                           clus
vv                                                          1P GAIN WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                     441
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                         7
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                 0
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V10, continuous
D1V11, continuous
D1V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  1P GAIN MUTATED                                  0     1
  1P GAIN WILD-TYPE                                2    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  1P GAIN MUTATED                          13    58
  1P GAIN WILD-TYPE                        35   388
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                                         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"
D1V14, binary
                   cls
clus                  0   1
  1P GAIN MUTATED     5  66
  1P GAIN WILD-TYPE  21 393
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      5   66
  1P GAIN WILD-TYPE   21  393
                        clus
vv                       1P GAIN MUTATED 1P GAIN WILD-TYPE
  HISPANIC OR LATINO                   5                21
  NOT HISPANIC OR LATINO              66               393
[1] 2 2
[1] FALSE

Clustering(2) Variable = 1Q GAIN MUTATION ANALYSIS
D2V1, survival
                   sevent
clus2                 0   1
  1Q GAIN MUTATED    63  61
  1Q GAIN WILD-TYPE 238 158
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              124               396 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               61               158 
$`1Q GAIN MUTATED`
TCGA-BA-6871 TCGA-BB-A5HU TCGA-CN-4727 TCGA-CN-6023 TCGA-CN-6997 TCGA-CQ-7067 
        3.55        25.71        51.29        52.08        32.48        16.73 
TCGA-CR-6472 TCGA-CR-6478 TCGA-CX-7082 TCGA-DQ-5629 TCGA-DQ-7589 TCGA-UF-A71D 
       34.52         6.02         0.36        30.94        46.32        48.03 
TCGA-BA-5555 TCGA-BA-6870 TCGA-BA-6872 TCGA-BA-7269 TCGA-BA-A6DI TCGA-BB-4224 
       17.10        14.83        12.62        41.85        11.05         9.14 
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-CN-4728 TCGA-CN-4739 TCGA-CN-5359 TCGA-CN-5367 TCGA-CN-5374 TCGA-CN-6010 
       56.68        45.83        12.39        11.57        56.94        50.07 
TCGA-CN-6013 TCGA-CN-6020 TCGA-CN-A498 TCGA-CN-A49A TCGA-CN-A63U TCGA-CN-A6V6 
       23.90         6.74        25.41        17.29        31.69        20.88 
TCGA-CQ-7064 TCGA-CQ-A4C9 TCGA-CQ-A4CD TCGA-CQ-A4CI TCGA-CR-6482 TCGA-CR-7370 
       64.87        23.24        33.60        31.23        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        49.58       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-7263 TCGA-CV-7407 TCGA-CV-7409 TCGA-CV-7421 TCGA-CV-7422 
        2.10        18.41        35.54        17.85         0.07        34.09 
TCGA-CV-7423 TCGA-CV-7437 TCGA-CV-7440 TCGA-CV-A45R TCGA-CV-A45W TCGA-CV-A45X 
      100.57        16.64        22.19       180.16        45.96         6.51 
TCGA-CV-A461 TCGA-CV-A6JE TCGA-CV-A6JM TCGA-CV-A6JO TCGA-CX-7086 TCGA-D6-6827 
       67.86        35.34         6.38         6.48        18.84        18.67 
TCGA-D6-A6EP TCGA-D6-A74Q TCGA-DQ-5625 TCGA-DQ-7596 TCGA-F7-8298 TCGA-F7-A622 
       13.94        23.34        37.25        41.59        32.71        11.80 
TCGA-H7-7774 TCGA-H7-A76A TCGA-HD-7754 TCGA-HD-7917 TCGA-HL-7533 TCGA-IQ-A61H 
       13.38        20.94        25.74        27.48        34.75        37.41 
TCGA-IQ-A61I TCGA-IQ-A61O TCGA-IQ-A6SH TCGA-MT-A7BN TCGA-P3-A5Q5 TCGA-P3-A5Q6 
        0.07        13.84        15.48        15.42        29.92        15.78 
TCGA-P3-A6SW TCGA-P3-A6T5 TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z9 
       36.82        29.00        21.07        19.73        12.89        14.76 
TCGA-QK-A8ZA TCGA-QK-AA3J TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-TN-A7HJ TCGA-UF-A719 
       12.20        15.32        15.91         7.10        13.25        54.67 
TCGA-UF-A71E TCGA-UF-A7JD TCGA-UF-A7JH TCGA-KU-A66T 
       49.45        24.30        29.46        18.15 

$`1Q GAIN WILD-TYPE`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-A4IG TCGA-BA-A4II 
        9.30        37.28        20.48        68.48        28.11        30.18 
TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6024 TCGA-CN-6992 TCGA-CN-A6V1 TCGA-CN-A6V3 
        9.07         9.24        11.08        35.05        19.82        24.39 
TCGA-CQ-5323 TCGA-CQ-6221 TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CQ-A4C7 TCGA-CX-7219 
       48.20        32.88        70.13        43.04        11.61        34.36 
TCGA-DQ-7588 TCGA-DQ-7593 TCGA-H7-A6C5 TCGA-HD-8634 TCGA-HD-8635 TCGA-UF-A7JV 
       14.04        40.24        21.11        12.66        22.85         2.96 
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 
        3.35        15.19        13.64         9.07        26.50        23.74 
TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6869 
       42.35        57.93        23.84        65.59        15.52        21.17 
TCGA-BA-6873 TCGA-BA-A4IF TCGA-BA-A4IH TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB 
        4.01        29.42        20.45        27.95        11.54         7.10 
TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-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         4.80        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-6988 TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6998 
       10.45        32.22        38.89         3.68        17.42        11.74 
TCGA-CN-A497 TCGA-CN-A499 TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63V 
       35.01        23.57        29.72        21.21         7.40        22.32 
TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY 
       12.39        16.57         4.41        12.07         2.70        23.44 
TCGA-CN-A6V7 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 
       19.53        52.37        21.50         2.93        54.58        70.45 
TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 
       62.37        45.99        10.42        11.21         4.24        41.19 
TCGA-CQ-6220 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 
       32.38        46.95        56.58        13.25         4.24        14.99 
TCGA-CQ-6229 TCGA-CQ-7065 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 
       38.76        53.52        41.88        43.10        77.56        44.48 
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-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6484 
       36.99        18.54        16.90        11.90        10.22        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-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-7380 TCGA-CR-7382 
       29.23         0.99        31.96         9.17        19.92        26.17 
TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 
       17.13        32.78        47.01        30.02        46.85        32.65 
TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 
       44.25        30.58        24.79         5.13         5.95        35.41 
TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5432 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 
       29.95        48.39       129.21        76.24        19.20        17.95 
TCGA-CV-5441 TCGA-CV-5443 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 
       94.88        91.53        17.92        13.35        23.05        86.83 
TCGA-CV-5976 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6934 
       48.59        54.74        21.07        62.43         9.60         2.14 
TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6948 
        4.73        21.90       140.78        19.79        12.03        42.38 
TCGA-CV-6950 TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-6955 TCGA-CV-6956 
       15.09         6.08        53.95        65.82        10.98         7.13 
TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7097 
        8.42        28.34         2.50        64.83       172.67        12.66 
TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-7180 
        7.99         9.01        52.31        12.92        21.80        10.75 
TCGA-CV-7183 TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7245 TCGA-CV-7247 
      130.88         4.73        89.65        36.00        26.20        18.97 
TCGA-CV-7248 TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7410 
       17.13         4.96        11.87        49.71        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-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ 
        5.98        29.79        28.01         3.62        21.24        23.47 
TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-A4AQ TCGA-D6-6515 
       19.92        22.52        10.42        10.55        51.12        13.25 
TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 
       25.41         9.60        23.05         2.53        16.14        11.44 
TCGA-D6-8568 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-DQ-5624 TCGA-DQ-5630 
       22.59        24.95        12.10        12.79        58.45        33.86 
TCGA-DQ-5631 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7594 TCGA-DQ-7595 
       18.02        46.45        20.45        37.58        40.04        39.12 
TCGA-F7-7848 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S 
       37.18        21.63        20.25         3.02        31.13        18.94 
TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A623 TCGA-F7-A624 TCGA-H7-8501 
       24.95         0.46        17.85        20.25        12.43        15.16 
TCGA-H7-8502 TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-8224 
       15.06        33.76        28.47        21.93        27.48        14.66 
TCGA-HD-8314 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 
       22.03         0.36        13.84         4.27         3.65         6.90 
TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61J 
       15.95        38.53        14.50        37.71        11.84        33.57 
TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A6SG TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W 
        5.29        13.68        19.04        19.27        10.75        14.37 
TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A5BI 
        7.96        30.05         1.84        12.62         6.25         7.13 
TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SX 
       16.08        17.98        71.74        51.25        10.85        47.01 
TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T6 TCGA-P3-A6T7 
       19.00        75.55        18.97         2.04        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-A8Z8 TCGA-QK-A8ZB TCGA-QK-AA3K 
        9.34        12.72        27.39         5.62        17.82         8.32 
TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6X2 TCGA-T3-A92M TCGA-T3-A92N 
       12.72        16.96         6.87        32.45        13.71         3.12 
TCGA-TN-A7HI TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A7J9 
       13.55        20.35        64.80         2.83        49.51        44.65 
TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JF TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO 
       74.47        17.95        55.43        18.05        13.94        20.75 
TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 TCGA-KU-A66S 
       22.36        32.65        17.03        20.55        14.56        13.35 

  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
             0.07              0.36 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
           180.16            210.97 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
            23.62             20.88 
[1] "0.1 - 180.2 (23.6)" "0.4 - 211.0 (20.9)"
[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        16        63         4         0
  1Q GAIN WILD-TYPE      22       62        66       189         8         1
D2V3, multiclass
           clus
vv          1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  STAGE I                 5                22
  STAGE II               14                62
  STAGE III              16                66
  STAGE IVA              63               189
  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  21  44
  1Q GAIN WILD-TYPE    44 105  79 129
D2V4, multiclass
       clus
vv      1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  T0+T1               6                44
  T2                 32               105
  T3                 21                79
  T4                 44               129
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  1Q GAIN MUTATED    31  15  44   3
  1Q GAIN WILD-TYPE 148  53 124   5
D2V5, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  N0              31               148
  N1              15                53
  N2              44               124
  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    35   0
  1Q GAIN WILD-TYPE 155   1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     35    0
  1Q GAIN WILD-TYPE  155    1
   clus
vv  1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  0              35               155
  1               0                 1
[1] 2 2
[1] FALSE
D2V7, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED    28  96
  1Q GAIN WILD-TYPE 112 286
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     28   96
  1Q GAIN WILD-TYPE  112  286
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  FEMALE              28               112
  MALE                96               286
[1] 2 2
[1] FALSE
D2V8, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED    28  81
  1Q GAIN WILD-TYPE 134 220
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     28   81
  1Q GAIN WILD-TYPE  134  220
     clus
vv    1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  NO               28               134
  YES              81               220
[1] 2 2
[1] FALSE
                   vv
clus                HEAD & NECK SQUAMOUS CELL CARCINOMA
  1Q GAIN MUTATED                                   117
  1Q GAIN WILD-TYPE                                 394
                   vv
clus                HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  1Q GAIN MUTATED                                                   6
  1Q GAIN WILD-TYPE                                                 4
                   vv
clus                HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  1Q GAIN MUTATED                                                           1
  1Q GAIN WILD-TYPE                                                         0
D2V9, multiclass
                                                           clus
vv                                                          1Q GAIN MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                   117
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       6
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT               1
                                                           clus
vv                                                          1Q GAIN WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                     394
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                         4
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                 0
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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    98
  1Q GAIN WILD-TYPE                        27   348
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                                         98               348
[1] 4 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     7 107
  1Q GAIN WILD-TYPE  19 352
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      7  107
  1Q GAIN WILD-TYPE   19  352
                        clus
vv                       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   7                19
  NOT HISPANIC OR LATINO             107               352
[1] 2 2
[1] FALSE

Clustering(3) Variable = 2P GAIN MUTATION ANALYSIS
D3V1, survival
                   sevent
clus2                 0   1
  2P GAIN MUTATED    55  41
  2P GAIN WILD-TYPE 246 178
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               96               424 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               41               178 
$`2P GAIN MUTATED`
TCGA-BA-4075 TCGA-CN-4727 TCGA-CN-6023 TCGA-CN-6024 TCGA-CX-7219 TCGA-DQ-5629 
        9.30        51.29        52.08        11.08        34.36        30.94 
TCGA-DQ-7589 TCGA-BA-5555 TCGA-BA-A4IF TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-7864 
       46.32        17.10        29.42        20.48        16.41        50.20 
TCGA-BB-8596 TCGA-CN-4742 TCGA-CN-5356 TCGA-CN-5359 TCGA-CN-5374 TCGA-CN-6010 
       71.05        13.05        46.32        12.39        56.94        50.07 
TCGA-CN-6012 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-A63T 
       48.00        10.45        32.22        38.89         3.68         7.40 
TCGA-CQ-5329 TCGA-CQ-6225 TCGA-CQ-7072 TCGA-CR-5247 TCGA-CR-6477 TCGA-CR-7365 
       70.45        13.25        77.56        11.77        16.90        39.16 
TCGA-CR-7372 TCGA-CR-7380 TCGA-CR-7383 TCGA-CR-7398 TCGA-CR-7399 TCGA-CV-5430 
       24.95        19.92        17.13         5.13         5.95       139.43 
TCGA-CV-5440 TCGA-CV-6933 TCGA-CV-6937 TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6941 
      107.51        90.12        20.52        21.90        26.43        11.24 
TCGA-CV-6950 TCGA-CV-6962 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7103 TCGA-CV-7178 
       15.09         4.14       172.67       111.16        52.31        71.21 
TCGA-CV-7235 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7250 
       77.16        36.00        31.36        26.20        18.97        95.34 
TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7263 TCGA-CV-7409 TCGA-CV-7415 TCGA-CV-7421 
       47.97        49.71        18.41        17.85        22.85         0.07 
TCGA-CV-7422 TCGA-CV-7423 TCGA-CV-7429 TCGA-CV-7435 TCGA-CV-7437 TCGA-CV-A45U 
       34.09       100.57         3.52       153.86        16.64        35.47 
TCGA-CV-A45X TCGA-CV-A45Z TCGA-CX-7086 TCGA-D6-6516 TCGA-D6-6823 TCGA-D6-8569 
        6.51        48.20        18.84        25.41        23.05        25.32 
TCGA-D6-A4ZB TCGA-D6-A6EP TCGA-DQ-7592 TCGA-F7-A620 TCGA-F7-A623 TCGA-HD-A633 
       12.36        13.94        37.58        17.85        20.25        13.84 
TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-IQ-A61E TCGA-IQ-A61H TCGA-IQ-A6SH TCGA-MZ-A7D7 
        3.65         6.90        37.71        37.41        15.48        17.98 
TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8ZA TCGA-QK-AA3J TCGA-RS-A6TO 
       21.07        19.73        12.89        12.20        15.32        12.72 
TCGA-T2-A6WZ TCGA-UF-A71A TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JF TCGA-UF-A7JK 
       15.91         2.83        49.45        44.65        55.43        13.94 

$`2P GAIN WILD-TYPE`
TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4IG TCGA-BA-A4II 
       37.28        20.48        68.48         3.55        28.11        30.18 
TCGA-BB-A5HU TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-A6V1 
       25.71         9.07         9.24        35.05        32.48        19.82 
TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-6221 TCGA-CQ-7063 TCGA-CQ-7067 TCGA-CQ-7068 
       24.39        48.20        32.88        70.13        16.73        43.04 
TCGA-CQ-A4C7 TCGA-CR-6472 TCGA-CR-6478 TCGA-CX-7082 TCGA-DQ-7588 TCGA-DQ-7593 
       11.61        34.52         6.02         0.36        14.04        40.24 
TCGA-H7-A6C5 TCGA-HD-8634 TCGA-HD-8635 TCGA-UF-A71D TCGA-UF-A7JV TCGA-4P-AA8J 
       21.11        12.66        22.85        48.03         2.96         3.35 
TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 
       15.19        13.64         9.07        26.50        23.74        42.35 
TCGA-BA-5153 TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 
       57.93        23.84        65.59        15.52        21.17        14.83 
TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IH TCGA-BA-A6D8 TCGA-BA-A6DA 
       12.62         4.01        41.85        20.45        27.95        11.54 
TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-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-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 
       13.38         6.15       105.90         9.14         4.80         4.41 
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-8601 TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-BB-A6UM 
       24.66        38.40        20.52        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-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-4740 
       57.11        12.99        20.55        14.33        45.83        27.58 
TCGA-CN-4741 TCGA-CN-5355 TCGA-CN-5358 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5364 
       73.61        42.02         8.58        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-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-6020 TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 
        6.74        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-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V6 
       16.57         4.41        12.07         2.70        23.44        20.88 
TCGA-CN-A6V7 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5330 
       19.53        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-6220 
       45.99        10.42        11.21         4.24        41.19        32.38 
TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7064 
       46.95        56.58         4.24        14.99        38.76        64.87 
TCGA-CQ-7065 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CB 
       53.52        41.88        43.10        44.48        23.24        29.36 
TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 
       33.60        29.49        14.14        12.46        31.23        84.23 
TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 
       54.67        37.87        26.27        58.42        50.01        39.52 
TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 
       36.99        18.54        11.90        10.22        11.34        11.64 
TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 
        7.69        12.46        22.78        15.75         9.27        47.18 
TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7373 
       47.34        40.93        35.84         3.45         3.09        29.23 
TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7382 TCGA-CR-7385 
        0.99        31.96         9.17        34.06        26.17        32.78 
TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 
       47.01        27.06        12.89        49.58        30.02        46.85 
TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7401 TCGA-CR-7402 
       32.65        44.25        30.58        24.79        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-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 
       17.95        94.88        76.50        91.53        80.12        17.92 
TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 
       13.35        23.05        86.83        48.59        60.49         7.07 
TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6934 
       43.23        54.74        21.07        62.43         9.60         2.14 
TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6938 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 
        9.70         5.46         4.73       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-7089 TCGA-CV-7095 
        7.13         8.42        28.34         2.50        64.83        18.81 
TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7104 
       12.66         7.99         9.01         5.26         1.84        12.92 
TCGA-CV-7177 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7248 
       21.80        10.75       130.88         4.73        89.65        17.13 
TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7255 TCGA-CV-7406 TCGA-CV-7407 TCGA-CV-7410 
        4.96        11.87         2.10        57.47        35.54       210.97 
TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7414 TCGA-CV-7416 TCGA-CV-7418 TCGA-CV-7424 
       89.33         9.67         0.46        25.08        25.94        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-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-A45V TCGA-CV-A45W TCGA-CV-A45Y TCGA-CV-A460 
      180.16       159.65         1.05        45.96        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-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-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-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-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 
       24.95        12.10        12.79        23.34        58.45        37.25 
TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7594 TCGA-DQ-7595 
       33.86        18.02        46.45        20.45        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-A76A TCGA-HD-7229 TCGA-HD-7753 
       13.38        15.16        15.06        20.94        33.76        28.47 
TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 
       25.74        21.93        27.48        27.48        14.66        22.03 
TCGA-HD-A4C1 TCGA-HD-A634 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 
        0.36         4.27        34.75        15.95        38.53        14.50 
TCGA-IQ-A61G TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O 
       11.84         0.07        33.57         5.29        13.68        13.84 
TCGA-IQ-A6SG TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A 
       19.04        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        27.39         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-A7JA TCGA-UF-A7JC TCGA-UF-A7JD 
       64.80        54.67        49.51        74.47        17.95        24.30 
TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UP-A6WW 
       29.46        18.05        20.75        22.36        32.65        17.03 
TCGA-WA-A7GZ TCGA-WA-A7H4 TCGA-KU-A66S TCGA-KU-A66T 
       20.55        14.56        13.35        18.15 

  2P GAIN MUTATED 2P GAIN WILD-TYPE 
             0.07              0.07 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
           172.67            210.97 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
           22.375            21.070 
[1] "0.1 - 172.7 (22.4)" "0.1 - 211.0 (21.1)"
[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        15        49         3         0
  2P GAIN WILD-TYPE      22       61        67       203         9         1
D3V3, multiclass
           clus
vv          2P GAIN MUTATED 2P GAIN WILD-TYPE
  STAGE I                 5                22
  STAGE II               15                61
  STAGE III              15                67
  STAGE IVA              49               203
  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  21  38
  2P GAIN WILD-TYPE    42 114  79 135
D3V4, multiclass
       clus
vv      2P GAIN MUTATED 2P GAIN WILD-TYPE
  T0+T1               8                42
  T2                 23               114
  T3                 21                79
  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    37  10  34   2
  2P GAIN WILD-TYPE 142  58 134   6
D3V5, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  N0              37               142
  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 158   1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     32    0
  2P GAIN WILD-TYPE  158    1
   clus
vv  2P GAIN MUTATED 2P GAIN WILD-TYPE
  0              32               158
  1               0                 1
[1] 2 2
[1] FALSE
D3V7, binary
                   cls
clus                  0   1
  2P GAIN MUTATED    17  79
  2P GAIN WILD-TYPE 123 303
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     17   79
  2P GAIN WILD-TYPE  123  303
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  FEMALE              17               123
  MALE                79               303
[1] 2 2
[1] FALSE
D3V8, binary
                   cls
clus                  0   1
  2P GAIN MUTATED    22  56
  2P GAIN WILD-TYPE 140 245
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     22   56
  2P GAIN WILD-TYPE  140  245
     clus
vv    2P GAIN MUTATED 2P GAIN WILD-TYPE
  NO               22               140
  YES              56               245
[1] 2 2
[1] FALSE
                   vv
clus                HEAD & NECK SQUAMOUS CELL CARCINOMA
  2P GAIN MUTATED                                    93
  2P GAIN WILD-TYPE                                 418
                   vv
clus                HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  2P GAIN MUTATED                                                   3
  2P GAIN WILD-TYPE                                                 7
                   vv
clus                HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  2P GAIN MUTATED                                                           0
  2P GAIN WILD-TYPE                                                         1
D3V9, multiclass
                                                           clus
vv                                                          2P GAIN MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                    93
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       3
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT               0
                                                           clus
vv                                                          2P GAIN WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                     418
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                         7
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                 1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V10, continuous
D3V11, continuous
D3V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  2P GAIN MUTATED                                  1     0
  2P GAIN WILD-TYPE                                1    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  2P GAIN MUTATED                          13    80
  2P GAIN WILD-TYPE                        35   366
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                                         80               366
[1] 4 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  84
  2P GAIN WILD-TYPE  22 375
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      4   84
  2P GAIN WILD-TYPE   22  375
                        clus
vv                       2P GAIN MUTATED 2P GAIN WILD-TYPE
  HISPANIC OR LATINO                   4                22
  NOT HISPANIC OR LATINO              84               375
[1] 2 2
[1] FALSE

Clustering(4) Variable = 2Q GAIN MUTATION ANALYSIS
D4V1, survival
                   sevent
clus2                 0   1
  2Q GAIN MUTATED    41  32
  2Q GAIN WILD-TYPE 260 187
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               73               447 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               32               187 
$`2Q GAIN MUTATED`
TCGA-BA-4075 TCGA-CN-4727 TCGA-CN-6024 TCGA-CX-7219 TCGA-DQ-5629 TCGA-DQ-7588 
        9.30        51.29        11.08        34.36        30.94        14.04 
TCGA-DQ-7589 TCGA-BA-A4IF TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-7864 TCGA-BB-8596 
       46.32        29.42        20.48        16.41        50.20        71.05 
TCGA-CN-4742 TCGA-CN-5356 TCGA-CN-5359 TCGA-CN-5374 TCGA-CN-6012 TCGA-CN-6994 
       13.05        46.32        12.39        56.94        48.00        38.89 
TCGA-CN-A63T TCGA-CQ-5329 TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6228 TCGA-CQ-7072 
        7.40        70.45        56.58        13.25        14.99        77.56 
TCGA-CR-5247 TCGA-CR-6477 TCGA-CR-7365 TCGA-CR-7383 TCGA-CV-5430 TCGA-CV-5434 
       11.77        16.90        39.16        17.13       139.43       108.95 
TCGA-CV-5440 TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6950 TCGA-CV-6962 TCGA-CV-7091 
      107.51        26.43        11.24        15.09         4.14       111.16 
TCGA-CV-7103 TCGA-CV-7235 TCGA-CV-7242 TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7250 
       52.31        77.16        36.00        26.20        18.97        95.34 
TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7263 TCGA-CV-7415 TCGA-CV-7421 TCGA-CV-7422 
       47.97        49.71        18.41        22.85         0.07        34.09 
TCGA-CV-7423 TCGA-CV-7429 TCGA-CV-7435 TCGA-CV-A45X TCGA-CV-A45Z TCGA-CX-7086 
      100.57         3.52       153.86         6.51        48.20        18.84 
TCGA-D6-6823 TCGA-D6-8569 TCGA-D6-A4ZB TCGA-DQ-7592 TCGA-F7-A623 TCGA-HD-A6HZ 
       23.05        25.32        12.36        37.58        20.25         3.65 
TCGA-HD-A6I0 TCGA-IQ-A61E TCGA-IQ-A61H TCGA-MT-A67D TCGA-P3-A6T5 TCGA-QK-A6VB 
        6.90        37.71        37.41         1.84        29.00        21.07 
TCGA-QK-A8ZA TCGA-T2-A6WZ TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A7J9 
       12.20        15.91        54.67         2.83        49.51        44.65 
TCGA-UF-A7JF 
       55.43 

$`2Q GAIN WILD-TYPE`
TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4IG TCGA-BA-A4II 
       37.28        20.48        68.48         3.55        28.11        30.18 
TCGA-BB-A5HU TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6992 TCGA-CN-6997 
       25.71         9.07         9.24        52.08        35.05        32.48 
TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-6221 TCGA-CQ-7063 TCGA-CQ-7067 
       19.82        24.39        48.20        32.88        70.13        16.73 
TCGA-CQ-7068 TCGA-CQ-A4C7 TCGA-CR-6472 TCGA-CR-6478 TCGA-CX-7082 TCGA-DQ-7593 
       43.04        11.61        34.52         6.02         0.36        40.24 
TCGA-H7-A6C5 TCGA-HD-8634 TCGA-HD-8635 TCGA-UF-A71D TCGA-UF-A7JV TCGA-4P-AA8J 
       21.11        12.66        22.85        48.03         2.96         3.35 
TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 
       15.19        13.64         9.07        26.50        23.74        42.35 
TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6869 
       57.93        17.10        23.84        65.59        15.52        21.17 
TCGA-BA-6870 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IH TCGA-BA-A6D8 
       14.83        12.62         4.01        41.85        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-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 
       11.05        13.38         6.15       105.90         9.14         4.80 
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-A5HY TCGA-BB-A5HZ 
       66.28        24.66        38.40        20.52        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-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 
       38.04         4.67        56.68        12.89        26.86        32.81 
TCGA-CN-4733 TCGA-CN-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-5355 TCGA-CN-5358 TCGA-CN-5360 TCGA-CN-5363 
       27.58        73.61        42.02         8.58        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-6010 TCGA-CN-6011 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 
       52.08        50.07        30.67        23.90        47.44        28.04 
TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6995 
       19.07        34.13         6.74        10.45        32.22         3.68 
TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A 
       17.42        11.74        35.01        25.41        23.57        17.29 
TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-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-A6V6 TCGA-CN-A6V7 
        4.41        12.07         2.70        23.44        20.88        19.53 
TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5330 TCGA-CQ-5331 
       52.37        21.50         2.93        54.58        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-6227 TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7069 TCGA-CQ-7071 
        4.24        38.76        64.87        53.52        41.88        43.10 
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-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-6473 TCGA-CR-6474 TCGA-CR-6480 
       58.42        50.01        39.52        36.99        18.54        11.90 
TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 
       10.22        11.34        11.64         7.69        12.46        22.78 
TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-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-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        49.58        30.02        46.85        32.65 
TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 
       44.25        30.58        24.79         5.13         5.95        35.41 
TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5435 TCGA-CV-5436 
       29.95        48.39        17.16       129.21        76.24        19.20 
TCGA-CV-5439 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 
       17.95        94.88        76.50        91.53        80.12        17.92 
TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 
       13.35        23.05        86.83        48.59        60.49         7.07 
TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6933 
       43.23        54.74        21.07        62.43         9.60        90.12 
TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6939 
        2.14         9.70         5.46        20.52         4.73        21.90 
TCGA-CV-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-7095 TCGA-CV-7097 TCGA-CV-7099 
        2.50        64.83       172.67        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-7236 TCGA-CV-7238 TCGA-CV-7243 TCGA-CV-7248 
       10.75       130.88         4.73        89.65        31.36        17.13 
TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7255 TCGA-CV-7406 TCGA-CV-7407 TCGA-CV-7409 
        4.96        11.87         2.10        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-7424 TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7430 TCGA-CV-7432 
       14.89        56.48       156.49        54.94        16.27        84.49 
TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7437 TCGA-CV-7438 TCGA-CV-7440 TCGA-CV-A45O 
       19.76         7.17        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-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-7085 TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6516 
       22.52        10.42        10.55        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-A4Z9 TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EN TCGA-D6-A6EO TCGA-D6-A6EP 
       17.72        28.77         7.63        22.59        24.95        13.94 
TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 
       12.10        12.79        23.34        58.45        37.25        33.86 
TCGA-DQ-5631 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 
       18.02        46.45        20.45        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-A76A TCGA-HD-7229 TCGA-HD-7753 
       13.38        15.16        15.06        20.94        33.76        28.47 
TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 
       25.74        21.93        27.48        27.48        14.66        22.03 
TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 
        0.36        13.84         4.27        34.75        15.95        38.53 
TCGA-IQ-7632 TCGA-IQ-A61G TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L 
       14.50        11.84         0.07        33.57         5.29        13.68 
TCGA-IQ-A61O TCGA-IQ-A6SG TCGA-IQ-A6SH TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W 
       13.84        19.04        15.48        19.27        10.75        14.37 
TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-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        27.39 
TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-A8ZB TCGA-QK-AA3J 
       19.73        12.89         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-A71E TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JH TCGA-UF-A7JJ 
       49.45        74.47        17.95        24.30        29.46        18.05 
TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UP-A6WW TCGA-WA-A7GZ 
       13.94        20.75        22.36        32.65        17.03        20.55 
TCGA-WA-A7H4 TCGA-KU-A66S TCGA-KU-A66T 
       14.56        13.35        18.15 

  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 
            29.00             20.75 
[1] "0.1 - 153.9 (29.0)" "0.1 - 211.0 (20.8)"
[1] "hr=" "1.2"
D4V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  2Q GAIN MUTATED         2       13        10        37         1         0
  2Q GAIN WILD-TYPE      25       63        72       215        11         1
D4V3, multiclass
           clus
vv          2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  STAGE I                 2                25
  STAGE II               13                63
  STAGE III              10                72
  STAGE IVA              37               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
  2Q GAIN MUTATED       6  20  13  27
  2Q GAIN WILD-TYPE    44 117  87 146
D4V4, multiclass
       clus
vv      2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  T0+T1               6                44
  T2                 20               117
  T3                 13                87
  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    31   5  24   1
  2Q GAIN WILD-TYPE 148  63 144   7
D4V5, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  N0              31               148
  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 168   1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     22    0
  2Q GAIN WILD-TYPE  168    1
   clus
vv  2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  0              22               168
  1               0                 1
[1] 2 2
[1] FALSE
D4V7, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED    14  59
  2Q GAIN WILD-TYPE 126 323
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     14   59
  2Q GAIN WILD-TYPE  126  323
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  FEMALE              14               126
  MALE                59               323
[1] 2 2
[1] FALSE
D4V8, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED    18  43
  2Q GAIN WILD-TYPE 144 258
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     18   43
  2Q GAIN WILD-TYPE  144  258
     clus
vv    2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  NO               18               144
  YES              43               258
[1] 2 2
[1] FALSE
                   vv
clus                HEAD & NECK SQUAMOUS CELL CARCINOMA
  2Q GAIN MUTATED                                    73
  2Q GAIN WILD-TYPE                                 438
                   vv
clus                HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  2Q GAIN MUTATED                                                   0
  2Q GAIN WILD-TYPE                                                10
                   vv
clus                HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  2Q GAIN MUTATED                                                           0
  2Q GAIN WILD-TYPE                                                         1
D4V9, multiclass
                                                           clus
vv                                                          2Q GAIN MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                    73
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       0
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT               0
                                                           clus
vv                                                          2Q GAIN WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                     438
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        10
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                 1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V10, continuous
D4V11, continuous
D4V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  2Q GAIN MUTATED                                  1     0
  2Q GAIN WILD-TYPE                                1    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  2Q GAIN MUTATED                           8    63
  2Q GAIN WILD-TYPE                        40   383
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                                         63               383
[1] 4 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  63
  2Q GAIN WILD-TYPE  22 396
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      4   63
  2Q GAIN WILD-TYPE   22  396
                        clus
vv                       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   4                22
  NOT HISPANIC OR LATINO              63               396
[1] 2 2
[1] FALSE

Clustering(5) Variable = 3P GAIN MUTATION ANALYSIS
D5V1, survival
                   sevent
clus2                 0   1
  3P GAIN MUTATED    50  32
  3P GAIN WILD-TYPE 251 187
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               82               438 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               32               187 
$`3P GAIN MUTATED`
TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-5559 TCGA-CN-6021 TCGA-CN-6023 TCGA-CN-A6V1 
       37.28        20.48        68.48         9.07        52.08        19.82 
TCGA-CQ-5323 TCGA-HD-8634 TCGA-UF-A71D TCGA-BA-5153 TCGA-BA-6868 TCGA-BA-6873 
       48.20        12.66        48.03        57.93        15.52         4.01 
TCGA-BA-A4IF TCGA-BA-A6DD TCGA-BB-4223 TCGA-BB-4225 TCGA-BB-7864 TCGA-CN-4723 
       29.42         5.69       105.90         4.80        50.20        55.86 
TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-6010 TCGA-CN-6013 TCGA-CN-6020 TCGA-CN-6988 
       26.86        32.81        50.07        23.90         6.74        10.45 
TCGA-CN-6994 TCGA-CN-A499 TCGA-CN-A49C TCGA-CN-A6V7 TCGA-CQ-6223 TCGA-CQ-6225 
       38.89        23.57        21.21        19.53        46.95        13.25 
TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6474 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 
       58.42        50.01        18.54        11.64         7.69        12.46 
TCGA-CR-7365 TCGA-CR-7368 TCGA-CR-7389 TCGA-CV-5431 TCGA-CV-5442 TCGA-CV-5977 
       39.16        40.93        12.89        17.16        76.50        60.49 
TCGA-CV-6433 TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-7097 TCGA-CV-7103 TCGA-CV-7178 
       21.07        21.90        26.43        12.66        52.31        71.21 
TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7243 TCGA-CV-7261 TCGA-CV-7407 TCGA-CV-7409 
        4.73        89.65        31.36        49.71        35.54        17.85 
TCGA-CV-7421 TCGA-CV-7437 TCGA-D6-A4ZB TCGA-D6-A6EM TCGA-DQ-5624 TCGA-DQ-7595 
        0.07        16.64        12.36         7.63        58.45        39.12 
TCGA-DQ-7596 TCGA-F7-8489 TCGA-F7-A623 TCGA-HD-7917 TCGA-HD-8314 TCGA-HD-A634 
       41.59        21.63        20.25        27.48        22.03         4.27 
TCGA-IQ-A61E TCGA-MT-A67G TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q6 
       37.71         6.25         7.13        16.08        17.98        15.78 
TCGA-P3-A6SX TCGA-P3-A6T5 TCGA-P3-A6T8 TCGA-QK-A6IJ TCGA-QK-A8Z7 TCGA-QK-A8Z8 
       47.01        29.00        13.15        12.72        12.89         5.62 
TCGA-RS-A6TO TCGA-T2-A6X0 TCGA-TN-A7HJ TCGA-UF-A7JA 
       12.72         7.10        13.25        74.47 

$`3P GAIN WILD-TYPE`
TCGA-BA-4075 TCGA-BA-6871 TCGA-BA-A4IG TCGA-BA-A4II TCGA-BB-A5HU TCGA-CN-4727 
        9.30         3.55        28.11        30.18        25.71        51.29 
TCGA-CN-6022 TCGA-CN-6024 TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-A6V3 TCGA-CQ-6221 
        9.24        11.08        35.05        32.48        24.39        32.88 
TCGA-CQ-7063 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-A4C7 TCGA-CR-6472 TCGA-CR-6478 
       70.13        16.73        43.04        11.61        34.52         6.02 
TCGA-CX-7082 TCGA-CX-7219 TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7593 
        0.36        34.36        30.94        14.04        46.32        40.24 
TCGA-H7-A6C5 TCGA-HD-8635 TCGA-UF-A7JV TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 
       21.11        22.85         2.96         3.35        15.19        13.64 
TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5555 TCGA-BA-5556 
        9.07        26.50        23.74        42.35        17.10        23.84 
TCGA-BA-5558 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6872 TCGA-BA-7269 TCGA-BA-A4IH 
       65.59        21.17        14.83        12.62        41.85        20.45 
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-7866 
        4.41        18.38        22.42        36.72        33.70        44.98 
TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-8601 TCGA-BB-A5HY 
       66.28        24.66        38.40        71.05        20.52        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-4725 TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4733 TCGA-CN-4735 
       38.04         4.67        56.68        12.89        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-6011 TCGA-CN-6012 TCGA-CN-6016 
        8.52        52.08        56.94        30.67        48.00        47.44 
TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6989 TCGA-CN-6995 TCGA-CN-6996 
       28.04        19.07        34.13        32.22         3.68        17.42 
TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A63T 
       11.74        35.01        25.41        17.29        29.72         7.40 
TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 
       31.69        22.32        12.39        16.57         4.41        12.07 
TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V6 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 
        2.70        23.44        20.88        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-6224 TCGA-CQ-6227 TCGA-CQ-6228 
        4.24        41.19        32.38        56.58         4.24        14.99 
TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 
       38.76        64.87        53.52        41.88        43.10        77.56 
TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG 
       44.48        23.24        29.36        33.60        29.49        14.14 
TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 
       12.46        31.23        84.23        11.77        54.67        37.87 
TCGA-CR-5250 TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6477 TCGA-CR-6480 TCGA-CR-6481 
       26.27        39.52        36.99        16.90        11.90        10.22 
TCGA-CR-6482 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7367 
       11.34        22.78        15.75         9.27        47.18        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        49.58        30.02        46.85 
TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 
       32.65        44.25        30.58        24.79         5.13         5.95 
TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5432 TCGA-CV-5434 
       35.41        29.95        48.39       139.43       129.21       108.95 
TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5443 
       76.24        19.20        17.95       107.51        94.88        91.53 
TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 
       80.12        17.92        13.35        23.05        86.83        48.59 
TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6933 
        7.07        43.23        54.74        62.43         9.60        90.12 
TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6941 
        2.14         9.70         5.46        20.52         4.73        11.24 
TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-6951 
      140.78        19.79        12.03        42.38        15.09        30.08 
TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-6955 TCGA-CV-6956 TCGA-CV-6959 
        6.08        53.95        65.82        10.98         7.13         8.42 
TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7091 
       28.34         2.50         4.14        64.83       172.67       111.16 
TCGA-CV-7095 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7104 
       18.81         7.99         9.01         5.26         1.84        12.92 
TCGA-CV-7177 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7242 TCGA-CV-7245 
       21.80        10.75       130.88        77.16        36.00        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-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-7416 TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7423 
        0.46        22.85        25.08        25.94        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-7438 TCGA-CV-7440 
       84.49        19.76         7.17       153.86         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-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 
       21.24        23.47        19.92        22.52        10.42        10.55 
TCGA-CX-7086 TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 
       18.84        51.12        13.25        25.41         9.60        23.05 
TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 
        2.53        16.14        11.44        18.67        24.95        25.32 
TCGA-D6-A4Z9 TCGA-D6-A6EK TCGA-D6-A6EN TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ 
       17.72        28.77        22.59        24.95        13.94        12.10 
TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7590 
       12.79        23.34        37.25        33.86        18.02        46.45 
TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7594 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-A50G 
       20.45        37.58        40.04        37.18        32.71        20.25 
TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 
        3.02        31.13        18.94        24.95         0.46        17.85 
TCGA-F7-A622 TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A76A 
       11.80        12.43        13.38        15.16        15.06        20.94 
TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-8224 
       33.76        28.47        25.74        21.93        27.48        14.66 
TCGA-HD-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-A6H7 
        5.29        13.68        13.84        19.04        15.48        19.27 
TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F 
       10.75        14.37         7.96        30.05         1.84        12.62 
TCGA-MT-A7BN TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW 
       15.42        29.92        71.74        51.25        10.85        36.82 
TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T6 TCGA-P3-A6T7 
       19.00        75.55        18.97         2.04        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-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB 
       27.39        21.07        19.73        14.76        12.20        17.82 
TCGA-QK-AA3J TCGA-QK-AA3K TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T2-A6X2 
       15.32         8.32        16.96         6.87        15.91        32.45 
TCGA-T3-A92M TCGA-T3-A92N TCGA-TN-A7HI TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A719 
       13.71         3.12        13.55        20.35        64.80        54.67 
TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JC TCGA-UF-A7JD 
        2.83        49.51        49.45        44.65        17.95        24.30 
TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS 
       55.43        29.46        18.05        13.94        20.75        22.36 
TCGA-UF-A7JT TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 TCGA-KU-A66S TCGA-KU-A66T 
       32.65        17.03        20.55        14.56        13.35        18.15 

  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 
            21.42             21.07 
[1] "0.1 - 105.9 (21.4)" "0.1 - 211.0 (21.1)"
[1] "hr=" "1.1"
D5V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  3P GAIN MUTATED         3       11        12        40         1         1
  3P GAIN WILD-TYPE      24       65        70       212        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              40               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
  3P GAIN MUTATED       7  25  10  27
  3P GAIN WILD-TYPE    43 112  90 146
D5V4, multiclass
       clus
vv      3P GAIN MUTATED 3P GAIN WILD-TYPE
  T0+T1               7                43
  T2                 25               112
  T3                 10                90
  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
  3P GAIN MUTATED    22  13  29   1
  3P GAIN WILD-TYPE 157  55 139   7
D5V5, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  N0              22               157
  N1              13                55
  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"
D5V6, binary
                   cls
clus                  0   1
  3P GAIN MUTATED    21   1
  3P GAIN WILD-TYPE 169   0
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     21    1
  3P GAIN WILD-TYPE  169    0
   clus
vv  3P GAIN MUTATED 3P GAIN WILD-TYPE
  0              21               169
  1               1                 0
[1] 2 2
[1] FALSE
D5V7, binary
                   cls
clus                  0   1
  3P GAIN MUTATED    23  59
  3P GAIN WILD-TYPE 117 323
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     23   59
  3P GAIN WILD-TYPE  117  323
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  FEMALE              23               117
  MALE                59               323
[1] 2 2
[1] FALSE
D5V8, binary
                   cls
clus                  0   1
  3P GAIN MUTATED    25  46
  3P GAIN WILD-TYPE 137 255
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     25   46
  3P GAIN WILD-TYPE  137  255
     clus
vv    3P GAIN MUTATED 3P GAIN WILD-TYPE
  NO               25               137
  YES              46               255
[1] 2 2
[1] FALSE
                   vv
clus                HEAD & NECK SQUAMOUS CELL CARCINOMA
  3P GAIN MUTATED                                    80
  3P GAIN WILD-TYPE                                 431
                   vv
clus                HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  3P GAIN MUTATED                                                   2
  3P GAIN WILD-TYPE                                                 8
                   vv
clus                HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  3P GAIN MUTATED                                                           0
  3P GAIN WILD-TYPE                                                         1
D5V9, multiclass
                                                           clus
vv                                                          3P GAIN MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                    80
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       2
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT               0
                                                           clus
vv                                                          3P GAIN WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                     431
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                         8
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                 1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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                           7    72
  3P GAIN WILD-TYPE                        41   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                      7                41
  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  73
  3P GAIN WILD-TYPE  22 386
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      4   73
  3P GAIN WILD-TYPE   22  386
                        clus
vv                       3P GAIN MUTATED 3P GAIN WILD-TYPE
  HISPANIC OR LATINO                   4                22
  NOT HISPANIC OR LATINO              73               386
[1] 2 2
[1] FALSE

Clustering(6) Variable = 3Q GAIN MUTATION ANALYSIS
D6V1, survival
                   sevent
clus2                 0   1
  3Q GAIN MUTATED   143 113
  3Q GAIN WILD-TYPE 158 106
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
              256               264 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
              113               106 
$`3Q GAIN MUTATED`
TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-5559 TCGA-BB-A5HU TCGA-CN-4727 TCGA-CN-6021 
       37.28        20.48        68.48        25.71        51.29         9.07 
TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-7067 
       52.08        11.08        19.82        24.39        48.20        16.73 
TCGA-CR-6478 TCGA-CX-7219 TCGA-DQ-7589 TCGA-HD-8634 TCGA-UF-A71D TCGA-BA-4078 
        6.02        34.36        46.32        12.66        48.03         9.07 
TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5153 TCGA-BA-6868 TCGA-BA-6870 TCGA-BA-6872 
       26.50        23.74        57.93        15.52        14.83        12.62 
TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IH TCGA-BA-A6D8 TCGA-BA-A6DD 
        4.01        41.85        29.42        20.45        27.95         5.69 
TCGA-BA-A6DI TCGA-BA-A8YP TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 
       11.05        16.41       105.90         9.14         4.80         4.41 
TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-8601 
       33.70        50.20        24.66        38.40        71.05        20.52 
TCGA-BB-A5HY TCGA-BB-A6UM TCGA-C9-A47Z TCGA-CN-4723 TCGA-CN-4726 TCGA-CN-4728 
       10.55        12.92         6.28        55.86         4.67        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-5366 TCGA-CN-5367 TCGA-CN-5373 
       71.31         8.32        16.21        11.84        11.57        52.08 
TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6019 
       56.94        50.07        48.00        23.90        47.44        34.13 
TCGA-CN-6020 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-6998 TCGA-CN-A497 
        6.74        10.45        32.22        38.89        11.74        35.01 
TCGA-CN-A499 TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A6V6 TCGA-CN-A6V7 
       23.57        29.72        21.21         7.40        20.88        19.53 
TCGA-CQ-5329 TCGA-CQ-6220 TCGA-CQ-6223 TCGA-CQ-6225 TCGA-CQ-6228 TCGA-CQ-7064 
       70.45        32.38        46.95        13.25        14.99        64.87 
TCGA-CQ-7065 TCGA-CQ-7069 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CE 
       53.52        41.88        77.56        44.48        23.24        29.49 
TCGA-CQ-A4CG TCGA-CR-5243 TCGA-CR-5249 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6474 
       14.14        84.23        37.87        58.42        50.01        18.54 
TCGA-CR-6480 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 
       11.90        11.64         7.69        12.46        22.78        15.75 
TCGA-CR-7365 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7380 
       39.16        40.93        35.84         3.09        24.95        19.92 
TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7397 TCGA-CR-7401 
       32.78        47.01        27.06        12.89        24.79        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-5442 TCGA-CV-5444 TCGA-CV-5973 TCGA-CV-5977 
       17.95       107.51        76.50        80.12        86.83        60.49 
TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6933 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6939 
       54.74        21.07        90.12         9.70         5.46        21.90 
TCGA-CV-6940 TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6951 TCGA-CV-6954 TCGA-CV-6959 
       26.43        12.03        42.38        30.08        65.82         8.42 
TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7097 TCGA-CV-7101 
        4.14        64.83       172.67       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 
       89.65        36.00        31.36        26.20        18.97        17.13 
TCGA-CV-7250 TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7263 TCGA-CV-7406 
       95.34        11.87        47.97        49.71        18.41        57.47 
TCGA-CV-7407 TCGA-CV-7409 TCGA-CV-7410 TCGA-CV-7414 TCGA-CV-7415 TCGA-CV-7416 
       35.54        17.85       210.97         0.46        22.85        25.08 
TCGA-CV-7421 TCGA-CV-7424 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7437 TCGA-CV-A45R 
        0.07        14.89         7.17       153.86        16.64       180.16 
TCGA-CV-A45U TCGA-CV-A45W TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A465 
       35.47        45.96        48.20        60.43        67.86         7.07 
TCGA-CV-A6JZ TCGA-CX-7086 TCGA-D6-8569 TCGA-D6-A4ZB TCGA-D6-A6EM TCGA-D6-A74Q 
       23.47        18.84        25.32        12.36         7.63        23.34 
TCGA-DQ-5624 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7592 TCGA-DQ-7595 TCGA-DQ-7596 
       58.45        33.86        18.02        37.58        39.12        41.59 
TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61V 
       32.71        21.63        20.25         3.02        31.13        24.95 
TCGA-F7-A623 TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 
       20.25        25.74        21.93        27.48        14.66        22.03 
TCGA-HD-A634 TCGA-HL-7533 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61J 
        4.27        34.75        37.71        11.84        37.41        33.57 
TCGA-IQ-A61K TCGA-MT-A67G TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 
        5.29         6.25         7.13        16.08        17.98        29.92 
TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T3 
       15.78        71.74        10.85        36.82        47.01        18.97 
TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A652 TCGA-QK-A6IJ 
        2.04        29.00        16.01        13.15        21.21        12.72 
TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WZ 
       12.89         5.62        14.76        12.72        16.96        15.91 
TCGA-T2-A6X0 TCGA-T3-A92M TCGA-T3-A92N TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL 
        7.10        13.71         3.12        13.55        13.25        20.35 
TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JD 
       54.67         2.83        49.45        44.65        74.47        24.30 
TCGA-UF-A7JF TCGA-UF-A7JK TCGA-UF-A7JO TCGA-KU-A66T 
       55.43        13.94        20.75        18.15 

$`3Q GAIN WILD-TYPE`
TCGA-BA-4075 TCGA-BA-6871 TCGA-BA-A4IG TCGA-BA-A4II TCGA-CN-6022 TCGA-CN-6992 
        9.30         3.55        28.11        30.18         9.24        35.05 
TCGA-CN-6997 TCGA-CQ-6221 TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CQ-A4C7 TCGA-CR-6472 
       32.48        32.88        70.13        43.04        11.61        34.52 
TCGA-CX-7082 TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7593 TCGA-H7-A6C5 TCGA-HD-8635 
        0.36        30.94        14.04        40.24        21.11        22.85 
TCGA-UF-A7JV TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-5152 TCGA-BA-5555 
        2.96         3.35        15.19        13.64        42.35        17.10 
TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-6869 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DE 
       23.84        65.59        21.17        11.54         7.10        14.47 
TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BB-4217 TCGA-BB-4228 
        7.82         2.27        13.38        20.48         6.15        18.38 
TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-A5HZ TCGA-BB-A6UO 
       22.42        36.72        44.98        66.28        27.19         8.81 
TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4725 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4738 
       12.69        48.76        38.04        52.14        57.11        14.33 
TCGA-CN-5355 TCGA-CN-5365 TCGA-CN-5369 TCGA-CN-5370 TCGA-CN-6011 TCGA-CN-6017 
       42.02        11.54        12.49         8.52        30.67        28.04 
TCGA-CN-6018 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-A498 TCGA-CN-A49A TCGA-CN-A63U 
       19.07         3.68        17.42        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-6224 
       45.99        10.42        11.21         4.24        41.19        56.58 
TCGA-CQ-6227 TCGA-CQ-6229 TCGA-CQ-7071 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CH 
        4.24        38.76        43.10        29.36        33.60        12.46 
TCGA-CQ-A4CI TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5250 TCGA-CR-6471 TCGA-CR-6473 
       31.23        11.77        54.67        26.27        39.52        36.99 
TCGA-CR-6477 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7367 
       16.90        10.22        11.34         9.27        47.18        47.34 
TCGA-CR-7370 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 
        3.45        29.23         0.99        31.96         9.17        34.06 
TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 
       26.17        17.13        49.58        30.02        46.85        32.65 
TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7398 TCGA-CR-7399 TCGA-CV-5434 TCGA-CV-5435 
       44.25        30.58         5.13         5.95       108.95        76.24 
TCGA-CV-5441 TCGA-CV-5443 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5976 
       94.88        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-6960 TCGA-CV-6961 TCGA-CV-7095 
       53.95        10.98         7.13        28.34         2.50        18.81 
TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7177 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7252 
        7.99         9.01        21.80       130.88        77.16         4.96 
TCGA-CV-7255 TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7423 
        2.10        89.33         9.67        25.94        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-7433 TCGA-CV-7438 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45Q 
       19.76         6.38        22.19        27.98        21.01       169.38 
TCGA-CV-A45T TCGA-CV-A45V TCGA-CV-A45X TCGA-CV-A45Y TCGA-CV-A463 TCGA-CV-A464 
      159.65         1.05         6.51        88.87         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-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-7085 TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 
       10.55        51.12        13.25        25.41         9.60        23.05 
TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-A4Z9 
        2.53        16.14        11.44        18.67        24.95        17.72 
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-DQ-5625 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7594 TCGA-F7-7848 TCGA-F7-A61S 
       37.25        46.45        20.45        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-A76A TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7832 TCGA-HD-A4C1 
       15.06        20.94        33.76        28.47        27.48         0.36 
TCGA-HD-A633 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 
       13.84         3.65         6.90        15.95        38.53        14.50 
TCGA-IQ-A61I TCGA-IQ-A61L TCGA-IQ-A61O TCGA-IQ-A6SG TCGA-IQ-A6SH TCGA-KU-A6H7 
        0.07        13.68        13.84        19.04        15.48        19.27 
TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F 
       10.75        14.37         7.96        30.05         1.84        12.62 
TCGA-MT-A7BN TCGA-P3-A5QE TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T6 TCGA-QK-A64Z 
       15.42        51.25        19.00        75.55        12.99        21.07 
TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6V9 TCGA-QK-A6VB 
       23.15         7.30        21.47         9.34        27.39        21.07 
TCGA-QK-A6VC TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-T2-A6WX 
       19.73        12.20        17.82        15.32         8.32         6.87 
TCGA-T2-A6X2 TCGA-UF-A718 TCGA-UF-A71B TCGA-UF-A7JC TCGA-UF-A7JH TCGA-UF-A7JJ 
       32.45        64.80        49.51        17.95        29.46        18.05 
TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 TCGA-KU-A66S 
       22.36        32.65        17.03        20.55        14.56        13.35 

  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 
           23.655            19.500 
[1] "0.1 - 211.0 (23.7)" "0.1 - 169.4 (19.5)"
[1] "hr=" "1.1"
D6V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  3Q GAIN MUTATED        11       36        40       129         6         1
  3Q GAIN WILD-TYPE      16       40        42       123         6         0
D6V3, multiclass
           clus
vv          3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  STAGE I                11                16
  STAGE II               36                40
  STAGE III              40                42
  STAGE IVA             129               123
  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      23 68 50 87
  3Q GAIN WILD-TYPE    27 69 50 86
D6V4, multiclass
       clus
vv      3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  T0+T1              23                27
  T2                 68                69
  T3                 50                50
  T4                 87                86
[1] 4 2
[1] TRUE
[1] "dimension of 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    74  36  97   5
  3Q GAIN WILD-TYPE 105  32  71   3
D6V5, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  N0              74               105
  N1              36                32
  N2              97                71
  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"
D6V6, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED    88   1
  3Q GAIN WILD-TYPE 102   0
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     88    1
  3Q GAIN WILD-TYPE  102    0
   clus
vv  3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  0              88               102
  1               1                 0
[1] 2 2
[1] FALSE
D6V7, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED    58 199
  3Q GAIN WILD-TYPE  82 183
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     58  199
  3Q GAIN WILD-TYPE   82  183
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  FEMALE              58                82
  MALE               199               183
[1] 2 2
[1] FALSE
D6V8, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED    72 152
  3Q GAIN WILD-TYPE  90 149
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     72  152
  3Q GAIN WILD-TYPE   90  149
     clus
vv    3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  NO               72                90
  YES             152               149
[1] 2 2
[1] FALSE
                   vv
clus                HEAD & NECK SQUAMOUS CELL CARCINOMA
  3Q GAIN MUTATED                                   251
  3Q GAIN WILD-TYPE                                 260
                   vv
clus                HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  3Q GAIN MUTATED                                                   6
  3Q GAIN WILD-TYPE                                                 4
                   vv
clus                HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  3Q GAIN MUTATED                                                           0
  3Q GAIN WILD-TYPE                                                         1
D6V9, multiclass
                                                           clus
vv                                                          3Q GAIN MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                   251
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       6
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT               0
                                                           clus
vv                                                          3Q GAIN WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                     260
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                         4
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                 1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V10, continuous
D6V11, continuous
D6V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  3Q GAIN MUTATED                                  1     6
  3Q GAIN WILD-TYPE                                1     5
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  3Q GAIN MUTATED                          24   215
  3Q GAIN WILD-TYPE                        24   231
D6V13, multiclass
                                  clus
vv                                 3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 1
  ASIAN                                          6                 5
  BLACK OR AFRICAN AMERICAN                     24                24
  WHITE                                        215               231
[1] 4 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    13 222
  3Q GAIN WILD-TYPE  13 237
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     13  222
  3Q GAIN WILD-TYPE   13  237
                        clus
vv                       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  HISPANIC OR LATINO                  13                13
  NOT HISPANIC OR LATINO             222               237
[1] 2 2
[1] FALSE

Clustering(7) Variable = 4P GAIN MUTATION ANALYSIS
D7V1, survival
                   sevent
clus2                 0   1
  4P GAIN MUTATED    22  19
  4P GAIN WILD-TYPE 279 200
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               41               479 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               19               200 
$`4P GAIN MUTATED`
TCGA-CN-4727 TCGA-CX-7219 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A6DI 
       51.29        34.36        12.62         4.01        41.85        11.05 
TCGA-BB-4225 TCGA-CN-4737 TCGA-CN-4740 TCGA-CQ-6224 TCGA-CQ-7069 TCGA-CR-5247 
        4.80        20.55        27.58        56.58        41.88        11.77 
TCGA-CR-7389 TCGA-CV-5430 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-6003 
       12.89       139.43        86.83        48.59        60.49        54.74 
TCGA-CV-6939 TCGA-CV-6945 TCGA-CV-6954 TCGA-CV-7090 TCGA-CV-7102 TCGA-CV-7180 
       21.90        12.03        65.82       172.67         1.84        10.75 
TCGA-CV-7255 TCGA-CV-7263 TCGA-CV-7416 TCGA-CV-7433 TCGA-CV-A45W TCGA-DQ-5625 
        2.10        18.41        25.08        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        27.39        14.76        13.94 

$`4P GAIN WILD-TYPE`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4IG 
        9.30        37.28        20.48        68.48         3.55        28.11 
TCGA-BA-A4II TCGA-BB-A5HU TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 
       30.18        25.71         9.07         9.24        52.08        11.08 
TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-6221 
       35.05        32.48        19.82        24.39        48.20        32.88 
TCGA-CQ-7063 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-A4C7 TCGA-CR-6472 TCGA-CR-6478 
       70.13        16.73        43.04        11.61        34.52         6.02 
TCGA-CX-7082 TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7593 TCGA-H7-A6C5 
        0.36        30.94        14.04        46.32        40.24        21.11 
TCGA-HD-8634 TCGA-HD-8635 TCGA-UF-A71D TCGA-UF-A7JV TCGA-4P-AA8J TCGA-BA-4074 
       12.66        22.85        48.03         2.96         3.35        15.19 
TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 
       13.64         9.07        26.50        23.74        42.35        57.93 
TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 
       17.10        23.84        65.59        15.52        21.17        14.83 
TCGA-BA-A4IF TCGA-BA-A4IH TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD 
       29.42        20.45        27.95        11.54         7.10         5.69 
TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BA-A8YP 
       14.47         7.82         2.27        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-A5HY TCGA-BB-A5HZ TCGA-BB-A6UM 
       38.40        71.05        20.52        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-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-4738 TCGA-CN-4739 TCGA-CN-4741 TCGA-CN-4742 
       57.11        12.99        14.33        45.83        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-6011 TCGA-CN-6012 TCGA-CN-6013 
       52.08        56.94        50.07        30.67        48.00        23.90 
TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6988 
       47.44        28.04        19.07        34.13         6.74        10.45 
TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A497 
       32.22        38.89         3.68        17.42        11.74        35.01 
TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T 
       25.41        23.57        17.29        29.72        21.21         7.40 
TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 
       31.69        22.32        12.39        16.57         4.41        12.07 
TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5324 TCGA-CQ-5325 
        2.70        23.44        20.88        19.53        52.37        21.50 
TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 
        2.93        54.58        70.45        62.37        45.99        10.42 
TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6220 TCGA-CQ-6223 TCGA-CQ-6225 
       11.21         4.24        41.19        32.38        46.95        13.25 
TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7071 
        4.24        14.99        38.76        64.87        53.52        43.10 
TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE 
       77.56        44.48        23.24        29.36        33.60        29.49 
TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5248 TCGA-CR-5249 
       14.14        12.46        31.23        84.23        54.67        37.87 
TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6474 
       26.27        58.42        50.01        39.52        36.99        18.54 
TCGA-CR-6477 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 
       16.90        11.90        10.22        11.34        11.64         7.69 
TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 
       12.46        22.78        15.75         9.27        47.18        39.16 
TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 
       47.34        40.93        35.84         3.45         3.09        24.95 
TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 
       29.23         0.99        31.96         9.17        34.06        19.92 
TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7390 
       26.17        17.13        32.78        47.01        27.06        49.58 
TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 
       30.02        46.85        32.65        44.25        30.58        24.79 
TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5431 
        5.13         5.95        35.41        29.95        48.39        17.16 
TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 
      129.21       108.95        76.24        19.20        17.95       107.51 
TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 
       94.88        76.50        91.53        80.12        17.92        13.35 
TCGA-CV-5971 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 
       23.05         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-6940 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6948 TCGA-CV-6950 
       26.43        11.24       140.78        19.79        42.38        15.09 
TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6955 TCGA-CV-6956 TCGA-CV-6959 
       30.08         6.08        53.95        10.98         7.13         8.42 
TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7091 TCGA-CV-7095 
       28.34         2.50         4.14        64.83       111.16        18.81 
TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7103 TCGA-CV-7104 
       12.66         7.99         9.01         5.26        52.31        12.92 
TCGA-CV-7177 TCGA-CV-7178 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7238 
       21.80        71.21       130.88        77.16         4.73        89.65 
TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7248 TCGA-CV-7250 
       36.00        31.36        26.20        18.97        17.13        95.34 
TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7407 
        4.96        11.87        47.97        49.71        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-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-A45X 
      169.38       180.16       159.65        35.47         1.05         6.51 
TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A463 TCGA-CV-A464 
       88.87        48.20        60.43        67.86         0.76        56.61 
TCGA-CV-A465 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JM TCGA-CV-A6JN 
        7.07        15.25         5.98        35.34         6.38        29.79 
TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 
        6.48        28.01         3.62        21.24        23.47        19.92 
TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-A4AQ TCGA-D6-6515 
       22.52        10.42        10.55        18.84        51.12        13.25 
TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 
       25.41         9.60        23.05         2.53        16.14        11.44 
TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK 
       18.67        24.95        25.32        17.72        12.36        28.77 
TCGA-D6-A6EM TCGA-D6-A6EN TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES 
        7.63        22.59        24.95        13.94        12.10        12.79 
TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7590 TCGA-DQ-7591 
       23.34        58.45        33.86        18.02        46.45        20.45 
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-A76A TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 
       20.94        33.76        28.47        25.74        21.93        27.48 
TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 
       27.48        14.66        22.03         0.36        13.84         4.27 
TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-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-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X 
       13.84        19.04        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-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-A6T6 TCGA-P3-A6T7 
       47.01        19.00        75.55        18.97        12.99        16.01 
TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH 
       13.15        21.07        21.21        23.15         7.30        21.47 
TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z8 
        9.34        12.72        21.07        19.73        12.89         5.62 
TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-RS-A6TO TCGA-RS-A6TP 
       12.20        17.82        15.32         8.32        12.72        16.96 
TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-T3-A92M TCGA-T3-A92N 
        6.87        15.91         7.10        32.45        13.71         3.12 
TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A 
       13.55        13.25        20.35        64.80        54.67         2.83 
TCGA-UF-A71B TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD 
       49.51        49.45        44.65        74.47        17.95        24.30 
TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT 
       55.43        29.46        18.05        20.75        22.36        32.65 
TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 TCGA-KU-A66S TCGA-KU-A66T 
       17.03        20.55        14.56        13.35        18.15 

  4P GAIN MUTATED 4P GAIN WILD-TYPE 
             1.84              0.07 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
           172.67            210.97 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
            20.55             21.11 
[1] "1.8 - 172.7 (20.6)" "0.1 - 211.0 (21.1)"
[1] "hr=" "1.1"
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       231        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               231
  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   3  16
  4P GAIN WILD-TYPE    49 124  97 157
D7V4, multiclass
       clus
vv      4P GAIN MUTATED 4P GAIN WILD-TYPE
  T0+T1               1                49
  T2                 13               124
  T3                  3                97
  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
  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 179   1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED     11    0
  4P GAIN WILD-TYPE  179    1
   clus
vv  4P GAIN MUTATED 4P GAIN WILD-TYPE
  0              11               179
  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  23
  4P GAIN WILD-TYPE 150 278
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED     12   23
  4P GAIN WILD-TYPE  150  278
     clus
vv    4P GAIN MUTATED 4P GAIN WILD-TYPE
  NO               12               150
  YES              23               278
[1] 2 2
[1] FALSE
                   vv
clus                HEAD & NECK SQUAMOUS CELL CARCINOMA
  4P GAIN MUTATED                                    41
  4P GAIN WILD-TYPE                                 470
                   vv
clus                HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  4P GAIN MUTATED                                                   0
  4P GAIN WILD-TYPE                                                10
                   vv
clus                HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  4P GAIN MUTATED                                                           0
  4P GAIN WILD-TYPE                                                         1
D7V9, multiclass
                                                           clus
vv                                                          4P GAIN MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                    41
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       0
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT               0
                                                           clus
vv                                                          4P GAIN WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                     470
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        10
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                 1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V10, continuous
D7V11, continuous
D7V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  4P GAIN MUTATED                                  1     0
  4P GAIN WILD-TYPE                                1    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  4P GAIN MUTATED                           8    31
  4P GAIN WILD-TYPE                        40   415
D7V13, multiclass
                                  clus
vv                                 4P GAIN MUTATED 4P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 1
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                      8                40
  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    20  17
  4Q GAIN WILD-TYPE 281 202
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               37               483 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               17               202 
$`4Q GAIN MUTATED`
TCGA-CN-4727 TCGA-CX-7219 TCGA-BA-6872 TCGA-BB-4225 TCGA-BB-A5HZ TCGA-CN-4740 
       51.29        34.36        12.62         4.80        27.19        27.58 
TCGA-CN-5363 TCGA-CQ-7069 TCGA-CR-5247 TCGA-CR-6491 TCGA-CR-7389 TCGA-CV-5436 
        8.32        41.88        11.77        22.78        12.89        19.20 
TCGA-CV-5977 TCGA-CV-6939 TCGA-CV-6945 TCGA-CV-7090 TCGA-CV-7102 TCGA-CV-7242 
       60.49        21.90        12.03       172.67         1.84        36.00 
TCGA-CV-7245 TCGA-CV-7263 TCGA-CV-7415 TCGA-CV-7433 TCGA-CV-A45W TCGA-CV-A45X 
       26.20        18.41        22.85        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        27.39        19.73        14.76 
TCGA-UF-A7J9 
       44.65 

$`4Q GAIN WILD-TYPE`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4IG 
        9.30        37.28        20.48        68.48         3.55        28.11 
TCGA-BA-A4II TCGA-BB-A5HU TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 
       30.18        25.71         9.07         9.24        52.08        11.08 
TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-6221 
       35.05        32.48        19.82        24.39        48.20        32.88 
TCGA-CQ-7063 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-A4C7 TCGA-CR-6472 TCGA-CR-6478 
       70.13        16.73        43.04        11.61        34.52         6.02 
TCGA-CX-7082 TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7593 TCGA-H7-A6C5 
        0.36        30.94        14.04        46.32        40.24        21.11 
TCGA-HD-8634 TCGA-HD-8635 TCGA-UF-A71D TCGA-UF-A7JV TCGA-4P-AA8J TCGA-BA-4074 
       12.66        22.85        48.03         2.96         3.35        15.19 
TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 
       13.64         9.07        26.50        23.74        42.35        57.93 
TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 
       17.10        23.84        65.59        15.52        21.17        14.83 
TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IH TCGA-BA-A6D8 TCGA-BA-A6DA 
        4.01        41.85        29.42        20.45        27.95        11.54 
TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DI 
        7.10         5.69        14.47         7.82         2.27        11.05 
TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 
       13.38        20.48        16.41         6.15       105.90         9.14 
TCGA-BB-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-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-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-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-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 
       12.49         8.52        52.08        56.94        50.07        30.67 
TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 
       48.00        23.90        47.44        28.04        19.07        34.13 
TCGA-CN-6020 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 
        6.74        10.45        32.22        38.89         3.68        17.42 
TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B 
       11.74        35.01        25.41        23.57        17.29        29.72 
TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y 
       21.21         7.40        31.69        22.32        12.39        16.57 
TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V6 TCGA-CN-A6V7 
        4.41        12.07         2.70        23.44        20.88        19.53 
TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 
       52.37        21.50         2.93        54.58        70.45        62.37 
TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6220 
       45.99        10.42        11.21         4.24        41.19        32.38 
TCGA-CQ-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-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C9 
       64.87        53.52        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-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-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6480 TCGA-CR-6481 
       39.52        36.99        18.54        16.90        11.90        10.22 
TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6492 TCGA-CR-6493 
       11.34        11.64         7.69        12.46        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        49.58        30.02        46.85        32.65        44.25 
TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 
       30.58        24.79         5.13         5.95        35.41        29.95 
TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 
       48.39       139.43        17.16       129.21       108.95        76.24 
TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 
       17.95       107.51        94.88        76.50        91.53        80.12 
TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-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-6940 
        2.14         9.70         5.46        20.52         4.73        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-6962 TCGA-CV-7089 TCGA-CV-7091 TCGA-CV-7095 
       28.34         2.50         4.14        64.83       111.16        18.81 
TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7103 TCGA-CV-7104 
       12.66         7.99         9.01         5.26        52.31        12.92 
TCGA-CV-7177 TCGA-CV-7178 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7236 
       21.80        71.21        10.75       130.88        77.16         4.73 
TCGA-CV-7238 TCGA-CV-7243 TCGA-CV-7247 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7252 
       89.65        31.36        18.97        17.13        95.34         4.96 
TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7255 TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7407 
       11.87        47.97         2.10        49.71        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-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-A45Y 
      169.38       180.16       159.65        35.47         1.05        88.87 
TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A463 TCGA-CV-A464 TCGA-CV-A465 
       48.20        60.43        67.86         0.76        56.61         7.07 
TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JM TCGA-CV-A6JN TCGA-CV-A6JO 
       15.25         5.98        35.34         6.38        29.79         6.48 
TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 
       28.01         3.62        21.24        23.47        19.92        22.52 
TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6516 
       10.42        10.55        18.84        51.12        13.25        25.41 
TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6827 TCGA-D6-8568 
        9.60        23.05         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-5624 
       24.95        13.94        12.10        12.79        23.34        58.45 
TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7594 
       33.86        18.02        46.45        20.45        37.58        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-A624 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A76A 
       11.80        12.43        13.38        15.16        15.06        20.94 
TCGA-HD-7229 TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-7917 TCGA-HD-8224 
       33.76        25.74        21.93        27.48        27.48        14.66 
TCGA-HD-8314 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 
       22.03         0.36        13.84         4.27         3.65         6.90 
TCGA-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-A61O TCGA-IQ-A6SG 
       37.41         0.07        33.57         5.29        13.84        19.04 
TCGA-IQ-A6SH TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A 
       15.48        19.27        10.75        14.37         7.96        30.05 
TCGA-MT-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-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-A6VB TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8ZA TCGA-QK-A8ZB 
       12.72        21.07        12.89         5.62        12.20        17.82 
TCGA-QK-AA3J TCGA-QK-AA3K TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ 
       15.32         8.32        12.72        16.96         6.87        15.91 
TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-T3-A92M TCGA-T3-A92N TCGA-TN-A7HI TCGA-TN-A7HJ 
        7.10        32.45        13.71         3.12        13.55        13.25 
TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71E 
       20.35        64.80        54.67         2.83        49.51        49.45 
TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ 
       74.47        17.95        24.30        55.43        29.46        18.05 
TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UP-A6WW TCGA-WA-A7GZ 
       13.94        20.75        22.36        32.65        17.03        20.55 
TCGA-WA-A7H4 TCGA-KU-A66S TCGA-KU-A66T 
       14.56        13.35        18.15 

  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
             1.84              0.07 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
           172.67            210.97 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
            20.25             21.11 
[1] "1.8 - 172.7 (20.2)" "0.1 - 211.0 (21.1)"
[1] "hr=" "1.2"
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       232        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               232
  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  13   2
  4Q GAIN WILD-TYPE 169  65 155   6
D8V5, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  N0              10               169
  N1               3                65
  N2              13               155
  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 176   1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED     14    0
  4Q GAIN WILD-TYPE  176    1
   clus
vv  4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  0              14               176
  1               0                 1
[1] 2 2
[1] FALSE
D8V7, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     8  29
  4Q GAIN WILD-TYPE 132 353
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      8   29
  4Q GAIN WILD-TYPE  132  353
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  FEMALE               8               132
  MALE                29               353
[1] 2 2
[1] FALSE
D8V8, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED    10  20
  4Q GAIN WILD-TYPE 152 281
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED     10   20
  4Q GAIN WILD-TYPE  152  281
     clus
vv    4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  NO               10               152
  YES              20               281
[1] 2 2
[1] FALSE
                   vv
clus                HEAD & NECK SQUAMOUS CELL CARCINOMA
  4Q GAIN MUTATED                                    36
  4Q GAIN WILD-TYPE                                 475
                   vv
clus                HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  4Q GAIN MUTATED                                                   1
  4Q GAIN WILD-TYPE                                                 9
                   vv
clus                HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  4Q GAIN MUTATED                                                           0
  4Q GAIN WILD-TYPE                                                         1
D8V9, multiclass
                                                           clus
vv                                                          4Q GAIN MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                    36
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       1
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT               0
                                                           clus
vv                                                          4Q GAIN WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                     475
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                         9
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                 1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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                           9    27
  4Q GAIN WILD-TYPE                        39   419
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                      9                39
  WHITE                                         27               419
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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 185 135
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
              200               320 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               84               135 
$`5P GAIN MUTATED`
TCGA-BA-4075 TCGA-BA-5559 TCGA-BA-A4IG TCGA-BB-A5HU TCGA-CN-4727 TCGA-CN-6023 
        9.30        68.48        28.11        25.71        51.29        52.08 
TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-A6V3 TCGA-CQ-6221 TCGA-CQ-7067 TCGA-DQ-5629 
       35.05        32.48        24.39        32.88        16.73        30.94 
TCGA-DQ-7589 TCGA-HD-8635 TCGA-UF-A71D TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4078 
       46.32        22.85        48.03         3.35        15.19         9.07 
TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 
       17.10        23.84        65.59        15.52        21.17        14.83 
TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A6D8 TCGA-BA-A6DB 
       12.62         4.01        41.85        29.42        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-C9-A47Z TCGA-CN-4723 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4736 
        6.28        55.86        12.89        26.86        32.81        12.99 
TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4742 TCGA-CN-5359 TCGA-CN-5363 
       20.55        14.33        45.83        13.05        12.39         8.32 
TCGA-CN-5366 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6994 
       11.84        50.07        30.67        34.13         6.74        38.89 
TCGA-CN-A498 TCGA-CN-A49B TCGA-CN-A63W TCGA-CN-A6UY TCGA-CN-A6V6 TCGA-CQ-5330 
       25.41        29.72        12.39        23.44        20.88        62.37 
TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-7064 TCGA-CQ-7072 TCGA-CQ-A4CD TCGA-CR-5243 
       56.58        13.25        64.87        77.56        33.60        84.23 
TCGA-CR-6467 TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6484 
       58.42        39.52        36.99        18.54        16.90        11.64 
TCGA-CR-6488 TCGA-CR-6492 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 
       12.46        15.75        39.16        47.34        40.93        35.84 
TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7383 TCGA-CR-7389 TCGA-CR-7392 TCGA-CR-7398 
       34.06        19.92        17.13        12.89        46.85         5.13 
TCGA-CR-7399 TCGA-CR-7404 TCGA-CV-5431 TCGA-CV-5435 TCGA-CV-5439 TCGA-CV-5440 
        5.95        48.39        17.16        76.24        17.95       107.51 
TCGA-CV-5442 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5978 TCGA-CV-6441 
       76.50        80.12        17.92        13.35         7.07         9.60 
TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6941 TCGA-CV-6945 TCGA-CV-6954 TCGA-CV-6956 
        5.46        20.52        11.24        12.03        65.82         7.13 
TCGA-CV-6959 TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7101 
        8.42         2.50       172.67       111.16        18.81         5.26 
TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-7178 TCGA-CV-7180 
        1.84        52.31        12.92        21.80        71.21        10.75 
TCGA-CV-7235 TCGA-CV-7245 TCGA-CV-7409 TCGA-CV-7416 TCGA-CV-7421 TCGA-CV-7424 
       77.16        26.20        17.85        25.08         0.07        14.89 
TCGA-CV-7429 TCGA-CV-7437 TCGA-CV-A45R TCGA-CV-A45U TCGA-CV-A45X TCGA-CV-A45Z 
        3.52        16.64       180.16        35.47         6.51        48.20 
TCGA-CV-A463 TCGA-CV-A465 TCGA-CV-A6JE TCGA-CX-7086 TCGA-D6-8568 TCGA-D6-8569 
        0.76         7.07        35.34        18.84        24.95        25.32 
TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7590 TCGA-DQ-7592 TCGA-DQ-7596 TCGA-F7-A50J 
       33.86        18.02        46.45        37.58        41.59        31.13 
TCGA-F7-A61S TCGA-F7-A620 TCGA-H7-8502 TCGA-H7-A76A TCGA-HD-7753 TCGA-HD-7831 
       18.94        17.85        15.06        20.94        28.47        21.93 
TCGA-HD-7832 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-A6HZ TCGA-HL-7533 TCGA-IQ-7630 
       27.48        27.48        14.66         3.65        34.75        15.95 
TCGA-IQ-A61E TCGA-IQ-A61J TCGA-IQ-A61O TCGA-IQ-A6SG TCGA-IQ-A6SH TCGA-KU-A6H7 
       37.71        33.57        13.84        19.04        15.48        19.27 
TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67D TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-MZ-A7D7 
       14.37         7.96         1.84        15.42         7.13        17.98 
TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T2 TCGA-P3-A6T3 
       15.78        71.74        36.82        47.01        75.55        18.97 
TCGA-P3-A6T4 TCGA-P3-A6T6 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IG 
        2.04        12.99        13.15        21.07        21.21         7.30 
TCGA-QK-A6IJ TCGA-QK-A6VC TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-AA3K 
       12.72        19.73         5.62        14.76        12.20         8.32 
TCGA-RS-A6TO TCGA-T2-A6WZ TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-UF-A71A TCGA-UF-A71B 
       12.72        15.91        13.55        13.25         2.83        49.51 
TCGA-UF-A7JA TCGA-UF-A7JF TCGA-UF-A7JK TCGA-UF-A7JS TCGA-UP-A6WW TCGA-WA-A7GZ 
       74.47        55.43        13.94        22.36        17.03        20.55 
TCGA-KU-A66S TCGA-KU-A66T 
       13.35        18.15 

$`5P GAIN WILD-TYPE`
TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-6871 TCGA-BA-A4II TCGA-CN-6021 TCGA-CN-6022 
       37.28        20.48         3.55        30.18         9.07         9.24 
TCGA-CN-6024 TCGA-CN-A6V1 TCGA-CQ-5323 TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CQ-A4C7 
       11.08        19.82        48.20        70.13        43.04        11.61 
TCGA-CR-6472 TCGA-CR-6478 TCGA-CX-7082 TCGA-CX-7219 TCGA-DQ-7588 TCGA-DQ-7593 
       34.52         6.02         0.36        34.36        14.04        40.24 
TCGA-H7-A6C5 TCGA-HD-8634 TCGA-UF-A7JV TCGA-BA-4076 TCGA-BA-5149 TCGA-BA-5151 
       21.11        12.66         2.96        13.64        26.50        23.74 
TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-A4IH TCGA-BA-A6DA TCGA-BA-A6DD TCGA-BA-A6DF 
       42.35        57.93        20.45        11.54         5.69         7.82 
TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BA-A8YP TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-7862 
        2.27        13.38        16.41         9.14         4.80        36.72 
TCGA-BB-7863 TCGA-BB-7866 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-A5HY TCGA-BB-A5HZ 
       33.70        44.98        24.66        38.40        10.55        27.19 
TCGA-BB-A6UM TCGA-BB-A6UO TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4725 TCGA-CN-4726 
       12.92         8.81        12.69        48.76        38.04         4.67 
TCGA-CN-4728 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-5355 
       56.68        52.14        57.11        27.58        73.61        42.02 
TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5360 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5367 
       46.32         8.58        71.31        16.21        11.54        11.57 
TCGA-CN-5369 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6012 TCGA-CN-6013 
       12.49         8.52        52.08        56.94        48.00        23.90 
TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6995 
       47.44        28.04        19.07        10.45        32.22         3.68 
TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49C 
       17.42        11.74        35.01        23.57        17.29        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-A6V7 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 
        2.70        19.53        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-7065 
       32.38        46.95         4.24        14.99        38.76        53.52 
TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CE 
       41.88        43.10        44.48        23.24        29.36        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-6470 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6487 
       26.27        50.01        11.90        10.22        11.34         7.69 
TCGA-CR-6491 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 
       22.78         9.27        47.18         3.45         3.09        24.95 
TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7382 TCGA-CR-7385 
       29.23         0.99        31.96         9.17        26.17        32.78 
TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7393 TCGA-CR-7394 
       47.01        27.06        49.58        30.02        32.65        44.25 
TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7401 TCGA-CR-7402 TCGA-CV-5430 TCGA-CV-5432 
       30.58        24.79        35.41        29.95       139.43       129.21 
TCGA-CV-5434 TCGA-CV-5436 TCGA-CV-5441 TCGA-CV-5443 TCGA-CV-5971 TCGA-CV-5973 
      108.95        19.20        94.88        91.53        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-6933 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6940 
       90.12         2.14         9.70         4.73        21.90        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-6960 TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7097 
       53.95        10.98        28.34         4.14        64.83        12.66 
TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7183 TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7242 
        7.99         9.01       130.88         4.73        89.65        36.00 
TCGA-CV-7243 TCGA-CV-7247 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 
       31.36        18.97        17.13        95.34         4.96        11.87 
TCGA-CV-7254 TCGA-CV-7255 TCGA-CV-7261 TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7407 
       47.97         2.10        49.71        18.41        57.47        35.54 
TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7414 TCGA-CV-7415 TCGA-CV-7418 
      210.97        89.33         9.67         0.46        22.85        25.94 
TCGA-CV-7422 TCGA-CV-7423 TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7430 
       34.09       100.57        56.48       156.49        54.94        16.27 
TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7438 TCGA-CV-7440 
       84.49        19.76         7.17       153.86         6.38        22.19 
TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45T TCGA-CV-A45V TCGA-CV-A45W 
       27.98        21.01       169.38       159.65         1.05        45.96 
TCGA-CV-A45Y TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JD 
       88.87        60.43        67.86        56.61        15.25         5.98 
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-A4AQ 
       23.47        19.92        22.52        10.42        10.55        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-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-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q 
       22.59        24.95        13.94        12.10        12.79        23.34 
TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-7591 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-F7-7848 
       58.45        37.25        20.45        40.04        39.12        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-A622 TCGA-F7-A623 TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 TCGA-HD-7229 
       11.80        20.25        12.43        13.38        15.16        33.76 
TCGA-HD-7754 TCGA-HD-8314 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6I0 
       25.74        22.03         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        27.39        21.07        12.89 
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-WA-A7H4 
       32.65        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            22.255 
[1] "0.1 - 180.2 (19.8)" "0.1 - 211.0 (22.3)"
[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       152         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               152
  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    71   1
  5P GAIN WILD-TYPE 119   0
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     71    1
  5P GAIN WILD-TYPE  119    0
   clus
vv  5P GAIN MUTATED 5P GAIN WILD-TYPE
  0              71               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    55 128
  5P GAIN WILD-TYPE 107 173
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     55  128
  5P GAIN WILD-TYPE  107  173
     clus
vv    5P GAIN MUTATED 5P GAIN WILD-TYPE
  NO               55               107
  YES             128               173
[1] 2 2
[1] FALSE
                   vv
clus                HEAD & NECK SQUAMOUS CELL CARCINOMA
  5P GAIN MUTATED                                   198
  5P GAIN WILD-TYPE                                 313
                   vv
clus                HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  5P GAIN MUTATED                                                   2
  5P GAIN WILD-TYPE                                                 8
                   vv
clus                HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  5P GAIN MUTATED                                                           1
  5P GAIN WILD-TYPE                                                         0
D9V9, multiclass
                                                           clus
vv                                                          5P GAIN MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                   198
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       2
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT               1
                                                           clus
vv                                                          5P GAIN WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                     313
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                         8
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                 0
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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    43  32
  5Q GAIN WILD-TYPE 258 187
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               75               445 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               32               187 
$`5Q GAIN MUTATED`
TCGA-BB-A5HU TCGA-CN-6023 TCGA-CN-6997 TCGA-CN-A6V3 TCGA-CQ-7067 TCGA-DQ-5629 
       25.71        52.08        32.48        24.39        16.73        30.94 
TCGA-HD-8635 TCGA-BA-4074 TCGA-BA-5149 TCGA-BA-5556 TCGA-BA-6869 TCGA-BA-6870 
       22.85        15.19        26.50        23.84        21.17        14.83 
TCGA-BA-A4IF TCGA-BA-A6DI TCGA-BA-A6DL TCGA-BB-4223 TCGA-BB-4227 TCGA-BB-7861 
       29.42        11.05        20.48       105.90         4.41        22.42 
TCGA-BB-7864 TCGA-C9-A47Z TCGA-CN-4731 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-5363 
       50.20         6.28        32.81        14.33        45.83         8.32 
TCGA-CN-6011 TCGA-CN-A49B TCGA-CN-A6UY TCGA-CQ-6224 TCGA-CR-5243 TCGA-CR-6467 
       30.67        29.72        23.44        56.58        84.23        58.42 
TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6484 TCGA-CR-7389 TCGA-CR-7399 TCGA-CV-5431 
       39.52        36.99        11.64        12.89         5.95        17.16 
TCGA-CV-5439 TCGA-CV-5442 TCGA-CV-5444 TCGA-CV-6441 TCGA-CV-6936 TCGA-CV-6945 
       17.95        76.50        80.12         9.60         5.46        12.03 
TCGA-CV-6954 TCGA-CV-6956 TCGA-CV-7102 TCGA-CV-7178 TCGA-CV-7235 TCGA-CV-7245 
       65.82         7.13         1.84        71.21        77.16        26.20 
TCGA-CV-7416 TCGA-CV-A45U TCGA-CV-A463 TCGA-D6-8569 TCGA-DQ-5630 TCGA-DQ-7590 
       25.08        35.47         0.76        25.32        33.86        46.45 
TCGA-F7-A50J TCGA-F7-A61S TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-A6HZ TCGA-IQ-A61O 
       31.13        18.94        21.93        27.48         3.65        13.84 
TCGA-MT-A51W TCGA-MT-A67D TCGA-MZ-A5BI TCGA-MZ-A7D7 TCGA-P3-A5Q6 TCGA-P3-A5QA 
       14.37         1.84         7.13        17.98        15.78        71.74 
TCGA-P3-A6T2 TCGA-P3-A6T4 TCGA-P3-A6T8 TCGA-QK-A6IG TCGA-QK-A8ZA TCGA-QK-AA3K 
       75.55         2.04        13.15         7.30        12.20         8.32 
TCGA-TN-A7HJ TCGA-UF-A7JS TCGA-WA-A7GZ 
       13.25        22.36        20.55 

$`5Q GAIN WILD-TYPE`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4IG 
        9.30        37.28        20.48        68.48         3.55        28.11 
TCGA-BA-A4II TCGA-CN-4727 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6024 TCGA-CN-6992 
       30.18        51.29         9.07         9.24        11.08        35.05 
TCGA-CN-A6V1 TCGA-CQ-5323 TCGA-CQ-6221 TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CQ-A4C7 
       19.82        48.20        32.88        70.13        43.04        11.61 
TCGA-CR-6472 TCGA-CR-6478 TCGA-CX-7082 TCGA-CX-7219 TCGA-DQ-7588 TCGA-DQ-7589 
       34.52         6.02         0.36        34.36        14.04        46.32 
TCGA-DQ-7593 TCGA-H7-A6C5 TCGA-HD-8634 TCGA-UF-A71D TCGA-UF-A7JV TCGA-4P-AA8J 
       40.24        21.11        12.66        48.03         2.96         3.35 
TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 
       13.64         9.07        23.74        42.35        57.93        17.10 
TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IH 
       65.59        15.52        12.62         4.01        41.85        20.45 
TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF 
       27.95        11.54         7.10         5.69        14.47         7.82 
TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4224 TCGA-BB-4225 
        2.27        13.38        16.41         6.15         9.14         4.80 
TCGA-BB-4228 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7871 
       18.38        36.72        33.70        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-BB-A6UO TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 
        8.81        12.69        48.76        55.86        38.04         4.67 
TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 
       56.68        12.89        26.86        52.14        57.11        12.99 
TCGA-CN-4737 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 
       20.55        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-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-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 
       48.00        23.90        47.44        28.04        19.07        34.13 
TCGA-CN-6020 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 
        6.74        10.45        32.22        38.89         3.68        17.42 
TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49C 
       11.74        35.01        25.41        23.57        17.29        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-A6V6 TCGA-CN-A6V7 TCGA-CQ-5324 TCGA-CQ-5325 
       12.07         2.70        20.88        19.53        52.37        21.50 
TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 
        2.93        54.58        70.45        62.37        45.99        10.42 
TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6220 TCGA-CQ-6223 TCGA-CQ-6225 
       11.21         4.24        41.19        32.38        46.95        13.25 
TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7069 
        4.24        14.99        38.76        64.87        53.52        41.88 
TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD 
       43.10        77.56        44.48        23.24        29.36        33.60 
TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-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-6474 TCGA-CR-6477 TCGA-CR-6480 
       37.87        26.27        50.01        18.54        16.90        11.90 
TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 
       10.22        11.34         7.69        12.46        22.78        15.75 
TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 
        9.27        47.18        39.16        47.34        40.93        35.84 
TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 
        3.45         3.09        24.95        29.23         0.99        31.96 
TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 
        9.17        34.06        19.92        26.17        17.13        32.78 
TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 
       47.01        27.06        49.58        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        24.79         5.13        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-5440 TCGA-CV-5441 TCGA-CV-5443 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 
      107.51        94.88        91.53        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-6937 
       21.07        62.43        90.12         2.14         9.70        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-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-6959 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7090 
        8.42        28.34         2.50         4.14        64.83       172.67 
TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 
      111.16        18.81        12.66         7.99         9.01         5.26 
TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-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-7247 TCGA-CV-7248 TCGA-CV-7250 
       89.65        36.00        31.36        18.97        17.13        95.34 
TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7255 TCGA-CV-7261 TCGA-CV-7263 
        4.96        11.87        47.97         2.10        49.71        18.41 
TCGA-CV-7406 TCGA-CV-7407 TCGA-CV-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-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-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-A465 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE 
       67.86        56.61         7.07        15.25         5.98        35.34 
TCGA-CV-A6JM TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY 
        6.38        29.79         6.48        28.01         3.62        21.24 
TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-7086 
       23.47        19.92        22.52        10.42        10.55        18.84 
TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 
       51.12        13.25        25.41         9.60        23.05         2.53 
TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-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-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-5631 TCGA-DQ-7591 
       12.79        23.34        58.45        37.25        18.02        20.45 
TCGA-DQ-7592 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 
       37.58        40.04        39.12        41.59        37.18        32.71 
TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 
       21.63        20.25         3.02        24.95         0.46        17.85 
TCGA-F7-A622 TCGA-F7-A623 TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 
       11.80        20.25        12.43        13.38        15.16        15.06 
TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8224 
       20.94        33.76        28.47        25.74        27.48        14.66 
TCGA-HD-8314 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6I0 TCGA-HL-7533 
       22.03         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-A6SG TCGA-IQ-A6SH 
        0.07        33.57         5.29        13.68        19.04        15.48 
TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67F TCGA-MT-A67G 
       19.27        10.75         7.96        30.05        12.62         6.25 
TCGA-MT-A7BN TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW 
       15.42        16.08        29.92        51.25        10.85        36.82 
TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T3 TCGA-P3-A6T5 TCGA-P3-A6T6 TCGA-P3-A6T7 
       47.01        19.00        18.97        29.00        12.99        16.01 
TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ 
       21.07        21.21        23.15        21.47         9.34        12.72 
TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8Z9 
       27.39        21.07        19.73        12.89         5.62        14.76 
TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ 
       17.82        15.32        12.72        16.96         6.87        15.91 
TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-T3-A92M TCGA-T3-A92N TCGA-TN-A7HI TCGA-TN-A7HL 
        7.10        32.45        13.71         3.12        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-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ 
       74.47        17.95        24.30        55.43        29.46        18.05 
TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JT TCGA-UP-A6WW TCGA-WA-A7H4 TCGA-KU-A66S 
       13.94        20.75        32.65        17.03        14.56        13.35 
TCGA-KU-A66T 
       18.15 

  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 
            22.36             21.07 
[1] "0.8 - 105.9 (22.4)" "0.1 - 211.0 (21.1)"
[1] "hr=" "1.1"
D10V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  5Q GAIN MUTATED         3        4        12        42         1         0
  5Q GAIN WILD-TYPE      24       72        70       210        11         1
D10V3, multiclass
           clus
vv          5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  STAGE I                 3                24
  STAGE II                4                72
  STAGE III              12                70
  STAGE IVA              42               210
  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  16  18  25
  5Q GAIN WILD-TYPE    44 121  82 148
D10V4, multiclass
       clus
vv      5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  T0+T1               6                44
  T2                 16               121
  T3                 18                82
  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
  5Q GAIN MUTATED    18  11  32   1
  5Q GAIN WILD-TYPE 161  57 136   7
D10V5, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  N0              18               161
  N1              11                57
  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"
D10V6, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED    25   0
  5Q GAIN WILD-TYPE 165   1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     25    0
  5Q GAIN WILD-TYPE  165    1
   clus
vv  5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  0              25               165
  1               0                 1
[1] 2 2
[1] FALSE
D10V7, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED    16  59
  5Q GAIN WILD-TYPE 124 323
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     16   59
  5Q GAIN WILD-TYPE  124  323
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  FEMALE              16               124
  MALE                59               323
[1] 2 2
[1] FALSE
D10V8, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED    18  50
  5Q GAIN WILD-TYPE 144 251
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     18   50
  5Q GAIN WILD-TYPE  144  251
     clus
vv    5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  NO               18               144
  YES              50               251
[1] 2 2
[1] FALSE
                   vv
clus                HEAD & NECK SQUAMOUS CELL CARCINOMA
  5Q GAIN MUTATED                                    74
  5Q GAIN WILD-TYPE                                 437
                   vv
clus                HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  5Q GAIN MUTATED                                                   0
  5Q GAIN WILD-TYPE                                                10
                   vv
clus                HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  5Q GAIN MUTATED                                                           1
  5Q GAIN WILD-TYPE                                                         0
D10V9, multiclass
                                                           clus
vv                                                          5Q GAIN MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                    74
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       0
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT               1
                                                           clus
vv                                                          5Q GAIN WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                     437
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        10
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                 0
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V10, continuous
D10V11, continuous
D10V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  5Q GAIN MUTATED                                  0     2
  5Q GAIN WILD-TYPE                                2     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  5Q GAIN MUTATED                           8    64
  5Q GAIN WILD-TYPE                        40   382
D10V13, multiclass
                                  clus
vv                                 5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          2                 9
  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"
D10V14, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED     7  65
  5Q GAIN WILD-TYPE  19 394
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      7   65
  5Q GAIN WILD-TYPE   19  394
                        clus
vv                       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   7                19
  NOT HISPANIC OR LATINO              65               394
[1] 2 2
[1] FALSE

Clustering(11) Variable = 6P GAIN MUTATION ANALYSIS
D11V1, survival
                   sevent
clus2                 0   1
  6P GAIN MUTATED    46  38
  6P GAIN WILD-TYPE 255 181
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               84               436 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               38               181 
$`6P GAIN MUTATED`
TCGA-BA-4075 TCGA-BA-A4II TCGA-CN-6022 TCGA-CN-6023 TCGA-CQ-7067 TCGA-CQ-A4C7 
        9.30        30.18         9.24        52.08        16.73        11.61 
TCGA-BA-5555 TCGA-BA-6870 TCGA-BA-6873 TCGA-BA-A6DI TCGA-BB-4224 TCGA-BB-7870 
       17.10        14.83         4.01        11.05         9.14        66.28 
TCGA-BB-A5HY TCGA-C9-A47Z TCGA-CN-4723 TCGA-CN-5356 TCGA-CN-5363 TCGA-CN-5367 
       10.55         6.28        55.86        46.32         8.32        11.57 
TCGA-CN-6020 TCGA-CN-6989 TCGA-CN-A49A TCGA-CN-A63U TCGA-CN-A63W TCGA-CN-A641 
        6.74        32.22        17.29        31.69        12.39        12.07 
TCGA-CN-A6V6 TCGA-CQ-5329 TCGA-CQ-5331 TCGA-CQ-5334 TCGA-CQ-6220 TCGA-CQ-A4CE 
       20.88        70.45        45.99         4.24        32.38        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-A465 TCGA-CV-A6JE TCGA-CV-A6JU 
       22.85        22.19        35.47         7.07        35.34         3.62 
TCGA-D6-A6EP TCGA-DQ-5625 TCGA-F7-A50I TCGA-H7-8502 TCGA-HD-7753 TCGA-HD-7831 
       13.94        37.25         3.02        15.06        28.47        21.93 
TCGA-HD-7917 TCGA-HD-A6I0 TCGA-IQ-A61E TCGA-IQ-A61L TCGA-IQ-A6SH TCGA-MT-A51W 
       27.48         6.90        37.71        13.68        15.48        14.37 
TCGA-MT-A67D TCGA-MZ-A5BI TCGA-P3-A5Q6 TCGA-P3-A6SW TCGA-P3-A6T3 TCGA-P3-A6T4 
        1.84         7.13        15.78        36.82        18.97         2.04 
TCGA-QK-A6IG TCGA-QK-A6VB TCGA-QK-A8Z7 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-RS-A6TO 
        7.30        21.07        12.89        14.76        12.20        12.72 
TCGA-TN-A7HJ TCGA-UF-A719 TCGA-UF-A7JD TCGA-UF-A7JH TCGA-UF-A7JK TCGA-KU-A66T 
       13.25        54.67        24.30        29.46        13.94        18.15 

$`6P GAIN WILD-TYPE`
TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4IG TCGA-BB-A5HU 
       37.28        20.48        68.48         3.55        28.11        25.71 
TCGA-CN-4727 TCGA-CN-6021 TCGA-CN-6024 TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-A6V1 
       51.29         9.07        11.08        35.05        32.48        19.82 
TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-6221 TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CR-6472 
       24.39        48.20        32.88        70.13        43.04        34.52 
TCGA-CR-6478 TCGA-CX-7082 TCGA-CX-7219 TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7589 
        6.02         0.36        34.36        30.94        14.04        46.32 
TCGA-DQ-7593 TCGA-H7-A6C5 TCGA-HD-8634 TCGA-HD-8635 TCGA-UF-A71D TCGA-UF-A7JV 
       40.24        21.11        12.66        22.85        48.03         2.96 
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 
        3.35        15.19        13.64         9.07        26.50        23.74 
TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6869 
       42.35        57.93        23.84        65.59        15.52        21.17 
TCGA-BA-6872 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IH TCGA-BA-A6D8 TCGA-BA-A6DA 
       12.62        41.85        29.42        20.45        27.95        11.54 
TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-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-4225 TCGA-BB-4227 
       20.48        16.41         6.15       105.90         4.80         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-A5HZ TCGA-BB-A6UM 
       24.66        38.40        71.05        20.52        27.19        12.92 
TCGA-BB-A6UO TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4728 
        8.81        12.69        48.76        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-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 
       20.55        14.33        45.83        27.58        73.61        13.05 
TCGA-CN-5355 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5364 TCGA-CN-5365 
       42.02         8.58        12.39        71.31        16.21        11.54 
TCGA-CN-5366 TCGA-CN-5369 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 
       11.84        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-6988 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6998 
       34.13        10.45        38.89         3.68        17.42        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-A642 TCGA-CN-A6UY TCGA-CN-A6V7 
       22.32        16.57         4.41         2.70        23.44        19.53 
TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5330 TCGA-CQ-5332 
       52.37        21.50         2.93        54.58        62.37        10.42 
TCGA-CQ-5333 TCGA-CQ-6218 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 
       11.21        41.19        46.95        56.58        13.25         4.24 
TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7069 TCGA-CQ-7071 
       14.99        38.76        64.87        53.52        41.88        43.10 
TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CG 
       77.56        44.48        23.24        29.36        33.60        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-6473 TCGA-CR-6474 TCGA-CR-6477 
       58.42        50.01        39.52        36.99        18.54        16.90 
TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6488 TCGA-CR-6491 
       11.90        10.22        11.34        11.64        12.46        22.78 
TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7369 
       15.75         9.27        47.18        39.16        47.34        35.84 
TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 
        3.45         3.09        24.95        29.23         0.99        31.96 
TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 
        9.17        34.06        19.92        26.17        17.13        32.78 
TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 
       47.01        27.06        49.58        30.02        46.85        32.65 
TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 
       44.25        30.58        24.79         5.13         5.95        35.41 
TCGA-CR-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-5443 TCGA-CV-5444 TCGA-CV-5966 
       17.95       107.51        94.88        91.53        80.12        17.92 
TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5978 TCGA-CV-5979 
       13.35        23.05        86.83        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-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-6955 TCGA-CV-6956 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-6962 TCGA-CV-7089 
       10.98         7.13        28.34         2.50         4.14        64.83 
TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 
      172.67       111.16        18.81        12.66         7.99         9.01 
TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-7178 
        5.26         1.84        52.31        12.92        21.80        71.21 
TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7245 
       10.75       130.88         4.73        89.65        36.00        26.20 
TCGA-CV-7247 TCGA-CV-7248 TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7261 
       18.97        17.13         4.96        11.87        47.97        49.71 
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-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-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-A6JM TCGA-CV-A6JN 
        0.76        56.61        15.25         5.98         6.38        29.79 
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-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        23.34        58.45 
TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7594 
       33.86        18.02        46.45        20.45        37.58        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-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 
       31.13        18.94        24.95         0.46        17.85        11.80 
TCGA-F7-A623 TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-A76A TCGA-HD-7229 
       20.25        12.43        13.38        15.16        20.94        33.76 
TCGA-HD-7754 TCGA-HD-7832 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-A4C1 TCGA-HD-A633 
       25.74        27.48        14.66        22.03         0.36        13.84 
TCGA-HD-A634 TCGA-HD-A6HZ TCGA-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-A6H7 TCGA-KU-A6H8 TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67F 
       19.04        19.27        10.75         7.96        30.05        12.62 
TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5QA 
        6.25        15.42        16.08        17.98        29.92        71.74 
TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T5 
       51.25        10.85        47.01        19.00        75.55        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        27.39        19.73         5.62 
TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ 
       17.82        15.32         8.32        16.96         6.87        15.91 
TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-T3-A92M TCGA-T3-A92N TCGA-TN-A7HI TCGA-TN-A7HL 
        7.10        32.45        13.71         3.12        13.55        20.35 
TCGA-UF-A718 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA 
       64.80         2.83        49.51        49.45        44.65        74.47 
TCGA-UF-A7JC TCGA-UF-A7JF TCGA-UF-A7JJ TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT 
       17.95        55.43        18.05        20.75        22.36        32.65 
TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 TCGA-KU-A66S 
       17.03        20.55        14.56        13.35 

  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 
           17.195            21.485 
[1] "1.8 - 139.4 (17.2)" "0.1 - 211.0 (21.5)"
[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        15        40         4         0
  6P GAIN WILD-TYPE      23       64        67       212         8         1
D11V3, multiclass
           clus
vv          6P GAIN MUTATED 6P GAIN WILD-TYPE
  STAGE I                 4                23
  STAGE II               12                64
  STAGE III              15                67
  STAGE IVA              40               212
  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  18  32
  6P GAIN WILD-TYPE    46 114  82 141
D11V4, multiclass
       clus
vv      6P GAIN MUTATED 6P GAIN WILD-TYPE
  T0+T1               4                46
  T2                 23               114
  T3                 18                82
  T4                 32               141
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  6P GAIN MUTATED    31  12  28   2
  6P GAIN WILD-TYPE 148  56 140   6
D11V5, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  N0              31               148
  N1              12                56
  N2              28               140
  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    34   0
  6P GAIN WILD-TYPE 156   1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     34    0
  6P GAIN WILD-TYPE  156    1
   clus
vv  6P GAIN MUTATED 6P GAIN WILD-TYPE
  0              34               156
  1               0                 1
[1] 2 2
[1] FALSE
D11V7, binary
                   cls
clus                  0   1
  6P GAIN MUTATED    19  66
  6P GAIN WILD-TYPE 121 316
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     19   66
  6P GAIN WILD-TYPE  121  316
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  FEMALE              19               121
  MALE                66               316
[1] 2 2
[1] FALSE
D11V8, binary
                   cls
clus                  0   1
  6P GAIN MUTATED    30  48
  6P GAIN WILD-TYPE 132 253
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     30   48
  6P GAIN WILD-TYPE  132  253
     clus
vv    6P GAIN MUTATED 6P GAIN WILD-TYPE
  NO               30               132
  YES              48               253
[1] 2 2
[1] FALSE
                   vv
clus                HEAD & NECK SQUAMOUS CELL CARCINOMA
  6P GAIN MUTATED                                    83
  6P GAIN WILD-TYPE                                 428
                   vv
clus                HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  6P GAIN MUTATED                                                   2
  6P GAIN WILD-TYPE                                                 8
                   vv
clus                HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  6P GAIN MUTATED                                                           0
  6P GAIN WILD-TYPE                                                         1
D11V9, multiclass
                                                           clus
vv                                                          6P GAIN MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                    83
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       2
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT               0
                                                           clus
vv                                                          6P GAIN WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                     428
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                         8
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                 1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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    64
  6P GAIN WILD-TYPE                        33   382
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                                         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"
D11V14, binary
                   cls
clus                  0   1
  6P GAIN MUTATED     5  72
  6P GAIN WILD-TYPE  21 387
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      5   72
  6P GAIN WILD-TYPE   21  387
                        clus
vv                       6P GAIN MUTATED 6P GAIN WILD-TYPE
  HISPANIC OR LATINO                   5                21
  NOT HISPANIC OR LATINO              72               387
[1] 2 2
[1] FALSE

Clustering(12) Variable = 6Q GAIN MUTATION ANALYSIS
D12V1, survival
                   sevent
clus2                 0   1
  6Q GAIN MUTATED    36  27
  6Q GAIN WILD-TYPE 265 192
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               63               457 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               27               192 
$`6Q GAIN MUTATED`
TCGA-BA-4075 TCGA-BA-A4II TCGA-BB-A5HU TCGA-CN-6022 TCGA-CQ-7067 TCGA-CX-7219 
        9.30        30.18        25.71         9.24        16.73        34.36 
TCGA-BA-6873 TCGA-BB-7870 TCGA-C9-A47Z TCGA-CN-4723 TCGA-CN-5356 TCGA-CN-5363 
        4.01        66.28         6.28        55.86        46.32         8.32 
TCGA-CN-A49A TCGA-CN-A63U TCGA-CN-A63W TCGA-CN-A6V6 TCGA-CQ-5331 TCGA-CQ-5334 
       17.29        31.69        12.39        20.88        45.99         4.24 
TCGA-CQ-6220 TCGA-CQ-A4CE TCGA-CR-5247 TCGA-CR-7380 TCGA-CR-7389 TCGA-CV-5430 
       32.38        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-A6JE TCGA-CV-A6JM TCGA-CV-A6JU TCGA-D6-A6EP TCGA-DQ-5625 
        7.07        35.34         6.38         3.62        13.94        37.25 
TCGA-F7-A50I TCGA-HD-7753 TCGA-HD-7831 TCGA-HD-7917 TCGA-HD-A6I0 TCGA-IQ-A61E 
        3.02        28.47        21.93        27.48         6.90        37.71 
TCGA-IQ-A61L TCGA-IQ-A6SH TCGA-MT-A51W TCGA-MT-A67D TCGA-MZ-A5BI TCGA-P3-A5Q6 
       13.68        15.48        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        12.89        12.20        12.72 
TCGA-UF-A719 TCGA-UF-A71E TCGA-KU-A66T 
       54.67        49.45        18.15 

$`6Q GAIN WILD-TYPE`
TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4IG TCGA-CN-4727 
       37.28        20.48        68.48         3.55        28.11        51.29 
TCGA-CN-6021 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-A6V1 
        9.07        52.08        11.08        35.05        32.48        19.82 
TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-6221 TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CQ-A4C7 
       24.39        48.20        32.88        70.13        43.04        11.61 
TCGA-CR-6472 TCGA-CR-6478 TCGA-CX-7082 TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7589 
       34.52         6.02         0.36        30.94        14.04        46.32 
TCGA-DQ-7593 TCGA-H7-A6C5 TCGA-HD-8634 TCGA-HD-8635 TCGA-UF-A71D TCGA-UF-A7JV 
       40.24        21.11        12.66        22.85        48.03         2.96 
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 
        3.35        15.19        13.64         9.07        26.50        23.74 
TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-6868 
       42.35        57.93        17.10        23.84        65.59        15.52 
TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6872 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IH 
       21.17        14.83        12.62        41.85        29.42        20.45 
TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF 
       27.95        11.54         7.10         5.69        14.47         7.82 
TCGA-BA-A6DG TCGA-BA-A6DI TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 
        2.27        11.05        13.38        20.48        16.41         6.15 
TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 
      105.90         9.14         4.80         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-8596 TCGA-BB-8601 TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO 
       71.05        20.52        10.55        27.19        12.92         8.81 
TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4729 
       12.69        48.76        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-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-6020 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-6995 
       34.13         6.74        10.45        32.22        38.89         3.68 
TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49B 
       17.42        11.74        35.01        25.41        23.57        29.72 
TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 
       21.21         7.40        22.32        16.57         4.41        12.07 
TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V7 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 
        2.70        23.44        19.53        52.37        21.50         2.93 
TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-6218 
       54.58        70.45        62.37        10.42        11.21        41.19 
TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 
       46.95        56.58        13.25         4.24        14.99        38.76 
TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 
       64.87        53.52        41.88        43.10        77.56        44.48 
TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI 
       23.24        29.36        33.60        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-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6480 TCGA-CR-6481 
       39.52        36.99        18.54        16.90        11.90        10.22 
TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 
       11.34        11.64         7.69        12.46        22.78        15.75 
TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 
        9.27        47.18        39.16        47.34        40.93        35.84 
TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 
        3.45         3.09        24.95        29.23         0.99        31.96 
TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-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-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 
       27.06        49.58        30.02        46.85        32.65        44.25 
TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 
       30.58        24.79         5.13         5.95        35.41        29.95 
TCGA-CR-7404 TCGA-CV-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-5443 TCGA-CV-5444 TCGA-CV-5966 
       17.95       107.51        94.88        91.53        80.12        17.92 
TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5976 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6433 
       13.35        23.05        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-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-7089 
       65.82        10.98         7.13        28.34         2.50        64.83 
TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 
      172.67       111.16        18.81        12.66         7.99         9.01 
TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-7178 
        5.26         1.84        52.31        12.92        21.80        71.21 
TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7242 
       10.75       130.88        77.16         4.73        89.65        36.00 
TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7252 
       31.36        26.20        18.97        17.13        95.34         4.96 
TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7407 
       11.87        47.97        49.71        18.41        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-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-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-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-A468 
       48.20        60.43        67.86         0.76        56.61        15.25 
TCGA-CV-A6JD TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JY TCGA-CV-A6JZ 
        5.98        29.79         6.48        28.01        21.24        23.47 
TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-A4AQ 
       19.92        22.52        10.42        10.55        18.84        51.12 
TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 
       13.25        25.41         9.60        23.05         2.53        16.14 
TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB 
       11.44        18.67        24.95        25.32        17.72        12.36 
TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EN TCGA-D6-A6EO TCGA-D6-A6EQ TCGA-D6-A6ES 
       28.77         7.63        22.59        24.95        12.10        12.79 
TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7590 TCGA-DQ-7591 
       23.34        58.45        33.86        18.02        46.45        20.45 
TCGA-DQ-7592 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 
       37.58        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-H7-8502 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7754 TCGA-HD-7832 TCGA-HD-8224 
       15.06        20.94        33.76        25.74        27.48        14.66 
TCGA-HD-8314 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HL-7533 
       22.03         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-A6H7 TCGA-KU-A6H8 
       33.57         5.29        13.84        19.04        19.27        10.75 
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-A6T3 TCGA-P3-A6T5 TCGA-P3-A6T6 
       47.01        19.00        75.55        18.97        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-A6VC TCGA-QK-A8Z8 TCGA-QK-A8Z9 
        9.34        12.72        27.39        19.73         5.62        14.76 
TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ 
       17.82        15.32         8.32        16.96         6.87        15.91 
TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-T3-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-A7J9 TCGA-UF-A7JA 
       20.35        64.80         2.83        49.51        44.65        74.47 
TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK 
       17.95        24.30        55.43        29.46        18.05        13.94 
TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 
       20.75        22.36        32.65        17.03        20.55        14.56 
TCGA-KU-A66S 
       13.35 

  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 
            17.29             21.24 
[1] "1.8 - 180.2 (17.3)" "0.1 - 211.0 (21.2)"
[1] "hr=" "1.1"
D12V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  6Q GAIN MUTATED         3        8        14        27         4         0
  6Q GAIN WILD-TYPE      24       68        68       225         8         1
D12V3, multiclass
           clus
vv          6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  STAGE I                 3                24
  STAGE II                8                68
  STAGE III              14                68
  STAGE IVA              27               225
  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
  6Q GAIN MUTATED       3  17  12  26
  6Q GAIN WILD-TYPE    47 120  88 147
D12V4, multiclass
       clus
vv      6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  T0+T1               3                47
  T2                 17               120
  T3                 12                88
  T4                 26               147
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  6Q GAIN MUTATED    27  11  16   1
  6Q GAIN WILD-TYPE 152  57 152   7
D12V5, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  N0              27               152
  N1              11                57
  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    23   0
  6Q GAIN WILD-TYPE 167   1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED     23    0
  6Q GAIN WILD-TYPE  167    1
   clus
vv  6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  0              23               167
  1               0                 1
[1] 2 2
[1] FALSE
D12V7, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED    16  48
  6Q GAIN WILD-TYPE 124 334
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED     16   48
  6Q GAIN WILD-TYPE  124  334
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  FEMALE              16               124
  MALE                48               334
[1] 2 2
[1] FALSE
D12V8, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED    28  32
  6Q GAIN WILD-TYPE 134 269
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED     28   32
  6Q GAIN WILD-TYPE  134  269
     clus
vv    6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  NO               28               134
  YES              32               269
[1] 2 2
[1] FALSE
                   vv
clus                HEAD & NECK SQUAMOUS CELL CARCINOMA
  6Q GAIN MUTATED                                    62
  6Q GAIN WILD-TYPE                                 449
                   vv
clus                HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  6Q GAIN MUTATED                                                   2
  6Q GAIN WILD-TYPE                                                 8
                   vv
clus                HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  6Q GAIN MUTATED                                                           0
  6Q GAIN WILD-TYPE                                                         1
D12V9, multiclass
                                                           clus
vv                                                          6Q GAIN MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                    62
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       2
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT               0
                                                           clus
vv                                                          6Q GAIN WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                     449
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                         8
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                 1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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                           9    51
  6Q GAIN WILD-TYPE                        39   395
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                      9                39
  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"
D12V14, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED     7  52
  6Q GAIN WILD-TYPE  19 407
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      7   52
  6Q GAIN WILD-TYPE   19  407
                        clus
vv                       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   7                19
  NOT HISPANIC OR LATINO              52               407
[1] 2 2
[1] FALSE

Clustering(13) Variable = 7P GAIN MUTATION ANALYSIS
D13V1, survival
                   sevent
clus2                 0   1
  7P GAIN MUTATED    86  97
  7P GAIN WILD-TYPE 215 122
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              183               337 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               97               122 
$`7P GAIN MUTATED`
TCGA-BA-4075 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CQ-7067 TCGA-CQ-7068 
        9.30         9.24        52.08        11.08        16.73        43.04 
TCGA-CQ-A4C7 TCGA-CR-6478 TCGA-CX-7219 TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7589 
       11.61         6.02        34.36        30.94        14.04        46.32 
TCGA-H7-A6C5 TCGA-HD-8634 TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-5149 TCGA-BA-5555 
       21.11        12.66        15.19        13.64        26.50        17.10 
TCGA-BA-6870 TCGA-BA-A6DI TCGA-BA-A6DL TCGA-BB-4224 TCGA-BB-7863 TCGA-BB-7870 
       14.83        11.05        20.48         9.14        33.70        66.28 
TCGA-BB-8596 TCGA-BB-8601 TCGA-BB-A5HY TCGA-C9-A47Z TCGA-CN-4722 TCGA-CN-4729 
       71.05        20.52        10.55         6.28        48.76        12.89 
TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-5356 
       26.86        32.81        20.55        14.33        45.83        46.32 
TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5363 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 
        8.58        12.39         8.32        11.54        11.84        11.57 
TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6020 TCGA-CN-6988 TCGA-CN-6989 
       30.67        48.00        23.90         6.74        10.45        32.22 
TCGA-CN-6995 TCGA-CN-A49A TCGA-CN-A63T TCGA-CN-A63V TCGA-CN-A641 TCGA-CQ-5329 
        3.68        17.29         7.40        22.32        12.07        70.45 
TCGA-CQ-5334 TCGA-CQ-6220 TCGA-CQ-6225 TCGA-CQ-7069 TCGA-CQ-7072 TCGA-CQ-A4C9 
        4.24        32.38        13.25        41.88        77.56        23.24 
TCGA-CQ-A4CH TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6484 TCGA-CR-7364 TCGA-CR-7365 
       12.46        18.54        16.90        11.64        47.18        39.16 
TCGA-CR-7367 TCGA-CR-7370 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7382 
       47.34         3.45         9.17        34.06        19.92        26.17 
TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7398 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 
       12.89        49.58         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       172.67       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 
       49.71        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-D6-6516 TCGA-D6-6823 
        6.48        28.01        23.47        18.84        25.41        23.05 
TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8569 TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EP 
       11.44        18.67        25.32        28.77         7.63        13.94 
TCGA-DQ-5625 TCGA-DQ-5631 TCGA-DQ-7592 TCGA-F7-8298 TCGA-F7-A50I TCGA-F7-A50J 
       37.25        18.02        37.58        32.71         3.02        31.13 
TCGA-F7-A61S TCGA-F7-A622 TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7831 TCGA-HD-7917 
       18.94        11.80        33.76        28.47        21.93        27.48 
TCGA-HD-A633 TCGA-IQ-7631 TCGA-IQ-A61H TCGA-IQ-A61K TCGA-IQ-A61O TCGA-IQ-A6SG 
       13.84        38.53        37.41         5.29        13.84        19.04 
TCGA-IQ-A6SH TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67G TCGA-MZ-A7D7 
       15.48        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        12.89        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 TCGA-KU-A66T 
       13.94        20.55        18.15 

$`7P GAIN WILD-TYPE`
TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4IG TCGA-BA-A4II 
       37.28        20.48        68.48         3.55        28.11        30.18 
TCGA-BB-A5HU TCGA-CN-4727 TCGA-CN-6021 TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-A6V1 
       25.71        51.29         9.07        35.05        32.48        19.82 
TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-6221 TCGA-CQ-7063 TCGA-CR-6472 TCGA-CX-7082 
       24.39        48.20        32.88        70.13        34.52         0.36 
TCGA-DQ-7593 TCGA-HD-8635 TCGA-UF-A71D TCGA-UF-A7JV TCGA-4P-AA8J TCGA-BA-4078 
       40.24        22.85        48.03         2.96         3.35         9.07 
TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-6868 
       23.74        42.35        57.93        23.84        65.59        15.52 
TCGA-BA-6869 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IH 
       21.17        12.62         4.01        41.85        29.42        20.45 
TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF 
       27.95        11.54         7.10         5.69        14.47         7.82 
TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4225 
        2.27        13.38        16.41         6.15       105.90         4.80 
TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7864 TCGA-BB-7866 
        4.41        18.38        22.42        36.72        50.20        44.98 
TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO TCGA-C9-A480 
       24.66        38.40        27.19        12.92         8.81        12.69 
TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4733 TCGA-CN-4735 
       55.86        38.04         4.67        56.68        52.14        57.11 
TCGA-CN-4736 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5360 
       12.99        27.58        73.61        13.05        42.02        71.31 
TCGA-CN-5364 TCGA-CN-5369 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 
       16.21        12.49         8.52        52.08        56.94        50.07 
TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6994 TCGA-CN-6996 
       47.44        28.04        19.07        34.13        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-A6V6 TCGA-CN-A6V7 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 
       20.88        19.53        52.37        21.50         2.93        54.58 
TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-6218 TCGA-CQ-6223 
       62.37        45.99        10.42        11.21        41.19        46.95 
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-7071 TCGA-CQ-A4C6 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG 
       43.10        44.48        29.36        33.60        29.49        14.14 
TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 
       31.23        84.23        11.77        54.67        37.87        26.27 
TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6480 TCGA-CR-6481 
       58.42        50.01        39.52        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-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7391 
       31.96        17.13        32.78        47.01        27.06        30.02 
TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7399 
       46.85        32.65        44.25        30.58        24.79         5.95 
TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5441 
       35.41        29.95        48.39        76.24        19.20        94.88 
TCGA-CV-5443 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 
       91.53        17.92        13.35        23.05        86.83        48.59 
TCGA-CV-5977 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 
       60.49        43.23        54.74        21.07        62.43         9.60 
TCGA-CV-6934 TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6941 TCGA-CV-6942 
        2.14        20.52         4.73        21.90        11.24       140.78 
TCGA-CV-6943 TCGA-CV-6948 TCGA-CV-6952 TCGA-CV-6955 TCGA-CV-6956 TCGA-CV-6959 
       19.79        42.38         6.08        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-7183 TCGA-CV-7238 
        9.01         1.84        52.31        12.92       130.88        89.65 
TCGA-CV-7242 TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7406 TCGA-CV-7410 
       36.00        95.34         4.96        11.87        57.47       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-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-A45O TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45R 
        7.17         6.38        27.98        21.01       169.38       180.16 
TCGA-CV-A45T TCGA-CV-A45W TCGA-CV-A45Y TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A464 
      159.65        45.96        88.87        60.43        67.86        56.61 
TCGA-CV-A465 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CV-A6JU 
        7.07        15.25         5.98        35.34        29.79         3.62 
TCGA-CV-A6JY TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-A4AQ 
       21.24        19.92        22.52        10.42        10.55        51.12 
TCGA-D6-6515 TCGA-D6-6517 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-8568 TCGA-D6-A4Z9 
       13.25         9.60         2.53        16.14        24.95        17.72 
TCGA-D6-A4ZB TCGA-D6-A6EN TCGA-D6-A6EO TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q 
       12.36        22.59        24.95        12.10        12.79        23.34 
TCGA-DQ-5624 TCGA-DQ-5630 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7594 TCGA-DQ-7595 
       58.45        33.86        46.45        20.45        40.04        39.12 
TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A61V TCGA-F7-A61W 
       41.59        37.18        21.63        20.25        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-A76A TCGA-HD-7754 TCGA-HD-7832 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-A4C1 
       20.94        25.74        27.48        14.66        22.03         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-A6H7 
       37.71        11.84         0.07        33.57        13.68        19.27 
TCGA-KU-A6H8 TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-MZ-A6I9 
       10.75         1.84        12.62        15.42         7.13        16.08 
TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6T0 
       29.92        71.74        51.25        10.85        36.82        19.00 
TCGA-P3-A6T2 TCGA-P3-A6T5 TCGA-P3-A6T7 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF 
       75.55        29.00        16.01        21.07        21.21        23.15 
TCGA-QK-A6IH TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A8Z8 TCGA-QK-A8Z9 
       21.47        12.72        27.39        21.07         5.62        14.76 
TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-RS-A6TP TCGA-T2-A6WX 
       12.20        17.82        15.32         8.32        16.96         6.87 
TCGA-T2-A6X0 TCGA-T3-A92M TCGA-TN-A7HI TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A719 
        7.10        13.71        13.55        20.35        64.80        54.67 
TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH 
        2.83        49.51        17.95        24.30        55.43        29.46 
TCGA-UF-A7JJ TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UP-A6WW TCGA-WA-A7H4 
       18.05        20.75        22.36        32.65        17.03        14.56 
TCGA-KU-A66S 
       13.35 

  7P GAIN MUTATED 7P GAIN WILD-TYPE 
             0.76              0.07 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
           172.67            210.97 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
            18.94             22.36 
[1] "0.8 - 172.7 (18.9)" "0.1 - 211.0 (22.4)"
[1] "hr=" "1.6"
D13V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  7P GAIN MUTATED         9       29        31        92         6         0
  7P GAIN WILD-TYPE      18       47        51       160         6         1
D13V3, multiclass
           clus
vv          7P GAIN MUTATED 7P GAIN WILD-TYPE
  STAGE I                 9                18
  STAGE II               29                47
  STAGE III              31                51
  STAGE IVA              92               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
  7P GAIN MUTATED      13  50  40  67
  7P GAIN WILD-TYPE    37  87  60 106
D13V4, multiclass
       clus
vv      7P GAIN MUTATED 7P GAIN WILD-TYPE
  T0+T1              13                37
  T2                 50                87
  T3                 40                60
  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
  7P GAIN MUTATED    65  23  61   4
  7P GAIN WILD-TYPE 114  45 107   4
D13V5, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  N0              65               114
  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    63   0
  7P GAIN WILD-TYPE 127   1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     63    0
  7P GAIN WILD-TYPE  127    1
   clus
vv  7P GAIN MUTATED 7P GAIN WILD-TYPE
  0              63               127
  1               0                 1
[1] 2 2
[1] FALSE
D13V7, binary
                   cls
clus                  0   1
  7P GAIN MUTATED    49 135
  7P GAIN WILD-TYPE  91 247
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     49  135
  7P GAIN WILD-TYPE   91  247
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  FEMALE              49                91
  MALE               135               247
[1] 2 2
[1] FALSE
D13V8, binary
                   cls
clus                  0   1
  7P GAIN MUTATED    56  98
  7P GAIN WILD-TYPE 106 203
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     56   98
  7P GAIN WILD-TYPE  106  203
     clus
vv    7P GAIN MUTATED 7P GAIN WILD-TYPE
  NO               56               106
  YES              98               203
[1] 2 2
[1] FALSE
                   vv
clus                HEAD & NECK SQUAMOUS CELL CARCINOMA
  7P GAIN MUTATED                                   181
  7P GAIN WILD-TYPE                                 330
                   vv
clus                HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  7P GAIN MUTATED                                                   2
  7P GAIN WILD-TYPE                                                 8
                   vv
clus                HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  7P GAIN MUTATED                                                           1
  7P GAIN WILD-TYPE                                                         0
D13V9, multiclass
                                                           clus
vv                                                          7P GAIN MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                   181
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       2
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT               1
                                                           clus
vv                                                          7P GAIN WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                     330
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                         8
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                 0
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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   153
  7P GAIN WILD-TYPE                        26   293
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                                        153               293
[1] 4 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     9 165
  7P GAIN WILD-TYPE  17 294
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      9  165
  7P GAIN WILD-TYPE   17  294
                        clus
vv                       7P GAIN MUTATED 7P GAIN WILD-TYPE
  HISPANIC OR LATINO                   9                17
  NOT HISPANIC OR LATINO             165               294
[1] 2 2
[1] FALSE

Clustering(14) Variable = 7Q GAIN MUTATION ANALYSIS
D14V1, survival
                   sevent
clus2                 0   1
  7Q GAIN MUTATED    60  67
  7Q GAIN WILD-TYPE 241 152
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              127               393 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               67               152 
$`7Q GAIN MUTATED`
TCGA-CN-4727 TCGA-CN-6023 TCGA-CN-6024 TCGA-CQ-7067 TCGA-CQ-A4C7 TCGA-CR-6478 
       51.29        52.08        11.08        16.73        11.61         6.02 
TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-BA-6870 TCGA-BA-A6DI TCGA-BB-7863 
       30.94        14.04        46.32        14.83        11.05        33.70 
TCGA-BB-7870 TCGA-BB-8596 TCGA-BB-8601 TCGA-BB-A5HY TCGA-C9-A47Z TCGA-CN-4722 
       66.28        71.05        20.52        10.55         6.28        48.76 
TCGA-CN-4729 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5360 
       12.89        14.33        45.83        46.32         8.58        71.31 
TCGA-CN-5363 TCGA-CN-5365 TCGA-CN-5367 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6020 
        8.32        11.54        11.57        48.00        23.90         6.74 
TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6995 TCGA-CN-A49A TCGA-CN-A63T TCGA-CN-A63V 
       10.45        32.22         3.68        17.29         7.40        22.32 
TCGA-CN-A641 TCGA-CQ-6225 TCGA-CQ-7069 TCGA-CQ-7072 TCGA-CQ-A4C9 TCGA-CR-7370 
       12.07        13.25        41.88        77.56        23.24         3.45 
TCGA-CR-7389 TCGA-CR-7390 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 
       12.89        49.58       139.43        17.16       129.21       108.95 
TCGA-CV-5435 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5442 TCGA-CV-5978 TCGA-CV-6933 
       76.24        17.95       107.51        76.50         7.07        90.12 
TCGA-CV-6935 TCGA-CV-6941 TCGA-CV-6945 TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6962 
        9.70        11.24        12.03        15.09        30.08         4.14 
TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7101 TCGA-CV-7177 TCGA-CV-7178 TCGA-CV-7235 
      172.67       111.16         5.26        21.80        71.21        77.16 
TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7248 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7263 
       26.20        18.97        17.13        47.97        49.71        18.41 
TCGA-CV-7407 TCGA-CV-7416 TCGA-CV-7422 TCGA-CV-7424 TCGA-CV-7425 TCGA-CV-7435 
       35.54        25.08        34.09        14.89        56.48       153.86 
TCGA-CV-7437 TCGA-CV-A45V TCGA-CV-A45Z TCGA-CV-A463 TCGA-CV-A6JM TCGA-CV-A6JZ 
       16.64         1.05        48.20         0.76         6.38        23.47 
TCGA-CX-7086 TCGA-D6-6516 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8569 TCGA-D6-A6EK 
       18.84        25.41        11.44        18.67        25.32        28.77 
TCGA-D6-A6EP TCGA-D6-A74Q TCGA-DQ-5625 TCGA-DQ-5631 TCGA-DQ-7592 TCGA-F7-8298 
       13.94        23.34        37.25        18.02        37.58        32.71 
TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S TCGA-HD-7753 TCGA-HD-7831 TCGA-HD-7917 
        3.02        31.13        18.94        28.47        21.93        27.48 
TCGA-IQ-7631 TCGA-IQ-A61H TCGA-IQ-A61K TCGA-IQ-A61O TCGA-IQ-A6SH TCGA-MT-A51W 
       38.53        37.41         5.29        13.84        15.48        14.37 
TCGA-MT-A67A TCGA-MT-A67G TCGA-MZ-A7D7 TCGA-P3-A5Q6 TCGA-P3-A6SX TCGA-P3-A6T4 
       30.05         6.25        17.98        15.78        47.01         2.04 
TCGA-P3-A6T6 TCGA-QK-A6II TCGA-QK-A8Z7 TCGA-QK-AA3J TCGA-RS-A6TO TCGA-T3-A92N 
       12.99         9.34        12.89        15.32        12.72         3.12 
TCGA-TN-A7HJ TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JK 
       13.25        54.67         2.83        44.65        74.47        13.94 
TCGA-WA-A7GZ 
       20.55 

$`7Q GAIN WILD-TYPE`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4IG 
        9.30        37.28        20.48        68.48         3.55        28.11 
TCGA-BA-A4II TCGA-BB-A5HU TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6992 TCGA-CN-6997 
       30.18        25.71         9.07         9.24        35.05        32.48 
TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-6221 TCGA-CQ-7063 TCGA-CQ-7068 
       19.82        24.39        48.20        32.88        70.13        43.04 
TCGA-CR-6472 TCGA-CX-7082 TCGA-CX-7219 TCGA-DQ-7593 TCGA-H7-A6C5 TCGA-HD-8634 
       34.52         0.36        34.36        40.24        21.11        12.66 
TCGA-HD-8635 TCGA-UF-A71D TCGA-UF-A7JV TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 
       22.85        48.03         2.96         3.35        15.19        13.64 
TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 
        9.07        26.50        23.74        42.35        57.93        17.10 
TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6872 TCGA-BA-6873 
       23.84        65.59        15.52        21.17        12.62         4.01 
TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IH TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB 
       41.85        29.42        20.45        27.95        11.54         7.10 
TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-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         4.80         4.41 
TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7871 
       18.38        22.42        36.72        50.20        44.98        24.66 
TCGA-BB-7872 TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO TCGA-C9-A480 TCGA-CN-4723 
       38.40        27.19        12.92         8.81        12.69        55.86 
TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 
       38.04         4.67        56.68        26.86        32.81        52.14 
TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 
       57.11        12.99        20.55        27.58        73.61        13.05 
TCGA-CN-5355 TCGA-CN-5359 TCGA-CN-5364 TCGA-CN-5366 TCGA-CN-5369 TCGA-CN-5370 
       42.02        12.39        16.21        11.84        12.49         8.52 
TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6016 TCGA-CN-6017 
       52.08        56.94        50.07        30.67        47.44        28.04 
TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A497 
       19.07        34.13        38.89        17.42        11.74        35.01 
TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63U TCGA-CN-A63W 
       25.41        23.57        29.72        21.21        31.69        12.39 
TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V6 TCGA-CN-A6V7 
       16.57         4.41         2.70        23.44        20.88        19.53 
TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 
       52.37        21.50         2.93        54.58        70.45        62.37 
TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6220 
       45.99        10.42        11.21         4.24        41.19        32.38 
TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7064 
       46.95        56.58         4.24        14.99        38.76        64.87 
TCGA-CQ-7065 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE 
       53.52        43.10        44.48        29.36        33.60        29.49 
TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 
       14.14        12.46        31.23        84.23        11.77        54.67 
TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6473 
       37.87        26.27        58.42        50.01        39.52        36.99 
TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 
       18.54        16.90        11.90        10.22        11.34        11.64 
TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 
        7.69        12.46        22.78        15.75         9.27        47.18 
TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-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-7391 
       26.17        17.13        32.78        47.01        27.06        30.02 
TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 
       46.85        32.65        44.25        30.58        24.79         5.13 
TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5436 TCGA-CV-5441 
        5.95        35.41        29.95        48.39        19.20        94.88 
TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 
       91.53        80.12        17.92        13.35        23.05        86.83 
TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-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-6936 TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6939 
        9.60         2.14         5.46        20.52         4.73        21.90 
TCGA-CV-6940 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6948 TCGA-CV-6952 TCGA-CV-6953 
       26.43       140.78        19.79        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-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-7180 TCGA-CV-7183 TCGA-CV-7236 TCGA-CV-7238 
       52.31        12.92        10.75       130.88         4.73        89.65 
TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7255 
       36.00        31.36        95.34         4.96        11.87         2.10 
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-7415 TCGA-CV-7418 TCGA-CV-7421 TCGA-CV-7423 TCGA-CV-7427 TCGA-CV-7428 
       22.85        25.94         0.07       100.57       156.49        54.94 
TCGA-CV-7429 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7438 
        3.52        16.27        84.49        19.76         7.17         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-A45W TCGA-CV-A45X TCGA-CV-A45Y TCGA-CV-A460 TCGA-CV-A461 
       35.47        45.96         6.51        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-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6K0 TCGA-CV-A6K1 
        6.48        28.01         3.62        21.24        19.92        22.52 
TCGA-CV-A6K2 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-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EM 
        2.53        16.14        24.95        17.72        12.36         7.63 
TCGA-D6-A6EN TCGA-D6-A6EO TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-DQ-5624 TCGA-DQ-5630 
       22.59        24.95        12.10        12.79        58.45        33.86 
TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 
       46.45        20.45        40.04        39.12        41.59        37.18 
TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 
       21.63        20.25        24.95         0.46        17.85        11.80 
TCGA-F7-A623 TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A76A 
       20.25        12.43        13.38        15.16        15.06        20.94 
TCGA-HD-7229 TCGA-HD-7754 TCGA-HD-7832 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-A4C1 
       33.76        25.74        27.48        14.66        22.03         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-7632 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61L 
       14.50        37.71        11.84         0.07        33.57        13.68 
TCGA-IQ-A6SG TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51X TCGA-MT-A67D TCGA-MT-A67F 
       19.04        19.27        10.75         7.96         1.84        12.62 
TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE 
       15.42         7.13        16.08        29.92        71.74        51.25 
TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T5 
       10.85        36.82        19.00        75.55        18.97        29.00 
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-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z8 
       21.47        12.72        27.39        21.07        19.73         5.62 
TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3K TCGA-RS-A6TP TCGA-T2-A6WX 
       14.76        12.20        17.82         8.32        16.96         6.87 
TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-T3-A92M TCGA-TN-A7HI TCGA-TN-A7HL 
       15.91         7.10        32.45        13.71        13.55        20.35 
TCGA-UF-A718 TCGA-UF-A71B TCGA-UF-A71E TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF 
       64.80        49.51        49.45        17.95        24.30        55.43 
TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UP-A6WW 
       29.46        18.05        20.75        22.36        32.65        17.03 
TCGA-WA-A7H4 TCGA-KU-A66S TCGA-KU-A66T 
       14.56        13.35        18.15 

  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
             0.76              0.07 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
           172.67            210.97 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
            18.94             21.21 
[1] "0.8 - 172.7 (18.9)" "0.1 - 211.0 (21.2)"
[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        61         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              61               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  31  27  47
  7Q GAIN WILD-TYPE    39 106  73 126
D14V4, multiclass
       clus
vv      7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  T0+T1              11                39
  T2                 31               106
  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  14  39   3
  7Q GAIN WILD-TYPE 131  54 129   5
D14V5, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  N0              48               131
  N1              14                54
  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 149   1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     41    0
  7Q GAIN WILD-TYPE  149    1
   clus
vv  7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  0              41               149
  1               0                 1
[1] 2 2
[1] FALSE
D14V7, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED    33  95
  7Q GAIN WILD-TYPE 107 287
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     33   95
  7Q GAIN WILD-TYPE  107  287
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  FEMALE              33               107
  MALE                95               287
[1] 2 2
[1] FALSE
D14V8, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED    37  67
  7Q GAIN WILD-TYPE 125 234
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     37   67
  7Q GAIN WILD-TYPE  125  234
     clus
vv    7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  NO               37               125
  YES              67               234
[1] 2 2
[1] FALSE
                   vv
clus                HEAD & NECK SQUAMOUS CELL CARCINOMA
  7Q GAIN MUTATED                                   125
  7Q GAIN WILD-TYPE                                 386
                   vv
clus                HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  7Q GAIN MUTATED                                                   2
  7Q GAIN WILD-TYPE                                                 8
                   vv
clus                HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  7Q GAIN MUTATED                                                           1
  7Q GAIN WILD-TYPE                                                         0
D14V9, multiclass
                                                           clus
vv                                                          7Q GAIN MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                   125
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       2
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT               1
                                                           clus
vv                                                          7Q GAIN WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                     386
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                         8
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                 0
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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   104
  7Q GAIN WILD-TYPE                        32   342
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                                        104               342
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V14, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED     8 110
  7Q GAIN WILD-TYPE  18 349
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      8  110
  7Q GAIN WILD-TYPE   18  349
                        clus
vv                       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   8                18
  NOT HISPANIC OR LATINO             110               349
[1] 2 2
[1] FALSE

Clustering(15) Variable = 8P GAIN MUTATION ANALYSIS
D15V1, survival
                   sevent
clus2                 0   1
  8P GAIN MUTATED    94  63
  8P GAIN WILD-TYPE 207 156
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
              157               363 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               63               156 
$`8P GAIN MUTATED`
TCGA-BA-4075 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4IG TCGA-BA-A4II 
        9.30        20.48        68.48         3.55        28.11        30.18 
TCGA-CN-6022 TCGA-CN-6024 TCGA-CQ-7068 TCGA-CR-6478 TCGA-DQ-5629 TCGA-DQ-7588 
        9.24        11.08        43.04         6.02        30.94        14.04 
TCGA-DQ-7589 TCGA-4P-AA8J TCGA-BA-5555 TCGA-BA-6868 TCGA-BA-A4IH TCGA-BA-A6DG 
       46.32         3.35        17.10        15.52        20.45         2.27 
TCGA-BA-A6DL TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-7861 
       20.48         6.15       105.90         9.14         4.80        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-6994 TCGA-CN-6995 TCGA-CN-6998 TCGA-CN-A499 TCGA-CN-A63T TCGA-CN-A63U 
       38.89         3.68        11.74        23.57         7.40        31.69 
TCGA-CN-A63V TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5330 TCGA-CQ-6224 TCGA-CQ-A4C9 
       22.32        52.37        21.50        62.37        56.58        23.24 
TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-6467 TCGA-CR-6470 
       29.49        14.14        31.23        84.23        58.42        50.01 
TCGA-CR-6477 TCGA-CR-6482 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6493 TCGA-CR-7365 
       16.90        11.34         7.69        12.46         9.27        39.16 
TCGA-CR-7367 TCGA-CR-7370 TCGA-CR-7376 TCGA-CR-7379 TCGA-CR-7382 TCGA-CR-7383 
       47.34         3.45        31.96        34.06        26.17        17.13 
TCGA-CR-7389 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5435 TCGA-CV-5440 
       12.89        48.39       139.43        17.16        76.24       107.51 
TCGA-CV-5442 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6934 
       76.50        48.59        60.49        54.74        21.07         2.14 
TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 
        5.46        20.52         4.73       140.78        19.79        12.03 
TCGA-CV-6948 TCGA-CV-6953 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7180 
       42.38        53.95       111.16        18.81        12.66        10.75 
TCGA-CV-7243 TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7263 TCGA-CV-7407 TCGA-CV-7409 
       31.36        11.87        47.97        18.41        35.54        17.85 
TCGA-CV-7415 TCGA-CV-7424 TCGA-CV-7428 TCGA-CV-A45P TCGA-CV-A45R TCGA-CV-A45T 
       22.85        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-A6EO 
       18.84        25.41        23.05        24.95        28.77        24.95 
TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-F7-7848 TCGA-F7-8489 TCGA-F7-A50I TCGA-F7-A61S 
       13.94        12.10        37.18        21.63         3.02        18.94 
TCGA-F7-A624 TCGA-H7-A76A TCGA-HD-7831 TCGA-HD-7917 TCGA-HD-8314 TCGA-HD-A634 
       12.43        20.94        21.93        27.48        22.03         4.27 
TCGA-IQ-A61O TCGA-MT-A51W TCGA-MT-A67D TCGA-MT-A67G TCGA-MZ-A5BI TCGA-MZ-A7D7 
       13.84        14.37         1.84         6.25         7.13        17.98 
TCGA-P3-A5QE TCGA-P3-A6T3 TCGA-P3-A6T5 TCGA-QK-A6IG TCGA-QK-A6IJ TCGA-RS-A6TO 
       51.25        18.97        29.00         7.30        12.72        12.72 
TCGA-T2-A6WX TCGA-T3-A92M TCGA-T3-A92N TCGA-TN-A7HI TCGA-UF-A719 TCGA-UF-A7JA 
        6.87        13.71         3.12        13.55        54.67        74.47 
TCGA-UF-A7JC TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS 
       17.95        55.43        29.46        13.94        20.75        22.36 
TCGA-KU-A66S 
       13.35 

$`8P GAIN WILD-TYPE`
TCGA-BA-4077 TCGA-BB-A5HU TCGA-CN-4727 TCGA-CN-6021 TCGA-CN-6023 TCGA-CN-6992 
       37.28        25.71        51.29         9.07        52.08        35.05 
TCGA-CN-6997 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-6221 TCGA-CQ-7063 
       32.48        19.82        24.39        48.20        32.88        70.13 
TCGA-CQ-7067 TCGA-CQ-A4C7 TCGA-CR-6472 TCGA-CX-7082 TCGA-CX-7219 TCGA-DQ-7593 
       16.73        11.61        34.52         0.36        34.36        40.24 
TCGA-H7-A6C5 TCGA-HD-8634 TCGA-HD-8635 TCGA-UF-A71D TCGA-UF-A7JV TCGA-BA-4074 
       21.11        12.66        22.85        48.03         2.96        15.19 
TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 
       13.64         9.07        26.50        23.74        42.35        57.93 
TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6872 TCGA-BA-6873 
       23.84        65.59        21.17        14.83        12.62         4.01 
TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD 
       41.85        29.42        27.95        11.54         7.10         5.69 
TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DI TCGA-BA-A6DJ TCGA-BA-A8YP TCGA-BB-4227 
       14.47         7.82        11.05        13.38        16.41         4.41 
TCGA-BB-4228 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7866 TCGA-BB-7871 TCGA-BB-A5HY 
       18.38        36.72        33.70        44.98        24.66        10.55 
TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4725 
       27.19        12.92         8.81         6.28        12.69        38.04 
TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4730 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 
        4.67        56.68        26.86        52.14        57.11        12.99 
TCGA-CN-4737 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5358 TCGA-CN-5360 TCGA-CN-5363 
       20.55        73.61        13.05         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-6011 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 
       56.94        30.67        23.90        47.44        28.04        19.07 
TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6996 TCGA-CN-A497 
       34.13         6.74        10.45        32.22        17.42        35.01 
TCGA-CN-A498 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63W TCGA-CN-A63Y 
       25.41        17.29        29.72        21.21        12.39        16.57 
TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V6 TCGA-CN-A6V7 
        4.41        12.07         2.70        23.44        20.88        19.53 
TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 
        2.93        54.58        70.45        45.99        10.42        11.21 
TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6220 TCGA-CQ-6223 TCGA-CQ-6225 TCGA-CQ-6227 
        4.24        41.19        32.38        46.95        13.25         4.24 
TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7069 TCGA-CQ-7071 
       14.99        38.76        64.87        53.52        41.88        43.10 
TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CH TCGA-CR-5247 
       77.56        44.48        29.36        33.60        12.46        11.77 
TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6474 
       54.67        37.87        26.27        39.52        36.99        18.54 
TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6484 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-7364 
       11.90        10.22        11.64        22.78        15.75        47.18 
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-7377 TCGA-CR-7380 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7390 
        9.17        19.92        32.78        47.01        27.06        49.58 
TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 
       30.02        46.85        32.65        44.25        30.58        24.79 
TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CV-5432 TCGA-CV-5434 
        5.13         5.95        35.41        29.95       129.21       108.95 
TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5441 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 
       19.20        17.95        94.88        91.53        80.12        17.92 
TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6436 
       13.35        23.05        86.83         7.07        43.23        62.43 
TCGA-CV-6441 TCGA-CV-6933 TCGA-CV-6935 TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6941 
        9.60        90.12         9.70        21.90        26.43        11.24 
TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6954 TCGA-CV-6955 TCGA-CV-6956 
       15.09        30.08         6.08        65.82        10.98         7.13 
TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7090 
        8.42        28.34         2.50         4.14        64.83       172.67 
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        89.65 
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-7255 TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 
        2.10        49.71        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-7425 TCGA-CV-7427 TCGA-CV-7429 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 
       56.48       156.49         3.52        16.27        84.49        19.76 
TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7437 TCGA-CV-7438 TCGA-CV-7440 TCGA-CV-A45O 
        7.17       153.86        16.64         6.38        22.19        27.98 
TCGA-CV-A45Q TCGA-CV-A45U TCGA-CV-A45V TCGA-CV-A45W TCGA-CV-A45Y TCGA-CV-A460 
      169.38        35.47         1.05        45.96        88.87        60.43 
TCGA-CV-A463 TCGA-CV-A464 TCGA-CV-A465 TCGA-CV-A6JD TCGA-CV-A6JM TCGA-CV-A6JN 
        0.76        56.61         7.07         5.98         6.38        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-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-D6-6826 TCGA-D6-6827 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB 
       16.14        11.44        18.67        25.32        17.72        12.36 
TCGA-D6-A6EM TCGA-D6-A6EN TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 
        7.63        22.59        12.79        23.34        58.45        37.25 
TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7594 
       33.86        18.02        46.45        20.45        37.58        40.04 
TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-8298 TCGA-F7-A50G TCGA-F7-A50J TCGA-F7-A61V 
       39.12        41.59        32.71        20.25        31.13        24.95 
TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A623 TCGA-H7-7774 TCGA-H7-8501 
        0.46        17.85        11.80        20.25        13.38        15.16 
TCGA-H7-8502 TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7832 TCGA-HD-8224 
       15.06        33.76        28.47        25.74        27.48        14.66 
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-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-A6H7 
       33.57         5.29        13.68        19.04        15.48        19.27 
TCGA-KU-A6H8 TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67F TCGA-MT-A7BN TCGA-MZ-A6I9 
       10.75         7.96        30.05        12.62        15.42        16.08 
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-A6T4 TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-P3-A6T8 
       19.00        75.55         2.04        12.99        16.01        13.15 
TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6V9 
       21.07        21.21        23.15        21.47         9.34        27.39 
TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-A8ZA 
       21.07        19.73        12.89         5.62        14.76        12.20 
TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-RS-A6TP TCGA-T2-A6WZ TCGA-T2-A6X0 
       17.82        15.32         8.32        16.96        15.91         7.10 
TCGA-T2-A6X2 TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A71A TCGA-UF-A71B 
       32.45        13.25        20.35        64.80         2.83        49.51 
TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JD TCGA-UF-A7JJ TCGA-UF-A7JT TCGA-UP-A6WW 
       49.45        44.65        24.30        18.05        32.65        17.03 
TCGA-WA-A7GZ TCGA-WA-A7H4 TCGA-KU-A66T 
       20.55        14.56        18.15 

  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 
            21.50             21.07 
[1] "1.8 - 180.2 (21.5)" "0.1 - 211.0 (21.1)"
[1] "hr=" "1.1"
D15V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  8P GAIN MUTATED         9       26        26        72         2         0
  8P GAIN WILD-TYPE      18       50        56       180        10         1
D15V3, multiclass
           clus
vv          8P GAIN MUTATED 8P GAIN WILD-TYPE
  STAGE I                 9                18
  STAGE II               26                50
  STAGE III              26                56
  STAGE IVA              72               180
  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
  8P GAIN MUTATED      18  49  25  46
  8P GAIN WILD-TYPE    32  88  75 127
D15V4, multiclass
       clus
vv      8P GAIN MUTATED 8P GAIN WILD-TYPE
  T0+T1              18                32
  T2                 49                88
  T3                 25                75
  T4                 46               127
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  8P GAIN MUTATED    50  24  51   2
  8P GAIN WILD-TYPE 129  44 117   6
D15V5, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  N0              50               129
  N1              24                44
  N2              51               117
  N3               2                 6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V6, binary
                   cls
clus                  0   1
  8P GAIN MUTATED    58   0
  8P GAIN WILD-TYPE 132   1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     58    0
  8P GAIN WILD-TYPE  132    1
   clus
vv  8P GAIN MUTATED 8P GAIN WILD-TYPE
  0              58               132
  1               0                 1
[1] 2 2
[1] FALSE
D15V7, binary
                   cls
clus                  0   1
  8P GAIN MUTATED    35 123
  8P GAIN WILD-TYPE 105 259
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     35  123
  8P GAIN WILD-TYPE  105  259
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  FEMALE              35               105
  MALE               123               259
[1] 2 2
[1] FALSE
D15V8, binary
                   cls
clus                  0   1
  8P GAIN MUTATED    53  84
  8P GAIN WILD-TYPE 109 217
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     53   84
  8P GAIN WILD-TYPE  109  217
     clus
vv    8P GAIN MUTATED 8P GAIN WILD-TYPE
  NO               53               109
  YES              84               217
[1] 2 2
[1] FALSE
                   vv
clus                HEAD & NECK SQUAMOUS CELL CARCINOMA
  8P GAIN MUTATED                                   152
  8P GAIN WILD-TYPE                                 359
                   vv
clus                HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  8P GAIN MUTATED                                                   5
  8P GAIN WILD-TYPE                                                 5
                   vv
clus                HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  8P GAIN MUTATED                                                           1
  8P GAIN WILD-TYPE                                                         0
D15V9, multiclass
                                                           clus
vv                                                          8P GAIN MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                   152
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       5
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT               1
                                                           clus
vv                                                          8P GAIN WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                     359
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                         5
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                 0
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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                          17   132
  8P GAIN WILD-TYPE                        31   314
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                     17                31
  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"
D15V14, binary
                   cls
clus                  0   1
  8P GAIN MUTATED     9 135
  8P GAIN WILD-TYPE  17 324
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      9  135
  8P GAIN WILD-TYPE   17  324
                        clus
vv                       8P GAIN MUTATED 8P GAIN WILD-TYPE
  HISPANIC OR LATINO                   9                17
  NOT HISPANIC OR LATINO             135               324
[1] 2 2
[1] FALSE

Clustering(16) Variable = 8Q GAIN MUTATION ANALYSIS
D16V1, survival
                   sevent
clus2                 0   1
  8Q GAIN MUTATED   177 140
  8Q GAIN WILD-TYPE 124  79
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              317               203 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              140                79 
$`8Q GAIN MUTATED`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4IG 
        9.30        37.28        20.48        68.48         3.55        28.11 
TCGA-BA-A4II TCGA-CN-6022 TCGA-CN-6024 TCGA-CN-6992 TCGA-CQ-7067 TCGA-CQ-7068 
       30.18         9.24        11.08        35.05        16.73        43.04 
TCGA-CQ-A4C7 TCGA-CR-6478 TCGA-CX-7082 TCGA-CX-7219 TCGA-DQ-5629 TCGA-DQ-7588 
       11.61         6.02         0.36        34.36        30.94        14.04 
TCGA-DQ-7589 TCGA-HD-8634 TCGA-HD-8635 TCGA-UF-A7JV TCGA-4P-AA8J TCGA-BA-5149 
       46.32        12.66        22.85         2.96         3.35        26.50 
TCGA-BA-5152 TCGA-BA-5555 TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6870 TCGA-BA-6872 
       42.35        17.10        65.59        15.52        14.83        12.62 
TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IH TCGA-BA-A6DA TCGA-BA-A6DD TCGA-BA-A6DG 
        4.01        41.85        20.45        11.54         5.69         2.27 
TCGA-BA-A6DI TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 
       11.05        20.48        16.41         6.15       105.90         9.14 
TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7863 TCGA-BB-7864 
        4.80         4.41        18.38        22.42        33.70        50.20 
TCGA-BB-7870 TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-8601 TCGA-BB-A5HY TCGA-BB-A5HZ 
       66.28        38.40        71.05        20.52        10.55        27.19 
TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4728 
        6.28        12.69        48.76        55.86        38.04        56.68 
TCGA-CN-4729 TCGA-CN-4731 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 
       12.89        32.81        12.99        20.55        14.33        45.83 
TCGA-CN-4740 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5363 TCGA-CN-5364 
       27.58        13.05        42.02        46.32         8.32        16.21 
TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-6012 TCGA-CN-6013 
       11.54        11.84         8.52        52.08        48.00        23.90 
TCGA-CN-6016 TCGA-CN-6020 TCGA-CN-6988 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 
       47.44         6.74        10.45        38.89         3.68        17.42 
TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A63T 
       11.74        25.41        23.57        17.29        29.72         7.40 
TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A640 TCGA-CN-A642 TCGA-CQ-5324 
       31.69        22.32        12.39         4.41         2.70        52.37 
TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5334 TCGA-CQ-6218 
       21.50         2.93        70.45        62.37         4.24        41.19 
TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7065 TCGA-CQ-7069 
       56.58         4.24        14.99        38.76        53.52        41.88 
TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CE TCGA-CQ-A4CG 
       77.56        44.48        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-6471 
       31.23        84.23        11.77        58.42        50.01        39.52 
TCGA-CR-6473 TCGA-CR-6477 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 
       36.99        16.90        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        24.79         5.95        35.41 
TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5435 TCGA-CV-5436 
       48.39       139.43        17.16       129.21        76.24        19.20 
TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5976 
      107.51        94.88        76.50        80.12        17.92        48.59 
TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6934 
       60.49         7.07        54.74        21.07        62.43         2.14 
TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6942 
        5.46        20.52         4.73        26.43        11.24       140.78 
TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6952 
       19.79        12.03        42.38        15.09        30.08         6.08 
TCGA-CV-6953 TCGA-CV-6959 TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7091 
       53.95         8.42         4.14        64.83       172.67       111.16 
TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7102 TCGA-CV-7104 TCGA-CV-7178 TCGA-CV-7180 
       18.81        12.66         1.84        12.92        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        89.65        31.36        26.20 
TCGA-CV-7247 TCGA-CV-7248 TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7255 TCGA-CV-7263 
       18.97        17.13        11.87        47.97         2.10        18.41 
TCGA-CV-7407 TCGA-CV-7409 TCGA-CV-7414 TCGA-CV-7415 TCGA-CV-7416 TCGA-CV-7421 
       35.54        17.85         0.46        22.85        25.08         0.07 
TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7434 TCGA-CV-7437 
      100.57        14.89       156.49        54.94         7.17        16.64 
TCGA-CV-7438 TCGA-CV-A45P TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45U TCGA-CV-A45X 
        6.38        21.01       180.16       159.65        35.47         6.51 
TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A461 TCGA-CV-A464 TCGA-CV-A465 TCGA-CV-A468 
       88.87        48.20        67.86        56.61         7.07        15.25 
TCGA-CV-A6JE TCGA-CV-A6JM TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JZ TCGA-CV-A6K0 
       35.34         6.38        29.79         6.48        23.47        19.92 
TCGA-CX-7086 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6826 TCGA-D6-8568 
       18.84        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-5630 
       13.94        12.10        12.79        58.45        37.25        33.86 
TCGA-DQ-7592 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50I TCGA-F7-A50J 
       37.58        37.18        32.71        21.63         3.02        31.13 
TCGA-F7-A61S TCGA-F7-A620 TCGA-F7-A624 TCGA-H7-8501 TCGA-H7-A76A TCGA-HD-7831 
       18.94        17.85        12.43        15.16        20.94        21.93 
TCGA-HD-7832 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-A634 TCGA-HL-7533 
       27.48        27.48        14.66        22.03         4.27        34.75 
TCGA-IQ-7630 TCGA-IQ-A61E TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O TCGA-IQ-A6SG 
       15.95        37.71         5.29        13.68        13.84        19.04 
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-WA-A7H4 TCGA-KU-A66S TCGA-KU-A66T 
       22.36        32.65        14.56        13.35        18.15 

$`8Q GAIN WILD-TYPE`
TCGA-BB-A5HU TCGA-CN-4727 TCGA-CN-6021 TCGA-CN-6023 TCGA-CN-6997 TCGA-CN-A6V1 
       25.71        51.29         9.07        52.08        32.48        19.82 
TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-6221 TCGA-CQ-7063 TCGA-CR-6472 TCGA-DQ-7593 
       24.39        48.20        32.88        70.13        34.52        40.24 
TCGA-H7-A6C5 TCGA-UF-A71D TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-5151 
       21.11        48.03        15.19        13.64         9.07        23.74 
TCGA-BA-5153 TCGA-BA-5556 TCGA-BA-6869 TCGA-BA-A4IF TCGA-BA-A6D8 TCGA-BA-A6DB 
       57.93        23.84        21.17        29.42        27.95         7.10 
TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DJ TCGA-BB-7862 TCGA-BB-7866 TCGA-BB-7871 
       14.47         7.82        13.38        36.72        44.98        24.66 
TCGA-BB-A6UM TCGA-BB-A6UO TCGA-CN-4726 TCGA-CN-4730 TCGA-CN-4733 TCGA-CN-4735 
       12.92         8.81         4.67        26.86        52.14        57.11 
TCGA-CN-4741 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5367 TCGA-CN-5369 
       73.61         8.58        12.39        71.31        11.57        12.49 
TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 
       56.94        50.07        30.67        28.04        19.07        34.13 
TCGA-CN-6989 TCGA-CN-A497 TCGA-CN-A49C TCGA-CN-A63Y TCGA-CN-A641 TCGA-CN-A6UY 
       32.22        35.01        21.21        16.57        12.07        23.44 
TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5327 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 
       20.88        19.53        54.58        45.99        10.42        11.21 
TCGA-CQ-6220 TCGA-CQ-6223 TCGA-CQ-6225 TCGA-CQ-7064 TCGA-CQ-7071 TCGA-CQ-A4CD 
       32.38        46.95        13.25        64.87        43.10        33.60 
TCGA-CQ-A4CH TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6474 TCGA-CR-6480 
       12.46        54.67        37.87        26.27        18.54        11.90 
TCGA-CR-6481 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-7364 TCGA-CR-7368 TCGA-CR-7371 
       10.22        22.78        15.75        47.18        40.93         3.09 
TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7385 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 
       29.23         0.99        32.78        49.58        30.02        46.85 
TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7398 TCGA-CR-7402 TCGA-CV-5434 
       32.65        44.25        30.58         5.13        29.95       108.95 
TCGA-CV-5439 TCGA-CV-5443 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5979 
       17.95        91.53        13.35        23.05        86.83        43.23 
TCGA-CV-6441 TCGA-CV-6933 TCGA-CV-6935 TCGA-CV-6939 TCGA-CV-6954 TCGA-CV-6955 
        9.60        90.12         9.70        21.90        65.82        10.98 
TCGA-CV-6956 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 
        7.13        28.34         2.50         7.99         9.01         5.26 
TCGA-CV-7103 TCGA-CV-7177 TCGA-CV-7242 TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7261 
       52.31        21.80        36.00        95.34         4.96        49.71 
TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7418 TCGA-CV-7422 
       57.47       210.97        89.33         9.67        25.94        34.09 
TCGA-CV-7425 TCGA-CV-7429 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7435 
       56.48         3.52        16.27        84.49        19.76       153.86 
TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A45V TCGA-CV-A45W TCGA-CV-A460 
       22.19        27.98       169.38         1.05        45.96        60.43 
TCGA-CV-A463 TCGA-CV-A6JD TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6K1 
        0.76         5.98        28.01         3.62        21.24        22.52 
TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6824 TCGA-D6-6825 
       10.42        10.55        51.12        13.25         2.53        16.14 
TCGA-D6-6827 TCGA-D6-A6EM TCGA-D6-A74Q TCGA-DQ-5631 TCGA-DQ-7590 TCGA-DQ-7591 
       18.67         7.63        23.34        18.02        46.45        20.45 
TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-A50G TCGA-F7-A61V TCGA-F7-A61W 
       40.04        39.12        41.59        20.25        24.95         0.46 
TCGA-F7-A622 TCGA-F7-A623 TCGA-H7-7774 TCGA-H7-8502 TCGA-HD-7229 TCGA-HD-7753 
       11.80        20.25        13.38        15.06        33.76        28.47 
TCGA-HD-7754 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-IQ-7631 
       25.74         0.36        13.84         3.65         6.90        38.53 
TCGA-IQ-7632 TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A6SH 
       14.50        11.84        37.41         0.07        33.57        15.48 
TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A67A TCGA-MT-A67F TCGA-MZ-A6I9 TCGA-P3-A5Q5 
       19.27        10.75        30.05        12.62        16.08        29.92 
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-A6IF TCGA-QK-A6V9 TCGA-QK-A6VB 
       12.99        16.01        13.15        23.15        27.39        21.07 
TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-AA3J TCGA-RS-A6TP 
       12.89         5.62        14.76        12.20        15.32        16.96 
TCGA-T2-A6X0 TCGA-TN-A7HL TCGA-UF-A71B TCGA-UP-A6WW TCGA-WA-A7GZ 
        7.10        20.35        49.51        17.03        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 
            20.52             22.19 
[1] "0.1 - 180.2 (20.5)" "0.1 - 211.0 (22.2)"
[1] "hr=" "1.2"
D16V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  8Q GAIN MUTATED        17       45        54       153        10         0
  8Q GAIN WILD-TYPE      10       31        28        99         2         1
D16V3, multiclass
           clus
vv          8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  STAGE I                17                10
  STAGE II               45                31
  STAGE III              54                28
  STAGE IVA             153                99
  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  79  65 107
  8Q GAIN WILD-TYPE    18  58  35  66
D16V4, multiclass
       clus
vv      8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  T0+T1              32                18
  T2                 79                58
  T3                 65                35
  T4                107                66
[1] 4 2
[1] TRUE
[1] "dimension of 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   104  44 106   7
  8Q GAIN WILD-TYPE  75  24  62   1
D16V5, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  N0             104                75
  N1              44                24
  N2             106                62
  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   120   0
  8Q GAIN WILD-TYPE  70   1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED    120    0
  8Q GAIN WILD-TYPE   70    1
   clus
vv  8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  0             120                70
  1               0                 1
[1] 2 2
[1] FALSE
D16V7, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED    86 232
  8Q GAIN WILD-TYPE  54 150
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     86  232
  8Q GAIN WILD-TYPE   54  150
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  FEMALE              86                54
  MALE               232               150
[1] 2 2
[1] FALSE
D16V8, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED   109 172
  8Q GAIN WILD-TYPE  53 129
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED    109  172
  8Q GAIN WILD-TYPE   53  129
     clus
vv    8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  NO              109                53
  YES             172               129
[1] 2 2
[1] FALSE
                   vv
clus                HEAD & NECK SQUAMOUS CELL CARCINOMA
  8Q GAIN MUTATED                                   311
  8Q GAIN WILD-TYPE                                 200
                   vv
clus                HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  8Q GAIN MUTATED                                                   6
  8Q GAIN WILD-TYPE                                                 4
                   vv
clus                HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  8Q GAIN MUTATED                                                           1
  8Q GAIN WILD-TYPE                                                         0
D16V9, multiclass
                                                           clus
vv                                                          8Q GAIN MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                   311
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       6
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT               1
                                                           clus
vv                                                          8Q GAIN WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                     200
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                         4
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                 0
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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   265
  8Q GAIN WILD-TYPE                        17   181
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                                        265               181
[1] 4 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    19 273
  8Q GAIN WILD-TYPE   7 186
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     19  273
  8Q GAIN WILD-TYPE    7  186
                        clus
vv                       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  HISPANIC OR LATINO                  19                 7
  NOT HISPANIC OR LATINO             273               186
[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 246 172
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
              102               418 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               47               172 
$`9P GAIN MUTATED`
TCGA-BA-5557 TCGA-BA-5559 TCGA-CN-6023 TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CQ-A4C7 
       20.48        68.48        52.08        70.13        43.04        11.61 
TCGA-CX-7219 TCGA-BA-5149 TCGA-BA-5556 TCGA-BA-6873 TCGA-BA-A6DA TCGA-BA-A6DJ 
       34.36        26.50        23.84         4.01        11.54        13.38 
TCGA-BB-7870 TCGA-BB-A5HZ TCGA-CN-5355 TCGA-CN-5359 TCGA-CN-5363 TCGA-CN-5370 
       66.28        27.19        42.02        12.39         8.32         8.52 
TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-A499 
       50.07        30.67        38.89         3.68        17.42        23.57 
TCGA-CN-A640 TCGA-CN-A642 TCGA-CN-A6V6 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-6223 
        4.41         2.70        20.88        70.45        62.37        46.95 
TCGA-CQ-6229 TCGA-CQ-A4C6 TCGA-CQ-A4CD TCGA-CR-6467 TCGA-CR-6487 TCGA-CR-7370 
       38.76        44.48        33.60        58.42         7.69         3.45 
TCGA-CR-7371 TCGA-CR-7373 TCGA-CR-7395 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 
        3.09        29.23        30.58       107.51        94.88        76.50 
TCGA-CV-5966 TCGA-CV-5977 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6938 TCGA-CV-6939 
       17.92        60.49        21.07        62.43         4.73        21.90 
TCGA-CV-6941 TCGA-CV-6952 TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7099 TCGA-CV-7235 
       11.24         6.08         4.14        64.83         7.99        77.16 
TCGA-CV-7238 TCGA-CV-7247 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7407 TCGA-CV-7409 
       89.65        18.97        47.97        49.71        35.54        17.85 
TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7429 TCGA-CV-A45Q TCGA-CV-A463 TCGA-CV-A465 
       56.48       156.49         3.52       169.38         0.76         7.07 
TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JO TCGA-CV-A6JZ TCGA-D6-6516 TCGA-D6-A6EM 
       15.25         5.98         6.48        23.47        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-BA-4075 TCGA-BA-4077 TCGA-BA-6871 TCGA-BA-A4IG TCGA-BA-A4II TCGA-BB-A5HU 
        9.30        37.28         3.55        28.11        30.18        25.71 
TCGA-CN-4727 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6024 TCGA-CN-6992 TCGA-CN-6997 
       51.29         9.07         9.24        11.08        35.05        32.48 
TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-6221 TCGA-CQ-7067 TCGA-CR-6472 
       19.82        24.39        48.20        32.88        16.73        34.52 
TCGA-CR-6478 TCGA-CX-7082 TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7593 
        6.02         0.36        30.94        14.04        46.32        40.24 
TCGA-H7-A6C5 TCGA-HD-8634 TCGA-HD-8635 TCGA-UF-A71D TCGA-UF-A7JV TCGA-4P-AA8J 
       21.11        12.66        22.85        48.03         2.96         3.35 
TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 
       15.19        13.64         9.07        23.74        42.35        57.93 
TCGA-BA-5555 TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6872 
       17.10        65.59        15.52        21.17        14.83        12.62 
TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IH TCGA-BA-A6D8 TCGA-BA-A6DB TCGA-BA-A6DD 
       41.85        29.42        20.45        27.95         7.10         5.69 
TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DI TCGA-BA-A6DL TCGA-BA-A8YP 
       14.47         7.82         2.27        11.05        20.48        16.41 
TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 
        6.15       105.90         9.14         4.80         4.41        18.38 
TCGA-BB-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-A5HY TCGA-BB-A6UM TCGA-BB-A6UO 
       38.40        71.05        20.52        10.55        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-4735 
       56.68        12.89        26.86        32.81        52.14        57.11 
TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 
       12.99        20.55        14.33        45.83        27.58        73.61 
TCGA-CN-4742 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5360 TCGA-CN-5364 TCGA-CN-5365 
       13.05        46.32         8.58        71.31        16.21        11.54 
TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5369 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6012 
       11.84        11.57        12.49        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-6988 TCGA-CN-6989 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A49A 
       10.45        32.22        11.74        35.01        25.41        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-A641 TCGA-CN-A6UY TCGA-CN-A6V7 TCGA-CQ-5324 TCGA-CQ-5325 
       16.57        12.07        23.44        19.53        52.37        21.50 
TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 
        2.93        54.58        45.99        10.42        11.21         4.24 
TCGA-CQ-6218 TCGA-CQ-6220 TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 
       41.19        32.38        56.58        13.25         4.24        14.99 
TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C9 
       64.87        53.52        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-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-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 
       11.64        12.46        22.78        15.75         9.27        47.18 
TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7372 TCGA-CR-7374 
       39.16        47.34        40.93        35.84        24.95         0.99 
TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7383 
       31.96         9.17        34.06        19.92        26.17        17.13 
TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 
       32.78        47.01        27.06        12.89        49.58        30.02 
TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 
       46.85        32.65        44.25        24.79         5.13         5.95 
TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 
       35.41        29.95        48.39       139.43        17.16       129.21 
TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5443 TCGA-CV-5444 
      108.95        76.24        19.20        17.95        91.53        80.12 
TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5978 TCGA-CV-5979 
       13.35        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       172.67       111.16        18.81 
TCGA-CV-7097 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7104 
       12.66         9.01         5.26         1.84        52.31        12.92 
TCGA-CV-7177 TCGA-CV-7178 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7236 TCGA-CV-7242 
       21.80        71.21        10.75       130.88         4.73        36.00 
TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 
       31.36        26.20        17.13        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-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-7428 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 
      100.57        14.89        54.94        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-A45R TCGA-CV-A45T TCGA-CV-A45U TCGA-CV-A45V TCGA-CV-A45W 
       21.01       180.16       159.65        35.47         1.05        45.96 
TCGA-CV-A45X TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A464 
        6.51        88.87        48.20        60.43        67.86        56.61 
TCGA-CV-A6JE TCGA-CV-A6JM TCGA-CV-A6JN TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY 
       35.34         6.38        29.79        28.01         3.62        21.24 
TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-A4AQ 
       19.92        22.52        10.42        10.55        18.84        51.12 
TCGA-D6-6515 TCGA-D6-6517 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-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK 
       18.67        24.95        25.32        17.72        12.36        28.77 
TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5630 
       24.95        13.94        12.79        23.34        58.45        33.86 
TCGA-DQ-5631 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7594 TCGA-DQ-7595 
       18.02        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-A50J TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A623 TCGA-F7-A624 
       31.13        24.95         0.46        17.85        20.25        12.43 
TCGA-H7-8501 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7831 
       15.16        20.94        33.76        28.47        25.74        21.93 
TCGA-HD-7832 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A6HZ 
       27.48        14.66        22.03         0.36        13.84         3.65 
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-A61O TCGA-IQ-A6SG TCGA-IQ-A6SH TCGA-KU-A6H7 
        0.07        33.57        13.84        19.04        15.48        19.27 
TCGA-KU-A6H8 TCGA-MT-A51X TCGA-MT-A67D TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-MZ-A6I9 
       10.75         7.96         1.84        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-A6SX TCGA-P3-A6T0 TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T6 TCGA-P3-A6T8 
       47.01        19.00        18.97         2.04        12.99        13.15 
TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ 
       21.07        21.21        23.15        21.47         9.34        12.72 
TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8ZA 
       27.39        21.07        19.73        12.89         5.62        12.20 
TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-RS-A6TP TCGA-T2-A6X0 TCGA-T2-A6X2 
       17.82        15.32         8.32        16.96         7.10        32.45 
TCGA-T3-A92M TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A 
       13.71        13.25        20.35        64.80        54.67         2.83 
TCGA-UF-A71B TCGA-UF-A71E TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF 
       49.51        49.45        74.47        17.95        24.30        55.43 
TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UP-A6WW 
       29.46        18.05        13.94        20.75        22.36        17.03 
TCGA-WA-A7GZ TCGA-WA-A7H4 TCGA-KU-A66S TCGA-KU-A66T 
       20.55        14.56        13.35        18.15 

  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            21.140 
[1] "0.8 - 169.4 (21.0)" "0.1 - 211.0 (21.1)"
[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       200         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               200
  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 153   1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED     37    0
  9P GAIN WILD-TYPE  153    1
   clus
vv  9P GAIN MUTATED 9P GAIN WILD-TYPE
  0              37               153
  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    34  58
  9P GAIN WILD-TYPE 128 243
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED     34   58
  9P GAIN WILD-TYPE  128  243
     clus
vv    9P GAIN MUTATED 9P GAIN WILD-TYPE
  NO               34               128
  YES              58               243
[1] 2 2
[1] FALSE
                   vv
clus                HEAD & NECK SQUAMOUS CELL CARCINOMA
  9P GAIN MUTATED                                   101
  9P GAIN WILD-TYPE                                 410
                   vv
clus                HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  9P GAIN MUTATED                                                   1
  9P GAIN WILD-TYPE                                                 9
                   vv
clus                HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  9P GAIN MUTATED                                                           0
  9P GAIN WILD-TYPE                                                         1
D17V9, multiclass
                                                           clus
vv                                                          9P GAIN MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                   101
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       1
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT               0
                                                           clus
vv                                                          9P GAIN WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                     410
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                         9
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                 1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V10, continuous
D17V11, continuous
D17V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  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    75  69
  9Q GAIN WILD-TYPE 226 150
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
              144               376 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               69               150 
$`9Q GAIN MUTATED`
TCGA-BA-5557 TCGA-BA-5559 TCGA-CN-4727 TCGA-CN-6021 TCGA-CN-6023 TCGA-CN-A6V3 
       20.48        68.48        51.29         9.07        52.08        24.39 
TCGA-CQ-5323 TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CQ-A4C7 TCGA-CX-7219 TCGA-BA-5149 
       48.20        70.13        43.04        11.61        34.36        26.50 
TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-6870 TCGA-BA-6873 TCGA-BA-A6DA TCGA-BA-A6DD 
       17.10        23.84        14.83         4.01        11.54         5.69 
TCGA-BA-A6DJ TCGA-BB-4224 TCGA-BB-7864 TCGA-BB-7870 TCGA-BB-A5HZ TCGA-CN-4723 
       13.38         9.14        50.20        66.28        27.19        55.86 
TCGA-CN-4728 TCGA-CN-4741 TCGA-CN-5355 TCGA-CN-5359 TCGA-CN-5363 TCGA-CN-5367 
       56.68        73.61        42.02        12.39         8.32        11.57 
TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-A499 
       50.07        30.67        38.89         3.68        17.42        23.57 
TCGA-CN-A49A TCGA-CN-A63T TCGA-CN-A640 TCGA-CN-A642 TCGA-CN-A6V6 TCGA-CQ-5325 
       17.29         7.40         4.41         2.70        20.88        21.50 
TCGA-CQ-5330 TCGA-CQ-6223 TCGA-CQ-6225 TCGA-CQ-6229 TCGA-CQ-A4C6 TCGA-CQ-A4CD 
       62.37        46.95        13.25        38.76        44.48        33.60 
TCGA-CQ-A4CG TCGA-CR-6467 TCGA-CR-6477 TCGA-CR-7368 TCGA-CR-7373 TCGA-CR-7379 
       14.14        58.42        16.90        40.93        29.23        34.06 
TCGA-CR-7380 TCGA-CR-7389 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5436 TCGA-CV-5439 
       19.92        12.89       129.21       108.95        19.20        17.95 
TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 
      107.51        94.88        76.50        80.12        17.92        13.35 
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-7100 TCGA-CV-7177 
        6.08         4.14        64.83         7.99         9.01        21.80 
TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7261 
       77.16         4.73        89.65        26.20        18.97        49.71 
TCGA-CV-7263 TCGA-CV-7407 TCGA-CV-7409 TCGA-CV-7415 TCGA-CV-7422 TCGA-CV-7425 
       18.41        35.54        17.85        22.85        34.09        56.48 
TCGA-CV-7427 TCGA-CV-7429 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7434 TCGA-CV-A45Q 
      156.49         3.52        16.27        84.49         7.17       169.38 
TCGA-CV-A45Z TCGA-CV-A461 TCGA-CV-A463 TCGA-CV-A465 TCGA-CV-A468 TCGA-CV-A6JD 
       48.20        67.86         0.76         7.07        15.25         5.98 
TCGA-CV-A6JZ TCGA-CX-A4AQ TCGA-D6-6516 TCGA-D6-8569 TCGA-D6-A6EM TCGA-D6-A6EN 
       23.47        51.12        25.41        25.32         7.63        22.59 
TCGA-D6-A6EQ TCGA-D6-A74Q TCGA-DQ-5625 TCGA-F7-A61S TCGA-F7-A622 TCGA-H7-7774 
       12.10        23.34        37.25        18.94        11.80        13.38 
TCGA-H7-8502 TCGA-HD-7832 TCGA-HD-7917 TCGA-HD-8314 TCGA-HD-A634 TCGA-HD-A6I0 
       15.06        27.48        27.48        22.03         4.27         6.90 
TCGA-IQ-7630 TCGA-IQ-A61L TCGA-MT-A51W TCGA-MT-A67A TCGA-MT-A67G TCGA-P3-A6SW 
       15.95        13.68        14.37        30.05         6.25        36.82 
TCGA-P3-A6T2 TCGA-P3-A6T5 TCGA-P3-A6T7 TCGA-QK-A64Z TCGA-QK-A6IG TCGA-QK-A8Z9 
       75.55        29.00        16.01        21.07         7.30        14.76 
TCGA-RS-A6TO TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-T3-A92N TCGA-TN-A7HI 
       12.72         6.87        15.91         7.10         3.12        13.55 
TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JH TCGA-UF-A7JS TCGA-UF-A7JT 
       49.45        44.65        74.47        29.46        22.36        32.65 

$`9Q GAIN WILD-TYPE`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-6871 TCGA-BA-A4IG TCGA-BA-A4II TCGA-BB-A5HU 
        9.30        37.28         3.55        28.11        30.18        25.71 
TCGA-CN-6022 TCGA-CN-6024 TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-A6V1 TCGA-CQ-6221 
        9.24        11.08        35.05        32.48        19.82        32.88 
TCGA-CQ-7067 TCGA-CR-6472 TCGA-CR-6478 TCGA-CX-7082 TCGA-DQ-5629 TCGA-DQ-7588 
       16.73        34.52         6.02         0.36        30.94        14.04 
TCGA-DQ-7589 TCGA-DQ-7593 TCGA-H7-A6C5 TCGA-HD-8634 TCGA-HD-8635 TCGA-UF-A71D 
       46.32        40.24        21.11        12.66        22.85        48.03 
TCGA-UF-A7JV TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-5151 
        2.96         3.35        15.19        13.64         9.07        23.74 
TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6872 
       42.35        57.93        65.59        15.52        21.17        12.62 
TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IH TCGA-BA-A6D8 TCGA-BA-A6DB TCGA-BA-A6DE 
       41.85        29.42        20.45        27.95         7.10        14.47 
TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DI TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 
        7.82         2.27        11.05        20.48        16.41         6.15 
TCGA-BB-4223 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 
      105.90         4.80         4.41        18.38        22.42        36.72 
TCGA-BB-7863 TCGA-BB-7866 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-8601 
       33.70        44.98        24.66        38.40        71.05        20.52 
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-6988 TCGA-CN-6989 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A49B 
       10.45        32.22        11.74        35.01        25.41        29.72 
TCGA-CN-A49C TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A641 
       21.21        31.69        22.32        12.39        16.57        12.07 
TCGA-CN-A6UY TCGA-CN-A6V7 TCGA-CQ-5324 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 
       23.44        19.53        52.37         2.93        54.58        70.45 
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-6224 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7069 
       56.58         4.24        14.99        64.87        53.52        41.88 
TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CE TCGA-CQ-A4CH 
       43.10        77.56        23.24        29.36        29.49        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-6473 TCGA-CR-6474 TCGA-CR-6480 TCGA-CR-6481 
       50.01        39.52        36.99        18.54        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-7369 TCGA-CR-7370 
        9.27        47.18        39.16        47.34        35.84         3.45 
TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7382 
        3.09        24.95         0.99        31.96         9.17        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        49.58        30.02 
TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 
       46.85        32.65        44.25        30.58        24.79         5.13 
TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 
        5.95        35.41        29.95        48.39       139.43        17.16 
TCGA-CV-5435 TCGA-CV-5443 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5978 
       76.24        91.53        23.05        86.83        48.59         7.07 
TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6441 TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6935 
       43.23        54.74         9.60        90.12         2.14         9.70 
TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6940 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 
        5.46        20.52        26.43       140.78        19.79        12.03 
TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-6955 
       42.38        15.09        30.08        53.95        65.82        10.98 
TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7091 
        7.13         8.42        28.34         2.50       172.67       111.16 
TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7104 
       18.81        12.66         5.26         1.84        52.31        12.92 
TCGA-CV-7178 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7248 
       71.21        10.75       130.88        36.00        31.36        17.13 
TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7255 TCGA-CV-7406 
       95.34         4.96        11.87        47.97         2.10        57.47 
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-7423 TCGA-CV-7424 TCGA-CV-7428 TCGA-CV-7433 TCGA-CV-7435 
        0.07       100.57        14.89        54.94        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-7085 TCGA-CX-7086 TCGA-D6-6515 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 
       10.55        18.84        13.25         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-A6EO TCGA-D6-A6EP TCGA-D6-A6ES TCGA-DQ-5624 TCGA-DQ-5630 
       28.77        24.95        13.94        12.79        58.45        33.86 
TCGA-DQ-5631 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7594 TCGA-DQ-7595 
       18.02        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-A50J TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A623 TCGA-F7-A624 
       31.13        24.95         0.46        17.85        20.25        12.43 
TCGA-H7-8501 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7831 
       15.16        20.94        33.76        28.47        25.74        21.93 
TCGA-HD-8224 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A6HZ TCGA-HL-7533 TCGA-IQ-7631 
       14.66         0.36        13.84         3.65        34.75        38.53 
TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J 
       14.50        37.71        11.84        37.41         0.07        33.57 
TCGA-IQ-A61K TCGA-IQ-A61O TCGA-IQ-A6SG TCGA-IQ-A6SH TCGA-KU-A6H7 TCGA-KU-A6H8 
        5.29        13.84        19.04        15.48        19.27        10.75 
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-A6SX TCGA-P3-A6T0 TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T6 TCGA-P3-A6T8 
       47.01        19.00        18.97         2.04        12.99        13.15 
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        27.39 
TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8ZA TCGA-QK-A8ZB 
       21.07        19.73        12.89         5.62        12.20        17.82 
TCGA-QK-AA3J TCGA-QK-AA3K TCGA-RS-A6TP TCGA-T2-A6X2 TCGA-T3-A92M TCGA-TN-A7HJ 
       15.32         8.32        16.96        32.45        13.71        13.25 
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-A7JF TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UP-A6WW 
       24.30        55.43        18.05        13.94        20.75        17.03 
TCGA-WA-A7GZ TCGA-WA-A7H4 TCGA-KU-A66S TCGA-KU-A66T 
       20.55        14.56        13.35        18.15 

  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            20.845 
[1] "0.8 - 169.4 (22.0)" "0.1 - 211.0 (20.8)"
[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        81         6         0
  9Q GAIN WILD-TYPE      21       53        65       171         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              81               171
  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  28  62
  9Q GAIN WILD-TYPE    40 103  72 111
D18V4, multiclass
       clus
vv      9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  T0+T1              10                40
  T2                 34               103
  T3                 28                72
  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
  9Q GAIN MUTATED    53  18  48   4
  9Q GAIN WILD-TYPE 126  50 120   4
D18V5, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  N0              53               126
  N1              18                50
  N2              48               120
  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    48   0
  9Q GAIN WILD-TYPE 142   1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     48    0
  9Q GAIN WILD-TYPE  142    1
   clus
vv  9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  0              48               142
  1               0                 1
[1] 2 2
[1] FALSE
D18V7, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED    42 103
  9Q GAIN WILD-TYPE  98 279
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     42  103
  9Q GAIN WILD-TYPE   98  279
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  FEMALE              42                98
  MALE               103               279
[1] 2 2
[1] FALSE
D18V8, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED    42  85
  9Q GAIN WILD-TYPE 120 216
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     42   85
  9Q GAIN WILD-TYPE  120  216
     clus
vv    9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  NO               42               120
  YES              85               216
[1] 2 2
[1] FALSE
                   vv
clus                HEAD & NECK SQUAMOUS CELL CARCINOMA
  9Q GAIN MUTATED                                   142
  9Q GAIN WILD-TYPE                                 369
                   vv
clus                HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  9Q GAIN MUTATED                                                   3
  9Q GAIN WILD-TYPE                                                 7
                   vv
clus                HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  9Q GAIN MUTATED                                                           0
  9Q GAIN WILD-TYPE                                                         1
D18V9, multiclass
                                                           clus
vv                                                          9Q GAIN MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                   142
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       3
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT               0
                                                           clus
vv                                                          9Q GAIN WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                     369
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                         7
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                 1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V10, continuous
D18V11, continuous
D18V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  9Q GAIN MUTATED                                  0     2
  9Q GAIN WILD-TYPE                                2     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  9Q GAIN MUTATED                          14   125
  9Q GAIN WILD-TYPE                        34   321
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                     14                34
  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"
D18V14, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED    11 123
  9Q GAIN WILD-TYPE  15 336
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     11  123
  9Q GAIN WILD-TYPE   15  336
                        clus
vv                       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  HISPANIC OR LATINO                  11                15
  NOT HISPANIC OR LATINO             123               336
[1] 2 2
[1] FALSE

Clustering(19) Variable = 10P GAIN MUTATION ANALYSIS
D19V1, survival
                    sevent
clus2                  0   1
  10P GAIN MUTATED    29  13
  10P GAIN WILD-TYPE 272 206
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                42                478 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                13                206 
$`10P GAIN MUTATED`
TCGA-CN-4727 TCGA-CQ-7067 TCGA-DQ-7589 TCGA-UF-A71D TCGA-BA-5151 TCGA-BA-5555 
       51.29        16.73        46.32        48.03        23.74        17.10 
TCGA-BA-6869 TCGA-BA-6872 TCGA-BA-A6DL TCGA-BB-7861 TCGA-BB-A5HZ TCGA-CN-5356 
       21.17        12.62        20.48        22.42        27.19        46.32 
TCGA-CN-6013 TCGA-CN-6994 TCGA-CN-A63T TCGA-CR-5247 TCGA-CR-6488 TCGA-CR-7399 
       23.90        38.89         7.40        11.77        12.46         5.95 
TCGA-CV-5441 TCGA-CV-6003 TCGA-CV-6934 TCGA-CV-6937 TCGA-CV-7091 TCGA-CV-7250 
       94.88        54.74         2.14        20.52       111.16        95.34 
TCGA-CV-7254 TCGA-CV-7421 TCGA-CV-7435 TCGA-CV-A45Z TCGA-CV-A6JM TCGA-CV-A6JY 
       47.97         0.07       153.86        48.20         6.38        21.24 
TCGA-D6-6825 TCGA-F7-7848 TCGA-HD-7753 TCGA-HD-7917 TCGA-HD-A6HZ TCGA-IQ-A6SG 
       16.14        37.18        28.47        27.48         3.65        19.04 
TCGA-P3-A5QE TCGA-QK-A6IG TCGA-QK-A6VB TCGA-QK-A6VC TCGA-T2-A6WZ TCGA-TN-A7HI 
       51.25         7.30        21.07        19.73        15.91        13.55 

$`10P GAIN WILD-TYPE`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4IG 
        9.30        37.28        20.48        68.48         3.55        28.11 
TCGA-BA-A4II TCGA-BB-A5HU TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 
       30.18        25.71         9.07         9.24        52.08        11.08 
TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-6221 
       35.05        32.48        19.82        24.39        48.20        32.88 
TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CQ-A4C7 TCGA-CR-6472 TCGA-CR-6478 TCGA-CX-7082 
       70.13        43.04        11.61        34.52         6.02         0.36 
TCGA-CX-7219 TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7593 TCGA-H7-A6C5 TCGA-HD-8634 
       34.36        30.94        14.04        40.24        21.11        12.66 
TCGA-HD-8635 TCGA-UF-A7JV TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4078 
       22.85         2.96         3.35        15.19        13.64         9.07 
TCGA-BA-5149 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-6868 
       26.50        42.35        57.93        23.84        65.59        15.52 
TCGA-BA-6870 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IH TCGA-BA-A6D8 
       14.83         4.01        41.85        29.42        20.45        27.95 
TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG 
       11.54         7.10         5.69        14.47         7.82         2.27 
TCGA-BA-A6DI TCGA-BA-A6DJ TCGA-BA-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-7862 TCGA-BB-7863 TCGA-BB-7864 
        4.80         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-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-6988 TCGA-CN-6989 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6998 
        6.74        10.45        32.22         3.68        17.42        11.74 
TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C 
       35.01        25.41        23.57        17.29        29.72        21.21 
TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 
       31.69        22.32        12.39        16.57         4.41        12.07 
TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5324 TCGA-CQ-5325 
        2.70        23.44        20.88        19.53        52.37        21.50 
TCGA-CQ-5326 TCGA-CQ-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-6223 TCGA-CQ-6224 
       11.21         4.24        41.19        32.38        46.95        56.58 
TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7065 
       13.25         4.24        14.99        38.76        64.87        53.52 
TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CB 
       41.88        43.10        77.56        44.48        23.24        29.36 
TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 
       33.60        29.49        14.14        12.46        31.23        84.23 
TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 
       54.67        37.87        26.27        58.42        50.01        39.52 
TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 
       36.99        18.54        16.90        11.90        10.22        11.34 
TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-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-7370 TCGA-CR-7371 
       39.16        47.34        40.93        35.84         3.45         3.09 
TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 
       24.95        29.23         0.99        31.96         9.17        34.06 
TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 
       19.92        26.17        17.13        32.78        47.01        27.06 
TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 
       12.89        49.58        30.02        46.85        32.65        44.25 
TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 
       30.58        24.79         5.13        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-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-5977 TCGA-CV-5978 
       13.35        23.05        86.83        48.59        60.49         7.07 
TCGA-CV-5979 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6933 TCGA-CV-6935 
       43.23        21.07        62.43         9.60        90.12         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-7095 TCGA-CV-7097 
        2.50         4.14        64.83       172.67        18.81        12.66 
TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7104 
        7.99         9.01         5.26         1.84        52.31        12.92 
TCGA-CV-7177 TCGA-CV-7178 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7236 
       21.80        71.21        10.75       130.88        77.16         4.73 
TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7248 
       89.65        36.00        31.36        26.20        18.97        17.13 
TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7255 TCGA-CV-7261 TCGA-CV-7263 TCGA-CV-7406 
        4.96        11.87         2.10        49.71        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-7422 TCGA-CV-7423 TCGA-CV-7424 
       22.85        25.08        25.94        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-7437 TCGA-CV-7438 TCGA-CV-7440 TCGA-CV-A45O 
       19.76         7.17        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-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-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 
        6.48        28.01         3.62        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-D6-8568 
        9.60        23.05         2.53        11.44        18.67        24.95 
TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EN 
       25.32        17.72        12.36        28.77         7.63        22.59 
TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 
       24.95        13.94        12.10        12.79        23.34        58.45 
TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 
       37.25        33.86        18.02        46.45        20.45        37.58 
TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G 
       40.04        39.12        41.59        32.71        21.63        20.25 
TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 
        3.02        31.13        18.94        24.95         0.46        17.85 
TCGA-F7-A622 TCGA-F7-A623 TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 
       11.80        20.25        12.43        13.38        15.16        15.06 
TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-8224 
       20.94        33.76        25.74        21.93        27.48        14.66 
TCGA-HD-8314 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6I0 TCGA-HL-7533 
       22.03         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-A6SH 
        0.07        33.57         5.29        13.68        13.84        15.48 
TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D 
       19.27        10.75        14.37         7.96        30.05         1.84 
TCGA-MT-A67F TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-MZ-A7D7 
       12.62         6.25        15.42         7.13        16.08        17.98 
TCGA-P3-A5Q5 TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-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-A6IH 
       16.01        13.15        21.07        21.21        23.15        21.47 
TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8Z9 
        9.34        12.72        27.39        12.89         5.62        14.76 
TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-RS-A6TO TCGA-RS-A6TP 
       12.20        17.82        15.32         8.32        12.72        16.96 
TCGA-T2-A6WX TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-T3-A92M TCGA-T3-A92N TCGA-TN-A7HJ 
        6.87         7.10        32.45        13.71         3.12        13.25 
TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71E 
       20.35        64.80        54.67         2.83        49.51        49.45 
TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH 
       44.65        74.47        17.95        24.30        55.43        29.46 
TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UP-A6WW 
       18.05        13.94        20.75        22.36        32.65        17.03 
TCGA-WA-A7GZ TCGA-WA-A7H4 TCGA-KU-A66S TCGA-KU-A66T 
       20.55        14.56        13.35        18.15 

  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             21.070 
[1] "0.1 - 153.9 (21.2)" "0.1 - 211.0 (21.1)"
[1] "hr=" "1.5"
D19V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  10P GAIN MUTATED         4        5         8        19         0         0
  10P GAIN WILD-TYPE      23       71        74       233        12         1
D19V3, multiclass
           clus
vv          10P GAIN MUTATED 10P GAIN WILD-TYPE
  STAGE I                  4                 23
  STAGE II                 5                 71
  STAGE III                8                 74
  STAGE IVA               19                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
  10P GAIN MUTATED       7   9   9  13
  10P GAIN WILD-TYPE    43 128  91 160
D19V4, multiclass
       clus
vv      10P GAIN MUTATED 10P GAIN WILD-TYPE
  T0+T1                7                 43
  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    20   8   9   0
  10P GAIN WILD-TYPE 159  60 159   8
D19V5, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  N0               20                159
  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 178   1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED     12    0
  10P GAIN WILD-TYPE  178    1
   clus
vv  10P GAIN MUTATED 10P GAIN WILD-TYPE
  0               12                178
  1                0                  1
[1] 2 2
[1] FALSE
D19V7, binary
                    cls
clus                   0   1
  10P GAIN MUTATED    10  32
  10P GAIN WILD-TYPE 130 350
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED     10   32
  10P GAIN WILD-TYPE  130  350
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  FEMALE               10                130
  MALE                 32                350
[1] 2 2
[1] FALSE
D19V8, binary
                    cls
clus                   0   1
  10P GAIN MUTATED    13  25
  10P GAIN WILD-TYPE 149 276
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED     13   25
  10P GAIN WILD-TYPE  149  276
     clus
vv    10P GAIN MUTATED 10P GAIN WILD-TYPE
  NO                13                149
  YES               25                276
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD & NECK SQUAMOUS CELL CARCINOMA
  10P GAIN MUTATED                                    41
  10P GAIN WILD-TYPE                                 470
                    vv
clus                 HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  10P GAIN MUTATED                                                   1
  10P GAIN WILD-TYPE                                                 9
                    vv
clus                 HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  10P GAIN MUTATED                                                           0
  10P GAIN WILD-TYPE                                                         1
D19V9, multiclass
                                                           clus
vv                                                          10P GAIN MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                     41
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        1
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                0
                                                           clus
vv                                                          10P GAIN WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                      470
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                          9
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                  1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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                           4    38
  10P GAIN WILD-TYPE                        44   408
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                       4                 44
  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"
D19V14, binary
                    cls
clus                   0   1
  10P GAIN MUTATED     1  40
  10P GAIN WILD-TYPE  25 419
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      1   40
  10P GAIN WILD-TYPE   25  419
                        clus
vv                       10P GAIN MUTATED 10P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                 25
  NOT HISPANIC OR LATINO               40                419
[1] 2 2
[1] FALSE

Clustering(20) Variable = 10Q GAIN MUTATION ANALYSIS
D20V1, survival
                    sevent
clus2                  0   1
  10Q GAIN MUTATED    21  13
  10Q GAIN WILD-TYPE 280 206
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                34                486 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                13                206 
$`10Q GAIN MUTATED`
TCGA-CN-4727 TCGA-CN-6023 TCGA-CQ-7067 TCGA-CQ-A4C7 TCGA-DQ-5629 TCGA-UF-A71D 
       51.29        52.08        16.73        11.61        30.94        48.03 
TCGA-BA-5151 TCGA-BA-6870 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-A6DL TCGA-BB-A5HY 
       23.74        14.83        12.62         4.01        20.48        10.55 
TCGA-BB-A5HZ TCGA-CN-6013 TCGA-CN-6994 TCGA-CN-A63T TCGA-CQ-5329 TCGA-CR-7390 
       27.19        23.90        38.89         7.40        70.45        49.58 
TCGA-CR-7399 TCGA-CV-5441 TCGA-CV-5966 TCGA-CV-6003 TCGA-CV-6441 TCGA-CV-6937 
        5.95        94.88        17.92        54.74         9.60        20.52 
TCGA-CV-7091 TCGA-CV-7435 TCGA-D6-6825 TCGA-F7-A620 TCGA-HD-7753 TCGA-HD-7917 
      111.16       153.86        16.14        17.85        28.47        27.48 
TCGA-HD-A6HZ TCGA-P3-A5Q6 TCGA-QK-A6IG TCGA-TN-A7HI 
        3.65        15.78         7.30        13.55 

$`10Q GAIN WILD-TYPE`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4IG 
        9.30        37.28        20.48        68.48         3.55        28.11 
TCGA-BA-A4II TCGA-BB-A5HU TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6024 TCGA-CN-6992 
       30.18        25.71         9.07         9.24        11.08        35.05 
TCGA-CN-6997 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-6221 TCGA-CQ-7063 
       32.48        19.82        24.39        48.20        32.88        70.13 
TCGA-CQ-7068 TCGA-CR-6472 TCGA-CR-6478 TCGA-CX-7082 TCGA-CX-7219 TCGA-DQ-7588 
       43.04        34.52         6.02         0.36        34.36        14.04 
TCGA-DQ-7589 TCGA-DQ-7593 TCGA-H7-A6C5 TCGA-HD-8634 TCGA-HD-8635 TCGA-UF-A7JV 
       46.32        40.24        21.11        12.66        22.85         2.96 
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5152 
        3.35        15.19        13.64         9.07        26.50        42.35 
TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6869 
       57.93        17.10        23.84        65.59        15.52        21.17 
TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IH TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB 
       41.85        29.42        20.45        27.95        11.54         7.10 
TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DI TCGA-BA-A6DJ 
        5.69        14.47         7.82         2.27        11.05        13.38 
TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 
       16.41         6.15       105.90         9.14         4.80         4.41 
TCGA-BB-4228 TCGA-BB-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-A6UM 
       66.28        24.66        38.40        71.05        20.52        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-4740 
       57.11        12.99        20.55        14.33        45.83        27.58 
TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 
       73.61        13.05        42.02        46.32         8.58        12.39 
TCGA-CN-5360 TCGA-CN-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-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-6988 TCGA-CN-6989 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A497 
       10.45        32.22         3.68        17.42        11.74        35.01 
TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63U 
       25.41        23.57        17.29        29.72        21.21        31.69 
TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 
       22.32        12.39        16.57         4.41        12.07         2.70 
TCGA-CN-A6UY TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 
       23.44        20.88        19.53        52.37        21.50         2.93 
TCGA-CQ-5327 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 
       54.58        62.37        45.99        10.42        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-7064 TCGA-CQ-7065 TCGA-CQ-7069 TCGA-CQ-7071 
       14.99        38.76        64.87        53.52        41.88        43.10 
TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE 
       77.56        44.48        23.24        29.36        33.60        29.49 
TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 
       14.14        12.46        31.23        84.23        11.77        54.67 
TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6473 
       37.87        26.27        58.42        50.01        39.52        36.99 
TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 
       18.54        16.90        11.90        10.22        11.34        11.64 
TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 
        7.69        12.46        22.78        15.75         9.27        47.18 
TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 
       39.16        47.34        40.93        35.84         3.45         3.09 
TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 
       24.95        29.23         0.99        31.96         9.17        34.06 
TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 
       19.92        26.17        17.13        32.78        47.01        27.06 
TCGA-CR-7389 TCGA-CR-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-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 
       24.79         5.13        35.41        29.95        48.39       139.43 
TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 
       17.16       129.21       108.95        76.24        19.20        17.95 
TCGA-CV-5440 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5970 TCGA-CV-5971 
      107.51        76.50        91.53        80.12        13.35        23.05 
TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6433 
       86.83        48.59        60.49         7.07        43.23        21.07 
TCGA-CV-6436 TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6938 
       62.43        90.12         2.14         9.70         5.46         4.73 
TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 
       21.90        26.43        11.24       140.78        19.79        12.03 
TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6954 
       42.38        15.09        30.08         6.08        53.95        65.82 
TCGA-CV-6955 TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-6962 
       10.98         7.13         8.42        28.34         2.50         4.14 
TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 
       64.83       172.67        18.81        12.66         7.99         9.01 
TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-7178 
        5.26         1.84        52.31        12.92        21.80        71.21 
TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7242 
       10.75       130.88        77.16         4.73        89.65        36.00 
TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7252 
       31.36        26.20        18.97        17.13        95.34         4.96 
TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7255 TCGA-CV-7261 TCGA-CV-7263 TCGA-CV-7406 
       11.87        47.97         2.10        49.71        18.41        57.47 
TCGA-CV-7407 TCGA-CV-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-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-A460 
        1.05        45.96         6.51        88.87        48.20        60.43 
TCGA-CV-A461 TCGA-CV-A463 TCGA-CV-A464 TCGA-CV-A465 TCGA-CV-A468 TCGA-CV-A6JD 
       67.86         0.76        56.61         7.07        15.25         5.98 
TCGA-CV-A6JE TCGA-CV-A6JM TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU 
       35.34         6.38        29.79         6.48        28.01         3.62 
TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 
       21.24        23.47        19.92        22.52        10.42        10.55 
TCGA-CX-7086 TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 
       18.84        51.12        13.25        25.41         9.60        23.05 
TCGA-D6-6824 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 
        2.53        11.44        18.67        24.95        25.32        17.72 
TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EN TCGA-D6-A6EO TCGA-D6-A6EP 
       12.36        28.77         7.63        22.59        24.95        13.94 
TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 
       12.10        12.79        23.34        58.45        37.25        33.86 
TCGA-DQ-5631 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7594 TCGA-DQ-7595 
       18.02        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-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A622 TCGA-F7-A623 
       31.13        18.94        24.95         0.46        11.80        20.25 
TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A76A TCGA-HD-7229 
       12.43        13.38        15.16        15.06        20.94        33.76 
TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-A4C1 
       25.74        21.93        27.48        14.66        22.03         0.36 
TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-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-A6H7 
        5.29        13.68        13.84        19.04        15.48        19.27 
TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F 
       10.75        14.37         7.96        30.05         1.84        12.62 
TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 
        6.25        15.42         7.13        16.08        17.98        29.92 
TCGA-P3-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-A8Z7 TCGA-QK-A8Z8 
       12.72        27.39        21.07        19.73        12.89         5.62 
TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-RS-A6TO 
       14.76        12.20        17.82        15.32         8.32        12.72 
TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-T3-A92M 
       16.96         6.87        15.91         7.10        32.45        13.71 
TCGA-T3-A92N TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A 
        3.12        13.25        20.35        64.80        54.67         2.83 
TCGA-UF-A71B TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD 
       49.51        49.45        44.65        74.47        17.95        24.30 
TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS 
       55.43        29.46        18.05        13.94        20.75        22.36 
TCGA-UF-A7JT TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 TCGA-KU-A66S TCGA-KU-A66T 
       32.65        17.03        20.55        14.56        13.35        18.15 

  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 
             20.50              21.14 
[1] "3.6 - 153.9 (20.5)" "0.1 - 211.0 (21.1)"
[1] "hr=" "1.2"
D20V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  10Q GAIN MUTATED         4        3         6        17         0         0
  10Q GAIN WILD-TYPE      23       73        76       235        12         1
D20V3, multiclass
           clus
vv          10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  STAGE I                  4                 23
  STAGE II                 3                 73
  STAGE III                6                 76
  STAGE IVA               17                235
  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       5   7   8  11
  10Q GAIN WILD-TYPE    45 130  92 162
D20V4, multiclass
       clus
vv      10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  T0+T1                5                 45
  T2                   7                130
  T3                   8                 92
  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
  10Q GAIN MUTATED    14   7  10   0
  10Q GAIN WILD-TYPE 165  61 158   8
D20V5, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  N0               14                165
  N1                7                 61
  N2               10                158
  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    11   0
  10Q GAIN WILD-TYPE 179   1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED     11    0
  10Q GAIN WILD-TYPE  179    1
   clus
vv  10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  0               11                179
  1                0                  1
[1] 2 2
[1] FALSE
D20V7, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED     9  25
  10Q GAIN WILD-TYPE 131 357
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      9   25
  10Q GAIN WILD-TYPE  131  357
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  FEMALE                9                131
  MALE                 25                357
[1] 2 2
[1] FALSE
D20V8, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED    11  20
  10Q GAIN WILD-TYPE 151 281
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED     11   20
  10Q GAIN WILD-TYPE  151  281
     clus
vv    10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  NO                11                151
  YES               20                281
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD & NECK SQUAMOUS CELL CARCINOMA
  10Q GAIN MUTATED                                    34
  10Q GAIN WILD-TYPE                                 477
                    vv
clus                 HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  10Q GAIN MUTATED                                                   0
  10Q GAIN WILD-TYPE                                                10
                    vv
clus                 HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  10Q GAIN MUTATED                                                           0
  10Q GAIN WILD-TYPE                                                         1
D20V9, multiclass
                                                           clus
vv                                                          10Q GAIN MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                     34
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        0
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                0
                                                           clus
vv                                                          10Q GAIN WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                      477
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                         10
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                  1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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                           2    32
  10Q GAIN WILD-TYPE                        46   414
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                       2                 46
  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"
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    39  29
  11P GAIN WILD-TYPE 262 190
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                68                452 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                29                190 
$`11P GAIN MUTATED`
TCGA-BA-4075 TCGA-CN-6997 TCGA-CQ-5323 TCGA-CQ-7063 TCGA-CQ-A4C7 TCGA-CX-7219 
        9.30        32.48        48.20        70.13        11.61        34.36 
TCGA-DQ-7588 TCGA-BA-5556 TCGA-BA-6868 TCGA-BA-A8YP TCGA-BB-4225 TCGA-BB-7861 
       14.04        23.84        15.52        16.41         4.80        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-CQ-5333 TCGA-CQ-5334 TCGA-CQ-7065 TCGA-CQ-7069 TCGA-CQ-A4C6 
       11.57        11.21         4.24        53.52        41.88        44.48 
TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CR-6484 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7370 
       29.49        14.14        11.64        39.16        47.34         3.45 
TCGA-CR-7382 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6937 TCGA-CV-6950 TCGA-CV-6959 
       26.17        54.74        21.07        20.52        15.09         8.42 
TCGA-CV-7247 TCGA-CV-7254 TCGA-CV-7255 TCGA-CV-7261 TCGA-CV-7409 TCGA-CV-7416 
       18.97        47.97         2.10        49.71        17.85        25.08 
TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CX-A4AQ TCGA-D6-6516 TCGA-D6-6827 TCGA-D6-8569 
       21.24        23.47        51.12        25.41        18.67        25.32 
TCGA-D6-A6EP TCGA-F7-A50J TCGA-F7-A622 TCGA-HD-7229 TCGA-IQ-7630 TCGA-IQ-A61K 
       13.94        31.13        11.80        33.76        15.95         5.29 
TCGA-IQ-A61L TCGA-IQ-A6SG TCGA-IQ-A6SH TCGA-MT-A67D TCGA-P3-A5QA TCGA-P3-A6T2 
       13.68        19.04        15.48         1.84        71.74        75.55 
TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-QK-A6IG TCGA-QK-A6IJ TCGA-QK-A6VB 
       18.97         2.04        29.00         7.30        12.72        21.07 
TCGA-T2-A6WX TCGA-UF-A7JC 
        6.87        17.95 

$`11P GAIN WILD-TYPE`
TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4IG TCGA-BA-A4II 
       37.28        20.48        68.48         3.55        28.11        30.18 
TCGA-BB-A5HU TCGA-CN-4727 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 
       25.71        51.29         9.07         9.24        52.08        11.08 
TCGA-CN-6992 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-6221 TCGA-CQ-7067 TCGA-CQ-7068 
       35.05        19.82        24.39        32.88        16.73        43.04 
TCGA-CR-6472 TCGA-CR-6478 TCGA-CX-7082 TCGA-DQ-5629 TCGA-DQ-7589 TCGA-DQ-7593 
       34.52         6.02         0.36        30.94        46.32        40.24 
TCGA-H7-A6C5 TCGA-HD-8634 TCGA-HD-8635 TCGA-UF-A71D TCGA-UF-A7JV TCGA-4P-AA8J 
       21.11        12.66        22.85        48.03         2.96         3.35 
TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 
       15.19        13.64         9.07        26.50        23.74        42.35 
TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5558 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6872 
       57.93        17.10        65.59        21.17        14.83        12.62 
TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IH TCGA-BA-A6D8 TCGA-BA-A6DA 
        4.01        41.85        29.42        20.45        27.95        11.54 
TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DI 
        7.10         5.69        14.47         7.82         2.27        11.05 
TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4227 
       13.38        20.48         6.15       105.90         9.14         4.41 
TCGA-BB-4228 TCGA-BB-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-A5HZ TCGA-BB-A6UM 
       24.66        38.40        71.05        20.52        27.19        12.92 
TCGA-BB-A6UO TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 
        8.81        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-4735 
       56.68        12.89        26.86        32.81        52.14        57.11 
TCGA-CN-4736 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-5356 TCGA-CN-5358 
       12.99        45.83        27.58        73.61        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-5369 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 
       12.49         8.52        52.08        56.94        50.07        30.67 
TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 
       48.00        23.90        47.44        28.04        19.07        34.13 
TCGA-CN-6020 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 
        6.74        10.45        32.22        38.89         3.68        17.42 
TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B 
       11.74        35.01        25.41        23.57        17.29        29.72 
TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y 
       21.21         7.40        31.69        22.32        12.39        16.57 
TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V6 TCGA-CN-A6V7 
        4.41        12.07         2.70        23.44        20.88        19.53 
TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 
       52.37        21.50         2.93        54.58        70.45        62.37 
TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-6218 TCGA-CQ-6220 TCGA-CQ-6223 TCGA-CQ-6224 
       45.99        10.42        41.19        32.38        46.95        56.58 
TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7071 
       13.25         4.24        14.99        38.76        64.87        43.10 
TCGA-CQ-7072 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CH TCGA-CQ-A4CI 
       77.56        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-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6480 
       50.01        39.52        36.99        18.54        16.90        11.90 
TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 
       10.22        11.34         7.69        12.46        22.78        15.75 
TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-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-7380 
       29.23         0.99        31.96         9.17        34.06        19.92 
TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 
       17.13        32.78        47.01        27.06        12.89        49.58 
TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 
       30.02        46.85        32.65        44.25        30.58        24.79 
TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 
        5.13         5.95        35.41        29.95        48.39       139.43 
TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 
       17.16       129.21       108.95        76.24        19.20        17.95 
TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 
      107.51        94.88        76.50        91.53        80.12        17.92 
TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 
       13.35        23.05        86.83        48.59        60.49         7.07 
TCGA-CV-5979 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6935 
       43.23        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-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-6960 TCGA-CV-6961 TCGA-CV-6962 
       65.82        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       172.67       111.16        18.81        12.66         7.99 
TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7177 
        9.01         5.26         1.84        52.31        12.92        21.80 
TCGA-CV-7178 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7238 
       71.21        10.75       130.88        77.16         4.73        89.65 
TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7252 
       36.00        31.36        26.20        17.13        95.34         4.96 
TCGA-CV-7253 TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7407 TCGA-CV-7410 TCGA-CV-7411 
       11.87        18.41        57.47        35.54       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-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-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 
       28.01         3.62        19.92        22.52        10.42        10.55 
TCGA-CX-7086 TCGA-D6-6515 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 
       18.84        13.25         9.60        23.05         2.53        16.14 
TCGA-D6-6826 TCGA-D6-8568 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM 
       11.44        24.95        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        23.34        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-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-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 
       20.25         3.02        18.94        24.95         0.46        17.85 
TCGA-F7-A623 TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A76A 
       20.25        12.43        13.38        15.16        15.06        20.94 
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-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 
       22.03         0.36        13.84         4.27         3.65         6.90 
TCGA-HL-7533 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H 
       34.75        38.53        14.50        37.71        11.84        37.41 
TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61O TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W 
        0.07        33.57        13.84        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-A5QE TCGA-P3-A5QF 
       16.08        17.98        29.92        15.78        51.25        10.85 
TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-P3-A6T8 
       36.82        47.01        19.00        12.99        16.01        13.15 
TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6V9 
       21.07        21.21        23.15        21.47         9.34        27.39 
TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB 
       19.73        12.89         5.62        14.76        12.20        17.82 
TCGA-QK-AA3J TCGA-QK-AA3K TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WZ TCGA-T2-A6X0 
       15.32         8.32        12.72        16.96        15.91         7.10 
TCGA-T2-A6X2 TCGA-T3-A92M TCGA-T3-A92N TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL 
       32.45        13.71         3.12        13.55        13.25        20.35 
TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71E TCGA-UF-A7J9 
       64.80        54.67         2.83        49.51        49.45        44.65 
TCGA-UF-A7JA TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK 
       74.47        24.30        55.43        29.46        18.05        13.94 
TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 
       20.75        22.36        32.65        17.03        20.55        14.56 
TCGA-KU-A66S TCGA-KU-A66T 
       13.35        18.15 

  11P GAIN MUTATED 11P GAIN WILD-TYPE 
              1.84               0.07 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
             75.55             210.97 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
            18.970             21.565 
[1] "1.8 - 75.5 (19.0)"  "0.1 - 211.0 (21.6)"
[1] "hr=" "1.2"
D21V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  11P GAIN MUTATED         5       14        15        27         2         0
  11P GAIN WILD-TYPE      22       62        67       225        10         1
D21V3, multiclass
           clus
vv          11P GAIN MUTATED 11P GAIN WILD-TYPE
  STAGE I                  5                 22
  STAGE II                14                 62
  STAGE III               15                 67
  STAGE IVA               27                225
  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  22  17  18
  11P GAIN WILD-TYPE    44 115  83 155
D21V4, multiclass
       clus
vv      11P GAIN MUTATED 11P GAIN WILD-TYPE
  T0+T1                6                 44
  T2                  22                115
  T3                  17                 83
  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
  11P GAIN MUTATED    32   9  15   2
  11P GAIN WILD-TYPE 147  59 153   6
D21V5, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  N0               32                147
  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    34   0
  11P GAIN WILD-TYPE 156   1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED     34    0
  11P GAIN WILD-TYPE  156    1
   clus
vv  11P GAIN MUTATED 11P GAIN WILD-TYPE
  0               34                156
  1                0                  1
[1] 2 2
[1] FALSE
D21V7, binary
                    cls
clus                   0   1
  11P GAIN MUTATED    20  48
  11P GAIN WILD-TYPE 120 334
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED     20   48
  11P GAIN WILD-TYPE  120  334
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  FEMALE               20                120
  MALE                 48                334
[1] 2 2
[1] FALSE
D21V8, binary
                    cls
clus                   0   1
  11P GAIN MUTATED    27  36
  11P GAIN WILD-TYPE 135 265
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED     27   36
  11P GAIN WILD-TYPE  135  265
     clus
vv    11P GAIN MUTATED 11P GAIN WILD-TYPE
  NO                27                135
  YES               36                265
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD & NECK SQUAMOUS CELL CARCINOMA
  11P GAIN MUTATED                                    68
  11P GAIN WILD-TYPE                                 443
                    vv
clus                 HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  11P GAIN MUTATED                                                   0
  11P GAIN WILD-TYPE                                                10
                    vv
clus                 HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  11P GAIN MUTATED                                                           0
  11P GAIN WILD-TYPE                                                         1
D21V9, multiclass
                                                           clus
vv                                                          11P GAIN MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                     68
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        0
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                0
                                                           clus
vv                                                          11P GAIN WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                      443
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                         10
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                  1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V10, continuous
D21V11, continuous
D21V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  11P GAIN MUTATED                                  0     4
  11P GAIN WILD-TYPE                                2     7
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  11P GAIN MUTATED                           7    55
  11P GAIN WILD-TYPE                        41   391
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                       7                 41
  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"
D21V14, binary
                    cls
clus                   0   1
  11P GAIN MUTATED     3  62
  11P GAIN WILD-TYPE  23 397
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      3   62
  11P GAIN WILD-TYPE   23  397
                        clus
vv                       11P GAIN MUTATED 11P GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                 23
  NOT HISPANIC OR LATINO               62                397
[1] 2 2
[1] FALSE

Clustering(22) Variable = 11Q GAIN MUTATION ANALYSIS
D22V1, survival
                    sevent
clus2                  0   1
  11Q GAIN MUTATED    41  30
  11Q GAIN WILD-TYPE 260 189
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                71                449 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                30                189 
$`11Q GAIN MUTATED`
TCGA-BA-4075 TCGA-CN-6997 TCGA-CQ-7063 TCGA-CQ-A4C7 TCGA-CX-7219 TCGA-UF-A71D 
        9.30        32.48        70.13        11.61        34.36        48.03 
TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4225 TCGA-BB-7861 
       23.84        65.59        20.48        16.41         4.80        22.42 
TCGA-CN-4731 TCGA-CN-4737 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5367 TCGA-CN-6018 
       32.81        20.55        13.05        42.02        11.57        19.07 
TCGA-CN-A63U TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6225 TCGA-CQ-7065 TCGA-CQ-7069 
       31.69        11.21         4.24        13.25        53.52        41.88 
TCGA-CQ-7072 TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CR-6484 TCGA-CR-7365 TCGA-CR-7367 
       77.56        29.49        14.14        11.64        39.16        47.34 
TCGA-CR-7370 TCGA-CR-7372 TCGA-CR-7383 TCGA-CV-6003 TCGA-CV-6937 TCGA-CV-6950 
        3.45        24.95        17.13        54.74        20.52        15.09 
TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-7248 TCGA-CV-7255 TCGA-CV-7261 TCGA-CV-7416 
        8.42        28.34        17.13         2.10        49.71        25.08 
TCGA-CV-7423 TCGA-CV-7440 TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-D6-6516 TCGA-D6-6826 
      100.57        22.19        21.24        23.47        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 
       33.76        21.93        15.95         5.29        13.68        19.04 
TCGA-IQ-A6SH TCGA-MT-A67D TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A6T3 TCGA-P3-A6T5 
       15.48         1.84        15.78        71.74        18.97        29.00 
TCGA-QK-A6IG TCGA-QK-A6IJ TCGA-UF-A718 TCGA-UF-A7JC TCGA-UF-A7JJ 
        7.30        12.72        64.80        17.95        18.05 

$`11Q GAIN WILD-TYPE`
TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4IG TCGA-BA-A4II 
       37.28        20.48        68.48         3.55        28.11        30.18 
TCGA-BB-A5HU TCGA-CN-4727 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 
       25.71        51.29         9.07         9.24        52.08        11.08 
TCGA-CN-6992 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-6221 TCGA-CQ-7067 
       35.05        19.82        24.39        48.20        32.88        16.73 
TCGA-CQ-7068 TCGA-CR-6472 TCGA-CR-6478 TCGA-CX-7082 TCGA-DQ-5629 TCGA-DQ-7588 
       43.04        34.52         6.02         0.36        30.94        14.04 
TCGA-DQ-7589 TCGA-DQ-7593 TCGA-H7-A6C5 TCGA-HD-8634 TCGA-HD-8635 TCGA-UF-A7JV 
       46.32        40.24        21.11        12.66        22.85         2.96 
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 
        3.35        15.19        13.64         9.07        26.50        23.74 
TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 
       42.35        57.93        17.10        15.52        21.17        14.83 
TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IH TCGA-BA-A6D8 
       12.62         4.01        41.85        29.42        20.45        27.95 
TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG 
       11.54         7.10         5.69        14.47         7.82         2.27 
TCGA-BA-A6DI TCGA-BA-A6DJ TCGA-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-A5HY TCGA-BB-A5HZ 
       24.66        38.40        71.05        20.52        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-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4733 
       38.04         4.67        56.68        12.89        26.86        52.14 
TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 
       57.11        12.99        14.33        45.83        27.58        73.61 
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-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-6019 TCGA-CN-6020 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-6995 
       34.13         6.74        10.45        32.22        38.89         3.68 
TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A 
       17.42        11.74        35.01        25.41        23.57        17.29 
TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-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-A6V6 TCGA-CN-A6V7 
        4.41        12.07         2.70        23.44        20.88        19.53 
TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 
       52.37        21.50         2.93        54.58        70.45        62.37 
TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-6218 TCGA-CQ-6220 TCGA-CQ-6223 TCGA-CQ-6224 
       45.99        10.42        41.19        32.38        46.95        56.58 
TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7071 TCGA-CQ-A4C6 
        4.24        14.99        38.76        64.87        43.10        44.48 
TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 
       23.24        29.36        33.60        12.46        31.23        84.23 
TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 
       11.77        54.67        37.87        26.27        58.42        50.01 
TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6480 TCGA-CR-6481 
       39.52        36.99        18.54        16.90        11.90        10.22 
TCGA-CR-6482 TCGA-CR-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-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-7379 TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7385 
       31.96         9.17        34.06        19.92        26.17        32.78 
TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 
       47.01        27.06        12.89        49.58        30.02        46.85 
TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 
       32.65        44.25        30.58        24.79         5.13         5.95 
TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 
       35.41        29.95        48.39       139.43        17.16       129.21 
TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 
      108.95        76.24        19.20        17.95       107.51        94.88 
TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 
       76.50        91.53        80.12        17.92        13.35        23.05 
TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-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-6938 TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 
        4.73        21.90        26.43        11.24       140.78        19.79 
TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6954 
       12.03        42.38        30.08         6.08        53.95        65.82 
TCGA-CV-6955 TCGA-CV-6956 TCGA-CV-6961 TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7090 
       10.98         7.13         2.50         4.14        64.83       172.67 
TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 
      111.16        18.81        12.66         7.99         9.01         5.26 
TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-7178 TCGA-CV-7180 
        1.84        52.31        12.92        21.80        71.21        10.75 
TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 
      130.88        77.16         4.73        89.65        36.00        31.36 
TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7254 
       26.20        18.97        95.34         4.96        11.87        47.97 
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-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-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-7085 TCGA-CX-7086 TCGA-CX-A4AQ 
       19.92        22.52        10.42        10.55        18.84        51.12 
TCGA-D6-6515 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-8568 
       13.25         9.60        23.05         2.53        16.14        24.95 
TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EN TCGA-D6-A6EO 
       25.32        17.72        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-5630 
       12.10        12.79        23.34        58.45        37.25        33.86 
TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 
       46.45        20.45        37.58        40.04        39.12        41.59 
TCGA-F7-7848 TCGA-F7-8298 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-A623 TCGA-F7-A624 TCGA-H7-7774 
       24.95         0.46        17.85        20.25        12.43        13.38 
TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A76A TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7832 
       15.16        15.06        20.94        28.47        25.74        27.48 
TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 
       27.48        14.66        22.03         0.36        13.84         4.27 
TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-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-A61O TCGA-KU-A6H7 
       11.84        37.41         0.07        33.57        13.84        19.27 
TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67F TCGA-MT-A67G 
       10.75        14.37         7.96        30.05        12.62         6.25 
TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5QE 
       15.42         7.13        16.08        17.98        29.92        51.25 
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        27.39        21.07        19.73        12.89 
TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K 
        5.62        14.76        12.20        17.82        15.32         8.32 
TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-T2-A6X2 
       12.72        16.96         6.87        15.91         7.10        32.45 
TCGA-T3-A92M TCGA-T3-A92N TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A719 
       13.71         3.12        13.55        13.25        20.35        54.67 
TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JD 
        2.83        49.51        49.45        44.65        74.47        24.30 
TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT 
       55.43        29.46        13.94        20.75        22.36        32.65 
TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 TCGA-KU-A66S TCGA-KU-A66T 
       17.03        20.55        14.56        13.35        18.15 

  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
              1.84               0.07 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
            100.57             210.97 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
             19.07              21.21 
[1] "1.8 - 100.6 (19.1)" "0.1 - 211.0 (21.2)"
[1] "hr=" "1.1"
D22V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  11Q GAIN MUTATED         6       13        16        30         1         0
  11Q GAIN WILD-TYPE      21       63        66       222        11         1
D22V3, multiclass
           clus
vv          11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  STAGE I                  6                 21
  STAGE II                13                 63
  STAGE III               16                 66
  STAGE IVA               30                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
  11Q GAIN MUTATED       8  19  18  22
  11Q GAIN WILD-TYPE    42 118  82 151
D22V4, multiclass
       clus
vv      11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  T0+T1                8                 42
  T2                  19                118
  T3                  18                 82
  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    35   7  18   1
  11Q GAIN WILD-TYPE 144  61 150   7
D22V5, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  N0               35                144
  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    34   0
  11Q GAIN WILD-TYPE 156   1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED     34    0
  11Q GAIN WILD-TYPE  156    1
   clus
vv  11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  0               34                156
  1                0                  1
[1] 2 2
[1] FALSE
D22V7, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED    24  47
  11Q GAIN WILD-TYPE 116 335
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED     24   47
  11Q GAIN WILD-TYPE  116  335
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  FEMALE               24                116
  MALE                 47                335
[1] 2 2
[1] FALSE
D22V8, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED    29  36
  11Q GAIN WILD-TYPE 133 265
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED     29   36
  11Q GAIN WILD-TYPE  133  265
     clus
vv    11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  NO                29                133
  YES               36                265
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD & NECK SQUAMOUS CELL CARCINOMA
  11Q GAIN MUTATED                                    71
  11Q GAIN WILD-TYPE                                 440
                    vv
clus                 HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  11Q GAIN MUTATED                                                   0
  11Q GAIN WILD-TYPE                                                10
                    vv
clus                 HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  11Q GAIN MUTATED                                                           0
  11Q GAIN WILD-TYPE                                                         1
D22V9, multiclass
                                                           clus
vv                                                          11Q GAIN MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                     71
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        0
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                0
                                                           clus
vv                                                          11Q GAIN WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                      440
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                         10
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                  1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V10, continuous
D22V11, continuous
D22V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  11Q GAIN MUTATED                                  0     2
  11Q GAIN WILD-TYPE                                2     9
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  11Q GAIN MUTATED                           7    59
  11Q GAIN WILD-TYPE                        41   387
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                       7                 41
  WHITE                                          59                387
[1] 4 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  61
  11Q GAIN WILD-TYPE  23 398
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      3   61
  11Q GAIN WILD-TYPE   23  398
                        clus
vv                       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                 23
  NOT HISPANIC OR LATINO               61                398
[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 214 158
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
               148                372 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                61                158 
$`12P GAIN MUTATED`
TCGA-BA-5559 TCGA-BA-6871 TCGA-CN-6023 TCGA-CN-6024 TCGA-CQ-7067 TCGA-CX-7219 
       68.48         3.55        52.08        11.08        16.73        34.36 
TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-4P-AA8J TCGA-BA-5555 TCGA-BA-A4IF 
       30.94        14.04        46.32         3.35        17.10        29.42 
TCGA-BA-A4IH TCGA-BA-A6DI TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4223 TCGA-BB-4224 
       20.45        11.05        20.48        16.41       105.90         9.14 
TCGA-BB-4225 TCGA-BB-7862 TCGA-BB-7870 TCGA-BB-A5HY TCGA-C9-A47Z TCGA-CN-4725 
        4.80        36.72        66.28        10.55         6.28        38.04 
TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-5356 
       56.68        12.89        20.55        14.33        45.83        46.32 
TCGA-CN-5359 TCGA-CN-5366 TCGA-CN-6012 TCGA-CN-6018 TCGA-CN-6988 TCGA-CN-6994 
       12.39        11.84        48.00        19.07        10.45        38.89 
TCGA-CN-6995 TCGA-CN-A497 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A63T 
        3.68        35.01        23.57        17.29        29.72         7.40 
TCGA-CN-A6V6 TCGA-CQ-5329 TCGA-CQ-5332 TCGA-CQ-6220 TCGA-CQ-6224 TCGA-CQ-A4CE 
       20.88        70.45        10.42        32.38        56.58        29.49 
TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-6467 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-7364 
       84.23        11.77        58.42         7.69        12.46        47.18 
TCGA-CR-7365 TCGA-CR-7372 TCGA-CR-7379 TCGA-CR-7383 TCGA-CR-7390 TCGA-CR-7397 
       39.16        24.95        34.06        17.13        49.58        24.79 
TCGA-CR-7398 TCGA-CR-7399 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 
        5.13         5.95       139.43        17.16       129.21       108.95 
TCGA-CV-5440 TCGA-CV-5978 TCGA-CV-6003 TCGA-CV-6933 TCGA-CV-6937 TCGA-CV-6940 
      107.51         7.07        54.74        90.12        20.52        26.43 
TCGA-CV-6941 TCGA-CV-6945 TCGA-CV-6959 TCGA-CV-6962 TCGA-CV-7091 TCGA-CV-7102 
       11.24        12.03         8.42         4.14       111.16         1.84 
TCGA-CV-7103 TCGA-CV-7177 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7247 
       52.31        21.80        36.00        31.36        26.20        18.97 
TCGA-CV-7248 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7407 TCGA-CV-7409 TCGA-CV-7416 
       17.13        47.97        49.71        35.54        17.85        25.08 
TCGA-CV-7418 TCGA-CV-7421 TCGA-CV-7422 TCGA-CV-7435 TCGA-CV-7437 TCGA-CV-7440 
       25.94         0.07        34.09       153.86        16.64        22.19 
TCGA-CV-A45R TCGA-CV-A45U TCGA-CV-A45W TCGA-CV-A45Z TCGA-CV-A6JM TCGA-CX-7086 
      180.16        35.47        45.96        48.20         6.38        18.84 
TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6823 TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-7591 
       13.25        25.41        23.05        23.34        58.45        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-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D 
       19.04        15.48        14.37         7.96        30.05         1.84 
TCGA-MT-A67G TCGA-MZ-A7D7 TCGA-P3-A5Q6 TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T4 
        6.25        17.98        15.78        75.55        18.97         2.04 
TCGA-QK-A64Z TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6VB TCGA-QK-A8Z9 TCGA-QK-A8ZA 
       21.07        23.15         7.30        21.07        14.76        12.20 
TCGA-RS-A6TO TCGA-T3-A92N TCGA-TN-A7HI TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71E 
       12.72         3.12        13.55         2.83        49.51        49.45 
TCGA-UF-A7J9 TCGA-UF-A7JC TCGA-UF-A7JH TCGA-KU-A66T 
       44.65        17.95        29.46        18.15 

$`12P GAIN WILD-TYPE`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-A4IG TCGA-BA-A4II TCGA-BB-A5HU 
        9.30        37.28        20.48        28.11        30.18        25.71 
TCGA-CN-4727 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-A6V1 
       51.29         9.07         9.24        35.05        32.48        19.82 
TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-6221 TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CQ-A4C7 
       24.39        48.20        32.88        70.13        43.04        11.61 
TCGA-CR-6472 TCGA-CR-6478 TCGA-CX-7082 TCGA-DQ-7593 TCGA-H7-A6C5 TCGA-HD-8634 
       34.52         6.02         0.36        40.24        21.11        12.66 
TCGA-HD-8635 TCGA-UF-A71D TCGA-UF-A7JV TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4078 
       22.85        48.03         2.96        15.19        13.64         9.07 
TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5556 TCGA-BA-5558 
       26.50        23.74        42.35        57.93        23.84        65.59 
TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 
       15.52        21.17        14.83        12.62         4.01        41.85 
TCGA-BA-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-A6DJ TCGA-BB-4217 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 
        2.27        13.38         6.15         4.41        18.38        22.42 
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-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-4726 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 
       55.86         4.67        26.86        32.81        52.14        57.11 
TCGA-CN-4736 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5358 
       12.99        27.58        73.61        13.05        42.02         8.58 
TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5367 TCGA-CN-5369 
       71.31         8.32        16.21        11.54        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-6019 TCGA-CN-6020 TCGA-CN-6989 TCGA-CN-6996 
       47.44        28.04        34.13         6.74        32.22        17.42 
TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A49C TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W 
       11.74        25.41        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-A6V7 
       16.57         4.41        12.07         2.70        23.44        19.53 
TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5330 TCGA-CQ-5331 
       52.37        21.50         2.93        54.58        62.37        45.99 
TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6223 TCGA-CQ-6225 TCGA-CQ-6227 
       11.21         4.24        41.19        46.95        13.25         4.24 
TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7069 TCGA-CQ-7071 
       14.99        38.76        64.87        53.52        41.88        43.10 
TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CG 
       77.56        44.48        23.24        29.36        33.60        14.14 
TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6470 
       12.46        31.23        54.67        37.87        26.27        50.01 
TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6480 TCGA-CR-6481 
       39.52        36.99        18.54        16.90        11.90        10.22 
TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7367 
       11.34        11.64        22.78        15.75         9.27        47.34 
TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7373 TCGA-CR-7374 
       40.93        35.84         3.45         3.09        29.23         0.99 
TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7385 TCGA-CR-7386 
       31.96         9.17        19.92        26.17        32.78        47.01 
TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 
       27.06        12.89        30.02        46.85        32.65        44.25 
TCGA-CR-7395 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5435 TCGA-CV-5436 
       30.58        35.41        29.95        48.39        76.24        19.20 
TCGA-CV-5439 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 
       17.95        94.88        76.50        91.53        80.12        17.92 
TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5979 
       13.35        23.05        86.83        48.59        60.49        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-6942 TCGA-CV-6943 TCGA-CV-6948 TCGA-CV-6950 
        4.73        21.90       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-6960 TCGA-CV-6961 TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7095 TCGA-CV-7097 
       28.34         2.50        64.83       172.67        18.81        12.66 
TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7104 TCGA-CV-7178 TCGA-CV-7180 
        7.99         9.01         5.26        12.92        71.21        10.75 
TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7250 TCGA-CV-7252 
      130.88        77.16         4.73        89.65        95.34         4.96 
TCGA-CV-7253 TCGA-CV-7255 TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7411 
       11.87         2.10        18.41        57.47       210.97        89.33 
TCGA-CV-7413 TCGA-CV-7414 TCGA-CV-7415 TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7425 
        9.67         0.46        22.85       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-7438 TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45T 
        7.17         6.38        27.98        21.01       169.38       159.65 
TCGA-CV-A45V TCGA-CV-A45X TCGA-CV-A45Y TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A463 
        1.05         6.51        88.87        60.43        67.86         0.76 
TCGA-CV-A464 TCGA-CV-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-7085 TCGA-CX-A4AQ TCGA-D6-6517 TCGA-D6-6824 
       22.52        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-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G 
       40.04        39.12        41.59        32.71        21.63        20.25 
TCGA-F7-A50I TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A623 
        3.02        24.95         0.46        17.85        11.80        20.25 
TCGA-H7-8502 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7832 TCGA-HD-8224 TCGA-HD-8314 
       15.06        20.94        33.76        27.48        14.66        22.03 
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-KU-A6H7 TCGA-KU-A6H8 
       33.57         5.29        13.68        13.84        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        27.39        19.73        12.89         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-A7JA TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO 
       74.47        24.30        55.43        18.05        13.94        20.75 
TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 TCGA-KU-A66S 
       22.36        32.65        17.03        20.55        14.56        13.35 

  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 
             21.07              21.14 
[1] "0.1 - 180.2 (21.1)" "0.1 - 211.0 (21.1)"
[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        72         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               72                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 140   1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     50    0
  12P GAIN WILD-TYPE  140    1
   clus
vv  12P GAIN MUTATED 12P GAIN WILD-TYPE
  0               50                140
  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    44  83
  12P GAIN WILD-TYPE 118 218
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     44   83
  12P GAIN WILD-TYPE  118  218
     clus
vv    12P GAIN MUTATED 12P GAIN WILD-TYPE
  NO                44                118
  YES               83                218
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD & NECK SQUAMOUS CELL CARCINOMA
  12P GAIN MUTATED                                   146
  12P GAIN WILD-TYPE                                 365
                    vv
clus                 HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  12P GAIN MUTATED                                                   2
  12P GAIN WILD-TYPE                                                 8
                    vv
clus                 HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  12P GAIN MUTATED                                                           0
  12P GAIN WILD-TYPE                                                         1
D23V9, multiclass
                                                           clus
vv                                                          12P GAIN MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                    146
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        2
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                0
                                                           clus
vv                                                          12P GAIN WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                      365
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                          8
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                  1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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    55  37
  12Q GAIN WILD-TYPE 246 182
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                92                428 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                37                182 
$`12Q GAIN MUTATED`
TCGA-BA-5559 TCGA-BA-6871 TCGA-CN-4727 TCGA-CN-6023 TCGA-CQ-7067 TCGA-DQ-7588 
       68.48         3.55        51.29        52.08        16.73        14.04 
TCGA-DQ-7589 TCGA-BA-A4IF TCGA-BA-A6DL TCGA-BB-4223 TCGA-BB-4225 TCGA-BB-7870 
       46.32        29.42        20.48       105.90         4.80        66.28 
TCGA-BB-A5HY TCGA-C9-A47Z TCGA-CN-4725 TCGA-CN-4728 TCGA-CN-4737 TCGA-CN-4739 
       10.55         6.28        38.04        56.68        20.55        45.83 
TCGA-CN-5356 TCGA-CN-5359 TCGA-CN-6010 TCGA-CN-6012 TCGA-CN-6988 TCGA-CN-6995 
       46.32        12.39        50.07        48.00        10.45         3.68 
TCGA-CN-A497 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A63T TCGA-CN-A6V6 
       35.01        23.57        17.29        29.72         7.40        20.88 
TCGA-CQ-5332 TCGA-CQ-6220 TCGA-CQ-6224 TCGA-CQ-A4CE TCGA-CR-5247 TCGA-CR-6467 
       10.42        32.38        56.58        29.49        11.77        58.42 
TCGA-CR-7365 TCGA-CR-7379 TCGA-CR-7383 TCGA-CR-7399 TCGA-CV-5430 TCGA-CV-5431 
       39.16        34.06        17.13         5.95       139.43        17.16 
TCGA-CV-5434 TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6959 TCGA-CV-6962 TCGA-CV-7091 
      108.95        26.43        11.24         8.42         4.14       111.16 
TCGA-CV-7102 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7248 
        1.84        36.00        31.36        26.20        18.97        17.13 
TCGA-CV-7416 TCGA-CV-7421 TCGA-CV-7422 TCGA-CV-7435 TCGA-CV-7437 TCGA-CV-7440 
       25.08         0.07        34.09       153.86        16.64        22.19 
TCGA-CV-A45R TCGA-CV-A45Z TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6823 TCGA-D6-A74Q 
      180.16        48.20        13.25        25.41        23.05        23.34 
TCGA-DQ-7591 TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A624 TCGA-H7-7774 TCGA-HD-7753 
       20.45        31.13        18.94        12.43        13.38        28.47 
TCGA-HD-A6HZ TCGA-IQ-A6SH TCGA-MT-A51W TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67G 
        3.65        15.48        14.37        30.05         1.84         6.25 
TCGA-MZ-A7D7 TCGA-P3-A6T4 TCGA-QK-A6IF TCGA-QK-A6VB TCGA-QK-A8Z9 TCGA-QK-A8ZA 
       17.98         2.04        23.15        21.07        14.76        12.20 
TCGA-RS-A6TO TCGA-T3-A92N TCGA-TN-A7HI TCGA-UF-A71A TCGA-UF-A71E TCGA-UF-A7J9 
       12.72         3.12        13.55         2.83        49.45        44.65 
TCGA-UF-A7JC TCGA-KU-A66T 
       17.95        18.15 

$`12Q GAIN WILD-TYPE`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-A4IG TCGA-BA-A4II TCGA-BB-A5HU 
        9.30        37.28        20.48        28.11        30.18        25.71 
TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6024 TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-A6V1 
        9.07         9.24        11.08        35.05        32.48        19.82 
TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-6221 TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CQ-A4C7 
       24.39        48.20        32.88        70.13        43.04        11.61 
TCGA-CR-6472 TCGA-CR-6478 TCGA-CX-7082 TCGA-CX-7219 TCGA-DQ-5629 TCGA-DQ-7593 
       34.52         6.02         0.36        34.36        30.94        40.24 
TCGA-H7-A6C5 TCGA-HD-8634 TCGA-HD-8635 TCGA-UF-A71D TCGA-UF-A7JV TCGA-4P-AA8J 
       21.11        12.66        22.85        48.03         2.96         3.35 
TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 
       15.19        13.64         9.07        26.50        23.74        42.35 
TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6869 
       57.93        17.10        23.84        65.59        15.52        21.17 
TCGA-BA-6870 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IH TCGA-BA-A6D8 
       14.83        12.62         4.01        41.85        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-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-A5HZ TCGA-BB-A6UM 
       24.66        38.40        71.05        20.52        27.19        12.92 
TCGA-BB-A6UO TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4726 TCGA-CN-4729 
        8.81        12.69        48.76        55.86         4.67        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-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5358 TCGA-CN-5360 
       27.58        73.61        13.05        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-5374 TCGA-CN-6011 TCGA-CN-6013 TCGA-CN-6016 
        8.52        52.08        56.94        30.67        23.90        47.44 
TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6989 TCGA-CN-6994 
       28.04        19.07        34.13         6.74        32.22        38.89 
TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A49C TCGA-CN-A63U TCGA-CN-A63V 
       17.42        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-A6V7 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 
       19.53        52.37        21.50         2.93        54.58        70.45 
TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6223 
       62.37        45.99        11.21         4.24        41.19        46.95 
TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7065 
       13.25         4.24        14.99        38.76        64.87        53.52 
TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CB 
       41.88        43.10        77.56        44.48        23.24        29.36 
TCGA-CQ-A4CD TCGA-CQ-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-6473 TCGA-CR-6474 
       37.87        26.27        50.01        39.52        36.99        18.54 
TCGA-CR-6477 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 
       16.90        11.90        10.22        11.34        11.64         7.69 
TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7367 
       12.46        22.78        15.75         9.27        47.18        47.34 
TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 
       40.93        35.84         3.45         3.09        24.95        29.23 
TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7385 
        0.99        31.96         9.17        19.92        26.17        32.78 
TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 
       47.01        27.06        12.89        49.58        30.02        46.85 
TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7401 
       32.65        44.25        30.58        24.79         5.13        35.41 
TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5432 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 
       29.95        48.39       129.21        76.24        19.20        17.95 
TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 
      107.51        94.88        76.50        91.53        80.12        17.92 
TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 
       13.35        23.05        86.83        48.59        60.49         7.07 
TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6933 
       43.23        54.74        21.07        62.43         9.60        90.12 
TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6939 
        2.14         9.70         5.46        20.52         4.73        21.90 
TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-6951 
      140.78        19.79        12.03        42.38        15.09        30.08 
TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-6955 TCGA-CV-6956 TCGA-CV-6960 
        6.08        53.95        65.82        10.98         7.13        28.34 
TCGA-CV-6961 TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 
        2.50        64.83       172.67        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-7235 TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7250 
       10.75       130.88        77.16         4.73        89.65        95.34 
TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7255 TCGA-CV-7261 TCGA-CV-7263 
        4.96        11.87        47.97         2.10        49.71        18.41 
TCGA-CV-7406 TCGA-CV-7407 TCGA-CV-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-7423 TCGA-CV-7424 TCGA-CV-7425 
        0.46        22.85        25.94       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-7438 TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45T 
        7.17         6.38        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-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-A6JM TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU 
       35.34         6.38        29.79         6.48        28.01         3.62 
TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 
       21.24        23.47        19.92        22.52        10.42        10.55 
TCGA-CX-7086 TCGA-CX-A4AQ TCGA-D6-6517 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 
       18.84        51.12         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-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7590 TCGA-DQ-7592 
       58.45        37.25        33.86        18.02        46.45        37.58 
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-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-H7-8501 TCGA-H7-8502 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7754 
       20.25        15.16        15.06        20.94        33.76        25.74 
TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-A4C1 
       21.93        27.48        27.48        14.66        22.03         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-KU-A6H7 TCGA-KU-A6H8 
        5.29        13.68        13.84        19.04        19.27        10.75 
TCGA-MT-A51X TCGA-MT-A67F TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-P3-A5Q5 
        7.96        12.62        15.42         7.13        16.08        29.92 
TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6SX 
       15.78        71.74        51.25        10.85        36.82        47.01 
TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-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-A6IG TCGA-QK-A6IH TCGA-QK-A6II 
       13.15        21.07        21.21         7.30        21.47         9.34 
TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8ZB 
       12.72        27.39        19.73        12.89         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-A71B TCGA-UF-A7JA TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ 
       49.51        74.47        24.30        55.43        29.46        18.05 
TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UP-A6WW TCGA-WA-A7GZ 
       13.94        20.75        22.36        32.65        17.03        20.55 
TCGA-WA-A7H4 TCGA-KU-A66S 
       14.56        13.35 

  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 
            20.715             21.190 
[1] "0.1 - 180.2 (20.7)" "0.1 - 211.0 (21.2)"
[1] "hr=" "1.1"
D24V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  12Q GAIN MUTATED         7       11        17        45         1         0
  12Q GAIN WILD-TYPE      20       65        65       207        11         1
D24V3, multiclass
           clus
vv          12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  STAGE I                  7                 20
  STAGE II                11                 65
  STAGE III               17                 65
  STAGE IVA               45                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
  12Q GAIN MUTATED      11  24  20  28
  12Q GAIN WILD-TYPE    39 113  80 145
D24V4, multiclass
       clus
vv      12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  T0+T1               11                 39
  T2                  24                113
  T3                  20                 80
  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    38  11  29   0
  12Q GAIN WILD-TYPE 141  57 139   8
D24V5, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  N0               38                141
  N1               11                 57
  N2               29                139
  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 160   1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     30    0
  12Q GAIN WILD-TYPE  160    1
   clus
vv  12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  0               30                160
  1                0                  1
[1] 2 2
[1] FALSE
D24V7, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED    23  69
  12Q GAIN WILD-TYPE 117 313
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     23   69
  12Q GAIN WILD-TYPE  117  313
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  FEMALE               23                117
  MALE                 69                313
[1] 2 2
[1] FALSE
D24V8, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED    26  54
  12Q GAIN WILD-TYPE 136 247
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     26   54
  12Q GAIN WILD-TYPE  136  247
     clus
vv    12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  NO                26                136
  YES               54                247
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD & NECK SQUAMOUS CELL CARCINOMA
  12Q GAIN MUTATED                                    91
  12Q GAIN WILD-TYPE                                 420
                    vv
clus                 HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  12Q GAIN MUTATED                                                   1
  12Q GAIN WILD-TYPE                                                 9
                    vv
clus                 HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  12Q GAIN MUTATED                                                           0
  12Q GAIN WILD-TYPE                                                         1
D24V9, multiclass
                                                           clus
vv                                                          12Q GAIN MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                     91
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        1
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                0
                                                           clus
vv                                                          12Q GAIN WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                      420
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                          9
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                  1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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    80
  12Q GAIN WILD-TYPE                        40   366
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                                          80                366
[1] 4 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  80
  12Q GAIN WILD-TYPE  21 379
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      5   80
  12Q GAIN WILD-TYPE   21  379
                        clus
vv                       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    5                 21
  NOT HISPANIC OR LATINO               80                379
[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 272 191
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                57                463 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                28                191 
$`13Q GAIN MUTATED`
TCGA-BA-4075 TCGA-DQ-5629 TCGA-BA-6870 TCGA-BA-A4IF TCGA-BB-4225 TCGA-CN-4726 
        9.30        30.94        14.83        29.42         4.80         4.67 
TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4737 TCGA-CN-4742 TCGA-CN-5370 TCGA-CN-6013 
       56.68        12.89        20.55        13.05         8.52        23.90 
TCGA-CN-6989 TCGA-CN-6996 TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CQ-7072 
       32.22        17.42        22.32        12.39        16.57        77.56 
TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5247 TCGA-CR-6484 TCGA-CR-6488 TCGA-CR-7365 
       12.46        31.23        11.77        11.64        12.46        39.16 
TCGA-CR-7367 TCGA-CR-7370 TCGA-CR-7380 TCGA-CR-7390 TCGA-CV-5440 TCGA-CV-6003 
       47.34         3.45        19.92        49.58       107.51        54.74 
TCGA-CV-6933 TCGA-CV-6939 TCGA-CV-6956 TCGA-CV-7090 TCGA-CV-7095 TCGA-CV-7097 
       90.12        21.90         7.13       172.67        18.81        12.66 
TCGA-CV-7178 TCGA-CV-7243 TCGA-CV-7247 TCGA-CV-7416 TCGA-CV-7423 TCGA-CV-7437 
       71.21        31.36        18.97        25.08       100.57        16.64 
TCGA-CV-A45X TCGA-CV-A463 TCGA-D6-6823 TCGA-D6-8569 TCGA-DQ-5631 TCGA-F7-A50J 
        6.51         0.76        23.05        25.32        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-BA-4077 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4IG TCGA-BA-A4II 
       37.28        20.48        68.48         3.55        28.11        30.18 
TCGA-BB-A5HU TCGA-CN-4727 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 
       25.71        51.29         9.07         9.24        52.08        11.08 
TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-6221 
       35.05        32.48        19.82        24.39        48.20        32.88 
TCGA-CQ-7063 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-A4C7 TCGA-CR-6472 TCGA-CR-6478 
       70.13        16.73        43.04        11.61        34.52         6.02 
TCGA-CX-7082 TCGA-CX-7219 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7593 TCGA-H7-A6C5 
        0.36        34.36        14.04        46.32        40.24        21.11 
TCGA-HD-8634 TCGA-HD-8635 TCGA-UF-A71D TCGA-UF-A7JV TCGA-4P-AA8J TCGA-BA-4074 
       12.66        22.85        48.03         2.96         3.35        15.19 
TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 
       13.64         9.07        26.50        23.74        42.35        57.93 
TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6872 
       17.10        23.84        65.59        15.52        21.17        12.62 
TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IH TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB 
        4.01        41.85        20.45        27.95        11.54         7.10 
TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DI TCGA-BA-A6DJ 
        5.69        14.47         7.82         2.27        11.05        13.38 
TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-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-8601 TCGA-BB-A5HY 
       66.28        24.66        38.40        71.05        20.52        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-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 
       55.86        38.04        26.86        32.81        52.14        57.11 
TCGA-CN-4736 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-5355 
       12.99        14.33        45.83        27.58        73.61        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-5373 TCGA-CN-5374 
       11.54        11.84        11.57        12.49        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-6020 TCGA-CN-6988 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6998 
       34.13         6.74        10.45        38.89         3.68        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-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY 
        7.40        31.69         4.41        12.07         2.70        23.44 
TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 
       20.88        19.53        52.37        21.50         2.93        54.58 
TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 
       70.45        62.37        45.99        10.42        11.21         4.24 
TCGA-CQ-6218 TCGA-CQ-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-7064 TCGA-CQ-7065 TCGA-CQ-7069 TCGA-CQ-7071 
       14.99        38.76        64.87        53.52        41.88        43.10 
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-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-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6480 TCGA-CR-6481 
       39.52        36.99        18.54        16.90        11.90        10.22 
TCGA-CR-6482 TCGA-CR-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-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-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-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-7399 TCGA-CR-7401 
       44.25        30.58        24.79         5.13         5.95        35.41 
TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 
       29.95        48.39       139.43        17.16       129.21       108.95 
TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 
       76.24        19.20        17.95        94.88        76.50        91.53 
TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 
       80.12        17.92        13.35        23.05        86.83        48.59 
TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 
       60.49         7.07        43.23        21.07        62.43         9.60 
TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6940 
        2.14         9.70         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-6959 
       30.08         6.08        53.95        65.82        10.98         8.42 
TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7091 TCGA-CV-7099 
       28.34         2.50         4.14        64.83       111.16         7.99 
TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7177 
        9.01         5.26         1.84        52.31        12.92        21.80 
TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7242 
       10.75       130.88        77.16         4.73        89.65        36.00 
TCGA-CV-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-7407 TCGA-CV-7409 
        2.10        49.71        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-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-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-A45Y TCGA-CV-A45Z 
      159.65        35.47         1.05        45.96        88.87        48.20 
TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A464 TCGA-CV-A465 TCGA-CV-A468 TCGA-CV-A6JD 
       60.43        67.86        56.61         7.07        15.25         5.98 
TCGA-CV-A6JE TCGA-CV-A6JM TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU 
       35.34         6.38        29.79         6.48        28.01         3.62 
TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 
       21.24        23.47        19.92        22.52        10.42        10.55 
TCGA-CX-7086 TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6824 
       18.84        51.12        13.25        25.41         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-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-7590 
       12.79        23.34        58.45        37.25        33.86        46.45 
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-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-A76A TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 
       15.16        15.06        20.94        33.76        28.47        25.74 
TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-A4C1 
       21.93        27.48        27.48        14.66        22.03         0.36 
TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 
       13.84         4.27         3.65         6.90        34.75        15.95 
TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J 
       38.53        14.50        37.71        37.41         0.07        33.57 
TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O TCGA-IQ-A6SG TCGA-IQ-A6SH TCGA-KU-A6H7 
        5.29        13.68        13.84        19.04        15.48        19.27 
TCGA-KU-A6H8 TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G TCGA-MT-A7BN 
       10.75        30.05         1.84        12.62         6.25        15.42 
TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5Q6 TCGA-P3-A5QA 
        7.13        16.08        17.98        29.92        15.78        71.74 
TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 
       51.25        10.85        36.82        47.01        19.00        75.55 
TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T6 TCGA-P3-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-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 
       21.21        23.15         7.30         9.34        12.72        27.39 
TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-A8ZA 
       21.07        19.73        12.89         5.62        14.76        12.20 
TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX 
       17.82        15.32         8.32        12.72        16.96         6.87 
TCGA-T2-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-A71E TCGA-UF-A7J9 
       20.35        64.80         2.83        49.51        49.45        44.65 
TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JJ TCGA-UF-A7JK 
       74.47        17.95        24.30        55.43        18.05        13.94 
TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UP-A6WW TCGA-WA-A7H4 TCGA-KU-A66S 
       20.75        22.36        32.65        17.03        14.56        13.35 
TCGA-KU-A66T 
       18.15 

  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
              0.76               0.07 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
            172.67             210.97 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
             20.55              21.17 
[1] "0.8 - 172.7 (20.6)" "0.1 - 211.0 (21.2)"
[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       229        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                229
  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 171   1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED     19    0
  13Q GAIN WILD-TYPE  171    1
   clus
vv  13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  0               19                171
  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    15  33
  13Q GAIN WILD-TYPE 147 268
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED     15   33
  13Q GAIN WILD-TYPE  147  268
     clus
vv    13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  NO                15                147
  YES               33                268
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD & NECK SQUAMOUS CELL CARCINOMA
  13Q GAIN MUTATED                                    56
  13Q GAIN WILD-TYPE                                 455
                    vv
clus                 HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  13Q GAIN MUTATED                                                   1
  13Q GAIN WILD-TYPE                                                 9
                    vv
clus                 HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  13Q GAIN MUTATED                                                           0
  13Q GAIN WILD-TYPE                                                         1
D25V9, multiclass
                                                           clus
vv                                                          13Q GAIN MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                     56
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        1
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                0
                                                           clus
vv                                                          13Q GAIN WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                      455
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                          9
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                  1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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    78  75
  14Q GAIN WILD-TYPE 223 144
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
               153                367 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                75                144 
$`14Q GAIN MUTATED`
TCGA-BA-4075 TCGA-BB-A5HU TCGA-CN-6021 TCGA-CQ-5323 TCGA-CQ-7067 TCGA-CX-7219 
        9.30        25.71         9.07        48.20        16.73        34.36 
TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7593 TCGA-BA-5555 TCGA-BA-6872 
       30.94        14.04        46.32        40.24        17.10        12.62 
TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A6DA TCGA-BA-A6DG TCGA-BA-A6DI 
        4.01        41.85        29.42        11.54         2.27        11.05 
TCGA-BA-A6DL TCGA-BB-8601 TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-BB-A6UO TCGA-C9-A47Z 
       20.48        20.52        10.55        27.19         8.81         6.28 
TCGA-C9-A480 TCGA-CN-4723 TCGA-CN-4730 TCGA-CN-4738 TCGA-CN-4740 TCGA-CN-5356 
       12.69        55.86        26.86        14.33        27.58        46.32 
TCGA-CN-5363 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-6994 TCGA-CN-A499 TCGA-CN-A49A 
        8.32        11.84        11.57        38.89        23.57        17.29 
TCGA-CN-A63T TCGA-CN-A63W TCGA-CN-A640 TCGA-CQ-5326 TCGA-CQ-5329 TCGA-CQ-5330 
        7.40        12.39         4.41         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-7069 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CR-6474 
       41.88        77.56        44.48        29.49        14.14        18.54 
TCGA-CR-6477 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7370 
       16.90        12.46        22.78        39.16        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 
       49.58       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       172.67 
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        89.65 
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-D6-6516 TCGA-D6-6823 TCGA-D6-6825 TCGA-D6-A4Z9 
       19.92        18.84        25.41        23.05        16.14        17.72 
TCGA-D6-A6EP TCGA-D6-A74Q TCGA-DQ-5625 TCGA-DQ-7592 TCGA-F7-A50I TCGA-F7-A50J 
       13.94        23.34        37.25        37.58         3.02        31.13 
TCGA-F7-A624 TCGA-HD-7753 TCGA-HD-7831 TCGA-HD-7917 TCGA-HD-A6HZ TCGA-IQ-A61E 
       12.43        28.47        21.93        27.48         3.65        37.71 
TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A6SH TCGA-MT-A51W TCGA-MT-A51X 
       33.57         5.29        13.68        15.48        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-A8Z7 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-AA3K TCGA-RS-A6TO 
       21.07        12.89        14.76        12.20         8.32        12.72 
TCGA-T2-A6WZ TCGA-T3-A92N TCGA-TN-A7HI TCGA-UF-A71A TCGA-UF-A7JD TCGA-UF-A7JH 
       15.91         3.12        13.55         2.83        24.30        29.46 
TCGA-UF-A7JK TCGA-UF-A7JO TCGA-KU-A66T 
       13.94        20.75        18.15 

$`14Q GAIN WILD-TYPE`
TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4IG TCGA-BA-A4II 
       37.28        20.48        68.48         3.55        28.11        30.18 
TCGA-CN-4727 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6992 TCGA-CN-6997 
       51.29         9.24        52.08        11.08        35.05        32.48 
TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-6221 TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CQ-A4C7 
       19.82        24.39        32.88        70.13        43.04        11.61 
TCGA-CR-6472 TCGA-CR-6478 TCGA-CX-7082 TCGA-H7-A6C5 TCGA-HD-8634 TCGA-HD-8635 
       34.52         6.02         0.36        21.11        12.66        22.85 
TCGA-UF-A71D TCGA-UF-A7JV TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4078 
       48.03         2.96         3.35        15.19        13.64         9.07 
TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5556 TCGA-BA-5558 
       26.50        23.74        42.35        57.93        23.84        65.59 
TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-A4IH TCGA-BA-A6D8 TCGA-BA-A6DB 
       15.52        21.17        14.83        20.45        27.95         7.10 
TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DJ TCGA-BA-A8YP TCGA-BB-4217 
        5.69        14.47         7.82        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         4.80         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-A6UM TCGA-CN-4722 TCGA-CN-4725 TCGA-CN-4726 
       38.40        71.05        12.92        48.76        38.04         4.67 
TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 
       56.68        12.89        32.81        52.14        57.11        12.99 
TCGA-CN-4737 TCGA-CN-4739 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5358 
       20.55        45.83        73.61        13.05        42.02         8.58 
TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5369 TCGA-CN-5370 
       12.39        71.31        16.21        11.54        12.49         8.52 
TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 
       52.08        56.94        50.07        30.67        48.00        23.90 
TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6988 
       47.44        28.04        19.07        34.13         6.74        10.45 
TCGA-CN-6989 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 
       32.22         3.68        17.42        11.74        35.01        25.41 
TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A641 
       29.72        21.21        31.69        22.32        16.57        12.07 
TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5324 TCGA-CQ-5325 
        2.70        23.44        20.88        19.53        52.37        21.50 
TCGA-CQ-5327 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-6218 TCGA-CQ-6223 
       54.58        45.99        10.42        11.21        41.19        46.95 
TCGA-CQ-6228 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7071 TCGA-CQ-A4C9 TCGA-CQ-A4CB 
       14.99        64.87        53.52        43.10        23.24        29.36 
TCGA-CQ-A4CD TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 
       33.60        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-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-7368 TCGA-CR-7369 TCGA-CR-7371 TCGA-CR-7373 
        9.27        47.18        40.93        35.84         3.09        29.23 
TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7382 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7389 
        0.99        31.96        26.17        32.78        47.01        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        24.79 
TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 
        5.13         5.95        35.41        29.95        48.39       139.43 
TCGA-CV-5431 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 
       17.16        76.24        19.20        94.88        76.50        91.53 
TCGA-CV-5966 TCGA-CV-5971 TCGA-CV-5976 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6433 
       17.92        23.05        48.59         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-6943 TCGA-CV-6948 TCGA-CV-6951 TCGA-CV-6952 
        4.73        21.90        19.79        42.38        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-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7102 
        4.14        64.83        12.66         7.99         9.01         1.84 
TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7236 
       52.31        12.92        21.80       130.88        77.16         4.73 
TCGA-CV-7242 TCGA-CV-7247 TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7261 
       36.00        18.97        95.34         4.96        11.87        49.71 
TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7407 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7414 
       18.41        57.47        35.54       210.97        89.33         0.46 
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-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7435 TCGA-CV-7438 
       54.94        16.27        84.49        19.76       153.86         6.38 
TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45V TCGA-CV-A45W 
       27.98        21.01       180.16       159.65         1.05        45.96 
TCGA-CV-A45X TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A463 
        6.51        88.87        48.20        60.43        67.86         0.76 
TCGA-CV-A464 TCGA-CV-A465 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JN TCGA-CV-A6JO 
       56.61         7.07        15.25         5.98        29.79         6.48 
TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K1 TCGA-CV-A6K2 
       28.01         3.62        21.24        23.47        22.52        10.42 
TCGA-CX-7085 TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6517 TCGA-D6-6824 TCGA-D6-6826 
       10.55        51.12        13.25         9.60         2.53        11.44 
TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM 
       18.67        24.95        25.32        12.36        28.77         7.63 
TCGA-D6-A6EN TCGA-D6-A6EO TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-DQ-5624 TCGA-DQ-5630 
       22.59        24.95        12.10        12.79        58.45        33.86 
TCGA-DQ-5631 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 
       18.02        46.45        20.45        40.04        39.12        41.59 
TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A61S TCGA-F7-A61V 
       37.18        32.71        21.63        20.25        18.94        24.95 
TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A623 TCGA-H7-7774 TCGA-H7-8501 
        0.46        17.85        11.80        20.25        13.38        15.16 
TCGA-H7-8502 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7754 TCGA-HD-7832 TCGA-HD-8224 
       15.06        20.94        33.76        25.74        27.48        14.66 
TCGA-HD-8314 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6I0 TCGA-HL-7533 
       22.03         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-A6H7 TCGA-KU-A6H8 TCGA-MT-A67A TCGA-MT-A67D 
       13.84        19.04        19.27        10.75        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-A5QA TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6T0 
       29.92        71.74        51.25        10.85        36.82        19.00 
TCGA-P3-A6T2 TCGA-P3-A6T5 TCGA-P3-A6T6 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 
       75.55        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-A6VC 
       23.15        21.47         9.34        12.72        27.39        19.73 
TCGA-QK-A8Z8 TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6X0 
        5.62        17.82        15.32        16.96         6.87         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-A71B TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JF 
       49.51        49.45        44.65        74.47        17.95        55.43 
TCGA-UF-A7JJ TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 
       18.05        22.36        32.65        17.03        20.55        14.56 
TCGA-KU-A66S 
       13.35 

  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
              2.04               0.07 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
            172.67             210.97 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
             18.84              21.63 
[1] "2.0 - 172.7 (18.8)" "0.1 - 211.0 (21.6)"
[1] "hr=" "1.3"
D26V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  14Q GAIN MUTATED        10       22        23        74         4         0
  14Q GAIN WILD-TYPE      17       54        59       178         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               74                178
  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  55
  14Q GAIN WILD-TYPE    38  97  71 118
D26V4, multiclass
       clus
vv      14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  T0+T1               12                 38
  T2                  40                 97
  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
  14Q GAIN MUTATED    51  18  54   2
  14Q GAIN WILD-TYPE 128  50 114   6
D26V5, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  N0               51                128
  N1               18                 50
  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"
D26V6, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED    53   0
  14Q GAIN WILD-TYPE 137   1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED     53    0
  14Q GAIN WILD-TYPE  137    1
   clus
vv  14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  0               53                137
  1                0                  1
[1] 2 2
[1] FALSE
D26V7, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED    45 108
  14Q GAIN WILD-TYPE  95 274
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED     45  108
  14Q GAIN WILD-TYPE   95  274
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  FEMALE               45                 95
  MALE                108                274
[1] 2 2
[1] FALSE
D26V8, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED    51  82
  14Q GAIN WILD-TYPE 111 219
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED     51   82
  14Q GAIN WILD-TYPE  111  219
     clus
vv    14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  NO                51                111
  YES               82                219
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD & NECK SQUAMOUS CELL CARCINOMA
  14Q GAIN MUTATED                                   152
  14Q GAIN WILD-TYPE                                 359
                    vv
clus                 HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  14Q GAIN MUTATED                                                   1
  14Q GAIN WILD-TYPE                                                 9
                    vv
clus                 HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  14Q GAIN MUTATED                                                           0
  14Q GAIN WILD-TYPE                                                         1
D26V9, multiclass
                                                           clus
vv                                                          14Q GAIN MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                    152
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        1
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                0
                                                           clus
vv                                                          14Q GAIN WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                      359
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                          9
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                  1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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                          22   122
  14Q GAIN WILD-TYPE                        26   324
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                      22                 26
  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"
D26V14, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED     6 136
  14Q GAIN WILD-TYPE  20 323
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      6  136
  14Q GAIN WILD-TYPE   20  323
                        clus
vv                       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    6                 20
  NOT HISPANIC OR LATINO              136                323
[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 261 187
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                72                448 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                32                187 
$`15Q GAIN MUTATED`
TCGA-BA-6871 TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-BA-6873 TCGA-BB-7861 
        3.55        30.94        14.04        46.32         4.01        22.42 
TCGA-BB-8596 TCGA-C9-A47Z TCGA-CN-4729 TCGA-CN-4737 TCGA-CN-4739 TCGA-CN-4740 
       71.05         6.28        12.89        20.55        45.83        27.58 
TCGA-CN-5356 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-6010 TCGA-CN-6995 TCGA-CN-A63U 
       46.32        11.54        11.84        50.07         3.68        31.69 
TCGA-CQ-6225 TCGA-CQ-6228 TCGA-CQ-7069 TCGA-CQ-A4C9 TCGA-CR-6474 TCGA-CR-6477 
       13.25        14.99        41.88        23.24        18.54        16.90 
TCGA-CR-6484 TCGA-CR-6491 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7379 TCGA-CR-7380 
       11.64        22.78        47.18        39.16        34.06        19.92 
TCGA-CR-7390 TCGA-CV-6003 TCGA-CV-6934 TCGA-CV-6959 TCGA-CV-7090 TCGA-CV-7091 
       49.58        54.74         2.14         8.42       172.67       111.16 
TCGA-CV-7101 TCGA-CV-7178 TCGA-CV-7235 TCGA-CV-7254 TCGA-CV-7255 TCGA-CV-7261 
        5.26        71.21        77.16        47.97         2.10        49.71 
TCGA-CV-7413 TCGA-CV-7415 TCGA-CV-7416 TCGA-CV-7418 TCGA-CV-7421 TCGA-CV-7427 
        9.67        22.85        25.08        25.94         0.07       156.49 
TCGA-CV-7433 TCGA-CV-7437 TCGA-CV-A6JD TCGA-CV-A6K2 TCGA-D6-6516 TCGA-D6-8569 
       19.76        16.64         5.98        10.42        25.41        25.32 
TCGA-D6-A6EM TCGA-F7-7848 TCGA-H7-8501 TCGA-HD-7753 TCGA-HD-7917 TCGA-HD-A633 
        7.63        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        12.89        13.25        49.45        29.46        13.94 

$`15Q GAIN WILD-TYPE`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-A4IG TCGA-BA-A4II 
        9.30        37.28        20.48        68.48        28.11        30.18 
TCGA-BB-A5HU TCGA-CN-4727 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 
       25.71        51.29         9.07         9.24        52.08        11.08 
TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-6221 
       35.05        32.48        19.82        24.39        48.20        32.88 
TCGA-CQ-7063 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-A4C7 TCGA-CR-6472 TCGA-CR-6478 
       70.13        16.73        43.04        11.61        34.52         6.02 
TCGA-CX-7082 TCGA-CX-7219 TCGA-DQ-7593 TCGA-H7-A6C5 TCGA-HD-8634 TCGA-HD-8635 
        0.36        34.36        40.24        21.11        12.66        22.85 
TCGA-UF-A71D TCGA-UF-A7JV TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4078 
       48.03         2.96         3.35        15.19        13.64         9.07 
TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 
       26.50        23.74        42.35        57.93        17.10        23.84 
TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6872 TCGA-BA-7269 
       65.59        15.52        21.17        14.83        12.62        41.85 
TCGA-BA-A4IF TCGA-BA-A4IH TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD 
       29.42        20.45        27.95        11.54         7.10         5.69 
TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DI TCGA-BA-A6DJ TCGA-BA-A6DL 
       14.47         7.82         2.27        11.05        13.38        20.48 
TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 
       16.41         6.15       105.90         9.14         4.80         4.41 
TCGA-BB-4228 TCGA-BB-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-8601 TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-BB-A6UM 
       24.66        38.40        20.52        10.55        27.19        12.92 
TCGA-BB-A6UO TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 
        8.81        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-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-6988 TCGA-CN-6989 
       28.04        19.07        34.13         6.74        10.45        32.22 
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-A63W 
       17.29        29.72        21.21         7.40        22.32        12.39 
TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V6 
       16.57         4.41        12.07         2.70        23.44        20.88 
TCGA-CN-A6V7 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 
       19.53        52.37        21.50         2.93        54.58        70.45 
TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 
       62.37        45.99        10.42        11.21         4.24        41.19 
TCGA-CQ-6220 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6229 TCGA-CQ-7064 
       32.38        46.95        56.58         4.24        38.76        64.87 
TCGA-CQ-7065 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4CB TCGA-CQ-A4CD 
       53.52        43.10        77.56        44.48        29.36        33.60 
TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 
       29.49        14.14        12.46        31.23        84.23        11.77 
TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 
       54.67        37.87        26.27        58.42        50.01        39.52 
TCGA-CR-6473 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6487 TCGA-CR-6488 
       36.99        11.90        10.22        11.34         7.69        12.46 
TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 
       15.75         9.27        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-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        24.79 
TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 
        5.13         5.95        35.41        29.95        48.39       139.43 
TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 
       17.16       129.21       108.95        76.24        19.20        17.95 
TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 
      107.51        94.88        76.50        91.53        80.12        17.92 
TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 
       13.35        23.05        86.83        48.59        60.49         7.07 
TCGA-CV-5979 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6933 TCGA-CV-6935 
       43.23        21.07        62.43         9.60        90.12         9.70 
TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6941 
        5.46        20.52         4.73        21.90        26.43        11.24 
TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-6951 
      140.78        19.79        12.03        42.38        15.09        30.08 
TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-6955 TCGA-CV-6956 TCGA-CV-6960 
        6.08        53.95        65.82        10.98         7.13        28.34 
TCGA-CV-6961 TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 
        2.50         4.14        64.83        18.81        12.66         7.99 
TCGA-CV-7100 TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-7180 
        9.01         1.84        52.31        12.92        21.80        10.75 
TCGA-CV-7183 TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 
      130.88         4.73        89.65        36.00        31.36        26.20 
TCGA-CV-7247 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7263 
       18.97        17.13        95.34         4.96        11.87        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-7422 TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7425 TCGA-CV-7428 TCGA-CV-7429 
       34.09       100.57        14.89        56.48        54.94         3.52 
TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7438 TCGA-CV-7440 
       16.27        84.49         7.17       153.86         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-A6JE 
       67.86         0.76        56.61         7.07        15.25        35.34 
TCGA-CV-A6JM TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY 
        6.38        29.79         6.48        28.01         3.62        21.24 
TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-A4AQ 
       23.47        19.92        22.52        10.55        18.84        51.12 
TCGA-D6-6515 TCGA-D6-6517 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        23.34        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-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G 
       40.04        39.12        41.59        32.71        21.63        20.25 
TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 
        3.02        31.13        18.94        24.95         0.46        17.85 
TCGA-F7-A622 TCGA-F7-A623 TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8502 TCGA-H7-A76A 
       11.80        20.25        12.43        13.38        15.06        20.94 
TCGA-HD-7229 TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-8224 TCGA-HD-8314 
       33.76        25.74        21.93        27.48        14.66        22.03 
TCGA-HD-A4C1 TCGA-HD-A634 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-A61E 
        0.36         4.27        34.75        15.95        38.53        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-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X 
       13.84        19.04        19.27        10.75        14.37         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-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        27.39        21.07        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-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-A7HL TCGA-UF-A718 TCGA-UF-A719 
       13.71         3.12        13.55        20.35        64.80        54.67 
TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD 
        2.83        49.51        44.65        74.47        17.95        24.30 
TCGA-UF-A7JF TCGA-UF-A7JJ TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UP-A6WW 
       55.43        18.05        20.75        22.36        32.65        17.03 
TCGA-WA-A7GZ TCGA-WA-A7H4 TCGA-KU-A66S TCGA-KU-A66T 
       20.55        14.56        13.35        18.15 

  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
              0.07               0.07 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
            172.67             210.97 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
             21.01              21.09 
[1] "0.1 - 172.7 (21.0)" "0.1 - 211.0 (21.1)"
[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       215         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                215
  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 164   1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED     26    0
  15Q GAIN WILD-TYPE  164    1
   clus
vv  15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  0               26                164
  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    21  41
  15Q GAIN WILD-TYPE 141 260
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED     21   41
  15Q GAIN WILD-TYPE  141  260
     clus
vv    15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  NO                21                141
  YES               41                260
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD & NECK SQUAMOUS CELL CARCINOMA
  15Q GAIN MUTATED                                    70
  15Q GAIN WILD-TYPE                                 441
                    vv
clus                 HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  15Q GAIN MUTATED                                                   2
  15Q GAIN WILD-TYPE                                                 8
                    vv
clus                 HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  15Q GAIN MUTATED                                                           0
  15Q GAIN WILD-TYPE                                                         1
D27V9, multiclass
                                                           clus
vv                                                          15Q GAIN MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                     70
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        2
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                0
                                                           clus
vv                                                          15Q GAIN WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                      441
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                          8
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                  1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V10, continuous
D27V11, continuous
D27V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  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    56  52
  16P GAIN WILD-TYPE 245 167
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
               108                412 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                52                167 
$`16P GAIN MUTATED`
TCGA-BA-4075 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4IG TCGA-CN-6022 TCGA-CQ-7067 
        9.30        68.48         3.55        28.11         9.24        16.73 
TCGA-CR-6478 TCGA-DQ-7588 TCGA-HD-8634 TCGA-BA-5555 TCGA-BA-6868 TCGA-BA-6869 
        6.02        14.04        12.66        17.10        15.52        21.17 
TCGA-BA-6870 TCGA-BA-6873 TCGA-BA-A4IF TCGA-BA-A6DI TCGA-BA-A6DL TCGA-C9-A47Z 
       14.83         4.01        29.42        11.05        20.48         6.28 
TCGA-CN-4728 TCGA-CN-4730 TCGA-CN-4737 TCGA-CN-4739 TCGA-CN-5356 TCGA-CN-6013 
       56.68        26.86        20.55        45.83        46.32        23.90 
TCGA-CN-6020 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-A497 TCGA-CN-A49A TCGA-CN-A63U 
        6.74        38.89        17.42        35.01        17.29        31.69 
TCGA-CQ-5326 TCGA-CQ-5329 TCGA-CQ-6220 TCGA-CQ-6223 TCGA-CQ-7072 TCGA-CR-5247 
        2.93        70.45        32.38        46.95        77.56        11.77 
TCGA-CR-6477 TCGA-CR-6481 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7370 TCGA-CR-7372 
       16.90        10.22        39.16        47.34         3.45        24.95 
TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7388 TCGA-CR-7390 TCGA-CR-7402 TCGA-CV-5439 
       34.06        19.92        27.06        49.58        29.95        17.95 
TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-6003 TCGA-CV-6933 TCGA-CV-6937 TCGA-CV-6939 
       60.49         7.07        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-7180 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7255 
       10.75        36.00        31.36        26.20        17.13         2.10 
TCGA-CV-7263 TCGA-CV-7409 TCGA-CV-7415 TCGA-CV-7423 TCGA-CV-7433 TCGA-CV-7435 
       18.41        17.85        22.85       100.57        19.76       153.86 
TCGA-CV-A45R TCGA-CV-A45U TCGA-CV-A45W TCGA-CV-A461 TCGA-CV-A465 TCGA-CV-A6JM 
      180.16        35.47        45.96        67.86         7.07         6.38 
TCGA-CV-A6JY TCGA-CX-7086 TCGA-D6-6516 TCGA-D6-6823 TCGA-D6-8569 TCGA-D6-A6EP 
       21.24        18.84        25.41        23.05        25.32        13.94 
TCGA-DQ-5625 TCGA-DQ-5631 TCGA-F7-A50J TCGA-F7-A623 TCGA-HD-7831 TCGA-IQ-7631 
       37.25        18.02        31.13        20.25        21.93        38.53 
TCGA-IQ-A61L TCGA-IQ-A6SH TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A7BN TCGA-P3-A6T4 
       13.68        15.48        14.37         7.96        15.42         2.04 
TCGA-P3-A6T5 TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6VB TCGA-QK-A8Z7 TCGA-RS-A6TO 
       29.00         9.34        12.72        21.07        12.89        12.72 
TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH 
       49.45        44.65        74.47        24.30        55.43        29.46 

$`16P GAIN WILD-TYPE`
TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-A4II TCGA-BB-A5HU TCGA-CN-4727 TCGA-CN-6021 
       37.28        20.48        30.18        25.71        51.29         9.07 
TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-A6V1 TCGA-CN-A6V3 
       52.08        11.08        35.05        32.48        19.82        24.39 
TCGA-CQ-5323 TCGA-CQ-6221 TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CQ-A4C7 TCGA-CR-6472 
       48.20        32.88        70.13        43.04        11.61        34.52 
TCGA-CX-7082 TCGA-CX-7219 TCGA-DQ-5629 TCGA-DQ-7589 TCGA-DQ-7593 TCGA-H7-A6C5 
        0.36        34.36        30.94        46.32        40.24        21.11 
TCGA-HD-8635 TCGA-UF-A71D TCGA-UF-A7JV TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 
       22.85        48.03         2.96         3.35        15.19        13.64 
TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5556 
        9.07        26.50        23.74        42.35        57.93        23.84 
TCGA-BA-5558 TCGA-BA-6872 TCGA-BA-7269 TCGA-BA-A4IH TCGA-BA-A6D8 TCGA-BA-A6DA 
       65.59        12.62        41.85        20.45        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         4.80         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-A5HY 
       66.28        24.66        38.40        71.05        20.52        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-4729 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 
       38.04         4.67        12.89        32.81        52.14        57.11 
TCGA-CN-4736 TCGA-CN-4738 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 
       12.99        14.33        27.58        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-6016 TCGA-CN-6017 TCGA-CN-6018 
       50.07        30.67        48.00        47.44        28.04        19.07 
TCGA-CN-6019 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6995 TCGA-CN-6998 TCGA-CN-A498 
       34.13        10.45        32.22         3.68        11.74        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-A6V6 
       16.57         4.41        12.07         2.70        23.44        20.88 
TCGA-CN-A6V7 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5330 TCGA-CQ-5331 
       19.53        52.37        21.50        54.58        62.37        45.99 
TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6224 TCGA-CQ-6225 
       10.42        11.21         4.24        41.19        56.58        13.25 
TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7069 
        4.24        14.99        38.76        64.87        53.52        41.88 
TCGA-CQ-7071 TCGA-CQ-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-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5248 TCGA-CR-5249 
       14.14        12.46        31.23        84.23        54.67        37.87 
TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6474 
       26.27        58.42        50.01        39.52        36.99        18.54 
TCGA-CR-6480 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 
       11.90        11.34        11.64         7.69        12.46        22.78 
TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7371 
       15.75         9.27        47.18        40.93        35.84         3.09 
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-7389 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 
       32.78        47.01        12.89        30.02        46.85        32.65 
TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 
       44.25        30.58        24.79         5.13         5.95        35.41 
TCGA-CR-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-5440 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 
       19.20       107.51        94.88        76.50        91.53        80.12 
TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5979 
       17.92        13.35        23.05        86.83        48.59        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-6940 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6948 TCGA-CV-6950 
        4.73        26.43       140.78        19.79        42.38        15.09 
TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6955 TCGA-CV-6956 TCGA-CV-6959 
       30.08         6.08        53.95        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       172.67        12.66 
TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7177 
        9.01         5.26         1.84        52.31        12.92        21.80 
TCGA-CV-7178 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7247 
       71.21       130.88        77.16         4.73        89.65        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        49.71        57.47 
TCGA-CV-7407 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7414 TCGA-CV-7416 
       35.54       210.97        89.33         9.67         0.46        25.08 
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-7434 TCGA-CV-7437 
       54.94         3.52        16.27        84.49         7.17        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-A45V TCGA-CV-A45X TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A463 
        1.05         6.51        88.87        48.20        60.43         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-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 
       28.01         3.62        23.47        19.92        22.52        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-D6-6826 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-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q 
        7.63        22.59        24.95        12.10        12.79        23.34 
TCGA-DQ-5624 TCGA-DQ-5630 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7594 
       58.45        33.86        46.45        20.45        37.58        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-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 
        3.02        18.94        24.95         0.46        17.85        11.80 
TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A76A TCGA-HD-7229 
       12.43        13.38        15.16        15.06        20.94        33.76 
TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7832 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 
       28.47        25.74        27.48        27.48        14.66        22.03 
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-A61K TCGA-IQ-A61O TCGA-IQ-A6SG TCGA-KU-A6H7 TCGA-KU-A6H8 
       33.57         5.29        13.84        19.04        19.27        10.75 
TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A5BI TCGA-MZ-A6I9 
       30.05         1.84        12.62         6.25         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-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-A6V9 TCGA-QK-A6VC TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-A8ZA 
       21.47        27.39        19.73         5.62        14.76        12.20 
TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ 
       17.82        15.32         8.32        16.96         6.87        15.91 
TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-T3-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-A7JC 
       20.35        64.80        54.67         2.83        49.51        17.95 
TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UP-A6WW 
       18.05        13.94        20.75        22.36        32.65        17.03 
TCGA-WA-A7GZ TCGA-WA-A7H4 TCGA-KU-A66S TCGA-KU-A66T 
       20.55        14.56        13.35        18.15 

  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 
             21.12              21.09 
[1] "2.0 - 180.2 (21.1)" "0.1 - 211.0 (21.1)"
[1] "hr=" "1.2"
D28V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  16P GAIN MUTATED         6       16        18        45         4         0
  16P GAIN WILD-TYPE      21       60        64       207         8         1
D28V3, multiclass
           clus
vv          16P GAIN MUTATED 16P GAIN WILD-TYPE
  STAGE I                  6                 21
  STAGE II                16                 60
  STAGE III               18                 64
  STAGE IVA               45                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      11  25  17  37
  16P GAIN WILD-TYPE    39 112  83 136
D28V4, multiclass
       clus
vv      16P GAIN MUTATED 16P GAIN WILD-TYPE
  T0+T1               11                 39
  T2                  25                112
  T3                  17                 83
  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  15  26   2
  16P GAIN WILD-TYPE 139  53 142   6
D28V5, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  N0               40                139
  N1               15                 53
  N2               26                142
  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    37   0
  16P GAIN WILD-TYPE 153   1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     37    0
  16P GAIN WILD-TYPE  153    1
   clus
vv  16P GAIN MUTATED 16P GAIN WILD-TYPE
  0               37                153
  1                0                  1
[1] 2 2
[1] FALSE
D28V7, binary
                    cls
clus                   0   1
  16P GAIN MUTATED    27  82
  16P GAIN WILD-TYPE 113 300
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     27   82
  16P GAIN WILD-TYPE  113  300
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  FEMALE               27                113
  MALE                 82                300
[1] 2 2
[1] FALSE
D28V8, binary
                    cls
clus                   0   1
  16P GAIN MUTATED    37  57
  16P GAIN WILD-TYPE 125 244
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     37   57
  16P GAIN WILD-TYPE  125  244
     clus
vv    16P GAIN MUTATED 16P GAIN WILD-TYPE
  NO                37                125
  YES               57                244
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD & NECK SQUAMOUS CELL CARCINOMA
  16P GAIN MUTATED                                   107
  16P GAIN WILD-TYPE                                 404
                    vv
clus                 HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  16P GAIN MUTATED                                                   2
  16P GAIN WILD-TYPE                                                 8
                    vv
clus                 HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  16P GAIN MUTATED                                                           0
  16P GAIN WILD-TYPE                                                         1
D28V9, multiclass
                                                           clus
vv                                                          16P GAIN MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                    107
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        2
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                0
                                                           clus
vv                                                          16P GAIN WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                      404
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                          8
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                  1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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    88
  16P GAIN WILD-TYPE                        32   358
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                                          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"
D28V14, binary
                    cls
clus                   0   1
  16P GAIN MUTATED     6  90
  16P GAIN WILD-TYPE  20 369
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      6   90
  16P GAIN WILD-TYPE   20  369
                        clus
vv                       16P GAIN MUTATED 16P GAIN WILD-TYPE
  HISPANIC OR LATINO                    6                 20
  NOT HISPANIC OR LATINO               90                369
[1] 2 2
[1] FALSE

Clustering(29) Variable = 16Q GAIN MUTATION ANALYSIS
D29V1, survival
                    sevent
clus2                  0   1
  16Q GAIN MUTATED    52  52
  16Q GAIN WILD-TYPE 249 167
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
               104                416 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                52                167 
$`16Q GAIN MUTATED`
TCGA-BA-4075 TCGA-BA-6871 TCGA-BA-A4IG TCGA-CN-6022 TCGA-CQ-7067 TCGA-CR-6478 
        9.30         3.55        28.11         9.24        16.73         6.02 
TCGA-DQ-7588 TCGA-HD-8634 TCGA-BA-6868 TCGA-BA-6870 TCGA-BA-6873 TCGA-BA-A4IF 
       14.04        12.66        15.52        14.83         4.01        29.42 
TCGA-BA-A6DA TCGA-BA-A6DI TCGA-BA-A6DL TCGA-C9-A47Z TCGA-CN-4728 TCGA-CN-4730 
       11.54        11.05        20.48         6.28        56.68        26.86 
TCGA-CN-4737 TCGA-CN-4739 TCGA-CN-6013 TCGA-CN-6020 TCGA-CN-6989 TCGA-CN-6994 
       20.55        45.83        23.90         6.74        32.22        38.89 
TCGA-CN-6996 TCGA-CN-A49A TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-6220 TCGA-CQ-6223 
       17.42        17.29        70.45        62.37        32.38        46.95 
TCGA-CQ-6225 TCGA-CQ-7072 TCGA-CR-5247 TCGA-CR-6477 TCGA-CR-7365 TCGA-CR-7372 
       13.25        77.56        11.77        16.90        39.16        24.95 
TCGA-CR-7374 TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7388 TCGA-CR-7390 TCGA-CV-5439 
        0.99        34.06        19.92        27.06        49.58        17.95 
TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6933 TCGA-CV-6937 
       60.49         7.07        43.23        54.74        90.12        20.52 
TCGA-CV-6939 TCGA-CV-6941 TCGA-CV-6945 TCGA-CV-6954 TCGA-CV-7091 TCGA-CV-7095 
       21.90        11.24        12.03        65.82       111.16        18.81 
TCGA-CV-7099 TCGA-CV-7102 TCGA-CV-7177 TCGA-CV-7178 TCGA-CV-7180 TCGA-CV-7242 
        7.99         1.84        21.80        71.21        10.75        36.00 
TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7409 
       31.36        26.20        17.13        18.41        57.47        17.85 
TCGA-CV-7415 TCGA-CV-7416 TCGA-CV-7423 TCGA-CV-7433 TCGA-CV-7435 TCGA-CV-A45R 
       22.85        25.08       100.57        19.76       153.86       180.16 
TCGA-CV-A45U TCGA-CV-A465 TCGA-CV-A6JM TCGA-CV-A6JY TCGA-D6-6516 TCGA-D6-6823 
       35.47         7.07         6.38        21.24        25.41        23.05 
TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A6EP TCGA-DQ-5631 TCGA-F7-A50J TCGA-F7-A623 
       24.95        25.32        13.94        18.02        31.13        20.25 
TCGA-HD-7753 TCGA-HD-7831 TCGA-HD-8314 TCGA-IQ-7631 TCGA-IQ-A61K TCGA-IQ-A61L 
       28.47        21.93        22.03        38.53         5.29        13.68 
TCGA-IQ-A6SH TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A7BN TCGA-P3-A5Q6 TCGA-P3-A6T4 
       15.48        14.37         7.96        15.42        15.78         2.04 
TCGA-P3-A6T5 TCGA-QK-A6IJ TCGA-QK-A6VB TCGA-QK-A8Z7 TCGA-UF-A7JA TCGA-UF-A7JD 
       29.00        12.72        21.07        12.89        74.47        24.30 
TCGA-UF-A7JF TCGA-UF-A7JH 
       55.43        29.46 

$`16Q GAIN WILD-TYPE`
TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-A4II TCGA-BB-A5HU TCGA-CN-4727 
       37.28        20.48        68.48        30.18        25.71        51.29 
TCGA-CN-6021 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-A6V1 
        9.07        52.08        11.08        35.05        32.48        19.82 
TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-6221 TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CQ-A4C7 
       24.39        48.20        32.88        70.13        43.04        11.61 
TCGA-CR-6472 TCGA-CX-7082 TCGA-CX-7219 TCGA-DQ-5629 TCGA-DQ-7589 TCGA-DQ-7593 
       34.52         0.36        34.36        30.94        46.32        40.24 
TCGA-H7-A6C5 TCGA-HD-8635 TCGA-UF-A71D TCGA-UF-A7JV TCGA-4P-AA8J TCGA-BA-4074 
       21.11        22.85        48.03         2.96         3.35        15.19 
TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 
       13.64         9.07        26.50        23.74        42.35        57.93 
TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-6869 TCGA-BA-6872 TCGA-BA-7269 
       17.10        23.84        65.59        21.17        12.62        41.85 
TCGA-BA-A4IH TCGA-BA-A6D8 TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF 
       20.45        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 
        4.80         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-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-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4729 TCGA-CN-4731 
       48.76        55.86        38.04         4.67        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-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-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6988 TCGA-CN-6995 
       47.44        28.04        19.07        34.13        10.45         3.68 
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-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 
        7.40        31.69        22.32        12.39        16.57         4.41 
TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5324 
       12.07         2.70        23.44        20.88        19.53        52.37 
TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 
       21.50         2.93        54.58        45.99        10.42        11.21 
TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 
        4.24        41.19        56.58         4.24        14.99        38.76 
TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C9 
       64.87        53.52        41.88        43.10        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-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-6473 TCGA-CR-6474 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 
       39.52        36.99        18.54        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-7376 TCGA-CR-7377 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 
       29.23        31.96         9.17        26.17        17.13        32.78 
TCGA-CR-7386 TCGA-CR-7389 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 
       47.01        12.89        30.02        46.85        32.65        44.25 
TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 
       30.58        24.79         5.13         5.95        35.41        29.95 
TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 
       48.39       139.43        17.16       129.21       108.95        76.24 
TCGA-CV-5436 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 
       19.20       107.51        94.88        76.50        91.53        80.12 
TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-6433 
       17.92        13.35        23.05        86.83        48.59        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-6940 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-6951 
       26.43       140.78        19.79        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-7097 TCGA-CV-7100 
        2.50         4.14        64.83       172.67        12.66         9.01 
TCGA-CV-7101 TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7236 
        5.26        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 
       89.65        18.97        95.34         4.96        11.87        47.97 
TCGA-CV-7255 TCGA-CV-7261 TCGA-CV-7407 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 
        2.10        49.71        35.54       210.97        89.33         9.67 
TCGA-CV-7414 TCGA-CV-7418 TCGA-CV-7421 TCGA-CV-7422 TCGA-CV-7424 TCGA-CV-7425 
        0.46        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-7434 
      156.49        54.94         3.52        16.27        84.49         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-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-A468 TCGA-CV-A6JD 
       60.43        67.86         0.76        56.61        15.25         5.98 
TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JZ 
       35.34        29.79         6.48        28.01         3.62        23.47 
TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-A4AQ 
       19.92        22.52        10.42        10.55        18.84        51.12 
TCGA-D6-6515 TCGA-D6-6517 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-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-5630 
       12.10        12.79        23.34        58.45        37.25        33.86 
TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 
       46.45        20.45        37.58        40.04        39.12        41.59 
TCGA-F7-7848 TCGA-F7-8298 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-A76A TCGA-HD-7229 TCGA-HD-7754 TCGA-HD-7832 
       15.16        15.06        20.94        33.76        25.74        27.48 
TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ 
       27.48        14.66         0.36        13.84         4.27         3.65 
TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G 
        6.90        34.75        15.95        14.50        37.71        11.84 
TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61O TCGA-IQ-A6SG TCGA-KU-A6H7 
       37.41         0.07        33.57        13.84        19.04        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-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-A6V9 TCGA-QK-A6VC TCGA-QK-A8Z8 TCGA-QK-A8Z9 
       21.47         9.34        27.39        19.73         5.62        14.76 
TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-RS-A6TO TCGA-RS-A6TP 
       12.20        17.82        15.32         8.32        12.72        16.96 
TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-T3-A92M TCGA-T3-A92N 
        6.87        15.91         7.10        32.45        13.71         3.12 
TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A 
       13.55        13.25        20.35        64.80        54.67         2.83 
TCGA-UF-A71B TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JC TCGA-UF-A7JJ TCGA-UF-A7JK 
       49.51        49.45        44.65        17.95        18.05        13.94 
TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 
       20.75        22.36        32.65        17.03        20.55        14.56 
TCGA-KU-A66S TCGA-KU-A66T 
       13.35        18.15 

  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 
            21.155             21.090 
[1] "1.0 - 180.2 (21.2)" "0.1 - 211.0 (21.1)"
[1] "hr=" "1.2"
D29V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  16Q GAIN MUTATED         7       18        16        45         4         0
  16Q GAIN WILD-TYPE      20       58        66       207         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               45                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
  16Q GAIN MUTATED      12  28  17  34
  16Q GAIN WILD-TYPE    38 109  83 139
D29V4, multiclass
       clus
vv      16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  T0+T1               12                 38
  T2                  28                109
  T3                  17                 83
  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  29   2
  16Q GAIN WILD-TYPE 141  55 139   6
D29V5, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  N0               38                141
  N1               13                 55
  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"
D29V6, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED    34   0
  16Q GAIN WILD-TYPE 156   1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     34    0
  16Q GAIN WILD-TYPE  156    1
   clus
vv  16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  0               34                156
  1                0                  1
[1] 2 2
[1] FALSE
D29V7, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED    31  74
  16Q GAIN WILD-TYPE 109 308
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     31   74
  16Q GAIN WILD-TYPE  109  308
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  FEMALE               31                109
  MALE                 74                308
[1] 2 2
[1] FALSE
D29V8, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED    33  54
  16Q GAIN WILD-TYPE 129 247
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     33   54
  16Q GAIN WILD-TYPE  129  247
     clus
vv    16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  NO                33                129
  YES               54                247
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD & NECK SQUAMOUS CELL CARCINOMA
  16Q GAIN MUTATED                                   103
  16Q GAIN WILD-TYPE                                 408
                    vv
clus                 HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  16Q GAIN MUTATED                                                   2
  16Q GAIN WILD-TYPE                                                 8
                    vv
clus                 HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  16Q GAIN MUTATED                                                           0
  16Q GAIN WILD-TYPE                                                         1
D29V9, multiclass
                                                           clus
vv                                                          16Q GAIN MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                    103
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        2
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                0
                                                           clus
vv                                                          16Q GAIN WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                      408
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                          8
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                  1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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    86
  16Q GAIN WILD-TYPE                        33   360
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                                          86                360
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V14, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED     6  88
  16Q GAIN WILD-TYPE  20 371
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      6   88
  16Q GAIN WILD-TYPE   20  371
                        clus
vv                       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    6                 20
  NOT HISPANIC OR LATINO               88                371
[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 263 190
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                67                453 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                29                190 
$`17P GAIN MUTATED`
TCGA-BA-4075 TCGA-CN-6023 TCGA-CR-6478 TCGA-BA-6872 TCGA-BA-7269 TCGA-BA-A4IF 
        9.30        52.08         6.02        12.62        41.85        29.42 
TCGA-BA-A6DI TCGA-BB-4225 TCGA-BB-8601 TCGA-BB-A5HY TCGA-C9-A47Z TCGA-CN-4728 
       11.05         4.80        20.52        10.55         6.28        56.68 
TCGA-CN-5356 TCGA-CN-5366 TCGA-CN-5370 TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-A63U 
       46.32        11.84         8.52        32.22        38.89        31.69 
TCGA-CQ-5329 TCGA-CQ-6229 TCGA-CQ-7072 TCGA-CQ-A4CE TCGA-CR-5247 TCGA-CR-6467 
       70.45        38.76        77.56        29.49        11.77        58.42 
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        49.71         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        12.89        54.67        49.45 
TCGA-UF-A7JH 
       29.46 

$`17P GAIN WILD-TYPE`
TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4IG TCGA-BA-A4II 
       37.28        20.48        68.48         3.55        28.11        30.18 
TCGA-BB-A5HU TCGA-CN-4727 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6024 TCGA-CN-6992 
       25.71        51.29         9.07         9.24        11.08        35.05 
TCGA-CN-6997 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-6221 TCGA-CQ-7063 
       32.48        19.82        24.39        48.20        32.88        70.13 
TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-A4C7 TCGA-CR-6472 TCGA-CX-7082 TCGA-CX-7219 
       16.73        43.04        11.61        34.52         0.36        34.36 
TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7593 TCGA-H7-A6C5 TCGA-HD-8634 
       30.94        14.04        46.32        40.24        21.11        12.66 
TCGA-HD-8635 TCGA-UF-A71D TCGA-UF-A7JV TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 
       22.85        48.03         2.96         3.35        15.19        13.64 
TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 
        9.07        26.50        23.74        42.35        57.93        17.10 
TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6873 
       23.84        65.59        15.52        21.17        14.83         4.01 
TCGA-BA-A4IH TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE 
       20.45        27.95        11.54         7.10         5.69        14.47 
TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-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-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 
      105.90         9.14         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-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO TCGA-C9-A480 TCGA-CN-4722 
       71.05        27.19        12.92         8.81        12.69        48.76 
TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 
       55.86        38.04         4.67        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-5358 TCGA-CN-5359 
       27.58        73.61        13.05        42.02         8.58        12.39 
TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5367 TCGA-CN-5369 
       71.31         8.32        16.21        11.54        11.57        12.49 
TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 
       52.08        56.94        50.07        30.67        48.00        23.90 
TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6988 
       47.44        28.04        19.07        34.13         6.74        10.45 
TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 
        3.68        17.42        11.74        35.01        25.41        23.57 
TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63V TCGA-CN-A63W 
       17.29        29.72        21.21         7.40        22.32        12.39 
TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V6 
       16.57         4.41        12.07         2.70        23.44        20.88 
TCGA-CN-A6V7 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5330 
       19.53        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-6220 
       45.99        10.42        11.21         4.24        41.19        32.38 
TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-7064 
       46.95        56.58        13.25         4.24        14.99        64.87 
TCGA-CQ-7065 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CB 
       53.52        41.88        43.10        44.48        23.24        29.36 
TCGA-CQ-A4CD TCGA-CQ-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-6473 TCGA-CR-6474 
       37.87        26.27        50.01        39.52        36.99        18.54 
TCGA-CR-6477 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 
       16.90        11.90        10.22        11.34        11.64         7.69 
TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7367 TCGA-CR-7368 
       22.78        15.75         9.27        47.18        47.34        40.93 
TCGA-CR-7369 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-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-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        49.58        30.02        46.85        32.65 
TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 
       44.25        30.58        24.79         5.13         5.95        35.41 
TCGA-CR-7402 TCGA-CV-5431 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5441 
       29.95        17.16        76.24        19.20        17.95        94.88 
TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 
       76.50        91.53        80.12        17.92        13.35        23.05 
TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6433 TCGA-CV-6436 
       86.83        48.59         7.07        43.23        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-6942 TCGA-CV-6943 TCGA-CV-6948 TCGA-CV-6952 TCGA-CV-6953 
       21.90       140.78        19.79        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-7097 TCGA-CV-7099 TCGA-CV-7100 
       64.83       172.67       111.16        12.66         7.99         9.01 
TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-7178 TCGA-CV-7180 
        1.84        52.31        12.92        21.80        71.21        10.75 
TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 
      130.88        77.16         4.73        89.65        36.00        31.36 
TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7255 
       26.20        18.97        95.34         4.96        11.87         2.10 
TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7407 TCGA-CV-7409 TCGA-CV-7410 TCGA-CV-7411 
       18.41        57.47        35.54        17.85       210.97        89.33 
TCGA-CV-7413 TCGA-CV-7415 TCGA-CV-7416 TCGA-CV-7418 TCGA-CV-7421 TCGA-CV-7422 
        9.67        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-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-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-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-7086 
       21.24        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-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-5630 TCGA-DQ-5631 
       12.79        23.34        58.45        37.25        33.86        18.02 
TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 
       46.45        20.45        37.58        40.04        39.12        41.59 
TCGA-F7-7848 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V 
       37.18        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-A76A TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 
       15.16        15.06        20.94        33.76        28.47        25.74 
TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-A4C1 TCGA-HD-A633 
       21.93        27.48        14.66        22.03         0.36        13.84 
TCGA-HD-A634 TCGA-HD-A6I0 TCGA-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-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A 
       15.48        19.27        10.75        14.37         7.96        30.05 
TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-MZ-A6I9 
        1.84        12.62         6.25        15.42         7.13        16.08 
TCGA-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-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-A6IH 
       16.01        13.15        21.07        21.21        23.15        21.47 
TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VC TCGA-QK-A8Z8 TCGA-QK-A8Z9 
        9.34        12.72        27.39        19.73         5.62        14.76 
TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-RS-A6TO TCGA-RS-A6TP 
       12.20        17.82        15.32         8.32        12.72        16.96 
TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-T3-A92M TCGA-T3-A92N 
        6.87        15.91         7.10        32.45        13.71         3.12 
TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A71A TCGA-UF-A71B 
       13.55        13.25        20.35        64.80         2.83        49.51 
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-UP-A6WW TCGA-WA-A7GZ 
       13.94        20.75        22.36        32.65        17.03        20.55 
TCGA-WA-A7H4 TCGA-KU-A66S TCGA-KU-A66T 
       14.56        13.35        18.15 

  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 
             23.47              21.07 
[1] "0.5 - 180.2 (23.5)" "0.1 - 211.0 (21.1)"
[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       225        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                225
  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 164   1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED     26    0
  17P GAIN WILD-TYPE  164    1
   clus
vv  17P GAIN MUTATED 17P GAIN WILD-TYPE
  0               26                164
  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  39
  17P GAIN WILD-TYPE 142 262
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED     20   39
  17P GAIN WILD-TYPE  142  262
     clus
vv    17P GAIN MUTATED 17P GAIN WILD-TYPE
  NO                20                142
  YES               39                262
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD & NECK SQUAMOUS CELL CARCINOMA
  17P GAIN MUTATED                                    64
  17P GAIN WILD-TYPE                                 447
                    vv
clus                 HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  17P GAIN MUTATED                                                   2
  17P GAIN WILD-TYPE                                                 8
                    vv
clus                 HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  17P GAIN MUTATED                                                           1
  17P GAIN WILD-TYPE                                                         0
D30V9, multiclass
                                                           clus
vv                                                          17P GAIN MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                     64
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        2
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                1
                                                           clus
vv                                                          17P GAIN WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                      447
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                          8
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                  0
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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    45  41
  17Q GAIN WILD-TYPE 256 178
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                86                434 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                41                178 
$`17Q GAIN MUTATED`
TCGA-CN-6022 TCGA-CN-6023 TCGA-CR-6478 TCGA-DQ-7588 TCGA-BA-6872 TCGA-BA-7269 
        9.24        52.08         6.02        14.04        12.62        41.85 
TCGA-BA-A4IF TCGA-BA-A6DI TCGA-BB-4225 TCGA-BB-8601 TCGA-BB-A5HY TCGA-C9-A47Z 
       29.42        11.05         4.80        20.52        10.55         6.28 
TCGA-CN-4728 TCGA-CN-4737 TCGA-CN-5356 TCGA-CN-5359 TCGA-CN-5366 TCGA-CN-6988 
       56.68        20.55        46.32        12.39        11.84        10.45 
TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-A63U TCGA-CN-A63W TCGA-CN-A641 TCGA-CQ-6220 
       32.22        38.89        31.69        12.39        12.07        32.38 
TCGA-CQ-6225 TCGA-CQ-7069 TCGA-CQ-7072 TCGA-CQ-A4C9 TCGA-CQ-A4CE TCGA-CR-5247 
       13.25        41.88        77.56        23.24        29.49        11.77 
TCGA-CR-6467 TCGA-CR-6473 TCGA-CR-7365 TCGA-CR-7370 TCGA-CR-7383 TCGA-CR-7390 
       58.42        36.99        39.16         3.45        17.13        49.58 
TCGA-CR-7399 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5432 TCGA-CV-5440 TCGA-CV-5970 
        5.95        48.39       139.43       129.21       107.51        13.35 
TCGA-CV-5977 TCGA-CV-6003 TCGA-CV-6933 TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6945 
       60.49        54.74        90.12        26.43        11.24        12.03 
TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6962 TCGA-CV-7095 TCGA-CV-7101 
       15.09        30.08         6.08         4.14        18.81         5.26 
TCGA-CV-7102 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7415 
        1.84        17.13        95.34        47.97        49.71        22.85 
TCGA-CV-7421 TCGA-CV-7424 TCGA-CV-A45R TCGA-CV-A45W TCGA-CV-A465 TCGA-CV-A6JZ 
        0.07        14.89       180.16        45.96         7.07        23.47 
TCGA-CX-A4AQ TCGA-D6-8569 TCGA-H7-8502 TCGA-HD-7753 TCGA-HD-7917 TCGA-HD-A6HZ 
       51.12        25.32        15.06        28.47        27.48         3.65 
TCGA-IQ-A61L TCGA-IQ-A61O TCGA-IQ-A6SG TCGA-MT-A67D TCGA-P3-A6T7 TCGA-QK-A6IG 
       13.68        13.84        19.04         1.84        16.01         7.30 
TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-AA3K TCGA-RS-A6TO 
       21.07        19.73        12.89         5.62         8.32        12.72 
TCGA-UF-A71E TCGA-UF-A7JH 
       49.45        29.46 

$`17Q GAIN WILD-TYPE`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4IG 
        9.30        37.28        20.48        68.48         3.55        28.11 
TCGA-BA-A4II TCGA-BB-A5HU TCGA-CN-4727 TCGA-CN-6021 TCGA-CN-6024 TCGA-CN-6992 
       30.18        25.71        51.29         9.07        11.08        35.05 
TCGA-CN-6997 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-6221 TCGA-CQ-7063 
       32.48        19.82        24.39        48.20        32.88        70.13 
TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-A4C7 TCGA-CR-6472 TCGA-CX-7082 TCGA-CX-7219 
       16.73        43.04        11.61        34.52         0.36        34.36 
TCGA-DQ-5629 TCGA-DQ-7589 TCGA-DQ-7593 TCGA-H7-A6C5 TCGA-HD-8634 TCGA-HD-8635 
       30.94        46.32        40.24        21.11        12.66        22.85 
TCGA-UF-A71D TCGA-UF-A7JV TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4078 
       48.03         2.96         3.35        15.19        13.64         9.07 
TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 
       26.50        23.74        42.35        57.93        17.10        23.84 
TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6873 TCGA-BA-A4IH 
       65.59        15.52        21.17        14.83         4.01        20.45 
TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF 
       27.95        11.54         7.10         5.69        14.47         7.82 
TCGA-BA-A6DG TCGA-BA-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-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-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-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-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 
       57.11        12.99        14.33        45.83        27.58        73.61 
TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5358 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5364 
       13.05        42.02         8.58        71.31         8.32        16.21 
TCGA-CN-5365 TCGA-CN-5367 TCGA-CN-5369 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 
       11.54        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-6995 TCGA-CN-6996 TCGA-CN-6998 
       19.07        34.13         6.74         3.68        17.42        11.74 
TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C 
       35.01        25.41        23.57        17.29        29.72        21.21 
TCGA-CN-A63T TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A642 TCGA-CN-A6UY 
        7.40        22.32        16.57         4.41         2.70        23.44 
TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 
       20.88        19.53        52.37        21.50         2.93        54.58 
TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 
       70.45        62.37        45.99        10.42        11.21         4.24 
TCGA-CQ-6218 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 
       41.19        46.95        56.58         4.24        14.99        38.76 
TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4CB TCGA-CQ-A4CD 
       64.87        53.52        43.10        44.48        29.36        33.60 
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-6470 TCGA-CR-6471 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6480 
       26.27        50.01        39.52        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-7385 TCGA-CR-7386 TCGA-CR-7388 
       34.06        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-7397 TCGA-CR-7398 TCGA-CR-7401 TCGA-CR-7402 TCGA-CV-5431 TCGA-CV-5434 
       24.79         5.13        35.41        29.95        17.16       108.95 
TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 
       76.24        19.20        17.95        94.88        76.50        91.53 
TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5978 
       80.12        17.92        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-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-6948 TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-6955 TCGA-CV-6956 TCGA-CV-6959 
       42.38        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-7097 
       28.34         2.50        64.83       172.67       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-7235 TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7242 
       10.75       130.88        77.16         4.73        89.65        36.00 
TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7255 
       31.36        26.20        18.97         4.96        11.87         2.10 
TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7407 TCGA-CV-7409 TCGA-CV-7410 TCGA-CV-7411 
       18.41        57.47        35.54        17.85       210.97        89.33 
TCGA-CV-7413 TCGA-CV-7414 TCGA-CV-7416 TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7423 
        9.67         0.46        25.08        25.94        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-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-A45T TCGA-CV-A45U TCGA-CV-A45V 
       27.98        21.01       169.38       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-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-A6JY TCGA-CV-A6K0 TCGA-CV-A6K1 
        6.48        28.01         3.62        21.24        19.92        22.52 
TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-7086 TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 
       10.42        10.55        18.84        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-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EN TCGA-D6-A6EO 
       17.72        12.36        28.77         7.63        22.59        24.95 
TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 
       13.94        12.10        12.79        23.34        58.45        37.25 
TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7594 
       33.86        18.02        46.45        20.45        37.58        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-A76A 
       11.80        20.25        12.43        13.38        15.16        20.94 
TCGA-HD-7229 TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-8224 TCGA-HD-8314 
       33.76        25.74        21.93        27.48        14.66        22.03 
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-A6SH TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W 
       33.57         5.29        15.48        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        27.39        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-A7J9 
       20.35        64.80        54.67         2.83        49.51        44.65 
TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-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-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 
       20.75        22.36        32.65        17.03        20.55        14.56 
TCGA-KU-A66S TCGA-KU-A66T 
       13.35        18.15 

  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 
            19.385             21.225 
[1] "0.1 - 180.2 (19.4)" "0.1 - 211.0 (21.2)"
[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        18        43         0         1
  17Q GAIN WILD-TYPE      25       64        64       209        12         0
D31V3, multiclass
           clus
vv          17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  STAGE I                  2                 25
  STAGE II                12                 64
  STAGE III               18                 64
  STAGE IVA               43                209
  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  23  27
  17Q GAIN WILD-TYPE    48 113  77 146
D31V4, multiclass
       clus
vv      17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  T0+T1                2                 48
  T2                  24                113
  T3                  23                 77
  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  14  31   0
  17Q GAIN WILD-TYPE 152  54 137   8
D31V5, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  N0               27                152
  N1               14                 54
  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    33   1
  17Q GAIN WILD-TYPE 157   0
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     33    1
  17Q GAIN WILD-TYPE  157    0
   clus
vv  17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  0               33                157
  1                1                  0
[1] 2 2
[1] FALSE
D31V7, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED    20  66
  17Q GAIN WILD-TYPE 120 316
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     20   66
  17Q GAIN WILD-TYPE  120  316
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  FEMALE               20                120
  MALE                 66                316
[1] 2 2
[1] FALSE
D31V8, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED    23  53
  17Q GAIN WILD-TYPE 139 248
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     23   53
  17Q GAIN WILD-TYPE  139  248
     clus
vv    17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  NO                23                139
  YES               53                248
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD & NECK SQUAMOUS CELL CARCINOMA
  17Q GAIN MUTATED                                    83
  17Q GAIN WILD-TYPE                                 428
                    vv
clus                 HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  17Q GAIN MUTATED                                                   2
  17Q GAIN WILD-TYPE                                                 8
                    vv
clus                 HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  17Q GAIN MUTATED                                                           1
  17Q GAIN WILD-TYPE                                                         0
D31V9, multiclass
                                                           clus
vv                                                          17Q GAIN MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                     83
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        2
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                1
                                                           clus
vv                                                          17Q GAIN WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                      428
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                          8
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                  0
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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    71
  17Q GAIN WILD-TYPE                        38   375
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                                          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"
D31V14, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED     9  73
  17Q GAIN WILD-TYPE  17 386
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      9   73
  17Q GAIN WILD-TYPE   17  386
                        clus
vv                       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    9                 17
  NOT HISPANIC OR LATINO               73                386
[1] 2 2
[1] FALSE

Clustering(32) Variable = 18P GAIN MUTATION ANALYSIS
D32V1, survival
                    sevent
clus2                  0   1
  18P GAIN MUTATED    68  56
  18P GAIN WILD-TYPE 233 163
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
               124                396 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                56                163 
$`18P GAIN MUTATED`
TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4IG TCGA-BB-A5HU TCGA-CN-6022 TCGA-CN-6024 
       68.48         3.55        28.11        25.71         9.24        11.08 
TCGA-CQ-7067 TCGA-H7-A6C5 TCGA-BA-4076 TCGA-BA-5151 TCGA-BA-5555 TCGA-BA-5558 
       16.73        21.11        13.64        23.74        17.10        65.59 
TCGA-BA-6869 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-A6DL TCGA-BB-4223 TCGA-BB-4224 
       21.17        12.62         4.01        20.48       105.90         9.14 
TCGA-BB-4225 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7870 TCGA-BB-A5HY TCGA-BB-A5HZ 
        4.80        22.42        36.72        66.28        10.55        27.19 
TCGA-BB-A6UO TCGA-C9-A47Z TCGA-CN-4728 TCGA-CN-4730 TCGA-CN-4736 TCGA-CN-4737 
        8.81         6.28        56.68        26.86        12.99        20.55 
TCGA-CN-5363 TCGA-CN-5366 TCGA-CN-6012 TCGA-CN-6020 TCGA-CN-6988 TCGA-CN-A497 
        8.32        11.84        48.00         6.74        10.45        35.01 
TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63W TCGA-CN-A641 TCGA-CN-A6UY TCGA-CQ-5332 
        7.40        31.69        12.39        12.07        23.44        10.42 
TCGA-CQ-6227 TCGA-CQ-A4C9 TCGA-CR-5247 TCGA-CR-6467 TCGA-CR-6477 TCGA-CR-6482 
        4.24        23.24        11.77        58.42        16.90        11.34 
TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7370 TCGA-CR-7372 TCGA-CR-7390 
        9.27        47.18        39.16         3.45        24.95        49.58 
TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5432 TCGA-CV-5434 
        5.95        35.41        29.95        48.39       129.21       108.95 
TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5973 TCGA-CV-5977 TCGA-CV-5979 TCGA-CV-6433 
      107.51        94.88        86.83        60.49        43.23        21.07 
TCGA-CV-6441 TCGA-CV-6935 TCGA-CV-6941 TCGA-CV-6945 TCGA-CV-6950 TCGA-CV-6951 
        9.60         9.70        11.24        12.03        15.09        30.08 
TCGA-CV-6962 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7180 TCGA-CV-7243 TCGA-CV-7247 
        4.14         5.26         1.84        10.75        31.36        18.97 
TCGA-CV-7253 TCGA-CV-7255 TCGA-CV-7406 TCGA-CV-7409 TCGA-CV-7415 TCGA-CV-7416 
       11.87         2.10        57.47        17.85        22.85        25.08 
TCGA-CV-7421 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7437 TCGA-CV-7440 TCGA-CV-A45W 
        0.07         7.17       153.86        16.64        22.19        45.96 
TCGA-CV-A45Z TCGA-CV-A461 TCGA-CV-A6JM TCGA-CX-A4AQ TCGA-D6-8568 TCGA-D6-8569 
       48.20        67.86         6.38        51.12        24.95        25.32 
TCGA-D6-A6EO TCGA-D6-A6EP TCGA-DQ-5631 TCGA-DQ-7590 TCGA-DQ-7595 TCGA-H7-8502 
       24.95        13.94        18.02        46.45        39.12        15.06 
TCGA-H7-A76A TCGA-HD-7831 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-IQ-A61G TCGA-IQ-A61K 
       20.94        21.93         4.27         3.65        11.84         5.29 
TCGA-IQ-A6SH TCGA-MZ-A7D7 TCGA-P3-A5Q6 TCGA-P3-A6T3 TCGA-QK-A8Z7 TCGA-QK-A8Z8 
       15.48        17.98        15.78        18.97        12.89         5.62 
TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-RS-A6TO TCGA-T2-A6WZ TCGA-T2-A6X2 TCGA-UF-A719 
       12.20        17.82        12.72        15.91        32.45        54.67 
TCGA-UF-A71A TCGA-UF-A71E TCGA-UF-A7JA TCGA-UF-A7JD 
        2.83        49.45        74.47        24.30 

$`18P GAIN WILD-TYPE`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-A4II TCGA-CN-4727 TCGA-CN-6021 
        9.30        37.28        20.48        30.18        51.29         9.07 
TCGA-CN-6023 TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 
       52.08        35.05        32.48        19.82        24.39        48.20 
TCGA-CQ-6221 TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CQ-A4C7 TCGA-CR-6472 TCGA-CR-6478 
       32.88        70.13        43.04        11.61        34.52         6.02 
TCGA-CX-7082 TCGA-CX-7219 TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7593 
        0.36        34.36        30.94        14.04        46.32        40.24 
TCGA-HD-8634 TCGA-HD-8635 TCGA-UF-A71D TCGA-UF-A7JV TCGA-4P-AA8J TCGA-BA-4074 
       12.66        22.85        48.03         2.96         3.35        15.19 
TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5556 TCGA-BA-6868 
        9.07        26.50        42.35        57.93        23.84        15.52 
TCGA-BA-6870 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IH TCGA-BA-A6D8 TCGA-BA-A6DA 
       14.83        41.85        29.42        20.45        27.95        11.54 
TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DI 
        7.10         5.69        14.47         7.82         2.27        11.05 
TCGA-BA-A6DJ TCGA-BA-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-4729 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4738 TCGA-CN-4739 
       12.89        32.81        52.14        57.11        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-5364 TCGA-CN-5365 TCGA-CN-5367 TCGA-CN-5369 
       12.39        71.31        16.21        11.54        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-6989 TCGA-CN-6994 
       47.44        28.04        19.07        34.13        32.22        38.89 
TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A 
        3.68        17.42        11.74        25.41        23.57        17.29 
TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A642 
       29.72        21.21        22.32        16.57         4.41         2.70 
TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 
       20.88        19.53        52.37        21.50         2.93        54.58 
TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-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-6224 TCGA-CQ-6225 TCGA-CQ-6228 TCGA-CQ-6229 
       32.38        46.95        56.58        13.25        14.99        38.76 
TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 
       64.87        53.52        41.88        43.10        77.56        44.48 
TCGA-CQ-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-6473 TCGA-CR-6474 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6484 TCGA-CR-6487 
       36.99        18.54        11.90        10.22        11.64         7.69 
TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 
       12.46        22.78        15.75        47.34        40.93        35.84 
TCGA-CR-7371 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 
        3.09        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-CV-5430 TCGA-CV-5431 TCGA-CV-5435 TCGA-CV-5436 
       24.79         5.13       139.43        17.16        76.24        19.20 
TCGA-CV-5439 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 
       17.95        76.50        91.53        80.12        17.92        13.35 
TCGA-CV-5971 TCGA-CV-5976 TCGA-CV-5978 TCGA-CV-6003 TCGA-CV-6436 TCGA-CV-6933 
       23.05        48.59         7.07        54.74        62.43        90.12 
TCGA-CV-6934 TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6940 
        2.14         5.46        20.52         4.73        21.90        26.43 
TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6948 TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6954 
      140.78        19.79        42.38         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-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 
      172.67       111.16        18.81        12.66         7.99         9.01 
TCGA-CV-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-7245 TCGA-CV-7248 TCGA-CV-7250 
        4.73        89.65        36.00        26.20        17.13        95.34 
TCGA-CV-7252 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7263 TCGA-CV-7407 TCGA-CV-7410 
        4.96        47.97        49.71        18.41        35.54       210.97 
TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7414 TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7423 
       89.33         9.67         0.46        25.94        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-7438 TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45Q 
       84.49        19.76         6.38        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-A460 TCGA-CV-A463 TCGA-CV-A464 TCGA-CV-A465 TCGA-CV-A468 TCGA-CV-A6JD 
       60.43         0.76        56.61         7.07        15.25         5.98 
TCGA-CV-A6JE TCGA-CV-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-CV-A6K2 TCGA-CX-7085 TCGA-CX-7086 
       23.47        19.92        22.52        10.42        10.55        18.84 
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        23.34        58.45        37.25 
TCGA-DQ-5630 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7594 TCGA-DQ-7596 TCGA-F7-7848 
       33.86        20.45        37.58        40.04        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-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7832 
       13.38        15.16        33.76        28.47        25.74        27.48 
TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A6I0 
       27.48        14.66        22.03         0.36        13.84         6.90 
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-A61J TCGA-IQ-A61L TCGA-IQ-A61O TCGA-IQ-A6SG TCGA-KU-A6H7 
        0.07        33.57        13.68        13.84        19.04        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-P3-A5Q5 TCGA-P3-A5QA 
        6.25        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-A6T2 
       51.25        10.85        36.82        47.01        19.00        75.55 
TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A64Z 
        2.04        29.00        12.99        16.01        13.15        21.07 
TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ 
       21.21        23.15         7.30        21.47         9.34        12.72 
TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z9 TCGA-QK-AA3J TCGA-QK-AA3K 
       27.39        21.07        19.73        14.76        15.32         8.32 
TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6X0 TCGA-T3-A92M TCGA-T3-A92N TCGA-TN-A7HI 
       16.96         6.87         7.10        13.71         3.12        13.55 
TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A71B TCGA-UF-A7J9 TCGA-UF-A7JC 
       13.25        20.35        64.80        49.51        44.65        17.95 
TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS 
       55.43        29.46        18.05        13.94        20.75        22.36 
TCGA-UF-A7JT TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 TCGA-KU-A66S TCGA-KU-A66T 
       32.65        17.03        20.55        14.56        13.35        18.15 

  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 
            18.495             21.715 
[1] "0.1 - 153.9 (18.5)" "0.1 - 211.0 (21.7)"
[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       188        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                188
  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    31  16  50   2
  18P GAIN WILD-TYPE 148  52 118   6
D32V5, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  N0               31                148
  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 153   0
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED     37    1
  18P GAIN WILD-TYPE  153    0
   clus
vv  18P GAIN MUTATED 18P GAIN WILD-TYPE
  0               37                153
  1                1                  0
[1] 2 2
[1] FALSE
D32V7, binary
                    cls
clus                   0   1
  18P GAIN MUTATED    18 106
  18P GAIN WILD-TYPE 122 276
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED     18  106
  18P GAIN WILD-TYPE  122  276
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  FEMALE               18                122
  MALE                106                276
[1] 2 2
[1] FALSE
D32V8, binary
                    cls
clus                   0   1
  18P GAIN MUTATED    33  71
  18P GAIN WILD-TYPE 129 230
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED     33   71
  18P GAIN WILD-TYPE  129  230
     clus
vv    18P GAIN MUTATED 18P GAIN WILD-TYPE
  NO                33                129
  YES               71                230
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD & NECK SQUAMOUS CELL CARCINOMA
  18P GAIN MUTATED                                   122
  18P GAIN WILD-TYPE                                 389
                    vv
clus                 HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  18P GAIN MUTATED                                                   2
  18P GAIN WILD-TYPE                                                 8
                    vv
clus                 HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  18P GAIN MUTATED                                                           0
  18P GAIN WILD-TYPE                                                         1
D32V9, multiclass
                                                           clus
vv                                                          18P GAIN MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                    122
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        2
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                0
                                                           clus
vv                                                          18P GAIN WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                      389
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                          8
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                  1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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   104
  18P GAIN WILD-TYPE                        34   342
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                                         104                342
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V14, binary
                    cls
clus                   0   1
  18P GAIN MUTATED     4 112
  18P GAIN WILD-TYPE  22 347
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      4  112
  18P GAIN WILD-TYPE   22  347
                        clus
vv                       18P GAIN MUTATED 18P GAIN WILD-TYPE
  HISPANIC OR LATINO                    4                 22
  NOT HISPANIC OR LATINO              112                347
[1] 2 2
[1] FALSE

Clustering(33) Variable = 18Q GAIN MUTATION ANALYSIS
D33V1, survival
                    sevent
clus2                  0   1
  18Q GAIN MUTATED    29  24
  18Q GAIN WILD-TYPE 272 195
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                53                467 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                24                195 
$`18Q GAIN MUTATED`
TCGA-BA-5559 TCGA-BA-6871 TCGA-CN-6024 TCGA-BA-5151 TCGA-BA-5555 TCGA-BB-4223 
       68.48         3.55        11.08        23.74        17.10       105.90 
TCGA-BB-4225 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7870 TCGA-CN-4736 TCGA-CN-6012 
        4.80        18.38        22.42        66.28        12.99        48.00 
TCGA-CN-6020 TCGA-CN-6988 TCGA-CN-A497 TCGA-CN-A6UY TCGA-CR-6467 TCGA-CR-6477 
        6.74        10.45        35.01        23.44        58.42        16.90 
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-7416 TCGA-CV-7421 
        4.14        52.31        57.47        22.85        25.08         0.07 
TCGA-CV-A45W TCGA-CV-A45Z TCGA-CV-A461 TCGA-CV-A6JM TCGA-CX-A4AQ TCGA-D6-A6EO 
       45.96        48.20        67.86         6.38        51.12        24.95 
TCGA-DQ-7590 TCGA-H7-A76A TCGA-HD-A634 TCGA-P3-A5Q6 TCGA-QK-A6IG TCGA-QK-A8Z7 
       46.45        20.94         4.27        15.78         7.30        12.89 
TCGA-QK-A8Z8 TCGA-T2-A6X2 TCGA-TN-A7HL TCGA-UF-A719 TCGA-UF-A71E 
        5.62        32.45        20.35        54.67        49.45 

$`18Q GAIN WILD-TYPE`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-A4IG TCGA-BA-A4II TCGA-BB-A5HU 
        9.30        37.28        20.48        28.11        30.18        25.71 
TCGA-CN-4727 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6992 TCGA-CN-6997 
       51.29         9.07         9.24        52.08        35.05        32.48 
TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-6221 TCGA-CQ-7063 TCGA-CQ-7067 
       19.82        24.39        48.20        32.88        70.13        16.73 
TCGA-CQ-7068 TCGA-CQ-A4C7 TCGA-CR-6472 TCGA-CR-6478 TCGA-CX-7082 TCGA-CX-7219 
       43.04        11.61        34.52         6.02         0.36        34.36 
TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7593 TCGA-H7-A6C5 TCGA-HD-8634 
       30.94        14.04        46.32        40.24        21.11        12.66 
TCGA-HD-8635 TCGA-UF-A71D TCGA-UF-A7JV TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 
       22.85        48.03         2.96         3.35        15.19        13.64 
TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5556 TCGA-BA-5558 
        9.07        26.50        42.35        57.93        23.84        65.59 
TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 
       15.52        21.17        14.83        12.62         4.01        41.85 
TCGA-BA-A4IF TCGA-BA-A4IH TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD 
       29.42        20.45        27.95        11.54         7.10         5.69 
TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DI TCGA-BA-A6DJ TCGA-BA-A6DL 
       14.47         7.82         2.27        11.05        13.38        20.48 
TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4224 TCGA-BB-4227 TCGA-BB-7862 TCGA-BB-7863 
       16.41         6.15         9.14         4.41        36.72        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-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-4737 TCGA-CN-4738 
       26.86        32.81        52.14        57.11        20.55        14.33 
TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 
       45.83        27.58        73.61        13.05        42.02        46.32 
TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-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-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-6989 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6998 
       34.13        32.22        38.89         3.68        17.42        11.74 
TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T 
       25.41        23.57        17.29        29.72        21.21         7.40 
TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 
       31.69        22.32        12.39        16.57         4.41        12.07 
TCGA-CN-A642 TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 
        2.70        20.88        19.53        52.37        21.50         2.93 
TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 
       54.58        70.45        62.37        45.99        10.42        11.21 
TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6220 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6225 
        4.24        41.19        32.38        46.95        56.58        13.25 
TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7069 
        4.24        14.99        38.76        64.87        53.52        41.88 
TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD 
       43.10        77.56        44.48        23.24        29.36        33.60 
TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 
       29.49        14.14        12.46        31.23        84.23        11.77 
TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6473 
       54.67        37.87        26.27        50.01        39.52        36.99 
TCGA-CR-6474 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 
       18.54        11.90        10.22        11.64         7.69        12.46 
TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7368 
       22.78        15.75         9.27        47.18        39.16        40.93 
TCGA-CR-7369 TCGA-CR-7371 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 
       35.84         3.09        29.23         0.99        31.96         9.17 
TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 
       34.06        19.92        26.17        17.13        32.78        47.01 
TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 
       27.06        12.89        49.58        30.02        46.85        32.65 
TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7402 
       44.25        30.58        24.79         5.13         5.95        29.95 
TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 
      139.43        17.16        76.24        19.20        17.95       107.51 
TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 
       94.88        76.50        91.53        80.12        17.92        13.35 
TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 
       23.05        86.83        48.59        60.49         7.07        43.23 
TCGA-CV-6003 TCGA-CV-6436 TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 
       54.74        62.43        90.12         2.14         9.70         5.46 
TCGA-CV-6937 TCGA-CV-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-6952 TCGA-CV-6953 TCGA-CV-6954 
       19.79        12.03        42.38         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-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 
      172.67       111.16        18.81        12.66         7.99         9.01 
TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-7178 TCGA-CV-7180 
        5.26         1.84        12.92        21.80        71.21        10.75 
TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 
      130.88        77.16         4.73        89.65        36.00        31.36 
TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 
       26.20        18.97        17.13        95.34         4.96        11.87 
TCGA-CV-7254 TCGA-CV-7255 TCGA-CV-7261 TCGA-CV-7263 TCGA-CV-7407 TCGA-CV-7409 
       47.97         2.10        49.71        18.41        35.54        17.85 
TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7414 TCGA-CV-7418 TCGA-CV-7422 
      210.97        89.33         9.67         0.46        25.94        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-A45U TCGA-CV-A45V TCGA-CV-A45X TCGA-CV-A45Y TCGA-CV-A460 
      159.65        35.47         1.05         6.51        88.87        60.43 
TCGA-CV-A463 TCGA-CV-A464 TCGA-CV-A465 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE 
        0.76        56.61         7.07        15.25         5.98        35.34 
TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ 
       29.79         6.48        28.01         3.62        21.24        23.47 
TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-7086 TCGA-D6-6515 
       19.92        22.52        10.42        10.55        18.84        13.25 
TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 
       25.41         9.60        23.05         2.53        16.14        11.44 
TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK 
       18.67        24.95        25.32        17.72        12.36        28.77 
TCGA-D6-A6EM TCGA-D6-A6EN TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q 
        7.63        22.59        13.94        12.10        12.79        23.34 
TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7591 TCGA-DQ-7592 
       58.45        37.25        33.86        18.02        20.45        37.58 
TCGA-DQ-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-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 
       15.06        33.76        28.47        25.74        21.93        27.48 
TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A6HZ 
       27.48        14.66        22.03         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-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W 
       13.84        19.04        15.48        19.27        10.75        14.37 
TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G TCGA-MT-A7BN 
        7.96        30.05         1.84        12.62         6.25        15.42 
TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-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-A6T5 TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A64Z 
        2.04        29.00        12.99        16.01        13.15        21.07 
TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 
       21.21        23.15        21.47         9.34        12.72        27.39 
TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J 
       21.07        19.73        14.76        12.20        17.82        15.32 
TCGA-QK-AA3K TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T2-A6X0 
        8.32        12.72        16.96         6.87        15.91         7.10 
TCGA-T3-A92M TCGA-T3-A92N TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-UF-A718 TCGA-UF-A71A 
       13.71         3.12        13.55        13.25        64.80         2.83 
TCGA-UF-A71B TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF 
       49.51        44.65        74.47        17.95        24.30        55.43 
TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT 
       29.46        18.05        13.94        20.75        22.36        32.65 
TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 TCGA-KU-A66S TCGA-KU-A66T 
       17.03        20.55        14.56        13.35        18.15 

  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 
             23.44              21.01 
[1] "0.1 - 129.2 (23.4)" "0.1 - 211.0 (21.0)"
[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        24         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               24                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  15
  18Q GAIN WILD-TYPE    44 127  89 158
D33V4, multiclass
       clus
vv      18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  T0+T1                6                 44
  T2                  10                127
  T3                  11                 89
  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
  18Q GAIN MUTATED    15   7  17   0
  18Q GAIN WILD-TYPE 164  61 151   8
D33V5, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  N0               15                164
  N1                7                 61
  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    15   1
  18Q GAIN WILD-TYPE 175   0
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED     15    1
  18Q GAIN WILD-TYPE  175    0
   clus
vv  18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  0               15                175
  1                1                  0
[1] 2 2
[1] FALSE
D33V7, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED     5  48
  18Q GAIN WILD-TYPE 135 334
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      5   48
  18Q GAIN WILD-TYPE  135  334
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  FEMALE                5                135
  MALE                 48                334
[1] 2 2
[1] FALSE
D33V8, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED    16  27
  18Q GAIN WILD-TYPE 146 274
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED     16   27
  18Q GAIN WILD-TYPE  146  274
     clus
vv    18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  NO                16                146
  YES               27                274
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD & NECK SQUAMOUS CELL CARCINOMA
  18Q GAIN MUTATED                                    51
  18Q GAIN WILD-TYPE                                 460
                    vv
clus                 HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  18Q GAIN MUTATED                                                   2
  18Q GAIN WILD-TYPE                                                 8
                    vv
clus                 HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  18Q GAIN MUTATED                                                           0
  18Q GAIN WILD-TYPE                                                         1
D33V9, multiclass
                                                           clus
vv                                                          18Q GAIN MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                     51
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        2
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                0
                                                           clus
vv                                                          18Q GAIN WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                      460
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                          8
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                  1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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  48
  18Q GAIN WILD-TYPE  24 411
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      2   48
  18Q GAIN WILD-TYPE   24  411
                        clus
vv                       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                 24
  NOT HISPANIC OR LATINO               48                411
[1] 2 2
[1] FALSE

Clustering(34) Variable = 19P GAIN MUTATION ANALYSIS
D34V1, survival
                    sevent
clus2                  0   1
  19P GAIN MUTATED    36  20
  19P GAIN WILD-TYPE 265 199
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                56                464 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                20                199 
$`19P GAIN MUTATED`
TCGA-BA-5559 TCGA-CN-6021 TCGA-CN-6023 TCGA-CN-6024 TCGA-CQ-5323 TCGA-CX-7219 
       68.48         9.07        52.08        11.08        48.20        34.36 
TCGA-BA-A8YP TCGA-BB-4223 TCGA-BB-4225 TCGA-BB-7861 TCGA-BB-7871 TCGA-BB-8601 
       16.41       105.90         4.80        22.42        24.66        20.52 
TCGA-CN-6989 TCGA-CN-A63T TCGA-CN-A63V TCGA-CN-A641 TCGA-CN-A6V6 TCGA-CR-6467 
       32.22         7.40        22.32        12.07        20.88        58.42 
TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-7389 TCGA-CR-7404 TCGA-CV-5431 TCGA-CV-5440 
        7.69        12.46        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-A45U TCGA-CV-A45Z TCGA-CV-A6JM TCGA-CV-A6K2 
       49.71        22.85        35.47        48.20         6.38        10.42 
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        27.39        21.07 
TCGA-QK-A8Z7 TCGA-QK-AA3K TCGA-T2-A6WZ TCGA-TN-A7HI TCGA-TN-A7HL TCGA-UF-A71A 
       12.89         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-BA-4075 TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-6871 TCGA-BA-A4IG TCGA-BA-A4II 
        9.30        37.28        20.48         3.55        28.11        30.18 
TCGA-BB-A5HU TCGA-CN-4727 TCGA-CN-6022 TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-A6V1 
       25.71        51.29         9.24        35.05        32.48        19.82 
TCGA-CN-A6V3 TCGA-CQ-6221 TCGA-CQ-7063 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-A4C7 
       24.39        32.88        70.13        16.73        43.04        11.61 
TCGA-CR-6472 TCGA-CR-6478 TCGA-CX-7082 TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7589 
       34.52         6.02         0.36        30.94        14.04        46.32 
TCGA-DQ-7593 TCGA-H7-A6C5 TCGA-HD-8634 TCGA-HD-8635 TCGA-UF-A71D TCGA-UF-A7JV 
       40.24        21.11        12.66        22.85        48.03         2.96 
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 
        3.35        15.19        13.64         9.07        26.50        23.74 
TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-6868 
       42.35        57.93        17.10        23.84        65.59        15.52 
TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF 
       21.17        14.83        12.62         4.01        41.85        29.42 
TCGA-BA-A4IH TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE 
       20.45        27.95        11.54         7.10         5.69        14.47 
TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DI TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-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-A5HY TCGA-BB-A5HZ 
       44.98        66.28        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-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 
       38.04         4.67        56.68        12.89        26.86        32.81 
TCGA-CN-4733 TCGA-CN-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-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 
       30.67        48.00        23.90        47.44        28.04        19.07 
TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6988 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 
       34.13         6.74        10.45        38.89         3.68        17.42 
TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B 
       11.74        35.01        25.41        23.57        17.29        29.72 
TCGA-CN-A49C TCGA-CN-A63U TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A642 
       21.21        31.69        12.39        16.57         4.41         2.70 
TCGA-CN-A6UY TCGA-CN-A6V7 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 
       23.44        19.53        52.37        21.50         2.93        54.58 
TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 
       70.45        62.37        45.99        10.42        11.21         4.24 
TCGA-CQ-6218 TCGA-CQ-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-7064 TCGA-CQ-7065 TCGA-CQ-7069 TCGA-CQ-7071 
       14.99        38.76        64.87        53.52        41.88        43.10 
TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE 
       77.56        44.48        23.24        29.36        33.60        29.49 
TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 
       14.14        12.46        31.23        84.23        11.77        54.67 
TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6474 
       37.87        26.27        50.01        39.52        36.99        18.54 
TCGA-CR-6477 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6491 
       16.90        11.90        10.22        11.34        11.64        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-7390 TCGA-CR-7391 TCGA-CR-7392 
       32.78        47.01        27.06        49.58        30.02        46.85 
TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 
       32.65        44.25        30.58        24.79         5.13         5.95 
TCGA-CR-7401 TCGA-CR-7402 TCGA-CV-5430 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 
       35.41        29.95       139.43       129.21       108.95        76.24 
TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5441 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 
       19.20        17.95        94.88        91.53        80.12        17.92 
TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5978 TCGA-CV-5979 
       13.35        23.05        86.83        48.59         7.07        43.23 
TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6933 TCGA-CV-6934 
       54.74        21.07        62.43         9.60        90.12         2.14 
TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6940 
        9.70         5.46        20.52         4.73        21.90        26.43 
TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6950 
       11.24       140.78        19.79        12.03        42.38        15.09 
TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-6955 TCGA-CV-6956 
       30.08         6.08        53.95        65.82        10.98         7.13 
TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7090 
        8.42        28.34         2.50         4.14        64.83       172.67 
TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7102 
      111.16        18.81        12.66         7.99         9.01         1.84 
TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-7178 TCGA-CV-7180 TCGA-CV-7183 
       52.31        12.92        21.80        71.21        10.75       130.88 
TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7248 TCGA-CV-7250 
        4.73        89.65        36.00        31.36        17.13        95.34 
TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7255 TCGA-CV-7263 TCGA-CV-7406 
        4.96        11.87        47.97         2.10        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-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-A45V 
       27.98        21.01       169.38       180.16       159.65         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-7085 TCGA-CX-7086 TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6516 
       22.52        10.55        18.84        51.12        13.25        25.41 
TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 
        9.60        23.05         2.53        16.14        11.44        18.67 
TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM 
       24.95        25.32        17.72        12.36        28.77         7.63 
TCGA-D6-A6EN TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q 
       22.59        24.95        13.94        12.10        12.79        23.34 
TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7590 TCGA-DQ-7591 
       58.45        37.25        33.86        18.02        46.45        20.45 
TCGA-DQ-7592 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8489 
       37.58        40.04        39.12        41.59        37.18        21.63 
TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 
       20.25         3.02        18.94        24.95         0.46        17.85 
TCGA-F7-A622 TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-HD-7229 
       11.80        12.43        13.38        15.16        15.06        33.76 
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-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6I0 TCGA-HL-7533 
       22.03         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-A61L TCGA-IQ-A61O TCGA-IQ-A6SG TCGA-IQ-A6SH 
        0.07        33.57        13.68        13.84        19.04        15.48 
TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D 
       19.27        10.75        14.37         7.96        30.05         1.84 
TCGA-MT-A67F TCGA-MT-A7BN TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5QA 
       12.62        15.42        16.08        17.98        29.92        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-A6T5 TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A64Z 
       18.97        29.00        12.99        16.01        13.15        21.07 
TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ 
       21.21        23.15         7.30        21.47         9.34        12.72 
TCGA-QK-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-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-T3-A92M 
       12.72        16.96         6.87         7.10        32.45        13.71 
TCGA-T3-A92N TCGA-TN-A7HJ TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71B TCGA-UF-A7J9 
        3.12        13.25        64.80        54.67        49.51        44.65 
TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ 
       74.47        17.95        24.30        55.43        29.46        18.05 
TCGA-UF-A7JK TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 
       13.94        22.36        32.65        17.03        20.55        14.56 
TCGA-KU-A66S TCGA-KU-A66T 
       13.35        18.15 

  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 
            20.635             21.225 
[1] "2.0 - 107.5 (20.6)" "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        32         1         0
  19P GAIN WILD-TYPE      24       71        76       220        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               32                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
  19P GAIN MUTATED       7   9  12  20
  19P GAIN WILD-TYPE    43 128  88 153
D34V4, multiclass
       clus
vv      19P GAIN MUTATED 19P GAIN WILD-TYPE
  T0+T1                7                 43
  T2                   9                128
  T3                  12                 88
  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
  19P GAIN MUTATED    15   5  26   1
  19P GAIN WILD-TYPE 164  63 142   7
D34V5, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  N0               15                164
  N1                5                 63
  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"
D34V6, binary
                    cls
clus                   0   1
  19P GAIN MUTATED    21   0
  19P GAIN WILD-TYPE 169   1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     21    0
  19P GAIN WILD-TYPE  169    1
   clus
vv  19P GAIN MUTATED 19P GAIN WILD-TYPE
  0               21                169
  1                0                  1
[1] 2 2
[1] FALSE
D34V7, binary
                    cls
clus                   0   1
  19P GAIN MUTATED     9  47
  19P GAIN WILD-TYPE 131 335
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      9   47
  19P GAIN WILD-TYPE  131  335
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  FEMALE                9                131
  MALE                 47                335
[1] 2 2
[1] FALSE
D34V8, binary
                    cls
clus                   0   1
  19P GAIN MUTATED    13  36
  19P GAIN WILD-TYPE 149 265
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     13   36
  19P GAIN WILD-TYPE  149  265
     clus
vv    19P GAIN MUTATED 19P GAIN WILD-TYPE
  NO                13                149
  YES               36                265
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD & NECK SQUAMOUS CELL CARCINOMA
  19P GAIN MUTATED                                    54
  19P GAIN WILD-TYPE                                 457
                    vv
clus                 HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  19P GAIN MUTATED                                                   2
  19P GAIN WILD-TYPE                                                 8
                    vv
clus                 HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  19P GAIN MUTATED                                                           0
  19P GAIN WILD-TYPE                                                         1
D34V9, multiclass
                                                           clus
vv                                                          19P GAIN MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                     54
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        2
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                0
                                                           clus
vv                                                          19P GAIN WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                      457
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                          8
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                  1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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    50  27
  19Q GAIN WILD-TYPE 251 192
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                77                443 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                27                192 
$`19Q GAIN MUTATED`
TCGA-BA-5559 TCGA-CN-6021 TCGA-CN-6023 TCGA-CN-6024 TCGA-CX-7219 TCGA-4P-AA8J 
       68.48         9.07        52.08        11.08        34.36         3.35 
TCGA-BA-5153 TCGA-BA-7269 TCGA-BA-A8YP TCGA-BB-4223 TCGA-BB-4225 TCGA-BB-7861 
       57.93        41.85        16.41       105.90         4.80        22.42 
TCGA-CN-6012 TCGA-CN-A63T TCGA-CN-A63V TCGA-CN-A641 TCGA-CN-A6UY TCGA-CN-A6V6 
       48.00         7.40        22.32        12.07        23.44        20.88 
TCGA-CQ-5324 TCGA-CQ-5330 TCGA-CQ-6223 TCGA-CQ-6225 TCGA-CR-6467 TCGA-CR-6487 
       52.37        62.37        46.95        13.25        58.42         7.69 
TCGA-CR-6488 TCGA-CR-7367 TCGA-CR-7389 TCGA-CR-7404 TCGA-CV-5431 TCGA-CV-5440 
       12.46        47.34        12.89        48.39        17.16       107.51 
TCGA-CV-5442 TCGA-CV-5977 TCGA-CV-6937 TCGA-CV-7101 TCGA-CV-7235 TCGA-CV-7243 
       76.50        60.49        20.52         5.26        77.16        31.36 
TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7253 TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7407 
       26.20        18.97        11.87        49.71        57.47        35.54 
TCGA-CV-7409 TCGA-CV-7415 TCGA-CV-7435 TCGA-CV-7437 TCGA-CV-A45U TCGA-CV-A45Z 
       17.85        22.85       153.86        16.64        35.47        48.20 
TCGA-CV-A6JM TCGA-CV-A6K2 TCGA-D6-6825 TCGA-DQ-7592 TCGA-F7-8298 TCGA-F7-A50I 
        6.38        10.42        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-MT-A67G TCGA-MZ-A5BI TCGA-P3-A5Q5 TCGA-P3-A6T4 
       11.84         5.29         6.25         7.13        29.92         2.04 
TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-AA3K TCGA-T2-A6WZ TCGA-TN-A7HI TCGA-TN-A7HJ 
       27.39        21.07         8.32        15.91        13.55        13.25 
TCGA-UF-A71A TCGA-UF-A71E TCGA-UF-A7JJ TCGA-UF-A7JO TCGA-KU-A66T 
        2.83        49.45        18.05        20.75        18.15 

$`19Q GAIN WILD-TYPE`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-6871 TCGA-BA-A4IG TCGA-BA-A4II 
        9.30        37.28        20.48         3.55        28.11        30.18 
TCGA-BB-A5HU TCGA-CN-4727 TCGA-CN-6022 TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-A6V1 
       25.71        51.29         9.24        35.05        32.48        19.82 
TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-6221 TCGA-CQ-7063 TCGA-CQ-7067 TCGA-CQ-7068 
       24.39        48.20        32.88        70.13        16.73        43.04 
TCGA-CQ-A4C7 TCGA-CR-6472 TCGA-CR-6478 TCGA-CX-7082 TCGA-DQ-5629 TCGA-DQ-7588 
       11.61        34.52         6.02         0.36        30.94        14.04 
TCGA-DQ-7589 TCGA-DQ-7593 TCGA-H7-A6C5 TCGA-HD-8634 TCGA-HD-8635 TCGA-UF-A71D 
       46.32        40.24        21.11        12.66        22.85        48.03 
TCGA-UF-A7JV TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 
        2.96        15.19        13.64         9.07        26.50        23.74 
TCGA-BA-5152 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6869 
       42.35        17.10        23.84        65.59        15.52        21.17 
TCGA-BA-6870 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-A4IF TCGA-BA-A4IH TCGA-BA-A6D8 
       14.83        12.62         4.01        29.42        20.45        27.95 
TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG 
       11.54         7.10         5.69        14.47         7.82         2.27 
TCGA-BA-A6DI TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BB-4217 TCGA-BB-4224 TCGA-BB-4227 
       11.05        13.38        20.48         6.15         9.14         4.41 
TCGA-BB-4228 TCGA-BB-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-A5HY TCGA-BB-A5HZ 
       24.66        38.40        71.05        20.52        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-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 
       38.04         4.67        56.68        12.89        26.86        32.81 
TCGA-CN-4733 TCGA-CN-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-6020 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 
        6.74        10.45        32.22        38.89         3.68        17.42 
TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B 
       11.74        35.01        25.41        23.57        17.29        29.72 
TCGA-CN-A49C TCGA-CN-A63U TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A642 
       21.21        31.69        12.39        16.57         4.41         2.70 
TCGA-CN-A6V7 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5331 
       19.53        21.50         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-6224 
       10.42        11.21         4.24        41.19        32.38        56.58 
TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7069 
        4.24        14.99        38.76        64.87        53.52        41.88 
TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD 
       43.10        77.56        44.48        23.24        29.36        33.60 
TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 
       29.49        14.14        12.46        31.23        84.23        11.77 
TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6473 
       54.67        37.87        26.27        50.01        39.52        36.99 
TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 
       18.54        16.90        11.90        10.22        11.34        11.64 
TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7368 
       22.78        15.75         9.27        47.18        39.16        40.93 
TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 
       35.84         3.45         3.09        24.95        29.23         0.99 
TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7383 
       31.96         9.17        34.06        19.92        26.17        17.13 
TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 
       32.78        47.01        27.06        49.58        30.02        46.85 
TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 
       32.65        44.25        30.58        24.79         5.13         5.95 
TCGA-CR-7401 TCGA-CR-7402 TCGA-CV-5430 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 
       35.41        29.95       139.43       129.21       108.95        76.24 
TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5441 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 
       19.20        17.95        94.88        91.53        80.12        17.92 
TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5978 TCGA-CV-5979 
       13.35        23.05        86.83        48.59         7.07        43.23 
TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6933 TCGA-CV-6934 
       54.74        21.07        62.43         9.60        90.12         2.14 
TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6941 
        9.70         5.46         4.73        21.90        26.43        11.24 
TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-6951 
      140.78        19.79        12.03        42.38        15.09        30.08 
TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-6955 TCGA-CV-6956 TCGA-CV-6959 
        6.08        53.95        65.82        10.98         7.13         8.42 
TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7091 
       28.34         2.50         4.14        64.83       172.67       111.16 
TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7102 TCGA-CV-7103 
       18.81        12.66         7.99         9.01         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-7248 TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7254 
       89.65        36.00        17.13        95.34         4.96        47.97 
TCGA-CV-7255 TCGA-CV-7263 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7414 
        2.10        18.41       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-7434 TCGA-CV-7438 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45P 
       19.76         7.17         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-A460 TCGA-CV-A461 TCGA-CV-A463 TCGA-CV-A464 TCGA-CV-A465 
       88.87        60.43        67.86         0.76        56.61         7.07 
TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-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-CX-7085 
        3.62        21.24        23.47        19.92        22.52        10.55 
TCGA-CX-7086 TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 
       18.84        51.12        13.25        25.41         9.60        23.05 
TCGA-D6-6824 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 
        2.53        11.44        18.67        24.95        25.32        17.72 
TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EN TCGA-D6-A6EO TCGA-D6-A6EP 
       12.36        28.77         7.63        22.59        24.95        13.94 
TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 
       12.10        12.79        23.34        58.45        37.25        33.86 
TCGA-DQ-5631 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 
       18.02        46.45        20.45        40.04        39.12        41.59 
TCGA-F7-7848 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W 
       37.18        21.63        20.25        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-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-7917 
       33.76        28.47        25.74        21.93        27.48        27.48 
TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6I0 
       14.66        22.03         0.36        13.84         4.27         6.90 
TCGA-IQ-7630 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J 
       15.95        14.50        37.71        37.41         0.07        33.57 
TCGA-IQ-A61L TCGA-IQ-A61O TCGA-IQ-A6SG TCGA-IQ-A6SH TCGA-KU-A6H7 TCGA-KU-A6H8 
       13.68        13.84        19.04        15.48        19.27        10.75 
TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A7BN 
       14.37         7.96        30.05         1.84        12.62        15.42 
TCGA-MZ-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-A8Z7 
        7.30        21.47         9.34        12.72        19.73        12.89 
TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-RS-A6TO 
        5.62        14.76        12.20        17.82        15.32        12.72 
TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-T3-A92M TCGA-T3-A92N 
       16.96         6.87         7.10        32.45        13.71         3.12 
TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71B TCGA-UF-A7J9 TCGA-UF-A7JA 
       20.35        64.80        54.67        49.51        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-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 TCGA-KU-A66S 
       32.65        17.03        20.55        14.56        13.35 

  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 
             20.94              21.17 
[1] "2.0 - 153.9 (20.9)" "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         9        40         2         0
  19Q GAIN WILD-TYPE      24       65        73       212        10         1
D35V3, multiclass
           clus
vv          19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  STAGE I                  3                 24
  STAGE II                11                 65
  STAGE III                9                 73
  STAGE IVA               40                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 GAIN MUTATED       7  20  15  25
  19Q GAIN WILD-TYPE    43 117  85 148
D35V4, multiclass
       clus
vv      19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  T0+T1                7                 43
  T2                  20                117
  T3                  15                 85
  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 GAIN MUTATED    25   7  29   2
  19Q GAIN WILD-TYPE 154  61 139   6
D35V5, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  N0               25                154
  N1                7                 61
  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    23   0
  19Q GAIN WILD-TYPE 167   1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     23    0
  19Q GAIN WILD-TYPE  167    1
   clus
vv  19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  0               23                167
  1                0                  1
[1] 2 2
[1] FALSE
D35V7, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED    13  64
  19Q GAIN WILD-TYPE 127 318
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     13   64
  19Q GAIN WILD-TYPE  127  318
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  FEMALE               13                127
  MALE                 64                318
[1] 2 2
[1] FALSE
D35V8, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED    21  43
  19Q GAIN WILD-TYPE 141 258
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     21   43
  19Q GAIN WILD-TYPE  141  258
     clus
vv    19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  NO                21                141
  YES               43                258
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD & NECK SQUAMOUS CELL CARCINOMA
  19Q GAIN MUTATED                                    75
  19Q GAIN WILD-TYPE                                 436
                    vv
clus                 HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  19Q GAIN MUTATED                                                   2
  19Q GAIN WILD-TYPE                                                 8
                    vv
clus                 HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  19Q GAIN MUTATED                                                           0
  19Q GAIN WILD-TYPE                                                         1
D35V9, multiclass
                                                           clus
vv                                                          19Q GAIN MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                     75
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        2
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                0
                                                           clus
vv                                                          19Q GAIN WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                      436
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                          8
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                  1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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                           7    67
  19Q GAIN WILD-TYPE                        41   379
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                       7                 41
  WHITE                                          67                379
[1] 4 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     4  67
  19Q GAIN WILD-TYPE  22 392
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      4   67
  19Q GAIN WILD-TYPE   22  392
                        clus
vv                       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    4                 22
  NOT HISPANIC OR LATINO               67                392
[1] 2 2
[1] FALSE

Clustering(36) Variable = 20P GAIN MUTATION ANALYSIS
D36V1, survival
                    sevent
clus2                  0   1
  20P GAIN MUTATED   112  80
  20P GAIN WILD-TYPE 189 139
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               192                328 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                80                139 
$`20P GAIN MUTATED`
TCGA-BA-5559 TCGA-BB-A5HU TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CQ-7067 
       68.48        25.71         9.24        52.08        11.08        16.73 
TCGA-CQ-A4C7 TCGA-CX-7082 TCGA-DQ-7588 TCGA-UF-A7JV TCGA-BA-4078 TCGA-BA-5149 
       11.61         0.36        14.04         2.96         9.07        26.50 
TCGA-BA-5151 TCGA-BA-5556 TCGA-BA-6868 TCGA-BA-6872 TCGA-BA-7269 TCGA-BA-A6DB 
       23.74        23.84        15.52        12.62        41.85         7.10 
TCGA-BA-A6DG TCGA-BA-A6DI TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-7861 TCGA-BB-7862 
        2.27        11.05         9.14         4.80        22.42        36.72 
TCGA-BB-7872 TCGA-BB-A5HY TCGA-C9-A47Z TCGA-CN-4728 TCGA-CN-4730 TCGA-CN-4731 
       38.40        10.55         6.28        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-5360 TCGA-CN-5363 
       73.61        13.05        46.32        12.39        71.31         8.32 
TCGA-CN-5366 TCGA-CN-5374 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6020 TCGA-CN-6988 
       11.84        56.94        48.00        23.90         6.74        10.45 
TCGA-CN-6989 TCGA-CN-A63T TCGA-CN-A63U TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-6220 
       32.22         7.40        31.69        70.45        62.37        32.38 
TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7069 
       46.95        56.58        13.25        38.76        64.87        41.88 
TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CE TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 
       44.48        23.24        29.49        31.23        84.23        11.77 
TCGA-CR-6467 TCGA-CR-6484 TCGA-CR-6488 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7370 
       58.42        11.64        12.46        39.16        47.34         3.45 
TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7377 TCGA-CR-7380 TCGA-CR-7389 TCGA-CR-7392 
       24.95        29.23         9.17        19.92        12.89        46.85 
TCGA-CR-7399 TCGA-CR-7401 TCGA-CV-5430 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 
        5.95        35.41       139.43       108.95        76.24        19.20 
TCGA-CV-5442 TCGA-CV-5444 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5977 
       76.50        80.12        13.35        23.05        86.83        60.49 
TCGA-CV-5978 TCGA-CV-6003 TCGA-CV-6933 TCGA-CV-6937 TCGA-CV-6939 TCGA-CV-6940 
        7.07        54.74        90.12        20.52        21.90        26.43 
TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6954 TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6962 
       12.03        42.38        65.82         7.13         8.42         4.14 
TCGA-CV-7090 TCGA-CV-7095 TCGA-CV-7177 TCGA-CV-7178 TCGA-CV-7180 TCGA-CV-7242 
      172.67        18.81        21.80        71.21        10.75        36.00 
TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7255 TCGA-CV-7263 TCGA-CV-7416 
       31.36        26.20        17.13         2.10        18.41        25.08 
TCGA-CV-7421 TCGA-CV-7423 TCGA-CV-7429 TCGA-CV-7437 TCGA-CV-7438 TCGA-CV-A45R 
        0.07       100.57         3.52        16.64         6.38       180.16 
TCGA-CV-A45T TCGA-CV-A45U TCGA-CV-A45X TCGA-CV-A45Z TCGA-CV-A464 TCGA-CV-A465 
      159.65        35.47         6.51        48.20        56.61         7.07 
TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 
       35.34        29.79         3.62        21.24        23.47        19.92 
TCGA-CX-7086 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6825 TCGA-D6-8569 TCGA-D6-A4ZB 
       18.84        25.41         9.60        16.14        25.32        12.36 
TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-DQ-5624 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-F7-A50J 
       13.94        12.10        58.45        20.45        37.58        31.13 
TCGA-F7-A61S TCGA-H7-8501 TCGA-HD-7753 TCGA-HD-7831 TCGA-HD-8314 TCGA-HD-A634 
       18.94        15.16        28.47        21.93        22.03         4.27 
TCGA-HD-A6HZ TCGA-IQ-7630 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61I 
        3.65        15.95        14.50        37.71        11.84         0.07 
TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A6SH TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67G 
        5.29        13.68        15.48        30.05         1.84         6.25 
TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-MZ-A7D7 TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A6T0 
       15.42         7.13        17.98        15.78        71.74        19.00 
TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-QK-A652 TCGA-QK-A6IG TCGA-QK-A6IJ 
       18.97         2.04        29.00        21.21         7.30        12.72 
TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z9 TCGA-T2-A6WZ TCGA-T3-A92M 
       21.07        19.73        12.89        14.76        15.91        13.71 
TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A71A TCGA-UF-A71E TCGA-UF-A7J9 
       13.55        13.25        20.35         2.83        49.45        44.65 
TCGA-UF-A7JA TCGA-UF-A7JF TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-WA-A7GZ TCGA-KU-A66T 
       74.47        55.43        18.05        13.94        20.55        18.15 

$`20P GAIN WILD-TYPE`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-6871 TCGA-BA-A4IG TCGA-BA-A4II 
        9.30        37.28        20.48         3.55        28.11        30.18 
TCGA-CN-4727 TCGA-CN-6021 TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-A6V1 TCGA-CN-A6V3 
       51.29         9.07        35.05        32.48        19.82        24.39 
TCGA-CQ-5323 TCGA-CQ-6221 TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CR-6472 TCGA-CR-6478 
       48.20        32.88        70.13        43.04        34.52         6.02 
TCGA-CX-7219 TCGA-DQ-5629 TCGA-DQ-7589 TCGA-DQ-7593 TCGA-H7-A6C5 TCGA-HD-8634 
       34.36        30.94        46.32        40.24        21.11        12.66 
TCGA-HD-8635 TCGA-UF-A71D TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-5152 
       22.85        48.03         3.35        15.19        13.64        42.35 
TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5558 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6873 
       57.93        17.10        65.59        21.17        14.83         4.01 
TCGA-BA-A4IF TCGA-BA-A4IH TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DD TCGA-BA-A6DE 
       29.42        20.45        27.95        11.54         5.69        14.47 
TCGA-BA-A6DF TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 
        7.82        13.38        20.48        16.41         6.15       105.90 
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-8596 TCGA-BB-8601 TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO 
       24.66        71.05        20.52        27.19        12.92         8.81 
TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4729 
       12.69        48.76        55.86        38.04         4.67        12.89 
TCGA-CN-4735 TCGA-CN-5355 TCGA-CN-5358 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5367 
       57.11        42.02         8.58        16.21        11.54        11.57 
TCGA-CN-5369 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6016 
       12.49         8.52        52.08        50.07        30.67        47.44 
TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 
       28.04        19.07        34.13        38.89         3.68        17.42 
TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B 
       11.74        35.01        25.41        23.57        17.29        29.72 
TCGA-CN-A49C TCGA-CN-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-A6UY TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5324 TCGA-CQ-5325 
        2.70        23.44        20.88        19.53        52.37        21.50 
TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 
        2.93        54.58        45.99        10.42        11.21         4.24 
TCGA-CQ-6218 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-7065 TCGA-CQ-7071 TCGA-CQ-7072 
       41.19         4.24        14.99        53.52        43.10        77.56 
TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CR-5248 TCGA-CR-5249 
       29.36        33.60        14.14        12.46        54.67        37.87 
TCGA-CR-5250 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 
       26.27        50.01        39.52        36.99        18.54        16.90 
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-7374 
        9.27        47.18        40.93        35.84         3.09         0.99 
TCGA-CR-7376 TCGA-CR-7379 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 
       31.96        34.06        26.17        17.13        32.78        47.01 
TCGA-CR-7388 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 
       27.06        49.58        30.02        32.65        44.25        30.58 
TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5431 TCGA-CV-5432 
       24.79         5.13        29.95        48.39        17.16       129.21 
TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5443 TCGA-CV-5966 TCGA-CV-5976 
       17.95       107.51        94.88        91.53        17.92        48.59 
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-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6950 
        5.46         4.73        11.24       140.78        19.79        15.09 
TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6955 TCGA-CV-6960 TCGA-CV-6961 
       30.08         6.08        53.95        10.98        28.34         2.50 
TCGA-CV-7089 TCGA-CV-7091 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 
       64.83       111.16        12.66         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 
       89.65        18.97        95.34         4.96        11.87        47.97 
TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7407 TCGA-CV-7409 TCGA-CV-7410 TCGA-CV-7411 
       49.71        57.47        35.54        17.85       210.97        89.33 
TCGA-CV-7413 TCGA-CV-7414 TCGA-CV-7415 TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7424 
        9.67         0.46        22.85        25.94        34.09        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-7435 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45Q 
        7.17       153.86        22.19        27.98        21.01       169.38 
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-7085 TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6823 TCGA-D6-6824 
       10.42        10.55        51.12        13.25        23.05         2.53 
TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-A4Z9 TCGA-D6-A6EK TCGA-D6-A6EM 
       11.44        18.67        24.95        17.72        28.77         7.63 
TCGA-D6-A6EN TCGA-D6-A6EO TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5625 TCGA-DQ-5630 
       22.59        24.95        12.79        23.34        37.25        33.86 
TCGA-DQ-5631 TCGA-DQ-7590 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 
       18.02        46.45        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-A623 TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8502 
       17.85        11.80        20.25        12.43        13.38        15.06 
TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7754 TCGA-HD-7832 TCGA-HD-7917 TCGA-HD-8224 
       20.94        33.76        25.74        27.48        27.48        14.66 
TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7631 TCGA-IQ-A61H 
        0.36        13.84         6.90        34.75        38.53        37.41 
TCGA-IQ-A61J TCGA-IQ-A61O TCGA-IQ-A6SG TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W 
       33.57        13.84        19.04        19.27        10.75        14.37 
TCGA-MT-A51X TCGA-MT-A67F TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5QE TCGA-P3-A5QF 
        7.96        12.62        16.08        29.92        51.25        10.85 
TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T2 TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-P3-A6T8 
       36.82        47.01        75.55        12.99        16.01        13.15 
TCGA-QK-A64Z TCGA-QK-A6IF TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6V9 TCGA-QK-A8Z8 
       21.07        23.15        21.47         9.34        27.39         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-A6X0 TCGA-T2-A6X2 TCGA-T3-A92N TCGA-UF-A718 TCGA-UF-A719 
        6.87         7.10        32.45         3.12        64.80        54.67 
TCGA-UF-A71B TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JH TCGA-UF-A7JO TCGA-UF-A7JS 
       49.51        17.95        24.30        29.46        20.75        22.36 
TCGA-UF-A7JT TCGA-UP-A6WW TCGA-WA-A7H4 TCGA-KU-A66S 
       32.65        17.03        14.56        13.35 

  20P GAIN MUTATED 20P GAIN WILD-TYPE 
              0.07               0.36 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
            180.16             210.97 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
            20.485             21.485 
[1] "0.1 - 180.2 (20.5)" "0.4 - 211.0 (21.5)"
[1] "hr=" "1"  
D36V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  20P GAIN MUTATED        12       24        36        94         5         0
  20P GAIN WILD-TYPE      15       52        46       158         7         1
D36V3, multiclass
           clus
vv          20P GAIN MUTATED 20P GAIN WILD-TYPE
  STAGE I                 12                 15
  STAGE II                24                 52
  STAGE III               36                 46
  STAGE IVA               94                158
  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  45  38  69
  20P GAIN WILD-TYPE    29  92  62 104
D36V4, multiclass
       clus
vv      20P GAIN MUTATED 20P GAIN WILD-TYPE
  T0+T1               21                 29
  T2                  45                 92
  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    61  34  62   3
  20P GAIN WILD-TYPE 118  34 106   5
D36V5, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  N0               61                118
  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    77   0
  20P GAIN WILD-TYPE 113   1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     77    0
  20P GAIN WILD-TYPE  113    1
   clus
vv  20P GAIN MUTATED 20P GAIN WILD-TYPE
  0               77                113
  1                0                  1
[1] 2 2
[1] FALSE
D36V7, binary
                    cls
clus                   0   1
  20P GAIN MUTATED    50 142
  20P GAIN WILD-TYPE  90 240
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     50  142
  20P GAIN WILD-TYPE   90  240
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  FEMALE               50                 90
  MALE                142                240
[1] 2 2
[1] FALSE
D36V8, binary
                    cls
clus                   0   1
  20P GAIN MUTATED    60 110
  20P GAIN WILD-TYPE 102 191
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     60  110
  20P GAIN WILD-TYPE  102  191
     clus
vv    20P GAIN MUTATED 20P GAIN WILD-TYPE
  NO                60                102
  YES              110                191
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD & NECK SQUAMOUS CELL CARCINOMA
  20P GAIN MUTATED                                   188
  20P GAIN WILD-TYPE                                 323
                    vv
clus                 HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  20P GAIN MUTATED                                                   4
  20P GAIN WILD-TYPE                                                 6
                    vv
clus                 HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  20P GAIN MUTATED                                                           0
  20P GAIN WILD-TYPE                                                         1
D36V9, multiclass
                                                           clus
vv                                                          20P GAIN MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                    188
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        4
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                0
                                                           clus
vv                                                          20P GAIN WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                      323
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                          6
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                  1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V10, continuous
D36V11, continuous
D36V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  20P GAIN MUTATED                                  1     4
  20P GAIN WILD-TYPE                                1     7
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  20P GAIN MUTATED                          20   159
  20P GAIN WILD-TYPE                        28   287
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                                         159                287
[1] 4 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    13 162
  20P GAIN WILD-TYPE  13 297
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     13  162
  20P GAIN WILD-TYPE   13  297
                        clus
vv                       20P GAIN MUTATED 20P GAIN WILD-TYPE
  HISPANIC OR LATINO                   13                 13
  NOT HISPANIC OR LATINO              162                297
[1] 2 2
[1] FALSE

Clustering(37) Variable = 20Q GAIN MUTATION ANALYSIS
D37V1, survival
                    sevent
clus2                  0   1
  20Q GAIN MUTATED   117  87
  20Q GAIN WILD-TYPE 184 132
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               204                316 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                87                132 
$`20Q GAIN MUTATED`
TCGA-BA-4075 TCGA-BB-A5HU TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-A6V3 
        9.30        25.71         9.24        52.08        11.08        24.39 
TCGA-CQ-7067 TCGA-CQ-A4C7 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-UF-A71D TCGA-UF-A7JV 
       16.73        11.61        14.04        46.32        48.03         2.96 
TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5556 TCGA-BA-6868 TCGA-BA-6872 
        9.07        26.50        23.74        23.84        15.52        12.62 
TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A6DB TCGA-BA-A6DG TCGA-BA-A6DI TCGA-BB-4225 
       41.85        29.42         7.10         2.27        11.05         4.80 
TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7864 TCGA-BB-7872 TCGA-BB-A5HY TCGA-C9-A47Z 
       22.42        36.72        50.20        38.40        10.55         6.28 
TCGA-CN-4725 TCGA-CN-4728 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4736 
       38.04        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-5363 TCGA-CN-5366 TCGA-CN-5374 TCGA-CN-6011 
       46.32        12.39         8.32        11.84        56.94        30.67 
TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6018 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6994 
       48.00        23.90        19.07        10.45        32.22        38.89 
TCGA-CN-6995 TCGA-CN-A49A TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A6UY TCGA-CQ-5329 
        3.68        17.29         7.40        31.69        23.44        70.45 
TCGA-CQ-5330 TCGA-CQ-6220 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6229 
       62.37        32.38        46.95        56.58        13.25        38.76 
TCGA-CQ-7064 TCGA-CQ-7069 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CE 
       64.87        41.88        77.56        44.48        23.24        29.49 
TCGA-CQ-A4CG TCGA-CR-5247 TCGA-CR-6467 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6484 
       14.14        11.77        58.42        18.54        16.90        11.64 
TCGA-CR-6488 TCGA-CR-6493 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7372 TCGA-CR-7373 
       12.46         9.27        39.16        47.34        24.95        29.23 
TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7383 TCGA-CR-7389 TCGA-CR-7392 
        9.17        34.06        19.92        17.13        12.89        46.85 
TCGA-CR-7401 TCGA-CV-5430 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 
       35.41       139.43       129.21       108.95        76.24        19.20 
TCGA-CV-5442 TCGA-CV-5444 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-6003 TCGA-CV-6933 
       76.50        80.12        60.49         7.07        54.74        90.12 
TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6940 TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6951 
        5.46        20.52        26.43        12.03        42.38        30.08 
TCGA-CV-6954 TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-6962 TCGA-CV-7090 
       65.82         7.13         8.42        28.34         4.14       172.67 
TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7177 TCGA-CV-7178 TCGA-CV-7180 TCGA-CV-7242 
       18.81        12.66        21.80        71.21        10.75        36.00 
TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7255 TCGA-CV-7263 TCGA-CV-7409 
       31.36        26.20        17.13         2.10        18.41        17.85 
TCGA-CV-7416 TCGA-CV-7421 TCGA-CV-7423 TCGA-CV-7429 TCGA-CV-7437 TCGA-CV-7438 
       25.08         0.07       100.57         3.52        16.64         6.38 
TCGA-CV-A45R TCGA-CV-A45U TCGA-CV-A45X TCGA-CV-A45Z TCGA-CV-A464 TCGA-CV-A465 
      180.16        35.47         6.51        48.20        56.61         7.07 
TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 
       35.34        29.79         3.62        21.24        23.47        19.92 
TCGA-CX-7086 TCGA-D6-6516 TCGA-D6-6823 TCGA-D6-6825 TCGA-D6-8569 TCGA-D6-A6EP 
       18.84        25.41        23.05        16.14        25.32        13.94 
TCGA-DQ-5624 TCGA-DQ-5631 TCGA-DQ-7592 TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A623 
       58.45        18.02        37.58        31.13        18.94        20.25 
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-7630 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61I TCGA-IQ-A61K 
       15.95        14.50        37.71        11.84         0.07         5.29 
TCGA-IQ-A61L TCGA-IQ-A6SH TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D 
       13.68        15.48        14.37         7.96        30.05         1.84 
TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-MZ-A7D7 TCGA-P3-A5Q6 TCGA-P3-A5QA 
        6.25        15.42         7.13        17.98        15.78        71.74 
TCGA-P3-A6T0 TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-QK-A652 TCGA-QK-A6IG 
       19.00        18.97         2.04        29.00        21.21         7.30 
TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z9 
       12.72        27.39        21.07        19.73        12.89        14.76 
TCGA-T2-A6WZ TCGA-T3-A92M TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-UF-A71E TCGA-UF-A7J9 
       15.91        13.71        13.55        13.25        49.45        44.65 
TCGA-UF-A7JA TCGA-UF-A7JF TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-WA-A7GZ TCGA-KU-A66T 
       74.47        55.43        18.05        13.94        20.55        18.15 

$`20Q GAIN WILD-TYPE`
TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4IG TCGA-BA-A4II 
       37.28        20.48        68.48         3.55        28.11        30.18 
TCGA-CN-4727 TCGA-CN-6021 TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-A6V1 TCGA-CQ-5323 
       51.29         9.07        35.05        32.48        19.82        48.20 
TCGA-CQ-6221 TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CR-6472 TCGA-CR-6478 TCGA-CX-7082 
       32.88        70.13        43.04        34.52         6.02         0.36 
TCGA-CX-7219 TCGA-DQ-5629 TCGA-DQ-7593 TCGA-H7-A6C5 TCGA-HD-8634 TCGA-HD-8635 
       34.36        30.94        40.24        21.11        12.66        22.85 
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 
        3.35        15.19        13.64        42.35        57.93        17.10 
TCGA-BA-5558 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6873 TCGA-BA-A4IH TCGA-BA-A6D8 
       65.59        21.17        14.83         4.01        20.45        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-4729 TCGA-CN-4735 TCGA-CN-5355 TCGA-CN-5358 TCGA-CN-5360 
        4.67        12.89        57.11        42.02         8.58        71.31 
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-6010 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6996 
       50.07        47.44        28.04        34.13         6.74        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-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-A6V6 TCGA-CN-A6V7 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 
       20.88        19.53        52.37        21.50         2.93        54.58 
TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6227 
       45.99        10.42        11.21         4.24        41.19         4.24 
TCGA-CQ-6228 TCGA-CQ-7065 TCGA-CQ-7071 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CH 
       14.99        53.52        43.10        29.36        33.60        12.46 
TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6470 
       31.23        84.23        54.67        37.87        26.27        50.01 
TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6487 
       39.52        36.99        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        49.58        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 
       24.79         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        94.88        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 
       89.65        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 
       49.71        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-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-D6-6826 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-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q 
        7.63        22.59        24.95        12.10        12.79        23.34 
TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7594 TCGA-DQ-7595 
       37.25        33.86        46.45        20.45        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-A624 TCGA-H7-7774 
       24.95         0.46        17.85        11.80        12.43        13.38 
TCGA-H7-8502 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7754 TCGA-HD-7832 TCGA-HD-7917 
       15.06        20.94        33.76        25.74        27.48        27.48 
TCGA-HD-8224 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7631 
       14.66         0.36        13.84         6.90        34.75        38.53 
TCGA-IQ-A61H TCGA-IQ-A61J TCGA-IQ-A61O TCGA-IQ-A6SG TCGA-KU-A6H7 TCGA-KU-A6H8 
       37.41        33.57        13.84        19.04        19.27        10.75 
TCGA-MT-A67F TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW 
       12.62        16.08        29.92        51.25        10.85        36.82 
TCGA-P3-A6SX TCGA-P3-A6T2 TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A64Z 
       47.01        75.55        12.99        16.01        13.15        21.07 
TCGA-QK-A6IF TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A8Z8 TCGA-QK-A8ZA TCGA-QK-A8ZB 
       23.15        21.47         9.34         5.62        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-A92N TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A 
       32.45         3.12        20.35        64.80        54.67         2.83 
TCGA-UF-A71B TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JH TCGA-UF-A7JO TCGA-UF-A7JS 
       49.51        17.95        24.30        29.46        20.75        22.36 
TCGA-UF-A7JT TCGA-UP-A6WW TCGA-WA-A7H4 TCGA-KU-A66S 
       32.65        17.03        14.56        13.35 

  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
              0.07               0.36 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
            180.16             210.97 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
             20.55              21.19 
[1] "0.1 - 180.2 (20.6)" "0.4 - 211.0 (21.2)"
[1] "hr=" "1"  
D37V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  20Q GAIN MUTATED        14       28        35        99         7         0
  20Q GAIN WILD-TYPE      13       48        47       153         5         1
D37V3, multiclass
           clus
vv          20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  STAGE I                 14                 13
  STAGE II                28                 48
  STAGE III               35                 47
  STAGE IVA               99                153
  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  48  40  73
  20Q GAIN WILD-TYPE    26  89  60 100
D37V4, multiclass
       clus
vv      20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  T0+T1               24                 26
  T2                  48                 89
  T3                  40                 60
  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    71  30  65   4
  20Q GAIN WILD-TYPE 108  38 103   4
D37V5, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  N0               71                108
  N1               30                 38
  N2               65                103
  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    81   0
  20Q GAIN WILD-TYPE 109   1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     81    0
  20Q GAIN WILD-TYPE  109    1
   clus
vv  20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  0               81                109
  1                0                  1
[1] 2 2
[1] FALSE
D37V7, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED    53 151
  20Q GAIN WILD-TYPE  87 231
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     53  151
  20Q GAIN WILD-TYPE   87  231
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  FEMALE               53                 87
  MALE                151                231
[1] 2 2
[1] FALSE
D37V8, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED    66 115
  20Q GAIN WILD-TYPE  96 186
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     66  115
  20Q GAIN WILD-TYPE   96  186
     clus
vv    20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  NO                66                 96
  YES              115                186
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD & NECK SQUAMOUS CELL CARCINOMA
  20Q GAIN MUTATED                                   201
  20Q GAIN WILD-TYPE                                 310
                    vv
clus                 HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  20Q GAIN MUTATED                                                   3
  20Q GAIN WILD-TYPE                                                 7
                    vv
clus                 HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  20Q GAIN MUTATED                                                           0
  20Q GAIN WILD-TYPE                                                         1
D37V9, multiclass
                                                           clus
vv                                                          20Q GAIN MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                    201
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        3
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                0
                                                           clus
vv                                                          20Q GAIN WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                      310
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                          7
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                  1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V10, continuous
D37V11, continuous
D37V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  20Q GAIN MUTATED                                  1     4
  20Q GAIN WILD-TYPE                                1     7
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  20Q GAIN MUTATED                          23   168
  20Q GAIN WILD-TYPE                        25   278
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                                         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"
D37V14, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED    12 175
  20Q GAIN WILD-TYPE  14 284
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     12  175
  20Q GAIN WILD-TYPE   14  284
                        clus
vv                       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   12                 14
  NOT HISPANIC OR LATINO              175                284
[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 280 205
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                35                485 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                14                205 
$`21Q GAIN MUTATED`
TCGA-CN-4727 TCGA-CN-6024 TCGA-CN-6992 TCGA-CR-6478 TCGA-BA-6873 TCGA-BA-A6DI 
       51.29        11.08        35.05         6.02         4.01        11.05 
TCGA-BA-A6DL TCGA-BB-4225 TCGA-CN-4729 TCGA-CN-4740 TCGA-CN-5356 TCGA-CN-6995 
       20.48         4.80        12.89        27.58        46.32         3.68 
TCGA-CN-A63U TCGA-CR-6467 TCGA-CR-7402 TCGA-CV-5430 TCGA-CV-5432 TCGA-CV-5441 
       31.69        58.42        29.95       139.43       129.21        94.88 
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-BA-4075 TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4IG 
        9.30        37.28        20.48        68.48         3.55        28.11 
TCGA-BA-A4II TCGA-BB-A5HU TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6997 
       30.18        25.71         9.07         9.24        52.08        32.48 
TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-6221 TCGA-CQ-7063 TCGA-CQ-7067 
       19.82        24.39        48.20        32.88        70.13        16.73 
TCGA-CQ-7068 TCGA-CQ-A4C7 TCGA-CR-6472 TCGA-CX-7082 TCGA-CX-7219 TCGA-DQ-5629 
       43.04        11.61        34.52         0.36        34.36        30.94 
TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7593 TCGA-H7-A6C5 TCGA-HD-8634 TCGA-HD-8635 
       14.04        46.32        40.24        21.11        12.66        22.85 
TCGA-UF-A71D TCGA-UF-A7JV TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4078 
       48.03         2.96         3.35        15.19        13.64         9.07 
TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 
       26.50        23.74        42.35        57.93        17.10        23.84 
TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6872 TCGA-BA-7269 
       65.59        15.52        21.17        14.83        12.62        41.85 
TCGA-BA-A4IF TCGA-BA-A4IH TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD 
       29.42        20.45        27.95        11.54         7.10         5.69 
TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-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-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 
      105.90         9.14         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-A5HY TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO 
       71.05        20.52        10.55        27.19        12.92         8.81 
TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-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-6988 TCGA-CN-6989 TCGA-CN-6994 
       19.07        34.13         6.74        10.45        32.22        38.89 
TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A 
       17.42        11.74        35.01        25.41        23.57        17.29 
TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-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-A6V6 TCGA-CN-A6V7 
        4.41        12.07         2.70        23.44        20.88        19.53 
TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 
       52.37        21.50         2.93        54.58        70.45        62.37 
TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6220 
       45.99        10.42        11.21         4.24        41.19        32.38 
TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 
       46.95        56.58        13.25         4.24        14.99        38.76 
TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 
       64.87        53.52        41.88        43.10        77.56        44.48 
TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH 
       23.24        29.36        33.60        29.49        14.14        12.46 
TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 
       31.23        84.23        11.77        54.67        37.87        26.27 
TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6480 
       50.01        39.52        36.99        18.54        16.90        11.90 
TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 
       10.22        11.34        11.64         7.69        12.46        22.78 
TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 
       15.75         9.27        47.18        39.16        47.34        40.93 
TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 
       35.84         3.45         3.09        24.95        29.23         0.99 
TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7383 
       31.96         9.17        34.06        19.92        26.17        17.13 
TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 
       32.78        47.01        27.06        12.89        49.58        30.02 
TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 
       46.85        32.65        44.25        30.58        24.79         5.13 
TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7404 TCGA-CV-5431 TCGA-CV-5434 TCGA-CV-5435 
        5.95        35.41        48.39        17.16       108.95        76.24 
TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 
       19.20        17.95       107.51        76.50        91.53        80.12 
TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 
       17.92        13.35        23.05        86.83        48.59        60.49 
TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-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-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       172.67 
TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 
      111.16        18.81        12.66         7.99         9.01         5.26 
TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-7178 TCGA-CV-7180 
        1.84        52.31        12.92        21.80        71.21        10.75 
TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 
      130.88        77.16         4.73        89.65        36.00        31.36 
TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 
       26.20        18.97        17.13        95.34         4.96        11.87 
TCGA-CV-7254 TCGA-CV-7255 TCGA-CV-7261 TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7407 
       47.97         2.10        49.71        18.41        57.47        35.54 
TCGA-CV-7409 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7416 TCGA-CV-7418 
       17.85       210.97        89.33         9.67        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-7434 TCGA-CV-7435 
       54.94         3.52        16.27        84.49         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-A45R TCGA-CV-A45T TCGA-CV-A45U TCGA-CV-A45V TCGA-CV-A45W TCGA-CV-A45X 
      180.16       159.65        35.47         1.05        45.96         6.51 
TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A463 TCGA-CV-A464 TCGA-CV-A465 
       88.87        48.20        60.43         0.76        56.61         7.07 
TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JM TCGA-CV-A6JN TCGA-CV-A6JO 
       15.25         5.98        35.34         6.38        29.79         6.48 
TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 
       28.01         3.62        21.24        23.47        19.92        22.52 
TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6516 
       10.42        10.55        18.84        51.12        13.25        25.41 
TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 
        9.60        23.05         2.53        16.14        11.44        18.67 
TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM 
       24.95        25.32        17.72        12.36        28.77         7.63 
TCGA-D6-A6EN TCGA-D6-A6EO TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 
       22.59        24.95        12.10        12.79        23.34        58.45 
TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7590 TCGA-DQ-7592 TCGA-DQ-7594 
       37.25        33.86        18.02        46.45        37.58        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-A76A TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 
       20.94        33.76        28.47        25.74        21.93        27.48 
TCGA-HD-7917 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 
       27.48         0.36        13.84         4.27         3.65         6.90 
TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G 
       34.75        15.95        38.53        14.50        37.71        11.84 
TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A6SG 
       37.41         0.07        33.57         5.29        13.68        19.04 
TCGA-IQ-A6SH TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A 
       15.48        19.27        10.75        14.37         7.96        30.05 
TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 
        1.84        12.62         6.25        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-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-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z8 
        9.34        12.72        27.39        19.73        12.89         5.62 
TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-RS-A6TO 
       14.76        12.20        17.82        15.32         8.32        12.72 
TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-T3-A92M 
       16.96         6.87        15.91         7.10        32.45        13.71 
TCGA-T3-A92N TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A 
        3.12        13.25        20.35        64.80        54.67         2.83 
TCGA-UF-A71B TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF 
       49.51        49.45        44.65        17.95        24.30        55.43 
TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT 
       29.46        18.05        13.94        20.75        22.36        32.65 
TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 TCGA-KU-A66S TCGA-KU-A66T 
       17.03        20.55        14.56        13.35        18.15 

  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 
             20.48              21.17 
[1] "0.5 - 139.4 (20.5)" "0.1 - 211.0 (21.2)"
[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       233        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                233
  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 180   1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED     10    0
  21Q GAIN WILD-TYPE  180    1
   clus
vv  21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  0               10                180
  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  22
  21Q GAIN WILD-TYPE 152 279
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED     10   22
  21Q GAIN WILD-TYPE  152  279
     clus
vv    21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  NO                10                152
  YES               22                279
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD & NECK SQUAMOUS CELL CARCINOMA
  21Q GAIN MUTATED                                    32
  21Q GAIN WILD-TYPE                                 479
                    vv
clus                 HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  21Q GAIN MUTATED                                                   2
  21Q GAIN WILD-TYPE                                                 8
                    vv
clus                 HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  21Q GAIN MUTATED                                                           1
  21Q GAIN WILD-TYPE                                                         0
D38V9, multiclass
                                                           clus
vv                                                          21Q GAIN MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                     32
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        2
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                1
                                                           clus
vv                                                          21Q GAIN WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                      479
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                          8
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                  0
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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 248 160
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
               112                408 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                59                160 
$`22Q GAIN MUTATED`
TCGA-BA-5557 TCGA-BB-A5HU TCGA-CN-6024 TCGA-CQ-6221 TCGA-CQ-7067 TCGA-CX-7219 
       20.48        25.71        11.08        32.88        16.73        34.36 
TCGA-DQ-5629 TCGA-DQ-7589 TCGA-HD-8634 TCGA-BA-4074 TCGA-BA-4078 TCGA-BA-5555 
       30.94        46.32        12.66        15.19         9.07        17.10 
TCGA-BA-7269 TCGA-BA-A6DA TCGA-BA-A6DI TCGA-BA-A6DL TCGA-BB-7870 TCGA-BB-8596 
       41.85        11.54        11.05        20.48        66.28        71.05 
TCGA-BB-8601 TCGA-C9-A480 TCGA-CN-4728 TCGA-CN-4737 TCGA-CN-4742 TCGA-CN-5356 
       20.52        12.69        56.68        20.55        13.05        46.32 
TCGA-CN-5367 TCGA-CN-6010 TCGA-CN-6012 TCGA-CN-6016 TCGA-CN-6989 TCGA-CN-6994 
       11.57        50.07        48.00        47.44        32.22        38.89 
TCGA-CN-A498 TCGA-CN-A49A TCGA-CQ-5326 TCGA-CQ-5332 TCGA-CQ-6220 TCGA-CQ-6224 
       25.41        17.29         2.93        10.42        32.38        56.58 
TCGA-CQ-6225 TCGA-CQ-6229 TCGA-CQ-7069 TCGA-CQ-7072 TCGA-CR-6471 TCGA-CR-6474 
       13.25        38.76        41.88        77.56        39.52        18.54 
TCGA-CR-6482 TCGA-CR-7365 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7383 TCGA-CR-7389 
       11.34        39.16         3.45         3.09        17.13        12.89 
TCGA-CR-7390 TCGA-CR-7397 TCGA-CR-7401 TCGA-CV-5430 TCGA-CV-5432 TCGA-CV-5434 
       49.58        24.79        35.41       139.43       129.21       108.95 
TCGA-CV-5970 TCGA-CV-5978 TCGA-CV-6933 TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6950 
       13.35         7.07        90.12        26.43        11.24        15.09 
TCGA-CV-7090 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7178 TCGA-CV-7245 TCGA-CV-7248 
      172.67         5.26         1.84        71.21        26.20        17.13 
TCGA-CV-7250 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7407 TCGA-CV-7422 TCGA-CV-7424 
       95.34        47.97        49.71        35.54        34.09        14.89 
TCGA-CV-7429 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7437 TCGA-CV-7440 TCGA-CV-A45W 
        3.52        19.76         7.17        16.64        22.19        45.96 
TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A6JE TCGA-CV-A6JM TCGA-CX-A4AQ TCGA-D6-A4ZB 
       88.87        48.20        35.34         6.38        51.12        12.36 
TCGA-D6-A6EP TCGA-DQ-5625 TCGA-HD-7753 TCGA-HD-7831 TCGA-HD-7917 TCGA-IQ-A61H 
       13.94        37.25        28.47        21.93        27.48        37.41 
TCGA-IQ-A61L TCGA-IQ-A61O TCGA-IQ-A6SH TCGA-MT-A51X TCGA-MZ-A5BI TCGA-MZ-A7D7 
       13.68        13.84        15.48         7.96         7.13        17.98 
TCGA-P3-A5Q6 TCGA-P3-A5QF TCGA-P3-A6SX TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T5 
       15.78        10.85        47.01        18.97         2.04        29.00 
TCGA-QK-A8Z7 TCGA-QK-A8ZA TCGA-T2-A6WZ TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B 
       12.89        12.20        15.91        54.67         2.83        49.51 
TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JD TCGA-KU-A66T 
       49.45        44.65        24.30        18.15 

$`22Q GAIN WILD-TYPE`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4IG TCGA-BA-A4II 
        9.30        37.28        68.48         3.55        28.11        30.18 
TCGA-CN-4727 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6992 TCGA-CN-6997 
       51.29         9.07         9.24        52.08        35.05        32.48 
TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CQ-A4C7 
       19.82        24.39        48.20        70.13        43.04        11.61 
TCGA-CR-6472 TCGA-CR-6478 TCGA-CX-7082 TCGA-DQ-7588 TCGA-DQ-7593 TCGA-H7-A6C5 
       34.52         6.02         0.36        14.04        40.24        21.11 
TCGA-HD-8635 TCGA-UF-A71D TCGA-UF-A7JV TCGA-4P-AA8J TCGA-BA-4076 TCGA-BA-5149 
       22.85        48.03         2.96         3.35        13.64        26.50 
TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-6868 
       23.74        42.35        57.93        23.84        65.59        15.52 
TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-A4IF TCGA-BA-A4IH 
       21.17        14.83        12.62         4.01        29.42        20.45 
TCGA-BA-A6D8 TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG 
       27.95         7.10         5.69        14.47         7.82         2.27 
TCGA-BA-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         4.80 
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-7872 TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-BB-A6UM 
       44.98        24.66        38.40        10.55        27.19        12.92 
TCGA-BB-A6UO TCGA-C9-A47Z TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 
        8.81         6.28        48.76        55.86        38.04         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-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-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-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-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6988 TCGA-CN-6995 
       28.04        19.07        34.13         6.74        10.45         3.68 
TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A499 TCGA-CN-A49B TCGA-CN-A49C 
       17.42        11.74        35.01        23.57        29.72        21.21 
TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 
        7.40        31.69        22.32        12.39        16.57         4.41 
TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5324 
       12.07         2.70        23.44        20.88        19.53        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-7064 
        4.24        41.19        46.95         4.24        14.99        64.87 
TCGA-CQ-7065 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD 
       53.52        43.10        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-6473 
       54.67        37.87        26.27        58.42        50.01        36.99 
TCGA-CR-6477 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 
       16.90        11.90        10.22        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-7372 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 
       35.84        24.95        29.23         0.99        31.96         9.17 
TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 
       34.06        19.92        26.17        32.78        47.01        27.06 
TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7398 
       30.02        46.85        32.65        44.25        30.58         5.13 
TCGA-CR-7399 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5431 TCGA-CV-5435 TCGA-CV-5436 
        5.95        29.95        48.39        17.16        76.24        19.20 
TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 
       17.95       107.51        94.88        76.50        91.53        80.12 
TCGA-CV-5966 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5979 
       17.92        23.05        86.83        48.59        60.49        43.23 
TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6935 
       54.74        21.07        62.43         9.60         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-6962 
       10.98         7.13         8.42        28.34         2.50         4.14 
TCGA-CV-7089 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 
       64.83       111.16        18.81        12.66         7.99         9.01 
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-7242 TCGA-CV-7243 TCGA-CV-7247 TCGA-CV-7252 
        4.73        89.65        36.00        31.36        18.97         4.96 
TCGA-CV-7253 TCGA-CV-7255 TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7409 TCGA-CV-7410 
       11.87         2.10        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-7423 TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7430 
        0.07       100.57        56.48       156.49        54.94        16.27 
TCGA-CV-7432 TCGA-CV-7435 TCGA-CV-7438 TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45Q 
       84.49       153.86         6.38        27.98        21.01       169.38 
TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45U TCGA-CV-A45V TCGA-CV-A45X TCGA-CV-A460 
      180.16       159.65        35.47         1.05         6.51        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-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ 
       29.79         6.48        28.01         3.62        21.24        23.47 
TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-7086 TCGA-D6-6515 
       19.92        22.52        10.42        10.55        18.84        13.25 
TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 
       25.41         9.60        23.05         2.53        16.14        11.44 
TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-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        23.34        58.45 
TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7594 
       33.86        18.02        46.45        20.45        37.58        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-A76A TCGA-HD-7229 TCGA-HD-7754 TCGA-HD-7832 TCGA-HD-8224 TCGA-HD-8314 
       20.94        33.76        25.74        27.48        14.66        22.03 
TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-HL-7533 
        0.36        13.84         4.27         3.65         6.90        34.75 
TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61I 
       15.95        38.53        14.50        37.71        11.84         0.07 
TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A6SG TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W 
       33.57         5.29        19.04        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        27.39        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-A7JA 
        3.12        13.55        13.25        20.35        64.80        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 TCGA-WA-A7H4 TCGA-KU-A66S 
       22.36        32.65        17.03        20.55        14.56        13.35 

  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
              1.84               0.07 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
            172.67             210.97 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
             22.06              21.07 
[1] "1.8 - 172.7 (22.1)" "0.1 - 211.0 (21.1)"
[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       195        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                195
  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 155   1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED     35    0
  22Q GAIN WILD-TYPE  155    1
   clus
vv  22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  0               35                155
  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  66
  22Q GAIN WILD-TYPE 130 235
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED     32   66
  22Q GAIN WILD-TYPE  130  235
     clus
vv    22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  NO                32                130
  YES               66                235
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD & NECK SQUAMOUS CELL CARCINOMA
  22Q GAIN MUTATED                                   109
  22Q GAIN WILD-TYPE                                 402
                    vv
clus                 HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  22Q GAIN MUTATED                                                   2
  22Q GAIN WILD-TYPE                                                 8
                    vv
clus                 HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  22Q GAIN MUTATED                                                           1
  22Q GAIN WILD-TYPE                                                         0
D39V9, multiclass
                                                           clus
vv                                                          22Q GAIN MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                    109
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        2
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                1
                                                           clus
vv                                                          22Q GAIN WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                      402
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                          8
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                  0
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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    29  22
  XP GAIN WILD-TYPE 272 197
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               51               469 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               22               197 
$`XP GAIN MUTATED`
TCGA-BA-4075 TCGA-BA-4077 TCGA-CN-6023 TCGA-CQ-7067 TCGA-BA-7269 TCGA-BB-4223 
        9.30        37.28        52.08        16.73        41.85       105.90 
TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-7864 TCGA-CN-4740 TCGA-CN-4742 TCGA-CN-A6V6 
        4.80         4.41        50.20        27.58        13.05        20.88 
TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-7064 TCGA-CQ-A4CG TCGA-CR-6467 TCGA-CR-6488 
       54.58        70.45        64.87        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-6951 TCGA-CV-7250 TCGA-CV-7254 TCGA-CV-7407 TCGA-CV-7409 
       86.83        30.08        95.34        47.97        35.54        17.85 
TCGA-CV-7415 TCGA-CV-7416 TCGA-CV-7421 TCGA-CV-7435 TCGA-CV-A45X TCGA-CV-A6JM 
       22.85        25.08         0.07       153.86         6.51         6.38 
TCGA-D6-6823 TCGA-D6-A6EP TCGA-HD-7832 TCGA-HD-A6I0 TCGA-IQ-A61G TCGA-IQ-A61J 
       23.05        13.94        27.48         6.90        11.84        33.57 
TCGA-IQ-A6SH TCGA-P3-A5QA TCGA-P3-A6T5 TCGA-P3-A6T6 TCGA-QK-A8ZA TCGA-RS-A6TO 
       15.48        71.74        29.00        12.99        12.20        12.72 
TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-UF-A7JA 
       13.55        13.25        74.47 

$`XP GAIN WILD-TYPE`
TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4IG TCGA-BA-A4II TCGA-BB-A5HU 
       20.48        68.48         3.55        28.11        30.18        25.71 
TCGA-CN-4727 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6024 TCGA-CN-6992 TCGA-CN-6997 
       51.29         9.07         9.24        11.08        35.05        32.48 
TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-6221 TCGA-CQ-7063 TCGA-CQ-7068 
       19.82        24.39        48.20        32.88        70.13        43.04 
TCGA-CQ-A4C7 TCGA-CR-6472 TCGA-CR-6478 TCGA-CX-7082 TCGA-CX-7219 TCGA-DQ-5629 
       11.61        34.52         6.02         0.36        34.36        30.94 
TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7593 TCGA-H7-A6C5 TCGA-HD-8634 TCGA-HD-8635 
       14.04        46.32        40.24        21.11        12.66        22.85 
TCGA-UF-A71D TCGA-UF-A7JV TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4078 
       48.03         2.96         3.35        15.19        13.64         9.07 
TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 
       26.50        23.74        42.35        57.93        17.10        23.84 
TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6872 TCGA-BA-6873 
       65.59        15.52        21.17        14.83        12.62         4.01 
TCGA-BA-A4IF TCGA-BA-A4IH TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD 
       29.42        20.45        27.95        11.54         7.10         5.69 
TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DI TCGA-BA-A6DJ TCGA-BA-A6DL 
       14.47         7.82         2.27        11.05        13.38        20.48 
TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4224 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 
       16.41         6.15         9.14        18.38        22.42        36.72 
TCGA-BB-7863 TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 
       33.70        44.98        66.28        24.66        38.40        71.05 
TCGA-BB-8601 TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO TCGA-C9-A47Z 
       20.52        10.55        27.19        12.92         8.81         6.28 
TCGA-C9-A480 TCGA-CN-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-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4741 TCGA-CN-5355 TCGA-CN-5356 
       20.55        14.33        45.83        73.61        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-6988 TCGA-CN-6989 TCGA-CN-6994 
       19.07        34.13         6.74        10.45        32.22        38.89 
TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 
        3.68        17.42        11.74        35.01        25.41        23.57 
TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V 
       17.29        29.72        21.21         7.40        31.69        22.32 
TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY 
       12.39        16.57         4.41        12.07         2.70        23.44 
TCGA-CN-A6V7 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5330 TCGA-CQ-5331 
       19.53        52.37        21.50         2.93        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-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7065 
       56.58        13.25         4.24        14.99        38.76        53.52 
TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CB 
       41.88        43.10        77.56        44.48        23.24        29.36 
TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 
       33.60        29.49        12.46        31.23        84.23        11.77 
TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6473 
       54.67        37.87        26.27        50.01        39.52        36.99 
TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 
       18.54        16.90        11.90        10.22        11.34        11.64 
TCGA-CR-6487 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 
        7.69        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        49.58        30.02 
TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 
       46.85        32.65        44.25        30.58        24.79         5.13 
TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 
        5.95        35.41        29.95        48.39       139.43        17.16 
TCGA-CV-5432 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 
      129.21        76.24        19.20        17.95       107.51        94.88 
TCGA-CV-5443 TCGA-CV-5966 TCGA-CV-5971 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 
       91.53        17.92        23.05        48.59        60.49         7.07 
TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6933 
       43.23        54.74        21.07        62.43         9.60        90.12 
TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6939 
        2.14         9.70         5.46        20.52         4.73        21.90 
TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6948 
       26.43        11.24       140.78        19.79        12.03        42.38 
TCGA-CV-6950 TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-6955 TCGA-CV-6956 
       15.09         6.08        53.95        65.82        10.98         7.13 
TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7090 
        8.42        28.34         2.50         4.14        64.83       172.67 
TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 
      111.16        18.81        12.66         7.99         9.01         5.26 
TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-7178 TCGA-CV-7180 
        1.84        52.31        12.92        21.80        71.21        10.75 
TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 
      130.88        77.16         4.73        89.65        36.00        31.36 
TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7248 TCGA-CV-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 
       49.71        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-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-D6-6824 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-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 
       24.95        12.10        12.79        23.34        58.45        37.25 
TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7594 
       33.86        18.02        46.45        20.45        37.58        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-A76A TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7917 
       20.94        33.76        28.47        25.74        21.93        27.48 
TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ 
       14.66        22.03         0.36        13.84         4.27         3.65 
TCGA-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-IQ-A6SG TCGA-KU-A6H7 
        0.07         5.29        13.68        13.84        19.04        19.27 
TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F 
       10.75        14.37         7.96        30.05         1.84        12.62 
TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 
        6.25        15.42         7.13        16.08        17.98        29.92 
TCGA-P3-A5Q6 TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 
       15.78        51.25        10.85        36.82        47.01        19.00 
TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A64Z 
       75.55        18.97         2.04        16.01        13.15        21.07 
TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ 
       21.21        23.15         7.30        21.47         9.34        12.72 
TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8Z9 
       27.39        21.07        19.73        12.89         5.62        14.76 
TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ 
       17.82        15.32         8.32        16.96         6.87        15.91 
TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-T3-A92M TCGA-T3-A92N TCGA-TN-A7HL TCGA-UF-A718 
        7.10        32.45        13.71         3.12        20.35        64.80 
TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JC 
       54.67         2.83        49.51        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-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 TCGA-KU-A66S 
       22.36        32.65        17.03        20.55        14.56        13.35 
TCGA-KU-A66T 
       18.15 

  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 
            23.05             21.07 
[1] "0.1 - 153.9 (23.1)" "0.1 - 211.0 (21.1)"
[1] "hr=" "1.1"
D40V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  XP GAIN MUTATED         2        5         8        30         1         0
  XP GAIN WILD-TYPE      25       71        74       222        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              30               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
  XP GAIN MUTATED       2  15   8  22
  XP GAIN WILD-TYPE    48 122  92 151
D40V4, multiclass
       clus
vv      XP GAIN MUTATED XP GAIN WILD-TYPE
  T0+T1               2                48
  T2                 15               122
  T3                  8                92
  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
  XP GAIN MUTATED    13   8  20   1
  XP GAIN WILD-TYPE 166  60 148   7
D40V5, multiclass
    clus
vv   XP GAIN MUTATED XP GAIN WILD-TYPE
  N0              13               166
  N1               8                60
  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"
D40V6, binary
                   cls
clus                  0   1
  XP GAIN MUTATED    17   0
  XP GAIN WILD-TYPE 173   1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED     17    0
  XP GAIN WILD-TYPE  173    1
   clus
vv  XP GAIN MUTATED XP GAIN WILD-TYPE
  0              17               173
  1               0                 1
[1] 2 2
[1] FALSE
D40V7, binary
                   cls
clus                  0   1
  XP GAIN MUTATED    18  33
  XP GAIN WILD-TYPE 122 349
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED     18   33
  XP GAIN WILD-TYPE  122  349
        clus
vv       XP GAIN MUTATED XP GAIN WILD-TYPE
  FEMALE              18               122
  MALE                33               349
[1] 2 2
[1] FALSE
D40V8, binary
                   cls
clus                  0   1
  XP GAIN MUTATED    15  30
  XP GAIN WILD-TYPE 147 271
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED     15   30
  XP GAIN WILD-TYPE  147  271
     clus
vv    XP GAIN MUTATED XP GAIN WILD-TYPE
  NO               15               147
  YES              30               271
[1] 2 2
[1] FALSE
                   vv
clus                HEAD & NECK SQUAMOUS CELL CARCINOMA
  XP GAIN MUTATED                                    51
  XP GAIN WILD-TYPE                                 460
                   vv
clus                HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  XP GAIN MUTATED                                                   0
  XP GAIN WILD-TYPE                                                10
                   vv
clus                HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  XP GAIN MUTATED                                                           0
  XP GAIN WILD-TYPE                                                         1
D40V9, multiclass
                                                           clus
vv                                                          XP GAIN MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                    51
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       0
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT               0
                                                           clus
vv                                                          XP GAIN WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                     460
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        10
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                 1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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    42
  XP GAIN WILD-TYPE                        41   404
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                                         42               404
[1] 4 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  46
  XP GAIN WILD-TYPE  24 413
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED      2   46
  XP GAIN WILD-TYPE   24  413
                        clus
vv                       XP GAIN MUTATED XP GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                24
  NOT HISPANIC OR LATINO              46               413
[1] 2 2
[1] FALSE

Clustering(41) Variable = XQ GAIN MUTATION ANALYSIS
D41V1, survival
                   sevent
clus2                 0   1
  XQ GAIN MUTATED    48  48
  XQ GAIN WILD-TYPE 253 171
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               96               424 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               48               171 
$`XQ GAIN MUTATED`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BB-A5HU TCGA-CN-6023 TCGA-CQ-A4C7 TCGA-DQ-5629 
        9.30        37.28        25.71        52.08        11.61        30.94 
TCGA-BA-5149 TCGA-BA-6872 TCGA-BA-7269 TCGA-BB-4223 TCGA-BB-4225 TCGA-BB-4227 
       26.50        12.62        41.85       105.90         4.80         4.41 
TCGA-BB-A6UO TCGA-CN-4728 TCGA-CN-4737 TCGA-CN-4740 TCGA-CN-4742 TCGA-CN-5359 
        8.81        56.68        20.55        27.58        13.05        12.39 
TCGA-CN-5367 TCGA-CN-6010 TCGA-CN-6012 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-A49B 
       11.57        50.07        48.00        10.45        32.22        29.72 
TCGA-CN-A6V6 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-6220 TCGA-CQ-6229 TCGA-CQ-7072 
       20.88        54.58        70.45        32.38        38.76        77.56 
TCGA-CQ-A4CG TCGA-CR-5247 TCGA-CR-6467 TCGA-CR-6477 TCGA-CR-6493 TCGA-CR-7370 
       14.14        11.77        58.42        16.90         9.27         3.45 
TCGA-CR-7380 TCGA-CR-7383 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5442 TCGA-CV-5444 
       19.92        17.13       108.95        76.24        76.50        80.12 
TCGA-CV-5970 TCGA-CV-6933 TCGA-CV-6936 TCGA-CV-6951 TCGA-CV-6959 TCGA-CV-7102 
       13.35        90.12         5.46        30.08         8.42         1.84 
TCGA-CV-7178 TCGA-CV-7235 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7250 TCGA-CV-7254 
       71.21        77.16        31.36        26.20        95.34        47.97 
TCGA-CV-7255 TCGA-CV-7407 TCGA-CV-7409 TCGA-CV-7415 TCGA-CV-7432 TCGA-CV-7437 
        2.10        35.54        17.85        22.85        84.49        16.64 
TCGA-CV-7438 TCGA-CV-A45Q TCGA-CV-A45X TCGA-CV-A465 TCGA-CV-A6JM TCGA-CV-A6JY 
        6.38       169.38         6.51         7.07         6.38        21.24 
TCGA-CX-7086 TCGA-D6-6516 TCGA-D6-6823 TCGA-D6-8568 TCGA-DQ-5625 TCGA-DQ-5631 
       18.84        25.41        23.05        24.95        37.25        18.02 
TCGA-DQ-7592 TCGA-HD-7832 TCGA-HD-7917 TCGA-HD-A6I0 TCGA-IQ-A61G TCGA-IQ-A61J 
       37.58        27.48        27.48         6.90        11.84        33.57 
TCGA-IQ-A6SG TCGA-IQ-A6SH TCGA-MT-A51X TCGA-MT-A7BN TCGA-P3-A6T5 TCGA-P3-A6T6 
       19.04        15.48         7.96        15.42        29.00        12.99 
TCGA-QK-A8ZA TCGA-RS-A6TO TCGA-T3-A92M TCGA-T3-A92N TCGA-TN-A7HI TCGA-TN-A7HJ 
       12.20        12.72        13.71         3.12        13.55        13.25 
TCGA-UF-A719 TCGA-UF-A71B TCGA-UF-A71E TCGA-UF-A7JH TCGA-WA-A7H4 TCGA-KU-A66T 
       54.67        49.51        49.45        29.46        14.56        18.15 

$`XQ GAIN WILD-TYPE`
TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4IG TCGA-BA-A4II TCGA-CN-4727 
       20.48        68.48         3.55        28.11        30.18        51.29 
TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6024 TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-A6V1 
        9.07         9.24        11.08        35.05        32.48        19.82 
TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-6221 TCGA-CQ-7063 TCGA-CQ-7067 TCGA-CQ-7068 
       24.39        48.20        32.88        70.13        16.73        43.04 
TCGA-CR-6472 TCGA-CR-6478 TCGA-CX-7082 TCGA-CX-7219 TCGA-DQ-7588 TCGA-DQ-7589 
       34.52         6.02         0.36        34.36        14.04        46.32 
TCGA-DQ-7593 TCGA-H7-A6C5 TCGA-HD-8634 TCGA-HD-8635 TCGA-UF-A71D TCGA-UF-A7JV 
       40.24        21.11        12.66        22.85        48.03         2.96 
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-5558 TCGA-BA-6868 TCGA-BA-6869 
       57.93        17.10        23.84        65.59        15.52        21.17 
TCGA-BA-6870 TCGA-BA-6873 TCGA-BA-A4IF TCGA-BA-A4IH TCGA-BA-A6D8 TCGA-BA-A6DA 
       14.83         4.01        29.42        20.45        27.95        11.54 
TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DI 
        7.10         5.69        14.47         7.82         2.27        11.05 
TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4224 TCGA-BB-4228 
       13.38        20.48        16.41         6.15         9.14        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-A5HY TCGA-BB-A5HZ 
       24.66        38.40        71.05        20.52        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-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 
        4.67        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-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-6994 
       47.44        28.04        19.07        34.13         6.74        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-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-A6V7 
       16.57         4.41        12.07         2.70        23.44        19.53 
TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 
       52.37        21.50         2.93        62.37        45.99        10.42 
TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6225 
       11.21         4.24        41.19        46.95        56.58        13.25 
TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7069 TCGA-CQ-7071 
        4.24        14.99        64.87        53.52        41.88        43.10 
TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CH 
       44.48        23.24        29.36        33.60        29.49        12.46 
TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6470 
       31.23        84.23        54.67        37.87        26.27        50.01 
TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 
       39.52        36.99        18.54        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-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-7382 
       29.23         0.99        31.96         9.17        34.06        26.17 
TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 
       32.78        47.01        27.06        12.89        49.58        30.02 
TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 
       46.85        32.65        44.25        30.58        24.79         5.13 
TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 
        5.95        35.41        29.95        48.39       139.43        17.16 
TCGA-CV-5432 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5443 
      129.21        19.20        17.95       107.51        94.88        91.53 
TCGA-CV-5966 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 
       17.92        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-6934 
       43.23        54.74        21.07        62.43         9.60         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-6945 TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-6952 
      140.78        19.79        12.03        42.38        15.09         6.08 
TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-6955 TCGA-CV-6956 TCGA-CV-6960 TCGA-CV-6961 
       53.95        65.82        10.98         7.13        28.34         2.50 
TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 
        4.14        64.83       172.67       111.16        18.81        12.66 
TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7177 
        7.99         9.01         5.26        52.31        12.92        21.80 
TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7247 
       10.75       130.88         4.73        89.65        36.00        18.97 
TCGA-CV-7248 TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7261 TCGA-CV-7263 TCGA-CV-7406 
       17.13         4.96        11.87        49.71        18.41        57.47 
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-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-7433 TCGA-CV-7434 TCGA-CV-7435 
       54.94         3.52        16.27        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-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-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN 
        0.76        56.61        15.25         5.98        35.34        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-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-D6-6826 TCGA-D6-6827 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB 
       16.14        11.44        18.67        25.32        17.72        12.36 
TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EN TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ 
       28.77         7.63        22.59        24.95        13.94        12.10 
TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5630 TCGA-DQ-7590 TCGA-DQ-7591 
       12.79        23.34        58.45        33.86        46.45        20.45 
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-A76A TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7831 
       15.06        20.94        33.76        28.47        25.74        21.93 
TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ 
       14.66        22.03         0.36        13.84         4.27         3.65 
TCGA-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-A6H7 TCGA-KU-A6H8 
        0.07         5.29        13.68        13.84        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-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-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        27.39        21.07 
TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-A8ZB TCGA-QK-AA3J 
       19.73        12.89         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-A7HL TCGA-UF-A718 TCGA-UF-A71A TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC 
       20.35        64.80         2.83        44.65        74.47        17.95 
TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS 
       24.30        55.43        18.05        13.94        20.75        22.36 
TCGA-UF-A7JT TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-KU-A66S 
       32.65        17.03        20.55        13.35 

  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 
           22.045            21.070 
[1] "1.8 - 169.4 (22.0)" "0.1 - 211.0 (21.1)"
[1] "hr=" "1.2"
D41V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  XQ GAIN MUTATED         3       13        14        52         2         0
  XQ GAIN WILD-TYPE      24       63        68       200        10         1
D41V3, multiclass
           clus
vv          XQ GAIN MUTATED XQ GAIN WILD-TYPE
  STAGE I                 3                24
  STAGE II               13                63
  STAGE III              14                68
  STAGE IVA              52               200
  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       4  25  18  37
  XQ GAIN WILD-TYPE    46 112  82 136
D41V4, multiclass
       clus
vv      XQ GAIN MUTATED XQ GAIN WILD-TYPE
  T0+T1               4                46
  T2                 25               112
  T3                 18                82
  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
  XQ GAIN MUTATED    31  10  37   1
  XQ GAIN WILD-TYPE 148  58 131   7
D41V5, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  N0              31               148
  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    29   0
  XQ GAIN WILD-TYPE 161   1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     29    0
  XQ GAIN WILD-TYPE  161    1
   clus
vv  XQ GAIN MUTATED XQ GAIN WILD-TYPE
  0              29               161
  1               0                 1
[1] 2 2
[1] FALSE
D41V7, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED    23  73
  XQ GAIN WILD-TYPE 117 309
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     23   73
  XQ GAIN WILD-TYPE  117  309
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  FEMALE              23               117
  MALE                73               309
[1] 2 2
[1] FALSE
D41V8, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED    27  58
  XQ GAIN WILD-TYPE 135 243
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     27   58
  XQ GAIN WILD-TYPE  135  243
     clus
vv    XQ GAIN MUTATED XQ GAIN WILD-TYPE
  NO               27               135
  YES              58               243
[1] 2 2
[1] FALSE
                   vv
clus                HEAD & NECK SQUAMOUS CELL CARCINOMA
  XQ GAIN MUTATED                                    95
  XQ GAIN WILD-TYPE                                 416
                   vv
clus                HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  XQ GAIN MUTATED                                                   1
  XQ GAIN WILD-TYPE                                                 9
                   vv
clus                HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  XQ GAIN MUTATED                                                           0
  XQ GAIN WILD-TYPE                                                         1
D41V9, multiclass
                                                           clus
vv                                                          XQ GAIN MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                    95
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       1
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT               0
                                                           clus
vv                                                          XQ GAIN WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                     416
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                         9
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                 1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V10, continuous
D41V11, continuous
D41V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  XQ GAIN MUTATED                                  1     1
  XQ GAIN WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  XQ GAIN MUTATED                          12    80
  XQ GAIN WILD-TYPE                        36   366
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                                         80               366
[1] 4 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  84
  XQ GAIN WILD-TYPE  21 375
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      5   84
  XQ GAIN WILD-TYPE   21  375
                        clus
vv                       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  HISPANIC OR LATINO                   5                21
  NOT HISPANIC OR LATINO              84               375
[1] 2 2
[1] FALSE

Clustering(42) Variable = 1P LOSS MUTATION ANALYSIS
D42V1, survival
                   sevent
clus2                 0   1
  1P LOSS MUTATED    27  28
  1P LOSS WILD-TYPE 274 191
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               55               465 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               28               191 
$`1P LOSS MUTATED`
TCGA-BA-4075 TCGA-BA-6871 TCGA-CN-6021 TCGA-CN-6024 TCGA-CN-6992 TCGA-CN-6997 
        9.30         3.55         9.07        11.08        35.05        32.48 
TCGA-DQ-7589 TCGA-HD-8634 TCGA-4P-AA8J TCGA-BA-5152 TCGA-BA-A6D8 TCGA-CN-4736 
       46.32        12.66         3.35        42.35        27.95        12.99 
TCGA-CN-5355 TCGA-CN-5360 TCGA-CN-6012 TCGA-CN-6018 TCGA-CN-6994 TCGA-CN-6995 
       42.02        71.31        48.00        19.07        38.89         3.68 
TCGA-CN-A63T TCGA-CN-A63W TCGA-CQ-5332 TCGA-CQ-6225 TCGA-CQ-7072 TCGA-CQ-A4CI 
        7.40        12.39        10.42        13.25        77.56        31.23 
TCGA-CR-7365 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CV-5432 TCGA-CV-5434 
       39.16         3.45         3.09        24.95       129.21       108.95 
TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-6003 TCGA-CV-6935 TCGA-CV-6940 TCGA-CV-6950 
       17.95       107.51        54.74         9.70        26.43        15.09 
TCGA-CV-6962 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7424 TCGA-D6-6516 TCGA-D6-A6EM 
        4.14        47.97        49.71        14.89        25.41         7.63 
TCGA-F7-8489 TCGA-F7-A61W TCGA-HD-A6HZ TCGA-IQ-A61L TCGA-MZ-A6I9 TCGA-P3-A6T5 
       21.63         0.46         3.65        13.68        16.08        29.00 
TCGA-P3-A6T8 TCGA-T3-A92N TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JD TCGA-UF-A7JO 
       13.15         3.12        49.45        44.65        24.30        20.75 
TCGA-WA-A7GZ 
       20.55 

$`1P LOSS WILD-TYPE`
TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-A4IG TCGA-BA-A4II TCGA-BB-A5HU 
       37.28        20.48        68.48        28.11        30.18        25.71 
TCGA-CN-4727 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 
       51.29         9.24        52.08        19.82        24.39        48.20 
TCGA-CQ-6221 TCGA-CQ-7063 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-A4C7 TCGA-CR-6472 
       32.88        70.13        16.73        43.04        11.61        34.52 
TCGA-CR-6478 TCGA-CX-7082 TCGA-CX-7219 TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7593 
        6.02         0.36        34.36        30.94        14.04        40.24 
TCGA-H7-A6C5 TCGA-HD-8635 TCGA-UF-A71D TCGA-UF-A7JV TCGA-BA-4074 TCGA-BA-4076 
       21.11        22.85        48.03         2.96        15.19        13.64 
TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 
        9.07        26.50        23.74        57.93        17.10        23.84 
TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6872 TCGA-BA-6873 
       65.59        15.52        21.17        14.83        12.62         4.01 
TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IH TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD 
       41.85        29.42        20.45        11.54         7.10         5.69 
TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DI TCGA-BA-A6DJ TCGA-BA-A6DL 
       14.47         7.82         2.27        11.05        13.38        20.48 
TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 
       16.41         6.15       105.90         9.14         4.80         4.41 
TCGA-BB-4228 TCGA-BB-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-A5HY 
       66.28        24.66        38.40        71.05        20.52        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-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-5356 TCGA-CN-5358 TCGA-CN-5359 
       27.58        73.61        13.05        46.32         8.58        12.39 
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-6019 TCGA-CN-6020 TCGA-CN-6988 TCGA-CN-6989 
       47.44        28.04        34.13         6.74        10.45        32.22 
TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A 
       17.42        11.74        35.01        25.41        23.57        17.29 
TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A640 
       29.72        21.21        31.69        22.32        16.57         4.41 
TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5324 
       12.07         2.70        23.44        20.88        19.53        52.37 
TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 
       21.50         2.93        54.58        70.45        62.37        45.99 
TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6220 TCGA-CQ-6223 TCGA-CQ-6224 
       11.21         4.24        41.19        32.38        46.95        56.58 
TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7069 
        4.24        14.99        38.76        64.87        53.52        41.88 
TCGA-CQ-7071 TCGA-CQ-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-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-6473 TCGA-CR-6474 
       26.27        58.42        50.01        39.52        36.99        18.54 
TCGA-CR-6477 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 
       16.90        11.90        10.22        11.34        11.64         7.69 
TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7367 
       12.46        22.78        15.75         9.27        47.18        47.34 
TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 
       40.93        35.84        29.23         0.99        31.96         9.17 
TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 
       34.06        19.92        26.17        17.13        32.78        47.01 
TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 
       27.06        12.89        49.58        30.02        46.85        32.65 
TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 
       44.25        30.58        24.79         5.13         5.95        35.41 
TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5435 TCGA-CV-5436 
       29.95        48.39       139.43        17.16        76.24        19.20 
TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 
       94.88        76.50        91.53        80.12        17.92        13.35 
TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 
       23.05        86.83        48.59        60.49         7.07        43.23 
TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6936 
       21.07        62.43         9.60        90.12         2.14         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-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-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 
      172.67       111.16        18.81        12.66         7.99         9.01 
TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-7178 
        5.26         1.84        52.31        12.92        21.80        71.21 
TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7242 
       10.75       130.88        77.16         4.73        89.65        36.00 
TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7252 
       31.36        26.20        18.97        17.13        95.34         4.96 
TCGA-CV-7253 TCGA-CV-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-7415 TCGA-CV-7416 
      210.97        89.33         9.67         0.46        22.85        25.08 
TCGA-CV-7418 TCGA-CV-7421 TCGA-CV-7422 TCGA-CV-7423 TCGA-CV-7425 TCGA-CV-7427 
       25.94         0.07        34.09       100.57        56.48       156.49 
TCGA-CV-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-7085 TCGA-CX-7086 TCGA-CX-A4AQ 
       19.92        22.52        10.42        10.55        18.84        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-D6-8569 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        23.34 
TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7590 TCGA-DQ-7591 
       58.45        37.25        33.86        18.02        46.45        20.45 
TCGA-DQ-7592 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 
       37.58        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-A76A TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 
       20.94        33.76        28.47        25.74        21.93        27.48 
TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 
       27.48        14.66        22.03         0.36        13.84         4.27 
TCGA-HD-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-IQ-A6SH TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X 
       19.04        15.48        19.27        10.75        14.37         7.96 
TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A5BI 
       30.05         1.84        12.62         6.25        15.42         7.13 
TCGA-MZ-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-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-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC 
       21.47         9.34        12.72        27.39        21.07        19.73 
TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J 
       12.89         5.62        14.76        12.20        17.82        15.32 
TCGA-QK-AA3K TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T2-A6X0 
        8.32        12.72        16.96         6.87        15.91         7.10 
TCGA-T2-A6X2 TCGA-T3-A92M TCGA-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-A7JA TCGA-UF-A7JC TCGA-UF-A7JF 
       54.67         2.83        49.51        74.47        17.95        55.43 
TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UP-A6WW 
       29.46        18.05        13.94        22.36        32.65        17.03 
TCGA-WA-A7H4 TCGA-KU-A66S TCGA-KU-A66T 
       14.56        13.35        18.15 

  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 
            20.55             21.17 
[1] "0.5 - 129.2 (20.6)" "0.1 - 211.0 (21.2)"
[1] "hr=" "1.3"
D42V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  1P LOSS MUTATED         3        5        10        31         0         0
  1P LOSS WILD-TYPE      24       71        72       221        12         1
D42V3, multiclass
           clus
vv          1P LOSS MUTATED 1P LOSS WILD-TYPE
  STAGE I                 3                24
  STAGE II                5                71
  STAGE III              10                72
  STAGE IVA              31               221
  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  14  13  20
  1P LOSS WILD-TYPE    46 123  87 153
D42V4, multiclass
       clus
vv      1P LOSS MUTATED 1P LOSS WILD-TYPE
  T0+T1               4                46
  T2                 14               123
  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    23   6  19   0
  1P LOSS WILD-TYPE 156  62 149   8
D42V5, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  N0              23               156
  N1               6                62
  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"
D42V6, binary
                   cls
clus                  0   1
  1P LOSS MUTATED    19   0
  1P LOSS WILD-TYPE 171   1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     19    0
  1P LOSS WILD-TYPE  171    1
   clus
vv  1P LOSS MUTATED 1P LOSS WILD-TYPE
  0              19               171
  1               0                 1
[1] 2 2
[1] FALSE
D42V7, binary
                   cls
clus                  0   1
  1P LOSS MUTATED    14  42
  1P LOSS WILD-TYPE 126 340
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     14   42
  1P LOSS WILD-TYPE  126  340
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  FEMALE              14               126
  MALE                42               340
[1] 2 2
[1] FALSE
D42V8, binary
                   cls
clus                  0   1
  1P LOSS MUTATED    22  26
  1P LOSS WILD-TYPE 140 275
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     22   26
  1P LOSS WILD-TYPE  140  275
     clus
vv    1P LOSS MUTATED 1P LOSS WILD-TYPE
  NO               22               140
  YES              26               275
[1] 2 2
[1] FALSE
                   vv
clus                HEAD & NECK SQUAMOUS CELL CARCINOMA
  1P LOSS MUTATED                                    54
  1P LOSS WILD-TYPE                                 457
                   vv
clus                HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  1P LOSS MUTATED                                                   2
  1P LOSS WILD-TYPE                                                 8
                   vv
clus                HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  1P LOSS MUTATED                                                           0
  1P LOSS WILD-TYPE                                                         1
D42V9, multiclass
                                                           clus
vv                                                          1P LOSS MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                    54
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       2
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT               0
                                                           clus
vv                                                          1P LOSS WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                     457
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                         8
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                 1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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    46
  1P LOSS WILD-TYPE                        42   400
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                                         46               400
[1] 4 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  47
  1P LOSS WILD-TYPE  24 412
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      2   47
  1P LOSS WILD-TYPE   24  412
                        clus
vv                       1P LOSS MUTATED 1P LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                24
  NOT HISPANIC OR LATINO              47               412
[1] 2 2
[1] FALSE

Clustering(43) Variable = 1Q LOSS MUTATION ANALYSIS
D43V1, survival
                   sevent
clus2                 0   1
  1Q LOSS MUTATED    18  20
  1Q LOSS WILD-TYPE 283 199
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               38               482 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               20               199 
$`1Q LOSS MUTATED`
TCGA-CQ-A4C7 TCGA-DQ-7588 TCGA-HD-8634 TCGA-4P-AA8J TCGA-BA-5149 TCGA-BA-5152 
       11.61        14.04        12.66         3.35        26.50        42.35 
TCGA-BB-A5HZ TCGA-C9-A47Z TCGA-CN-4736 TCGA-CN-5355 TCGA-CN-6012 TCGA-CN-6018 
       27.19         6.28        12.99        42.02        48.00        19.07 
TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-A63T TCGA-CN-A63W TCGA-CQ-6220 TCGA-CQ-6225 
       38.89         3.68         7.40        12.39        32.38        13.25 
TCGA-CQ-6227 TCGA-CR-7365 TCGA-CR-7372 TCGA-CV-5432 TCGA-CV-5439 TCGA-CV-5441 
        4.24        39.16        24.95       129.21        17.95        94.88 
TCGA-CV-6003 TCGA-CV-6950 TCGA-CV-7261 TCGA-CV-7416 TCGA-CV-7424 TCGA-F7-8489 
       54.74        15.09        49.71        25.08        14.89        21.63 
TCGA-F7-A61W TCGA-HD-A6HZ TCGA-IQ-A61L TCGA-MZ-A6I9 TCGA-P3-A6T8 TCGA-T3-A92N 
        0.46         3.65        13.68        16.08        13.15         3.12 
TCGA-UF-A7JC TCGA-WA-A7GZ 
       17.95        20.55 

$`1Q LOSS WILD-TYPE`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4IG 
        9.30        37.28        20.48        68.48         3.55        28.11 
TCGA-BA-A4II TCGA-BB-A5HU TCGA-CN-4727 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 
       30.18        25.71        51.29         9.07         9.24        52.08 
TCGA-CN-6024 TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 
       11.08        35.05        32.48        19.82        24.39        48.20 
TCGA-CQ-6221 TCGA-CQ-7063 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CR-6472 TCGA-CR-6478 
       32.88        70.13        16.73        43.04        34.52         6.02 
TCGA-CX-7082 TCGA-CX-7219 TCGA-DQ-5629 TCGA-DQ-7589 TCGA-DQ-7593 TCGA-H7-A6C5 
        0.36        34.36        30.94        46.32        40.24        21.11 
TCGA-HD-8635 TCGA-UF-A71D TCGA-UF-A7JV TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4078 
       22.85        48.03         2.96        15.19        13.64         9.07 
TCGA-BA-5151 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-6868 
       23.74        57.93        17.10        23.84        65.59        15.52 
TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF 
       21.17        14.83        12.62         4.01        41.85        29.42 
TCGA-BA-A4IH TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE 
       20.45        27.95        11.54         7.10         5.69        14.47 
TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DI TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BA-A8YP 
        7.82         2.27        11.05        13.38        20.48        16.41 
TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 
        6.15       105.90         9.14         4.80         4.41        18.38 
TCGA-BB-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-A5HY TCGA-BB-A6UM 
       24.66        38.40        71.05        20.52        10.55        12.92 
TCGA-BB-A6UO TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 
        8.81        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-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-6988 TCGA-CN-6989 TCGA-CN-6996 TCGA-CN-6998 
       34.13         6.74        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-A6V6 TCGA-CN-A6V7 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 
       23.44        20.88        19.53        52.37        21.50         2.93 
TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 
       54.58        70.45        62.37        45.99        10.42        11.21 
TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6228 TCGA-CQ-6229 
        4.24        41.19        46.95        56.58        14.99        38.76 
TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 
       64.87        53.52        41.88        43.10        77.56        44.48 
TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH 
       23.24        29.36        33.60        29.49        14.14        12.46 
TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 
       31.23        84.23        11.77        54.67        37.87        26.27 
TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 
       58.42        50.01        39.52        36.99        18.54        16.90 
TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 
       11.90        10.22        11.34        11.64         7.69        12.46 
TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7367 TCGA-CR-7368 
       22.78        15.75         9.27        47.18        47.34        40.93 
TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 
       35.84         3.45         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        49.58        30.02        46.85 
TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 
       32.65        44.25        30.58        24.79         5.13         5.95 
TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5434 
       35.41        29.95        48.39       139.43        17.16       108.95 
TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5440 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 
       76.24        19.20       107.51        76.50        91.53        80.12 
TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 
       17.92        13.35        23.05        86.83        48.59        60.49 
TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-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-6951 TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-6955 TCGA-CV-6956 
       30.08         6.08        53.95        65.82        10.98         7.13 
TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7090 
        8.42        28.34         2.50         4.14        64.83       172.67 
TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 
      111.16        18.81        12.66         7.99         9.01         5.26 
TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-7178 TCGA-CV-7180 
        1.84        52.31        12.92        21.80        71.21        10.75 
TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 
      130.88        77.16         4.73        89.65        36.00        31.36 
TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 
       26.20        18.97        17.13        95.34         4.96        11.87 
TCGA-CV-7254 TCGA-CV-7255 TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7407 TCGA-CV-7409 
       47.97         2.10        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-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-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-A45R TCGA-CV-A45T TCGA-CV-A45U TCGA-CV-A45V TCGA-CV-A45W TCGA-CV-A45X 
      180.16       159.65        35.47         1.05        45.96         6.51 
TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A463 TCGA-CV-A464 
       88.87        48.20        60.43        67.86         0.76        56.61 
TCGA-CV-A465 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JM TCGA-CV-A6JN 
        7.07        15.25         5.98        35.34         6.38        29.79 
TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 
        6.48        28.01         3.62        21.24        23.47        19.92 
TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-A4AQ TCGA-D6-6515 
       22.52        10.42        10.55        18.84        51.12        13.25 
TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 
       25.41         9.60        23.05         2.53        16.14        11.44 
TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK 
       18.67        24.95        25.32        17.72        12.36        28.77 
TCGA-D6-A6EM TCGA-D6-A6EN TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES 
        7.63        22.59        24.95        13.94        12.10        12.79 
TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7590 
       23.34        58.45        37.25        33.86        18.02        46.45 
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-A50G TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V 
       32.71        20.25         3.02        31.13        18.94        24.95 
TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A623 TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 
       17.85        11.80        20.25        12.43        13.38        15.16 
TCGA-H7-8502 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7831 
       15.06        20.94        33.76        28.47        25.74        21.93 
TCGA-HD-7832 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-A4C1 TCGA-HD-A633 
       27.48        27.48        14.66        22.03         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-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W 
       13.84        19.04        15.48        19.27        10.75        14.37 
TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G TCGA-MT-A7BN 
        7.96        30.05         1.84        12.62         6.25        15.42 
TCGA-MZ-A5BI TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QE 
        7.13        17.98        29.92        15.78        71.74        51.25 
TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T3 
       10.85        36.82        47.01        19.00        75.55        18.97 
TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-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        27.39 
TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-A8ZA 
       21.07        19.73        12.89         5.62        14.76        12.20 
TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX 
       17.82        15.32         8.32        12.72        16.96         6.87 
TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-T3-A92M TCGA-TN-A7HI TCGA-TN-A7HJ 
       15.91         7.10        32.45        13.71        13.55        13.25 
TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71E 
       20.35        64.80        54.67         2.83        49.51        49.45 
TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ 
       44.65        74.47        24.30        55.43        29.46        18.05 
TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UP-A6WW TCGA-WA-A7H4 
       13.94        20.75        22.36        32.65        17.03        14.56 
TCGA-KU-A66S TCGA-KU-A66T 
       13.35        18.15 

  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 
           17.015            21.225 
[1] "0.5 - 129.2 (17.0)" "0.1 - 211.0 (21.2)"
[1] "hr=" "1.5"
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       229        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               229
  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    15   5  15   0
  1Q LOSS WILD-TYPE 164  63 153   8
D43V5, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  N0              15               164
  N1               5                63
  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"
D43V6, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED    11   0
  1Q LOSS WILD-TYPE 179   1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED     11    0
  1Q LOSS WILD-TYPE  179    1
   clus
vv  1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  0              11               179
  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  14
  1Q LOSS WILD-TYPE 141 287
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED     21   14
  1Q LOSS WILD-TYPE  141  287
     clus
vv    1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  NO               21               141
  YES              14               287
[1] 2 2
[1] FALSE
                   vv
clus                HEAD & NECK SQUAMOUS CELL CARCINOMA
  1Q LOSS MUTATED                                    39
  1Q LOSS WILD-TYPE                                 472
                   vv
clus                HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  1Q LOSS MUTATED                                                   0
  1Q LOSS WILD-TYPE                                                10
                   vv
clus                HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  1Q LOSS MUTATED                                                           0
  1Q LOSS WILD-TYPE                                                         1
D43V9, multiclass
                                                           clus
vv                                                          1Q LOSS MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                    39
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       0
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT               0
                                                           clus
vv                                                          1Q LOSS WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                     472
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        10
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                 1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V10, continuous
D43V11, continuous
D43V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  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  36
  1Q LOSS WILD-TYPE  25 423
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      1   36
  1Q LOSS WILD-TYPE   25  423
                        clus
vv                       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                25
  NOT HISPANIC OR LATINO              36               423
[1] 2 2
[1] FALSE

Clustering(44) Variable = 2P LOSS MUTATION ANALYSIS
D44V1, survival
                   sevent
clus2                 0   1
  2P LOSS MUTATED    17  15
  2P LOSS WILD-TYPE 284 204
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               32               488 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               15               204 
$`2P LOSS MUTATED`
TCGA-BA-5559 TCGA-DQ-7588 TCGA-BA-6873 TCGA-BB-7861 TCGA-BB-7862 TCGA-C9-A47Z 
       68.48        14.04         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-F7-A50J 
       84.49       180.16         7.07        21.24        11.44        31.13 
TCGA-IQ-A61L TCGA-MT-A7BN TCGA-MZ-A6I9 TCGA-P3-A5Q6 TCGA-P3-A6T5 TCGA-QK-AA3K 
       13.68        15.42        16.08        15.78        29.00         8.32 
TCGA-UF-A7JS TCGA-KU-A66T 
       22.36        18.15 

$`2P LOSS WILD-TYPE`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-6871 TCGA-BA-A4IG TCGA-BA-A4II 
        9.30        37.28        20.48         3.55        28.11        30.18 
TCGA-BB-A5HU TCGA-CN-4727 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 
       25.71        51.29         9.07         9.24        52.08        11.08 
TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-6221 
       35.05        32.48        19.82        24.39        48.20        32.88 
TCGA-CQ-7063 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-A4C7 TCGA-CR-6472 TCGA-CR-6478 
       70.13        16.73        43.04        11.61        34.52         6.02 
TCGA-CX-7082 TCGA-CX-7219 TCGA-DQ-5629 TCGA-DQ-7589 TCGA-DQ-7593 TCGA-H7-A6C5 
        0.36        34.36        30.94        46.32        40.24        21.11 
TCGA-HD-8634 TCGA-HD-8635 TCGA-UF-A71D TCGA-UF-A7JV TCGA-4P-AA8J TCGA-BA-4074 
       12.66        22.85        48.03         2.96         3.35        15.19 
TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 
       13.64         9.07        26.50        23.74        42.35        57.93 
TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 
       17.10        23.84        65.59        15.52        21.17        14.83 
TCGA-BA-6872 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IH TCGA-BA-A6D8 TCGA-BA-A6DA 
       12.62        41.85        29.42        20.45        27.95        11.54 
TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DI 
        7.10         5.69        14.47         7.82         2.27        11.05 
TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 
       13.38        20.48        16.41         6.15       105.90         9.14 
TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 
        4.80         4.41        18.38        33.70        50.20        44.98 
TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-8601 TCGA-BB-A5HY 
       66.28        24.66        38.40        71.05        20.52        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-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 
       38.04         4.67        56.68        12.89        26.86        32.81 
TCGA-CN-4733 TCGA-CN-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-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 
       48.00        23.90        47.44        28.04        19.07        34.13 
TCGA-CN-6020 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 
        6.74        10.45        32.22        38.89         3.68        17.42 
TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A49A TCGA-CN-A49C TCGA-CN-A63T 
       11.74        35.01        25.41        17.29        21.21         7.40 
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-A6V6 TCGA-CN-A6V7 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 
       23.44        20.88        19.53        52.37        21.50         2.93 
TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 
       54.58        70.45        62.37        45.99        10.42        11.21 
TCGA-CQ-5334 TCGA-CQ-6220 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 
        4.24        32.38        46.95        56.58        13.25         4.24 
TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7065 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 
       14.99        38.76        53.52        41.88        43.10        77.56 
TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG 
       44.48        23.24        29.36        33.60        29.49        14.14 
TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 
       12.46        31.23        84.23        11.77        54.67        37.87 
TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6474 
       26.27        58.42        50.01        39.52        36.99        18.54 
TCGA-CR-6477 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 
       16.90        11.90        10.22        11.34        11.64         7.69 
TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 
       12.46        22.78        15.75         9.27        47.18        39.16 
TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 
       47.34        40.93        35.84         3.45         3.09        24.95 
TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 
       29.23         0.99        31.96         9.17        34.06        19.92 
TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 
       26.17        17.13        32.78        47.01        27.06        12.89 
TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 
       49.58        30.02        46.85        32.65        44.25        30.58 
TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 
       24.79         5.13         5.95        35.41        29.95        48.39 
TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 
      139.43        17.16       129.21       108.95        76.24        19.20 
TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 
       17.95       107.51        94.88        76.50        91.53        80.12 
TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 
       13.35        23.05        48.59        60.49         7.07        43.23 
TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6935 
       21.07        62.43         9.60        90.12         2.14         9.70 
TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6941 
        5.46        20.52         4.73        21.90        26.43        11.24 
TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-6951 
      140.78        19.79        12.03        42.38        15.09        30.08 
TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-6955 TCGA-CV-6956 TCGA-CV-6959 
        6.08        53.95        65.82        10.98         7.13         8.42 
TCGA-CV-6960 TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 
       28.34         4.14        64.83       172.67       111.16        18.81 
TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7103 
       12.66         7.99         9.01         5.26         1.84        52.31 
TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-7178 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 
       12.92        21.80        71.21        10.75       130.88        77.16 
TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7247 
        4.73        89.65        36.00        31.36        26.20        18.97 
TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7263 
       17.13        95.34        11.87        47.97        49.71        18.41 
TCGA-CV-7406 TCGA-CV-7407 TCGA-CV-7409 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 
       57.47        35.54        17.85       210.97        89.33         9.67 
TCGA-CV-7414 TCGA-CV-7415 TCGA-CV-7416 TCGA-CV-7418 TCGA-CV-7421 TCGA-CV-7422 
        0.46        22.85        25.08        25.94         0.07        34.09 
TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-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-A45T TCGA-CV-A45U 
       22.19        27.98        21.01       169.38       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-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-A6JZ 
        6.38        29.79         6.48        28.01         3.62        23.47 
TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-A4AQ 
       19.92        22.52        10.42        10.55        18.84        51.12 
TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 
       13.25        25.41         9.60        23.05         2.53        16.14 
TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK 
       18.67        24.95        25.32        17.72        12.36        28.77 
TCGA-D6-A6EM TCGA-D6-A6EN TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES 
        7.63        22.59        24.95        13.94        12.10        12.79 
TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7590 
       23.34        58.45        37.25        33.86        18.02        46.45 
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-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-A76A TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 
       15.16        15.06        20.94        33.76        28.47        25.74 
TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-A4C1 
       21.93        27.48        27.48        14.66        22.03         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-A61O TCGA-IQ-A6SG TCGA-IQ-A6SH TCGA-KU-A6H7 
       33.57         5.29        13.84        19.04        15.48        19.27 
TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F 
       10.75        14.37         7.96        30.05         1.84        12.62 
TCGA-MT-A67G TCGA-MZ-A5BI TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE 
        6.25         7.13        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-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        27.39 
TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-A8ZA 
       21.07        19.73        12.89         5.62        14.76        12.20 
TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ 
       17.82        15.32        12.72        16.96         6.87        15.91 
TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-T3-A92M TCGA-T3-A92N TCGA-TN-A7HI TCGA-TN-A7HJ 
        7.10        32.45        13.71         3.12        13.55        13.25 
TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71E 
       20.35        64.80        54.67         2.83        49.51        49.45 
TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH 
       44.65        74.47        17.95        24.30        55.43        29.46 
TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JT TCGA-UP-A6WW TCGA-WA-A7GZ 
       18.05        13.94        20.75        32.65        17.03        20.55 
TCGA-WA-A7H4 TCGA-KU-A66S 
       14.56        13.35 

  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 
           19.695            21.090 
[1] "2.1 - 180.2 (19.7)" "0.1 - 211.0 (21.1)"
[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       236        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               236
  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 182   1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      8    0
  2P LOSS WILD-TYPE  182    1
   clus
vv  2P LOSS MUTATED 2P LOSS WILD-TYPE
  0               8               182
  1               0                 1
[1] 2 2
[1] FALSE
D44V7, binary
                   cls
clus                  0   1
  2P LOSS MUTATED    15  17
  2P LOSS WILD-TYPE 125 365
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED     15   17
  2P LOSS WILD-TYPE  125  365
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  FEMALE              15               125
  MALE                17               365
[1] 2 2
[1] FALSE
D44V8, binary
                   cls
clus                  0   1
  2P LOSS MUTATED    12  20
  2P LOSS WILD-TYPE 150 281
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED     12   20
  2P LOSS WILD-TYPE  150  281
     clus
vv    2P LOSS MUTATED 2P LOSS WILD-TYPE
  NO               12               150
  YES              20               281
[1] 2 2
[1] FALSE
                   vv
clus                HEAD & NECK SQUAMOUS CELL CARCINOMA
  2P LOSS MUTATED                                    32
  2P LOSS WILD-TYPE                                 479
                   vv
clus                HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  2P LOSS MUTATED                                                   0
  2P LOSS WILD-TYPE                                                10
                   vv
clus                HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  2P LOSS MUTATED                                                           0
  2P LOSS WILD-TYPE                                                         1
D44V9, multiclass
                                                           clus
vv                                                          2P LOSS MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                    32
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       0
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT               0
                                                           clus
vv                                                          2P LOSS WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                     479
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        10
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                 1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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    29
  2P LOSS WILD-TYPE                        46   417
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                                         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"
D44V14, binary
                   cls
clus                  0   1
  2P LOSS MUTATED     4  26
  2P LOSS WILD-TYPE  22 433
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      4   26
  2P LOSS WILD-TYPE   22  433
                        clus
vv                       2P LOSS MUTATED 2P LOSS WILD-TYPE
  HISPANIC OR LATINO                   4                22
  NOT HISPANIC OR LATINO              26               433
[1] 2 2
[1] FALSE

Clustering(45) Variable = 2Q LOSS MUTATION ANALYSIS
D45V1, survival
                   sevent
clus2                 0   1
  2Q LOSS MUTATED    26  18
  2Q LOSS WILD-TYPE 275 201
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               44               476 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               18               201 
$`2Q LOSS MUTATED`
TCGA-BA-5559 TCGA-BA-6871 TCGA-CR-6472 TCGA-DQ-7593 TCGA-BA-5152 TCGA-BA-6873 
       68.48         3.55        34.52        40.24        42.35         4.01 
TCGA-BB-7861 TCGA-BB-7862 TCGA-C9-A47Z TCGA-CN-4736 TCGA-CN-6018 TCGA-CN-6995 
       22.42        36.72         6.28        12.99        19.07         3.68 
TCGA-CN-A499 TCGA-CN-A49B TCGA-CN-A63W TCGA-CQ-5327 TCGA-CQ-7064 TCGA-CR-6484 
       23.57        29.72        12.39        54.58        64.87        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-A45R TCGA-CV-A465 TCGA-CV-A6JY 
        2.50         4.96         2.10       180.16         7.07        21.24 
TCGA-D6-6826 TCGA-D6-A6EM TCGA-F7-A50J TCGA-F7-A620 TCGA-IQ-A61L TCGA-IQ-A6SH 
       11.44         7.63        31.13        17.85        13.68        15.48 
TCGA-KU-A6H7 TCGA-MZ-A6I9 TCGA-P3-A5Q6 TCGA-QK-A8Z7 TCGA-QK-AA3K TCGA-T3-A92N 
       19.27        16.08        15.78        12.89         8.32         3.12 
TCGA-UF-A71E TCGA-KU-A66T 
       49.45        18.15 

$`2Q LOSS WILD-TYPE`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-A4IG TCGA-BA-A4II TCGA-BB-A5HU 
        9.30        37.28        20.48        28.11        30.18        25.71 
TCGA-CN-4727 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6992 
       51.29         9.07         9.24        52.08        11.08        35.05 
TCGA-CN-6997 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-6221 TCGA-CQ-7063 
       32.48        19.82        24.39        48.20        32.88        70.13 
TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-A4C7 TCGA-CR-6478 TCGA-CX-7082 TCGA-CX-7219 
       16.73        43.04        11.61         6.02         0.36        34.36 
TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-H7-A6C5 TCGA-HD-8634 TCGA-HD-8635 
       30.94        14.04        46.32        21.11        12.66        22.85 
TCGA-UF-A71D TCGA-UF-A7JV TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4078 
       48.03         2.96         3.35        15.19        13.64         9.07 
TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5558 
       26.50        23.74        57.93        17.10        23.84        65.59 
TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6872 TCGA-BA-7269 TCGA-BA-A4IF 
       15.52        21.17        14.83        12.62        41.85        29.42 
TCGA-BA-A4IH TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE 
       20.45        27.95        11.54         7.10         5.69        14.47 
TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DI TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BA-A8YP 
        7.82         2.27        11.05        13.38        20.48        16.41 
TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 
        6.15       105.90         9.14         4.80         4.41        18.38 
TCGA-BB-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-A5HY TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO 
       71.05        20.52        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-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-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-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-6019 TCGA-CN-6020 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6994 
       28.04        34.13         6.74        10.45        32.22        38.89 
TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A49A TCGA-CN-A49C 
       17.42        11.74        35.01        25.41        17.29        21.21 
TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 
        7.40        31.69        22.32        16.57         4.41        12.07 
TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5324 TCGA-CQ-5325 
        2.70        23.44        20.88        19.53        52.37        21.50 
TCGA-CQ-5326 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 
        2.93        70.45        62.37        45.99        10.42        11.21 
TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6220 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6225 
        4.24        41.19        32.38        46.95        56.58        13.25 
TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7065 TCGA-CQ-7069 TCGA-CQ-7071 
        4.24        14.99        38.76        53.52        41.88        43.10 
TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE 
       77.56        44.48        23.24        29.36        33.60        29.49 
TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 
       14.14        12.46        31.23        84.23        11.77        54.67 
TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6473 
       37.87        26.27        58.42        50.01        39.52        36.99 
TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6487 
       18.54        16.90        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-7365 
       12.46        22.78        15.75         9.27        47.18        39.16 
TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7372 TCGA-CR-7373 
       47.34        40.93        35.84         3.45        24.95        29.23 
TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7382 
        0.99        31.96         9.17        34.06        19.92        26.17 
TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 
       17.13        32.78        47.01        27.06        12.89        49.58 
TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 
       30.02        46.85        32.65        44.25        30.58        24.79 
TCGA-CR-7398 TCGA-CR-7401 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 
        5.13        35.41        48.39       139.43        17.16       129.21 
TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 
      108.95        76.24        19.20        17.95       107.51        94.88 
TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 
       76.50        91.53        80.12        17.92        13.35        23.05 
TCGA-CV-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-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-6940 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 
       21.90        26.43        11.24       140.78        19.79        12.03 
TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6954 
       42.38        15.09        30.08         6.08        53.95        65.82 
TCGA-CV-6955 TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-6962 TCGA-CV-7089 
       10.98         7.13         8.42        28.34         4.14        64.83 
TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 
      172.67       111.16        18.81        12.66         7.99         9.01 
TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-7178 
        5.26         1.84        52.31        12.92        21.80        71.21 
TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7242 
       10.75       130.88        77.16         4.73        89.65        36.00 
TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7253 
       31.36        26.20        18.97        17.13        95.34        11.87 
TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7407 TCGA-CV-7409 
       47.97        49.71        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-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-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-D6-6827 TCGA-D6-8568 
        9.60        23.05         2.53        16.14        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        23.34        58.45        37.25 
TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7594 
       33.86        18.02        46.45        20.45        37.58        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-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A622 TCGA-F7-A623 
        3.02        18.94        24.95         0.46        11.80        20.25 
TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A76A TCGA-HD-7229 
       12.43        13.38        15.16        15.06        20.94        33.76 
TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-7917 TCGA-HD-8224 
       28.47        25.74        21.93        27.48        27.48        14.66 
TCGA-HD-8314 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 
       22.03         0.36        13.84         4.27         3.65         6.90 
TCGA-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-A61O TCGA-IQ-A6SG 
       37.41         0.07        33.57         5.29        13.84        19.04 
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-A5QA 
        6.25        15.42         7.13        17.98        29.92        71.74 
TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 
       51.25        10.85        36.82        47.01        19.00        75.55 
TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-P3-A6T8 
       18.97         2.04        29.00        12.99        16.01        13.15 
TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II 
       21.07        21.21        23.15         7.30        21.47         9.34 
TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z8 TCGA-QK-A8Z9 
       12.72        27.39        21.07        19.73         5.62        14.76 
TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX 
       12.20        17.82        15.32        12.72        16.96         6.87 
TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-T3-A92M TCGA-TN-A7HI TCGA-TN-A7HJ 
       15.91         7.10        32.45        13.71        13.55        13.25 
TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A7J9 
       20.35        64.80        54.67         2.83        49.51        44.65 
TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ 
       74.47        17.95        24.30        55.43        29.46        18.05 
TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UP-A6WW TCGA-WA-A7GZ 
       13.94        20.75        22.36        32.65        17.03        20.55 
TCGA-WA-A7H4 TCGA-KU-A66S 
       14.56        13.35 

  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            21.340 
[1] "2.1 - 180.2 (17.0)" "0.1 - 211.0 (21.3)"
[1] "hr=" "1.1"
D45V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  2Q LOSS MUTATED         0        3        14        20         0         0
  2Q LOSS WILD-TYPE      27       73        68       232        12         1
D45V3, multiclass
           clus
vv          2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  STAGE I                 0                27
  STAGE II                3                73
  STAGE III              14                68
  STAGE IVA              20               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
  2Q LOSS MUTATED       2  10  12  14
  2Q LOSS WILD-TYPE    48 127  88 159
D45V4, multiclass
       clus
vv      2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  T0+T1               2                48
  T2                 10               127
  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    12  12  13   0
  2Q LOSS WILD-TYPE 167  56 155   8
D45V5, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  N0              12               167
  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 173   1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED     17    0
  2Q LOSS WILD-TYPE  173    1
   clus
vv  2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  0              17               173
  1               0                 1
[1] 2 2
[1] FALSE
D45V7, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED    20  24
  2Q LOSS WILD-TYPE 120 358
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED     20   24
  2Q LOSS WILD-TYPE  120  358
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  FEMALE              20               120
  MALE                24               358
[1] 2 2
[1] FALSE
D45V8, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED    17  27
  2Q LOSS WILD-TYPE 145 274
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED     17   27
  2Q LOSS WILD-TYPE  145  274
     clus
vv    2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  NO               17               145
  YES              27               274
[1] 2 2
[1] FALSE
                   vv
clus                HEAD & NECK SQUAMOUS CELL CARCINOMA
  2Q LOSS MUTATED                                    42
  2Q LOSS WILD-TYPE                                 469
                   vv
clus                HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  2Q LOSS MUTATED                                                   2
  2Q LOSS WILD-TYPE                                                 8
                   vv
clus                HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  2Q LOSS MUTATED                                                           0
  2Q LOSS WILD-TYPE                                                         1
D45V9, multiclass
                                                           clus
vv                                                          2Q LOSS MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                    42
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       2
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT               0
                                                           clus
vv                                                          2Q LOSS WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                     469
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                         8
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                 1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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    36
  2Q LOSS WILD-TYPE                        43   410
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                                         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"
D45V14, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED     4  37
  2Q LOSS WILD-TYPE  22 422
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      4   37
  2Q LOSS WILD-TYPE   22  422
                        clus
vv                       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   4                22
  NOT HISPANIC OR LATINO              37               422
[1] 2 2
[1] FALSE

Clustering(46) Variable = 3P LOSS MUTATION ANALYSIS
D46V1, survival
                   sevent
clus2                 0   1
  3P LOSS MUTATED   158 136
  3P LOSS WILD-TYPE 143  83
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
              294               226 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
              136                83 
$`3P LOSS MUTATED`
TCGA-BA-4075 TCGA-BA-6871 TCGA-BA-A4II TCGA-BB-A5HU TCGA-CN-6024 TCGA-CN-6992 
        9.30         3.55        30.18        25.71        11.08        35.05 
TCGA-CN-6997 TCGA-CN-A6V3 TCGA-CQ-6221 TCGA-CQ-7067 TCGA-CQ-A4C7 TCGA-CR-6478 
       32.48        24.39        32.88        16.73        11.61         6.02 
TCGA-CX-7082 TCGA-CX-7219 TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-H7-A6C5 
        0.36        34.36        30.94        14.04        46.32        21.11 
TCGA-HD-8635 TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-5149 
       22.85         3.35        15.19        13.64         9.07        26.50 
TCGA-BA-5555 TCGA-BA-5558 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6872 TCGA-BA-7269 
       17.10        65.59        21.17        14.83        12.62        41.85 
TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BA-A6DI TCGA-BA-A6DL 
       27.95        11.54         7.10        14.47        11.05        20.48 
TCGA-BA-A8YP TCGA-BB-4224 TCGA-BB-4227 TCGA-BB-7862 TCGA-BB-7870 TCGA-BB-7871 
       16.41         9.14         4.41        36.72        66.28        24.66 
TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-8601 TCGA-BB-A5HZ TCGA-BB-A6UO TCGA-C9-A47Z 
       38.40        71.05        20.52        27.19         8.81         6.28 
TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4735 TCGA-CN-4736 
       38.04         4.67        56.68        12.89        57.11        12.99 
TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4742 TCGA-CN-5355 
       20.55        14.33        45.83        27.58        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-5373 TCGA-CN-6011 TCGA-CN-6012 
       11.54        11.84        11.57        52.08        30.67        48.00 
TCGA-CN-6016 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6989 TCGA-CN-6995 TCGA-CN-6996 
       47.44        19.07        34.13        32.22         3.68        17.42 
TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A63T 
       11.74        35.01        25.41        17.29        29.72         7.40 
TCGA-CN-A63U TCGA-CN-A63W TCGA-CN-A640 TCGA-CN-A641 TCGA-CQ-5326 TCGA-CQ-5330 
       31.69        12.39         4.41        12.07         2.93        62.37 
TCGA-CQ-5332 TCGA-CQ-6218 TCGA-CQ-6220 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 
       10.42        41.19        32.38        56.58         4.24        14.99 
TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7069 TCGA-CQ-7072 TCGA-CQ-A4C6 
       38.76        64.87        53.52        41.88        77.56        44.48 
TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CI TCGA-CR-5243 
       23.24        29.36        33.60        29.49        31.23        84.23 
TCGA-CR-5247 TCGA-CR-5250 TCGA-CR-6473 TCGA-CR-6477 TCGA-CR-6480 TCGA-CR-6482 
       11.77        26.27        36.99        16.90        11.90        11.34 
TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7367 TCGA-CR-7369 
       22.78        15.75         9.27        47.18        47.34        35.84 
TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7377 TCGA-CR-7379 
        3.45         3.09        24.95        29.23         9.17        34.06 
TCGA-CR-7380 TCGA-CR-7383 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7390 TCGA-CR-7397 
       19.92        17.13        47.01        27.06        49.58        24.79 
TCGA-CR-7398 TCGA-CR-7401 TCGA-CR-7402 TCGA-CV-5430 TCGA-CV-5432 TCGA-CV-5434 
        5.13        35.41        29.95       139.43       129.21       108.95 
TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5444 
       76.24        19.20        17.95       107.51        94.88        80.12 
TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5978 TCGA-CV-5979 
       17.92        13.35        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-6941 TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-6951 
       20.52        11.24        12.03        42.38        15.09        30.08 
TCGA-CV-6952 TCGA-CV-6954 TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-6961 
        6.08        65.82         7.13         8.42        28.34         2.50 
TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7099 TCGA-CV-7100 
        4.14        64.83       111.16        18.81         7.99         9.01 
TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-7180 TCGA-CV-7242 
        5.26         1.84        12.92        21.80        10.75        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-7255 TCGA-CV-7263 TCGA-CV-7410 TCGA-CV-7413 TCGA-CV-7414 TCGA-CV-7416 
        2.10        18.41       210.97         9.67         0.46        25.08 
TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7428 TCGA-CV-7429 
       25.94        34.09       100.57        14.89        54.94         3.52 
TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-A45R TCGA-CV-A45U 
       16.27        84.49         7.17       153.86       180.16        35.47 
TCGA-CV-A45W TCGA-CV-A45X TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A465 
       45.96         6.51        48.20        60.43        67.86         7.07 
TCGA-CV-A6JE TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JZ TCGA-CV-A6K1 TCGA-CX-7086 
       35.34        28.01         3.62        23.47        22.52        18.84 
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-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES 
       24.95        25.32        24.95        13.94        12.10        12.79 
TCGA-D6-A74Q TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-F7-7848 
       23.34        33.86        18.02        20.45        37.58        37.18 
TCGA-F7-8298 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61W 
       32.71        20.25         3.02        31.13        18.94         0.46 
TCGA-F7-A620 TCGA-F7-A622 TCGA-H7-8502 TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7831 
       17.85        11.80        15.06        33.76        28.47        21.93 
TCGA-HD-7832 TCGA-HD-8224 TCGA-HD-A633 TCGA-HD-A6HZ TCGA-IQ-7630 TCGA-IQ-A61G 
       27.48        14.66        13.84         3.65        15.95        11.84 
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-IQ-A6SH TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67D TCGA-P3-A5QA TCGA-P3-A6T3 
       15.48        14.37         7.96         1.84        71.74        18.97 
TCGA-P3-A6T4 TCGA-P3-A6T7 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IH TCGA-QK-A6V9 
        2.04        16.01        21.07        21.21        21.47        27.39 
TCGA-QK-A6VB TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K 
       21.07        14.76        12.20        17.82        15.32         8.32 
TCGA-T2-A6WZ TCGA-T3-A92M TCGA-T3-A92N TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A 
       15.91        13.71         3.12        64.80        54.67         2.83 
TCGA-UF-A71B TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF 
       49.51        49.45        44.65        17.95        24.30        55.43 
TCGA-UF-A7JH TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS TCGA-WA-A7GZ TCGA-KU-A66T 
       29.46        13.94        20.75        22.36        20.55        18.15 

$`3P LOSS WILD-TYPE`
TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-A4IG TCGA-CN-4727 TCGA-CN-6021 
       37.28        20.48        68.48        28.11        51.29         9.07 
TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-A6V1 TCGA-CQ-5323 TCGA-CQ-7063 TCGA-CQ-7068 
        9.24        52.08        19.82        48.20        70.13        43.04 
TCGA-CR-6472 TCGA-DQ-7593 TCGA-HD-8634 TCGA-UF-A71D TCGA-UF-A7JV TCGA-BA-5151 
       34.52        40.24        12.66        48.03         2.96        23.74 
TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5556 TCGA-BA-6868 TCGA-BA-6873 TCGA-BA-A4IF 
       42.35        57.93        23.84        15.52         4.01        29.42 
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-7864 
      105.90         4.80        18.38        22.42        33.70        50.20 
TCGA-BB-7866 TCGA-BB-A5HY TCGA-BB-A6UM TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 
       44.98        10.55        12.92        12.69        48.76        55.86 
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-6010 TCGA-CN-6013 TCGA-CN-6017 TCGA-CN-6020 TCGA-CN-6988 
       56.94        50.07        23.90        28.04         6.74        10.45 
TCGA-CN-6994 TCGA-CN-A499 TCGA-CN-A49C TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A642 
       38.89        23.57        21.21        22.32        16.57         2.70 
TCGA-CN-A6UY TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 
       23.44        20.88        19.53        52.37        21.50        54.58 
TCGA-CQ-5329 TCGA-CQ-5331 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6223 TCGA-CQ-6225 
       70.45        45.99        11.21         4.24        46.95        13.25 
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-6474 TCGA-CR-6481 TCGA-CR-6484 TCGA-CR-6487 
       50.01        39.52        18.54        10.22        11.64         7.69 
TCGA-CR-6488 TCGA-CR-7365 TCGA-CR-7368 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7382 
       12.46        39.16        40.93         0.99        31.96        26.17 
TCGA-CR-7385 TCGA-CR-7389 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 
       32.78        12.89        30.02        46.85        32.65        44.25 
TCGA-CR-7395 TCGA-CR-7399 TCGA-CR-7404 TCGA-CV-5431 TCGA-CV-5442 TCGA-CV-5443 
       30.58         5.95        48.39        17.16        76.50        91.53 
TCGA-CV-5971 TCGA-CV-5977 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6938 TCGA-CV-6939 
       23.05        60.49        21.07        62.43         4.73        21.90 
TCGA-CV-6940 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6953 TCGA-CV-6955 TCGA-CV-7090 
       26.43       140.78        19.79        53.95        10.98       172.67 
TCGA-CV-7097 TCGA-CV-7103 TCGA-CV-7178 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7236 
       12.66        52.31        71.21       130.88        77.16         4.73 
TCGA-CV-7238 TCGA-CV-7243 TCGA-CV-7250 TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7407 
       89.65        31.36        95.34        49.71        57.47        35.54 
TCGA-CV-7409 TCGA-CV-7411 TCGA-CV-7415 TCGA-CV-7421 TCGA-CV-7425 TCGA-CV-7427 
       17.85        89.33        22.85         0.07        56.48       156.49 
TCGA-CV-7433 TCGA-CV-7437 TCGA-CV-7438 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45P 
       19.76        16.64         6.38        22.19        27.98        21.01 
TCGA-CV-A45Q TCGA-CV-A45T TCGA-CV-A45V TCGA-CV-A45Y TCGA-CV-A463 TCGA-CV-A464 
      169.38       159.65         1.05        88.87         0.76        56.61 
TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JM TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JY 
       15.25         5.98         6.38        29.79         6.48        21.24 
TCGA-CV-A6K0 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-D6-6515 TCGA-D6-6824 TCGA-D6-6827 
       19.92        10.42        10.55        13.25         2.53        18.67 
TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EN TCGA-DQ-5624 
       17.72        12.36        28.77         7.63        22.59        58.45 
TCGA-DQ-5625 TCGA-DQ-7590 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-8489 
       37.25        46.45        40.04        39.12        41.59        21.63 
TCGA-F7-A61V TCGA-F7-A623 TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-A76A 
       24.95        20.25        12.43        13.38        15.16        20.94 
TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8314 TCGA-HD-A4C1 TCGA-HD-A634 TCGA-HD-A6I0 
       25.74        27.48        22.03         0.36         4.27         6.90 
TCGA-HL-7533 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61K TCGA-KU-A6H7 
       34.75        38.53        14.50        37.71         5.29        19.27 
TCGA-KU-A6H8 TCGA-MT-A67A TCGA-MT-A67F TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A5BI 
       10.75        30.05        12.62         6.25        15.42         7.13 
TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5Q6 TCGA-P3-A5QE TCGA-P3-A5QF 
       16.08        17.98        29.92        15.78        51.25        10.85 
TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T5 TCGA-P3-A6T6 
       36.82        47.01        19.00        75.55        29.00        12.99 
TCGA-P3-A6T8 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6VC 
       13.15        23.15         7.30         9.34        12.72        19.73 
TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6X0 
       12.89         5.62        12.72        16.96         6.87         7.10 
TCGA-T2-A6X2 TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A7JA TCGA-UF-A7JJ 
       32.45        13.55        13.25        20.35        74.47        18.05 
TCGA-UF-A7JT TCGA-UP-A6WW TCGA-WA-A7H4 TCGA-KU-A66S 
       32.65        17.03        14.56        13.35 

  3P LOSS MUTATED 3P LOSS WILD-TYPE 
             0.07              0.07 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
           210.97            172.67 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
           20.535            21.965 
[1] "0.1 - 211.0 (20.5)" "0.1 - 172.7 (22.0)"
[1] "hr=" "1.4"
D46V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  3P LOSS MUTATED        15       40        47       152         9         0
  3P LOSS WILD-TYPE      12       36        35       100         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             152               100
  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  66 106
  3P LOSS WILD-TYPE    24  66  34  67
D46V4, multiclass
       clus
vv      3P LOSS MUTATED 3P LOSS WILD-TYPE
  T0+T1              26                24
  T2                 71                66
  T3                 66                34
  T4                106                67
[1] 4 2
[1] TRUE
[1] "dimension of 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   101  38 107   5
  3P LOSS WILD-TYPE  78  30  61   3
D46V5, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  N0             101                78
  N1              38                30
  N2             107                61
  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  79   1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED    111    0
  3P LOSS WILD-TYPE   79    1
   clus
vv  3P LOSS MUTATED 3P LOSS WILD-TYPE
  0             111                79
  1               0                 1
[1] 2 2
[1] FALSE
D46V7, binary
                   cls
clus                  0   1
  3P LOSS MUTATED    66 230
  3P LOSS WILD-TYPE  74 152
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     66  230
  3P LOSS WILD-TYPE   74  152
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  FEMALE              66                74
  MALE               230               152
[1] 2 2
[1] FALSE
D46V8, binary
                   cls
clus                  0   1
  3P LOSS MUTATED    90 169
  3P LOSS WILD-TYPE  72 132
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     90  169
  3P LOSS WILD-TYPE   72  132
     clus
vv    3P LOSS MUTATED 3P LOSS WILD-TYPE
  NO               90                72
  YES             169               132
[1] 2 2
[1] FALSE
                   vv
clus                HEAD & NECK SQUAMOUS CELL CARCINOMA
  3P LOSS MUTATED                                   292
  3P LOSS WILD-TYPE                                 219
                   vv
clus                HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  3P LOSS MUTATED                                                   3
  3P LOSS WILD-TYPE                                                 7
                   vv
clus                HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  3P LOSS MUTATED                                                           1
  3P LOSS WILD-TYPE                                                         0
D46V9, multiclass
                                                           clus
vv                                                          3P LOSS MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                   292
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       3
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT               1
                                                           clus
vv                                                          3P LOSS WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                     219
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                         7
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                 0
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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                          37   241
  3P LOSS WILD-TYPE                        11   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                     37                11
  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    16 253
  3P LOSS WILD-TYPE  10 206
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     16  253
  3P LOSS WILD-TYPE   10  206
                        clus
vv                       3P LOSS MUTATED 3P LOSS WILD-TYPE
  HISPANIC OR LATINO                  16                10
  NOT HISPANIC OR LATINO             253               206
[1] 2 2
[1] FALSE

Clustering(47) Variable = 3Q LOSS MUTATION ANALYSIS
D47V1, survival
                   sevent
clus2                 0   1
  3Q LOSS MUTATED    27  31
  3Q LOSS WILD-TYPE 274 188
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               58               462 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               31               188 
$`3Q LOSS MUTATED`
TCGA-BA-6871 TCGA-CN-6997 TCGA-DQ-7588 TCGA-H7-A6C5 TCGA-BA-4076 TCGA-BA-5555 
        3.55        32.48        14.04        21.11        13.64        17.10 
TCGA-BA-5558 TCGA-BA-A6DB TCGA-BA-A6DL TCGA-BB-7870 TCGA-BB-A5HZ TCGA-CN-4725 
       65.59         7.10        20.48        66.28        27.19        38.04 
TCGA-CN-4735 TCGA-CN-4738 TCGA-CN-5365 TCGA-CN-6018 TCGA-CN-6995 TCGA-CN-A63U 
       57.11        14.33        11.54        19.07         3.68        31.69 
TCGA-CN-A63W TCGA-CQ-5332 TCGA-CQ-6224 TCGA-CQ-6229 TCGA-CQ-A4CD TCGA-CR-6473 
       12.39        10.42        56.58        38.76        33.60        36.99 
TCGA-CR-6493 TCGA-CR-7373 TCGA-CR-7377 TCGA-CR-7383 TCGA-CR-7390 TCGA-CR-7398 
        9.27        29.23         9.17        17.13        49.58         5.13 
TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5966 TCGA-CV-5976 TCGA-CV-6441 TCGA-CV-6937 
      108.95        76.24        17.92        48.59         9.60        20.52 
TCGA-CV-6950 TCGA-CV-6952 TCGA-CV-6961 TCGA-CV-7100 TCGA-CV-7252 TCGA-CV-7255 
       15.09         6.08         2.50         9.01         4.96         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-F7-A620 TCGA-HD-7753 TCGA-HD-7832 TCGA-IQ-A61I TCGA-MT-A51W TCGA-MT-A51X 
       17.85        28.47        27.48         0.07        14.37         7.96 
TCGA-QK-A6IH TCGA-QK-A8ZB TCGA-QK-AA3K TCGA-WA-A7GZ 
       21.47        17.82         8.32        20.55 

$`3Q LOSS WILD-TYPE`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-A4IG TCGA-BA-A4II 
        9.30        37.28        20.48        68.48        28.11        30.18 
TCGA-BB-A5HU TCGA-CN-4727 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 
       25.71        51.29         9.07         9.24        52.08        11.08 
TCGA-CN-6992 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-6221 TCGA-CQ-7063 
       35.05        19.82        24.39        48.20        32.88        70.13 
TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-A4C7 TCGA-CR-6472 TCGA-CR-6478 TCGA-CX-7082 
       16.73        43.04        11.61        34.52         6.02         0.36 
TCGA-CX-7219 TCGA-DQ-5629 TCGA-DQ-7589 TCGA-DQ-7593 TCGA-HD-8634 TCGA-HD-8635 
       34.36        30.94        46.32        40.24        12.66        22.85 
TCGA-UF-A71D TCGA-UF-A7JV TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4078 TCGA-BA-5149 
       48.03         2.96         3.35        15.19         9.07        26.50 
TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5556 TCGA-BA-6868 TCGA-BA-6869 
       23.74        42.35        57.93        23.84        15.52        21.17 
TCGA-BA-6870 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IH 
       14.83        12.62         4.01        41.85        29.42        20.45 
TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG 
       27.95        11.54         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 
        4.80         4.41        18.38        22.42        36.72        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-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-4726 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 
       55.86         4.67        56.68        12.89        26.86        32.81 
TCGA-CN-4733 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 
       52.14        12.99        20.55        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-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-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 
       52.08        56.94        50.07        30.67        48.00        23.90 
TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6988 TCGA-CN-6989 
       47.44        28.04        34.13         6.74        10.45        32.22 
TCGA-CN-6994 TCGA-CN-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-A6V6 TCGA-CN-A6V7 
        4.41        12.07         2.70        23.44        20.88        19.53 
TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 
       52.37        21.50         2.93        54.58        70.45        62.37 
TCGA-CQ-5331 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6220 TCGA-CQ-6223 
       45.99        11.21         4.24        41.19        32.38        46.95 
TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7069 
       13.25         4.24        14.99        64.87        53.52        41.88 
TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CE 
       43.10        77.56        44.48        23.24        29.36        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-6474 
       37.87        26.27        58.42        50.01        39.52        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-7364 TCGA-CR-7365 TCGA-CR-7367 
       12.46        22.78        15.75        47.18        39.16        47.34 
TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7374 
       40.93        35.84         3.45         3.09        24.95         0.99 
TCGA-CR-7376 TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7385 TCGA-CR-7386 
       31.96        34.06        19.92        26.17        32.78        47.01 
TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 
       27.06        12.89        30.02        46.85        32.65        44.25 
TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 
       30.58        24.79         5.95        35.41        29.95        48.39 
TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 
      139.43        17.16       129.21        19.20        17.95       107.51 
TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5970 TCGA-CV-5971 
       94.88        76.50        91.53        80.12        13.35        23.05 
TCGA-CV-5973 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 
       86.83        60.49         7.07        43.23        54.74        21.07 
TCGA-CV-6436 TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6938 
       62.43        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-6953 TCGA-CV-6954 TCGA-CV-6955 TCGA-CV-6956 
       42.38        30.08        53.95        65.82        10.98         7.13 
TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7091 
        8.42        28.34         4.14        64.83       172.67       111.16 
TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7103 
       18.81        12.66         7.99         5.26         1.84        52.31 
TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-7178 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 
       12.92        21.80        71.21        10.75       130.88        77.16 
TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7247 
        4.73        89.65        36.00        31.36        26.20        18.97 
TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7263 
       17.13        95.34        11.87        47.97        49.71        18.41 
TCGA-CV-7406 TCGA-CV-7407 TCGA-CV-7409 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 
       57.47        35.54        17.85       210.97        89.33         9.67 
TCGA-CV-7414 TCGA-CV-7415 TCGA-CV-7416 TCGA-CV-7421 TCGA-CV-7422 TCGA-CV-7423 
        0.46        22.85        25.08         0.07        34.09       100.57 
TCGA-CV-7424 TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7429 TCGA-CV-7432 TCGA-CV-7433 
       14.89        56.48       156.49         3.52        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-A45Y TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A463 
       45.96        88.87        48.20        60.43        67.86         0.76 
TCGA-CV-A464 TCGA-CV-A465 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JM TCGA-CV-A6JN 
       56.61         7.07        15.25         5.98         6.38        29.79 
TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 
        6.48        28.01         3.62        21.24        23.47        19.92 
TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-A4AQ TCGA-D6-6515 
       22.52        10.42        10.55        18.84        51.12        13.25 
TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6827 
       25.41         9.60        23.05         2.53        16.14        18.67 
TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM 
       24.95        25.32        17.72        12.36        28.77         7.63 
TCGA-D6-A6EN TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q 
       22.59        24.95        13.94        12.10        12.79        23.34 
TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7590 TCGA-DQ-7591 
       58.45        37.25        33.86        18.02        46.45        20.45 
TCGA-DQ-7592 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 
       37.58        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-A76A TCGA-HD-7229 TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7917 
       15.06        20.94        33.76        25.74        21.93        27.48 
TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ 
       14.66        22.03         0.36        13.84         4.27         3.65 
TCGA-HD-A6I0 TCGA-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-A61J TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O 
       11.84        37.41        33.57         5.29        13.68        13.84 
TCGA-IQ-A6SG TCGA-IQ-A6SH TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A67A TCGA-MT-A67D 
       19.04        15.48        19.27        10.75        30.05         1.84 
TCGA-MT-A67F TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-MZ-A7D7 
       12.62         6.25        15.42         7.13        16.08        17.98 
TCGA-P3-A5Q5 TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW 
       29.92        15.78        71.74        51.25        10.85        36.82 
TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T5 
       47.01        19.00        75.55        18.97         2.04        29.00 
TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF 
       12.99        16.01        13.15        21.07        21.21        23.15 
TCGA-QK-A6IG TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC 
        7.30         9.34        12.72        27.39        21.07        19.73 
TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-AA3J TCGA-RS-A6TO 
       12.89         5.62        14.76        12.20        15.32        12.72 
TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-T3-A92M 
       16.96         6.87        15.91         7.10        32.45        13.71 
TCGA-T3-A92N TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A719 
        3.12        13.55        13.25        20.35        64.80        54.67 
TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC 
        2.83        49.51        49.45        44.65        74.47        17.95 
TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO 
       24.30        55.43        29.46        18.05        13.94        20.75 
TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UP-A6WW TCGA-WA-A7H4 TCGA-KU-A66S TCGA-KU-A66T 
       22.36        32.65        17.03        14.56        13.35        18.15 

  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 
           17.835            21.715 
[1] "0.1 - 109.0 (17.8)" "0.1 - 211.0 (21.7)"
[1] "hr=" "1.6"
D47V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  3Q LOSS MUTATED         4        6         4        34         2         0
  3Q LOSS WILD-TYPE      23       70        78       218        10         1
D47V3, multiclass
           clus
vv          3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  STAGE I                 4                23
  STAGE II                6                70
  STAGE III               4                78
  STAGE IVA              34               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       7  11  11  23
  3Q LOSS WILD-TYPE    43 126  89 150
D47V4, multiclass
       clus
vv      3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  T0+T1               7                43
  T2                 11               126
  T3                 11                89
  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
  3Q LOSS MUTATED    24   5  22   1
  3Q LOSS WILD-TYPE 155  63 146   7
D47V5, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  N0              24               155
  N1               5                63
  N2              22               146
  N3               1                 7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V6, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED    17   0
  3Q LOSS WILD-TYPE 173   1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED     17    0
  3Q LOSS WILD-TYPE  173    1
   clus
vv  3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  0              17               173
  1               0                 1
[1] 2 2
[1] FALSE
D47V7, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED    12  46
  3Q LOSS WILD-TYPE 128 336
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED     12   46
  3Q LOSS WILD-TYPE  128  336
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  FEMALE              12               128
  MALE                46               336
[1] 2 2
[1] FALSE
D47V8, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED    20  30
  3Q LOSS WILD-TYPE 142 271
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED     20   30
  3Q LOSS WILD-TYPE  142  271
     clus
vv    3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  NO               20               142
  YES              30               271
[1] 2 2
[1] FALSE
                   vv
clus                HEAD & NECK SQUAMOUS CELL CARCINOMA
  3Q LOSS MUTATED                                    58
  3Q LOSS WILD-TYPE                                 453
                   vv
clus                HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  3Q LOSS MUTATED                                                   0
  3Q LOSS WILD-TYPE                                                10
                   vv
clus                HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  3Q LOSS MUTATED                                                           0
  3Q LOSS WILD-TYPE                                                         1
D47V9, multiclass
                                                           clus
vv                                                          3Q LOSS MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                    58
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       0
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT               0
                                                           clus
vv                                                          3Q LOSS WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                     453
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        10
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                 1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V10, continuous
D47V11, continuous
D47V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  3Q LOSS MUTATED                                  0     0
  3Q LOSS WILD-TYPE                                2    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  3Q LOSS MUTATED                           9    49
  3Q LOSS WILD-TYPE                        39   397
D47V13, multiclass
                                  clus
vv                                 3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                      9                39
  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"
D47V14, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED     1  55
  3Q LOSS WILD-TYPE  25 404
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      1   55
  3Q LOSS WILD-TYPE   25  404
                        clus
vv                       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                25
  NOT HISPANIC OR LATINO              55               404
[1] 2 2
[1] FALSE

Clustering(48) Variable = 4P LOSS MUTATION ANALYSIS
D48V1, survival
                   sevent
clus2                 0   1
  4P LOSS MUTATED   109  84
  4P LOSS WILD-TYPE 192 135
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
              193               327 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               84               135 
$`4P LOSS MUTATED`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-6871 TCGA-BA-A4IG TCGA-CN-6021 
        9.30        37.28        20.48         3.55        28.11         9.07 
TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-7067 TCGA-CR-6472 
       35.05        32.48        24.39        48.20        16.73        34.52 
TCGA-CX-7082 TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-H7-A6C5 TCGA-BA-4074 
        0.36        30.94        14.04        46.32        21.11        15.19 
TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5555 TCGA-BA-6870 TCGA-BA-A4IF 
       13.64         9.07        26.50        17.10        14.83        29.42 
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-6989 TCGA-CN-6994 TCGA-CN-6995 
       48.00        19.07        34.13        32.22        38.89         3.68 
TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A499 TCGA-CN-A49B TCGA-CN-A63T TCGA-CN-A63U 
       11.74        35.01        23.57        29.72         7.40        31.69 
TCGA-CN-A63W TCGA-CN-A641 TCGA-CQ-6220 TCGA-CQ-6223 TCGA-CQ-6225 TCGA-CQ-6228 
       12.39        12.07        32.38        46.95        13.25        14.99 
TCGA-CQ-7064 TCGA-CQ-7072 TCGA-CQ-A4C9 TCGA-CQ-A4CD TCGA-CQ-A4CI TCGA-CR-5248 
       64.87        77.56        23.24        33.60        31.23        54.67 
TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7369 
        7.69        12.46        22.78        39.16        47.34        35.84 
TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7383 
        3.45         3.09        24.95        29.23         0.99        17.13 
TCGA-CR-7388 TCGA-CR-7390 TCGA-CR-7398 TCGA-CR-7404 TCGA-CV-5431 TCGA-CV-5432 
       27.06        49.58         5.13        48.39        17.16       129.21 
TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5440 TCGA-CV-5444 TCGA-CV-5978 
      108.95        76.24        19.20       107.51        80.12         7.07 
TCGA-CV-6441 TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6940 TCGA-CV-6941 
        9.60        90.12         2.14         9.70        26.43        11.24 
TCGA-CV-6942 TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6956 TCGA-CV-6961 
      140.78        42.38        15.09        30.08         7.13         2.50 
TCGA-CV-6962 TCGA-CV-7091 TCGA-CV-7097 TCGA-CV-7101 TCGA-CV-7103 TCGA-CV-7235 
        4.14       111.16        12.66         5.26        52.31        77.16 
TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7248 
        4.73        89.65        36.00        26.20        18.97        17.13 
TCGA-CV-7261 TCGA-CV-7407 TCGA-CV-7413 TCGA-CV-7415 TCGA-CV-7418 TCGA-CV-7422 
       49.71        35.54         9.67        22.85        25.94        34.09 
TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7435 TCGA-CV-7438 
      100.57        14.89        16.27        84.49       153.86         6.38 
TCGA-CV-7440 TCGA-CV-A45X TCGA-CV-A465 TCGA-D6-6516 TCGA-D6-6823 TCGA-D6-A4Z9 
       22.19         6.51         7.07        25.41        23.05        17.72 
TCGA-D6-A6EM TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A74Q TCGA-F7-8298 TCGA-F7-A50G 
        7.63        24.95        13.94        23.34        32.71        20.25 
TCGA-F7-A61S TCGA-F7-A61V TCGA-H7-8502 TCGA-HD-7753 TCGA-HD-7831 TCGA-HD-7917 
       18.94        24.95        15.06        28.47        21.93        27.48 
TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-A633 TCGA-HD-A6HZ TCGA-IQ-A61E TCGA-IQ-A61G 
       14.66        22.03        13.84         3.65        37.71        11.84 
TCGA-IQ-A61H TCGA-IQ-A61J TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A6I9 TCGA-MZ-A7D7 
       37.41        33.57         6.25        15.42        16.08        17.98 
TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T8 TCGA-QK-A6VB 
       15.78        71.74        36.82        47.01        13.15        21.07 
TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8ZA TCGA-QK-AA3J TCGA-QK-AA3K 
       19.73        12.89         5.62        12.20        15.32         8.32 
TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-T3-A92M TCGA-T3-A92N TCGA-UF-A71A TCGA-UF-A71B 
       15.91         7.10        13.71         3.12         2.83        49.51 
TCGA-UF-A7J9 TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JS 
       44.65        17.95        24.30        55.43        29.46        22.36 
TCGA-WA-A7GZ 
       20.55 

$`4P LOSS WILD-TYPE`
TCGA-BA-5559 TCGA-BA-A4II TCGA-BB-A5HU TCGA-CN-4727 TCGA-CN-6022 TCGA-CN-6023 
       68.48        30.18        25.71        51.29         9.24        52.08 
TCGA-CN-6024 TCGA-CN-A6V1 TCGA-CQ-6221 TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CQ-A4C7 
       11.08        19.82        32.88        70.13        43.04        11.61 
TCGA-CR-6478 TCGA-CX-7219 TCGA-DQ-7593 TCGA-HD-8634 TCGA-HD-8635 TCGA-UF-A71D 
        6.02        34.36        40.24        12.66        22.85        48.03 
TCGA-UF-A7JV TCGA-4P-AA8J TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5556 
        2.96         3.35        23.74        42.35        57.93        23.84 
TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 
       65.59        15.52        21.17        12.62         4.01        41.85 
TCGA-BA-A4IH TCGA-BA-A6DA TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG 
       20.45        11.54         5.69        14.47         7.82         2.27 
TCGA-BA-A6DI TCGA-BA-A6DJ TCGA-BB-4217 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 
       11.05        13.38         6.15         4.80         4.41        18.38 
TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7872 
       36.72        33.70        50.20        44.98        66.28        38.40 
TCGA-BB-A6UM TCGA-BB-A6UO TCGA-CN-4722 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4736 
       12.92         8.81        48.76        32.81        52.14        12.99 
TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-5356 TCGA-CN-5358 
       20.55        14.33        27.58        73.61        46.32         8.58 
TCGA-CN-5359 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5369 TCGA-CN-5370 
       12.39        11.54        11.84        11.57        12.49         8.52 
TCGA-CN-5373 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6020 TCGA-CN-6988 
       52.08        23.90        47.44        28.04         6.74        10.45 
TCGA-CN-6996 TCGA-CN-A498 TCGA-CN-A49A TCGA-CN-A49C TCGA-CN-A63V TCGA-CN-A63Y 
       17.42        25.41        17.29        21.21        22.32        16.57 
TCGA-CN-A640 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5324 
        4.41         2.70        23.44        20.88        19.53        52.37 
TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 
       21.50         2.93        54.58        70.45        62.37        45.99 
TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6224 TCGA-CQ-6227 
       10.42        11.21         4.24        41.19        56.58         4.24 
TCGA-CQ-6229 TCGA-CQ-7065 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4CB 
       38.76        53.52        41.88        43.10        44.48        29.36 
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-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6492 
       16.90        11.90        10.22        11.34        11.64        15.75 
TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7368 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 
        9.27        47.18        40.93        31.96         9.17        34.06 
TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7389 TCGA-CR-7391 
       19.92        26.17        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-7399 
       46.85        32.65        44.25        30.58        24.79         5.95 
TCGA-CR-7401 TCGA-CR-7402 TCGA-CV-5430 TCGA-CV-5439 TCGA-CV-5441 TCGA-CV-5442 
       35.41        29.95       139.43        17.95        94.88        76.50 
TCGA-CV-5443 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 
       91.53        17.92        13.35        23.05        86.83        48.59 
TCGA-CV-5977 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6936 
       60.49        43.23        54.74        21.07        62.43         5.46 
TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6952 
       20.52         4.73        21.90        19.79        12.03         6.08 
TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-6955 TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-7089 
       53.95        65.82        10.98         8.42        28.34        64.83 
TCGA-CV-7090 TCGA-CV-7095 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7102 TCGA-CV-7104 
      172.67        18.81         7.99         9.01         1.84        12.92 
TCGA-CV-7177 TCGA-CV-7178 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7243 TCGA-CV-7250 
       21.80        71.21        10.75       130.88        31.36        95.34 
TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7255 TCGA-CV-7263 TCGA-CV-7406 
        4.96        11.87        47.97         2.10        18.41        57.47 
TCGA-CV-7409 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7414 TCGA-CV-7416 TCGA-CV-7421 
       17.85       210.97        89.33         0.46        25.08         0.07 
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-7594 TCGA-DQ-7595 TCGA-DQ-7596 
       46.45        20.45        37.58        40.04        39.12        41.59 
TCGA-F7-7848 TCGA-F7-8489 TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61W TCGA-F7-A620 
       37.18        21.63         3.02        31.13         0.46        17.85 
TCGA-F7-A622 TCGA-F7-A623 TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-A76A 
       11.80        20.25        12.43        13.38        15.16        20.94 
TCGA-HD-7229 TCGA-HD-7754 TCGA-HD-7832 TCGA-HD-A4C1 TCGA-HD-A634 TCGA-HD-A6I0 
       33.76        25.74        27.48         0.36         4.27         6.90 
TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61I TCGA-IQ-A61K 
       34.75        15.95        38.53        14.50         0.07         5.29 
TCGA-IQ-A61L TCGA-IQ-A61O TCGA-IQ-A6SG TCGA-IQ-A6SH TCGA-KU-A6H7 TCGA-KU-A6H8 
       13.68        13.84        19.04        15.48        19.27        10.75 
TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-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        27.39 
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-A71E 
       13.55        13.25        20.35        64.80        54.67        49.45 
TCGA-UF-A7JA TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JT TCGA-UP-A6WW 
       74.47        18.05        13.94        20.75        32.65        17.03 
TCGA-WA-A7H4 TCGA-KU-A66S TCGA-KU-A66T 
       14.56        13.35        18.15 

  4P LOSS MUTATED 4P LOSS WILD-TYPE 
             0.36              0.07 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
           153.86            210.97 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
            22.36             20.88 
[1] "0.4 - 153.9 (22.4)" "0.1 - 211.0 (20.9)"
[1] "hr=" "1.1"
D48V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  4P LOSS MUTATED        13       23        31        98         5         1
  4P LOSS WILD-TYPE      14       53        51       154         7         0
D48V3, multiclass
           clus
vv          4P LOSS MUTATED 4P LOSS WILD-TYPE
  STAGE I                13                14
  STAGE II               23                53
  STAGE III              31                51
  STAGE IVA              98               154
  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  62
  4P LOSS WILD-TYPE    29  93  52 111
D48V4, multiclass
       clus
vv      4P LOSS MUTATED 4P LOSS WILD-TYPE
  T0+T1              21                29
  T2                 44                93
  T3                 48                52
  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
  4P LOSS MUTATED    64  27  68   5
  4P LOSS WILD-TYPE 115  41 100   3
D48V5, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  N0              64               115
  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 129   0
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     61    1
  4P LOSS WILD-TYPE  129    0
   clus
vv  4P LOSS MUTATED 4P LOSS WILD-TYPE
  0              61               129
  1               1                 0
[1] 2 2
[1] FALSE
D48V7, binary
                   cls
clus                  0   1
  4P LOSS MUTATED    44 149
  4P LOSS WILD-TYPE  96 233
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     44  149
  4P LOSS WILD-TYPE   96  233
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  FEMALE              44                96
  MALE               149               233
[1] 2 2
[1] FALSE
D48V8, binary
                   cls
clus                  0   1
  4P LOSS MUTATED    57 115
  4P LOSS WILD-TYPE 105 186
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     57  115
  4P LOSS WILD-TYPE  105  186
     clus
vv    4P LOSS MUTATED 4P LOSS WILD-TYPE
  NO               57               105
  YES             115               186
[1] 2 2
[1] FALSE
                   vv
clus                HEAD & NECK SQUAMOUS CELL CARCINOMA
  4P LOSS MUTATED                                   188
  4P LOSS WILD-TYPE                                 323
                   vv
clus                HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  4P LOSS MUTATED                                                   5
  4P LOSS WILD-TYPE                                                 5
                   vv
clus                HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  4P LOSS MUTATED                                                           0
  4P LOSS WILD-TYPE                                                         1
D48V9, multiclass
                                                           clus
vv                                                          4P LOSS MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                   188
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       5
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT               0
                                                           clus
vv                                                          4P LOSS WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                     323
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                         5
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                 1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V10, continuous
D48V11, continuous
D48V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  4P LOSS MUTATED                                  0     3
  4P LOSS WILD-TYPE                                2     8
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  4P LOSS MUTATED                          24   160
  4P LOSS WILD-TYPE                        24   286
D48V13, multiclass
                                  clus
vv                                 4P LOSS MUTATED 4P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          3                 8
  BLACK OR AFRICAN AMERICAN                     24                24
  WHITE                                        160               286
[1] 4 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    11 169
  4P LOSS WILD-TYPE  15 290
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     11  169
  4P LOSS WILD-TYPE   15  290
                        clus
vv                       4P LOSS MUTATED 4P LOSS WILD-TYPE
  HISPANIC OR LATINO                  11                15
  NOT HISPANIC OR LATINO             169               290
[1] 2 2
[1] FALSE

Clustering(49) Variable = 4Q LOSS MUTATION ANALYSIS
D49V1, survival
                   sevent
clus2                 0   1
  4Q LOSS MUTATED    83  68
  4Q LOSS WILD-TYPE 218 151
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
              151               369 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               68               151 
$`4Q LOSS MUTATED`
TCGA-BA-4075 TCGA-BA-5557 TCGA-BA-A4IG TCGA-CN-6021 TCGA-CN-6997 TCGA-CQ-5323 
        9.30        20.48        28.11         9.07        32.48        48.20 
TCGA-CQ-7067 TCGA-CR-6472 TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-H7-A6C5 
       16.73        34.52        30.94        14.04        46.32        21.11 
TCGA-HD-8634 TCGA-BA-4078 TCGA-BA-5555 TCGA-BA-6870 TCGA-BA-6873 TCGA-BA-A4IF 
       12.66         9.07        17.10        14.83         4.01        29.42 
TCGA-BA-A6D8 TCGA-BA-A6DB TCGA-BA-A6DI TCGA-BA-A8YP TCGA-BB-4227 TCGA-BB-7870 
       27.95         7.10        11.05        16.41         4.41        66.28 
TCGA-BB-7871 TCGA-BB-8596 TCGA-BB-8601 TCGA-BB-A5HY TCGA-C9-A47Z TCGA-C9-A480 
       24.66        71.05        20.52        10.55         6.28        12.69 
TCGA-CN-4725 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4735 TCGA-CN-4737 TCGA-CN-4739 
       38.04        56.68        12.89        57.11        20.55        45.83 
TCGA-CN-4742 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 
       13.05        12.39        71.31        50.07        30.67        48.00 
TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6998 
       19.07        34.13        32.22        38.89         3.68        11.74 
TCGA-CN-A497 TCGA-CN-A499 TCGA-CN-A49B TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63W 
       35.01        23.57        29.72         7.40        31.69        12.39 
TCGA-CN-A6V7 TCGA-CQ-6220 TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6228 TCGA-CQ-7064 
       19.53        32.38        56.58        13.25        14.99        64.87 
TCGA-CQ-7072 TCGA-CQ-A4C9 TCGA-CQ-A4CI TCGA-CR-5248 TCGA-CR-6484 TCGA-CR-6487 
       77.56        23.24        31.23        54.67        11.64         7.69 
TCGA-CR-6488 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 
       12.46        39.16        47.34         3.45         3.09        24.95 
TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7383 TCGA-CR-7392 TCGA-CR-7398 TCGA-CR-7404 
       29.23         0.99        17.13        46.85         5.13        48.39 
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-5444 TCGA-CV-5976 TCGA-CV-6003 TCGA-CV-6441 TCGA-CV-6933 TCGA-CV-6935 
       80.12        48.59        54.74         9.60        90.12         9.70 
TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6954 TCGA-CV-6956 TCGA-CV-6962 TCGA-CV-7091 
       11.24       140.78        65.82         7.13         4.14       111.16 
TCGA-CV-7097 TCGA-CV-7101 TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7180 TCGA-CV-7247 
       12.66         5.26        52.31        12.92        10.75        18.97 
TCGA-CV-7248 TCGA-CV-7261 TCGA-CV-7407 TCGA-CV-7413 TCGA-CV-7416 TCGA-CV-7418 
       17.13        49.71        35.54         9.67        25.08        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-D6-6823 
       22.19        35.47        60.43         7.07        18.84        23.05 
TCGA-D6-A6EM TCGA-D6-A6EP TCGA-D6-A74Q TCGA-DQ-7592 TCGA-F7-A50G TCGA-F7-A61S 
        7.63        13.94        23.34        37.58        20.25        18.94 
TCGA-HD-7831 TCGA-HD-A6HZ TCGA-IQ-A61H TCGA-IQ-A61J TCGA-MT-A67G TCGA-P3-A5Q6 
       21.93         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        12.89 
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-BA-4077 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4II TCGA-BB-A5HU TCGA-CN-4727 
       37.28        68.48         3.55        30.18        25.71        51.29 
TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6992 TCGA-CN-A6V1 TCGA-CN-A6V3 
        9.24        52.08        11.08        35.05        19.82        24.39 
TCGA-CQ-6221 TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CQ-A4C7 TCGA-CR-6478 TCGA-CX-7082 
       32.88        70.13        43.04        11.61         6.02         0.36 
TCGA-CX-7219 TCGA-DQ-7593 TCGA-HD-8635 TCGA-UF-A71D TCGA-UF-A7JV TCGA-4P-AA8J 
       34.36        40.24        22.85        48.03         2.96         3.35 
TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 
       15.19        13.64        26.50        23.74        42.35        57.93 
TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6872 TCGA-BA-7269 
       23.84        65.59        15.52        21.17        12.62        41.85 
TCGA-BA-A4IH TCGA-BA-A6DA TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG 
       20.45        11.54         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         4.80 
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-7872 TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO TCGA-CN-4722 TCGA-CN-4723 
       38.40        27.19        12.92         8.81        48.76        55.86 
TCGA-CN-4726 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4736 TCGA-CN-4738 
        4.67        26.86        32.81        52.14        12.99        14.33 
TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5363 
       27.58        73.61        42.02        46.32         8.58         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-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6020 
       52.08        56.94        23.90        47.44        28.04         6.74 
TCGA-CN-6988 TCGA-CN-6996 TCGA-CN-A498 TCGA-CN-A49A TCGA-CN-A49C TCGA-CN-A63V 
       10.45        17.42        25.41        17.29        21.21        22.32 
TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V6 
       16.57         4.41        12.07         2.70        23.44        20.88 
TCGA-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-6223 
       45.99        10.42        11.21         4.24        41.19        46.95 
TCGA-CQ-6227 TCGA-CQ-6229 TCGA-CQ-7065 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C6 
        4.24        38.76        53.52        41.88        43.10        44.48 
TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CR-5243 
       29.36        33.60        29.49        14.14        12.46        84.23 
TCGA-CR-5247 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 
       11.77        37.87        26.27        58.42        50.01        39.52 
TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 
       36.99        18.54        16.90        11.90        10.22        11.34 
TCGA-CR-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-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-7393 
       47.01        27.06        12.89        49.58        30.02        32.65 
TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 
       44.25        30.58        24.79         5.95        35.41        29.95 
TCGA-CV-5430 TCGA-CV-5436 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5966 
      139.43        19.20        94.88        76.50        91.53        17.92 
TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 
       13.35        23.05        86.83        60.49         7.07        43.23 
TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6934 TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6938 
       21.07        62.43         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       172.67        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 
       89.65        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-7421 TCGA-CV-7425 
      210.97        89.33         0.46        22.85         0.07        56.48 
TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7437 
      156.49        54.94        84.49        19.76         7.17        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-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-A6JY TCGA-CV-A6JZ 
       29.79         6.48        28.01         3.62        21.24        23.47 
TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-A4AQ TCGA-D6-6515 
       19.92        22.52        10.42        10.55        51.12        13.25 
TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6824 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-A4ZB TCGA-D6-A6EK TCGA-D6-A6EN 
       24.95        25.32        17.72        12.36        28.77        22.59 
TCGA-D6-A6EO TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 
       24.95        12.10        12.79        58.45        37.25        33.86 
TCGA-DQ-5631 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 
       18.02        46.45        20.45        40.04        39.12        41.59 
TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61V 
       37.18        32.71        21.63         3.02        31.13        24.95 
TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A623 TCGA-F7-A624 TCGA-H7-7774 
        0.46        17.85        11.80        20.25        12.43        13.38 
TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 
       15.16        15.06        20.94        33.76        28.47        25.74 
TCGA-HD-7832 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-A4C1 TCGA-HD-A633 
       27.48        27.48        14.66        22.03         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-A61I TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O 
       37.71        11.84         0.07         5.29        13.68        13.84 
TCGA-IQ-A6SG TCGA-IQ-A6SH TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X 
       19.04        15.48        19.27        10.75        14.37         7.96 
TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-MZ-A6I9 
       30.05         1.84        12.62        15.42         7.13        16.08 
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-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-A6IH TCGA-QK-A6II TCGA-QK-A6IJ 
       13.15        21.07        21.21        21.47         9.34        12.72 
TCGA-QK-A6V9 TCGA-QK-A6VC TCGA-QK-A8Z9 TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-RS-A6TO 
       27.39        19.73        14.76        17.82        15.32        12.72 
TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-TN-A7HI TCGA-TN-A7HJ 
       16.96         6.87         7.10        32.45        13.55        13.25 
TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71E 
       20.35        64.80        54.67         2.83        49.51        49.45 
TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JJ TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UP-A6WW 
       44.65        74.47        18.05        22.36        32.65        17.03 
TCGA-WA-A7H4 TCGA-KU-A66S TCGA-KU-A66T 
       14.56        13.35        18.15 

  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 
            20.75             21.21 
[1] "1.0 - 153.9 (20.8)" "0.1 - 211.0 (21.2)"
[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       178        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               178
  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    43  24  55   1
  4Q LOSS WILD-TYPE 136  44 113   7
D49V5, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  N0              43               136
  N1              24                44
  N2              55               113
  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 146   0
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     44    1
  4Q LOSS WILD-TYPE  146    0
   clus
vv  4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  0              44               146
  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  94
  4Q LOSS WILD-TYPE 122 207
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     40   94
  4Q LOSS WILD-TYPE  122  207
     clus
vv    4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  NO               40               122
  YES              94               207
[1] 2 2
[1] FALSE
                   vv
clus                HEAD & NECK SQUAMOUS CELL CARCINOMA
  4Q LOSS MUTATED                                   149
  4Q LOSS WILD-TYPE                                 362
                   vv
clus                HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  4Q LOSS MUTATED                                                   2
  4Q LOSS WILD-TYPE                                                 8
                   vv
clus                HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  4Q LOSS MUTATED                                                           0
  4Q LOSS WILD-TYPE                                                         1
D49V9, multiclass
                                                           clus
vv                                                          4Q LOSS MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                   149
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       2
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT               0
                                                           clus
vv                                                          4Q LOSS WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                     362
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                         8
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                 1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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                          20   120
  4Q LOSS WILD-TYPE                        28   326
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                     20                28
  WHITE                                        120               326
[1] 4 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 272 197
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               51               469 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               22               197 
$`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-BA-4075 TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-A4IG TCGA-BA-A4II 
        9.30        37.28        20.48        68.48        28.11        30.18 
TCGA-BB-A5HU TCGA-CN-4727 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 
       25.71        51.29         9.07         9.24        52.08        11.08 
TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-6221 
       35.05        32.48        19.82        24.39        48.20        32.88 
TCGA-CQ-7063 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-A4C7 TCGA-CR-6472 TCGA-CR-6478 
       70.13        16.73        43.04        11.61        34.52         6.02 
TCGA-CX-7082 TCGA-CX-7219 TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7593 
        0.36        34.36        30.94        14.04        46.32        40.24 
TCGA-H7-A6C5 TCGA-HD-8634 TCGA-HD-8635 TCGA-UF-A71D TCGA-UF-A7JV TCGA-4P-AA8J 
       21.11        12.66        22.85        48.03         2.96         3.35 
TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 
       15.19        13.64         9.07        26.50        23.74        42.35 
TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6869 
       57.93        17.10        23.84        65.59        15.52        21.17 
TCGA-BA-6870 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IH 
       14.83        12.62         4.01        41.85        29.42        20.45 
TCGA-BA-A6D8 TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG 
       27.95         7.10         5.69        14.47         7.82         2.27 
TCGA-BA-A6DI TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4225 
       11.05        13.38        20.48         6.15       105.90         4.80 
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-7872 TCGA-BB-8596 TCGA-BB-8601 TCGA-BB-A5HZ 
       44.98        66.28        38.40        71.05        20.52        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-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 
       38.04         4.67        56.68        12.89        26.86        32.81 
TCGA-CN-4733 TCGA-CN-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-5358 TCGA-CN-5359 TCGA-CN-5360 
       27.58        73.61        13.05         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-6019 TCGA-CN-6020 
       23.90        47.44        28.04        19.07        34.13         6.74 
TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A497 
       32.22        38.89         3.68        17.42        11.74        35.01 
TCGA-CN-A498 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63V 
       25.41        17.29        29.72        21.21         7.40        22.32 
TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY 
       12.39        16.57         4.41        12.07         2.70        23.44 
TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 
       20.88        19.53        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-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-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4CB 
       64.87        53.52        43.10        77.56        44.48        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-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 
       54.67        37.87        26.27        58.42        50.01        39.52 
TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 
       36.99        18.54        16.90        11.90        10.22        11.34 
TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-7365 
       11.64         7.69        12.46        22.78        15.75        39.16 
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-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7382 
        0.99        31.96         9.17        34.06        19.92        26.17 
TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 
       17.13        32.78        47.01        27.06        12.89        49.58 
TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 
       30.02        46.85        32.65        44.25        30.58        24.79 
TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 
        5.13         5.95        35.41        29.95        48.39       139.43 
TCGA-CV-5431 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 
       17.16       108.95        76.24        19.20        17.95       107.51 
TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 
       94.88        76.50        91.53        80.12        17.92        13.35 
TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5978 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 
       23.05        86.83         7.07        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-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6952 
       11.24       140.78        19.79        12.03        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-7095 TCGA-CV-7097 
        2.50        64.83       172.67       111.16        18.81        12.66 
TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7104 
        7.99         9.01         5.26         1.84        52.31        12.92 
TCGA-CV-7177 TCGA-CV-7178 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7236 
       21.80        71.21        10.75       130.88        77.16         4.73 
TCGA-CV-7238 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7250 TCGA-CV-7252 
       89.65        31.36        26.20        18.97        95.34         4.96 
TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7255 TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7409 
       11.87        47.97         2.10        49.71        57.47        17.85 
TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7415 TCGA-CV-7416 TCGA-CV-7418 
      210.97        89.33         9.67        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-7437 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45R 
       16.64        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-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-A6ES TCGA-D6-A74Q TCGA-DQ-5624 
       22.59        24.95        13.94        12.79        23.34        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-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-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 
        3.02        31.13        18.94        24.95         0.46        17.85 
TCGA-F7-A622 TCGA-F7-A623 TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 
       11.80        20.25        12.43        13.38        15.16        15.06 
TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 
       20.94        33.76        28.47        25.74        21.93        27.48 
TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 
       27.48        14.66        22.03         0.36        13.84         4.27 
TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-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-IQ-A6SG TCGA-IQ-A6SH TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X 
       19.04        15.48        19.27        10.75        14.37         7.96 
TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A5BI 
       30.05         1.84        12.62         6.25        15.42         7.13 
TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QE 
       16.08        17.98        29.92        15.78        71.74        51.25 
TCGA-P3-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-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VC TCGA-QK-A8Z7 
        7.30         9.34        12.72        27.39        19.73        12.89 
TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3K TCGA-RS-A6TO 
        5.62        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-A719 
        3.12        13.55        13.25        20.35        64.80        54.67 
TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A7JA TCGA-UF-A7JF TCGA-UF-A7JJ TCGA-UF-A7JK 
        2.83        49.51        74.47        55.43        18.05        13.94 
TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 TCGA-KU-A66S 
       22.36        32.65        17.03        20.55        14.56        13.35 
TCGA-KU-A66T 
       18.15 

  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 
            23.57             21.01 
[1] "0.5 - 153.9 (23.6)" "0.1 - 211.0 (21.0)"
[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       223        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               223
  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 171   1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED     19    0
  5P LOSS WILD-TYPE  171    1
   clus
vv  5P LOSS MUTATED 5P LOSS WILD-TYPE
  0              19               171
  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  28
  5P LOSS WILD-TYPE 147 273
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED     15   28
  5P LOSS WILD-TYPE  147  273
     clus
vv    5P LOSS MUTATED 5P LOSS WILD-TYPE
  NO               15               147
  YES              28               273
[1] 2 2
[1] FALSE
                   vv
clus                HEAD & NECK SQUAMOUS CELL CARCINOMA
  5P LOSS MUTATED                                    49
  5P LOSS WILD-TYPE                                 462
                   vv
clus                HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  5P LOSS MUTATED                                                   2
  5P LOSS WILD-TYPE                                                 8
                   vv
clus                HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  5P LOSS MUTATED                                                           0
  5P LOSS WILD-TYPE                                                         1
D50V9, multiclass
                                                           clus
vv                                                          5P LOSS MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                    49
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       2
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT               0
                                                           clus
vv                                                          5P LOSS WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                     462
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                         8
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                 1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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    98  61
  5Q LOSS WILD-TYPE 203 158
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
              159               361 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               61               158 
$`5Q LOSS MUTATED`
TCGA-BA-4075 TCGA-BA-6871 TCGA-BA-A4IG TCGA-CN-4727 TCGA-CN-6024 TCGA-CN-6992 
        9.30         3.55        28.11        51.29        11.08        35.05 
TCGA-CX-7082 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-UF-A71D TCGA-BA-4078 TCGA-BA-5555 
        0.36        14.04        46.32        48.03         9.07        17.10 
TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB 
       12.62         4.01        41.85        27.95        11.54         7.10 
TCGA-BA-A6DE TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4224 TCGA-BB-7870 TCGA-BB-7871 
       14.47        16.41         6.15         9.14        66.28        24.66 
TCGA-BB-8596 TCGA-BB-8601 TCGA-BB-A5HY TCGA-CN-4725 TCGA-CN-4729 TCGA-CN-4730 
       71.05        20.52        10.55        38.04        12.89        26.86 
TCGA-CN-4737 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5360 TCGA-CN-5366 
       20.55        13.05        42.02        46.32        71.31        11.84 
TCGA-CN-6010 TCGA-CN-6012 TCGA-CN-6019 TCGA-CN-6988 TCGA-CN-A499 TCGA-CN-A63U 
       50.07        48.00        34.13        10.45        23.57        31.69 
TCGA-CN-A63W TCGA-CN-A641 TCGA-CQ-5326 TCGA-CQ-5332 TCGA-CQ-6225 TCGA-CQ-6227 
       12.39        12.07         2.93        10.42        13.25         4.24 
TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7069 TCGA-CQ-7072 TCGA-CQ-A4C9 
       38.76        64.87        53.52        41.88        77.56        23.24 
TCGA-CQ-A4CE TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5247 TCGA-CR-6474 TCGA-CR-6477 
       29.49        12.46        31.23        11.77        18.54        16.90 
TCGA-CR-6488 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7368 TCGA-CR-7369 
       12.46         9.27        47.18        39.16        40.93        35.84 
TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7379 TCGA-CR-7390 TCGA-CR-7398 
        3.45         3.09        24.95        34.06        49.58         5.13 
TCGA-CR-7404 TCGA-CV-5432 TCGA-CV-5435 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5973 
       48.39       129.21        76.24       107.51        94.88        86.83 
TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6933 
       48.59        60.49         7.07        43.23        54.74        90.12 
TCGA-CV-6940 TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-6962 
       26.43        15.09        30.08         8.42        28.34         4.14 
TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7101 TCGA-CV-7103 TCGA-CV-7177 
      172.67       111.16        18.81         5.26        52.31        21.80 
TCGA-CV-7180 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7248 TCGA-CV-7254 TCGA-CV-7261 
       10.75        36.00        31.36        17.13        47.97        49.71 
TCGA-CV-7263 TCGA-CV-7407 TCGA-CV-7414 TCGA-CV-7421 TCGA-CV-7424 TCGA-CV-7429 
       18.41        35.54         0.46         0.07        14.89         3.52 
TCGA-CV-7435 TCGA-CV-7438 TCGA-CV-A45R TCGA-CV-A45W TCGA-CV-A45X TCGA-CV-A45Z 
      153.86         6.38       180.16        45.96         6.51        48.20 
TCGA-CV-A465 TCGA-CV-A6JE TCGA-CX-7086 TCGA-D6-6823 TCGA-D6-A6EQ TCGA-D6-A74Q 
        7.07        35.34        18.84        23.05        12.10        23.34 
TCGA-DQ-5631 TCGA-DQ-7592 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-F7-7848 TCGA-F7-A50G 
       18.02        37.58        40.04        39.12        37.18        20.25 
TCGA-F7-A61W TCGA-F7-A622 TCGA-HD-7753 TCGA-HD-7917 TCGA-IQ-A61G TCGA-IQ-A61H 
        0.46        11.80        28.47        27.48        11.84        37.41 
TCGA-IQ-A6SG TCGA-IQ-A6SH TCGA-MT-A7BN TCGA-P3-A5QF TCGA-P3-A6SX TCGA-P3-A6T3 
       19.04        15.48        15.42        10.85        47.01        18.97 
TCGA-P3-A6T5 TCGA-QK-A652 TCGA-QK-A6IH TCGA-QK-A6IJ TCGA-QK-A6VB TCGA-QK-A6VC 
       29.00        21.21        21.47        12.72        21.07        19.73 
TCGA-QK-A8Z7 TCGA-QK-A8Z9 TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-T2-A6WZ TCGA-UF-A71B 
       12.89        14.76        17.82        15.32        15.91        49.51 
TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF 
       49.45        44.65        74.47        17.95        24.30        55.43 
TCGA-UF-A7JH TCGA-UF-A7JO TCGA-KU-A66T 
       29.46        20.75        18.15 

$`5Q LOSS WILD-TYPE`
TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-A4II TCGA-BB-A5HU TCGA-CN-6021 
       37.28        20.48        68.48        30.18        25.71         9.07 
TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6997 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 
        9.24        52.08        32.48        19.82        24.39        48.20 
TCGA-CQ-6221 TCGA-CQ-7063 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-A4C7 TCGA-CR-6472 
       32.88        70.13        16.73        43.04        11.61        34.52 
TCGA-CR-6478 TCGA-CX-7219 TCGA-DQ-5629 TCGA-DQ-7593 TCGA-H7-A6C5 TCGA-HD-8634 
        6.02        34.36        30.94        40.24        21.11        12.66 
TCGA-HD-8635 TCGA-UF-A7JV TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-5149 
       22.85         2.96         3.35        15.19        13.64        26.50 
TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-6868 
       23.74        42.35        57.93        23.84        65.59        15.52 
TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-A4IF TCGA-BA-A4IH TCGA-BA-A6DD TCGA-BA-A6DF 
       21.17        14.83        29.42        20.45         5.69         7.82 
TCGA-BA-A6DG TCGA-BA-A6DI TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BB-4223 TCGA-BB-4225 
        2.27        11.05        13.38        20.48       105.90         4.80 
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-7872 TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO TCGA-C9-A47Z 
       44.98        38.40        27.19        12.92         8.81         6.28 
TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4731 
       12.69        48.76        55.86         4.67        56.68        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-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-6989 
       23.90        47.44        28.04        19.07         6.74        32.22 
TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 
       38.89         3.68        17.42        11.74        35.01        25.41 
TCGA-CN-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-A642 TCGA-CN-A6UY TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5324 
        4.41         2.70        23.44        20.88        19.53        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-6220 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6228 
        4.24        41.19        32.38        46.95        56.58        14.99 
TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CG TCGA-CR-5243 
       43.10        44.48        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-6473 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 
       36.99        11.90        10.22        11.34        11.64         7.69 
TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-7367 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 
       22.78        15.75        47.34        29.23         0.99        31.96 
TCGA-CR-7377 TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 
        9.17        19.92        26.17        17.13        32.78        47.01 
TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 
       27.06        12.89        30.02        46.85        32.65        44.25 
TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CV-5430 
       30.58        24.79         5.95        35.41        29.95       139.43 
TCGA-CV-5431 TCGA-CV-5434 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5442 TCGA-CV-5443 
       17.16       108.95        19.20        17.95        76.50        91.53 
TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-6433 TCGA-CV-6436 
       80.12        17.92        13.35        23.05        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-6961 
        6.08        53.95        65.82        10.98         7.13         2.50 
TCGA-CV-7089 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7102 TCGA-CV-7104 
       64.83        12.66         7.99         9.01         1.84        12.92 
TCGA-CV-7178 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7245 
       71.21       130.88        77.16         4.73        89.65        26.20 
TCGA-CV-7247 TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7255 TCGA-CV-7406 
       18.97        95.34         4.96        11.87         2.10        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-7422 TCGA-CV-7423 TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7428 
       25.94        34.09       100.57        56.48       156.49        54.94 
TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7437 TCGA-CV-7440 
       16.27        84.49        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-A45Y TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A463 TCGA-CV-A464 TCGA-CV-A468 
       88.87        60.43        67.86         0.76        56.61        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-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-A6EM TCGA-D6-A6EN TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6ES 
       28.77         7.63        22.59        24.95        13.94        12.79 
TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7596 
       58.45        37.25        33.86        46.45        20.45        41.59 
TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V 
       32.71        21.63         3.02        31.13        18.94        24.95 
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-A76A TCGA-HD-7229 TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-8224 
       20.94        33.76        25.74        21.93        27.48        14.66 
TCGA-HD-8314 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 
       22.03         0.36        13.84         4.27         3.65         6.90 
TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61I 
       34.75        15.95        38.53        14.50        37.71         0.07 
TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A6H7 TCGA-KU-A6H8 
       33.57         5.29        13.68        13.84        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-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-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T4 TCGA-P3-A6T6 
       51.25        36.82        19.00        75.55         2.04        12.99 
TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6II 
       16.01        13.15        21.07        23.15         7.30         9.34 
TCGA-QK-A6V9 TCGA-QK-A8Z8 TCGA-QK-A8ZA TCGA-QK-AA3K TCGA-RS-A6TO TCGA-RS-A6TP 
       27.39         5.62        12.20         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-A719 TCGA-UF-A71A TCGA-UF-A7JJ 
       13.25        20.35        64.80        54.67         2.83        18.05 
TCGA-UF-A7JK TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 
       13.94        22.36        32.65        17.03        20.55        14.56 
TCGA-KU-A66S 
       13.35 

  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 
            23.05             20.94 
[1] "0.1 - 180.2 (23.1)" "0.1 - 211.0 (20.9)"
[1] "hr=" "1.2"
D51V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  5Q LOSS MUTATED         6       25        30        80         3         0
  5Q LOSS WILD-TYPE      21       51        52       172         9         1
D51V3, multiclass
           clus
vv          5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  STAGE I                 6                21
  STAGE II               25                51
  STAGE III              30                52
  STAGE IVA              80               172
  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  44  32  60
  5Q LOSS WILD-TYPE    41  93  68 113
D51V4, multiclass
       clus
vv      5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  T0+T1               9                41
  T2                 44                93
  T3                 32                68
  T4                 60               113
[1] 4 2
[1] TRUE
[1] "dimension of 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    52  25  53   2
  5Q LOSS WILD-TYPE 127  43 115   6
D51V5, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  N0              52               127
  N1              25                43
  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"
D51V6, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED    60   0
  5Q LOSS WILD-TYPE 130   1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     60    0
  5Q LOSS WILD-TYPE  130    1
   clus
vv  5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  0              60               130
  1               0                 1
[1] 2 2
[1] FALSE
D51V7, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED    37 123
  5Q LOSS WILD-TYPE 103 259
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     37  123
  5Q LOSS WILD-TYPE  103  259
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  FEMALE              37               103
  MALE               123               259
[1] 2 2
[1] FALSE
D51V8, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED    46  94
  5Q LOSS WILD-TYPE 116 207
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     46   94
  5Q LOSS WILD-TYPE  116  207
     clus
vv    5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  NO               46               116
  YES              94               207
[1] 2 2
[1] FALSE
                   vv
clus                HEAD & NECK SQUAMOUS CELL CARCINOMA
  5Q LOSS MUTATED                                   156
  5Q LOSS WILD-TYPE                                 355
                   vv
clus                HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  5Q LOSS MUTATED                                                   4
  5Q LOSS WILD-TYPE                                                 6
                   vv
clus                HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  5Q LOSS MUTATED                                                           0
  5Q LOSS WILD-TYPE                                                         1
D51V9, multiclass
                                                           clus
vv                                                          5Q LOSS MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                   156
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       4
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT               0
                                                           clus
vv                                                          5Q LOSS WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                     355
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                         6
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                 1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V10, continuous
D51V11, continuous
D51V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  5Q LOSS MUTATED                                  1     4
  5Q LOSS WILD-TYPE                                1     7
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  5Q LOSS MUTATED                          22   129
  5Q LOSS WILD-TYPE                        26   317
D51V13, multiclass
                                  clus
vv                                 5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 1
  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"
D51V14, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED     8 135
  5Q LOSS WILD-TYPE  18 324
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      8  135
  5Q LOSS WILD-TYPE   18  324
                        clus
vv                       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   8                18
  NOT HISPANIC OR LATINO             135               324
[1] 2 2
[1] FALSE

Clustering(52) Variable = 6P LOSS MUTATION ANALYSIS
D52V1, survival
                   sevent
clus2                 0   1
  6P LOSS MUTATED    38  29
  6P LOSS WILD-TYPE 263 190
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               67               453 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               29               190 
$`6P LOSS MUTATED`
TCGA-BA-5559 TCGA-CN-6024 TCGA-CN-6997 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-BA-5152 
       68.48        11.08        32.48        14.04        46.32        42.35 
TCGA-BB-4225 TCGA-BB-7862 TCGA-CN-4725 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4735 
        4.80        36.72        38.04        56.68        12.89        57.11 
TCGA-CN-4740 TCGA-CN-5359 TCGA-CN-6010 TCGA-CN-6988 TCGA-CN-6994 TCGA-CN-A63T 
       27.58        12.39        50.07        10.45        38.89         7.40 
TCGA-CN-A640 TCGA-CN-A6V7 TCGA-CQ-5332 TCGA-CQ-6223 TCGA-CQ-A4C9 TCGA-CR-6488 
        4.41        19.53        10.42        46.95        23.24        12.46 
TCGA-CR-6493 TCGA-CR-7365 TCGA-CR-7371 TCGA-CR-7373 TCGA-CR-7399 TCGA-CR-7404 
        9.27        39.16         3.09        29.23         5.95        48.39 
TCGA-CV-5434 TCGA-CV-5436 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-6441 TCGA-CV-6940 
      108.95        19.20        91.53        80.12         9.60        26.43 
TCGA-CV-6960 TCGA-CV-6962 TCGA-CV-7095 TCGA-CV-7101 TCGA-CV-7247 TCGA-CV-7248 
       28.34         4.14        18.81         5.26        18.97        17.13 
TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7263 TCGA-CV-7416 TCGA-CV-7418 TCGA-CV-A6JT 
       11.87        47.97        18.41        25.08        25.94        28.01 
TCGA-D6-6823 TCGA-D6-6826 TCGA-D6-A6EQ TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-7591 
       23.05        11.44        12.10        23.34        58.45        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-A5QA TCGA-P3-A6T0 TCGA-T3-A92N TCGA-UF-A71E TCGA-UF-A7JF 
       17.98        71.74        19.00         3.12        49.45        55.43 
TCGA-UP-A6WW 
       17.03 

$`6P LOSS WILD-TYPE`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-6871 TCGA-BA-A4IG TCGA-BA-A4II 
        9.30        37.28        20.48         3.55        28.11        30.18 
TCGA-BB-A5HU TCGA-CN-4727 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6992 
       25.71        51.29         9.07         9.24        52.08        35.05 
TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-6221 TCGA-CQ-7063 TCGA-CQ-7067 
       19.82        24.39        48.20        32.88        70.13        16.73 
TCGA-CQ-7068 TCGA-CQ-A4C7 TCGA-CR-6472 TCGA-CR-6478 TCGA-CX-7082 TCGA-CX-7219 
       43.04        11.61        34.52         6.02         0.36        34.36 
TCGA-DQ-5629 TCGA-DQ-7593 TCGA-H7-A6C5 TCGA-HD-8634 TCGA-HD-8635 TCGA-UF-A71D 
       30.94        40.24        21.11        12.66        22.85        48.03 
TCGA-UF-A7JV TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-5149 
        2.96         3.35        15.19        13.64         9.07        26.50 
TCGA-BA-5151 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-6868 
       23.74        57.93        17.10        23.84        65.59        15.52 
TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF 
       21.17        14.83        12.62         4.01        41.85        29.42 
TCGA-BA-A4IH TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE 
       20.45        27.95        11.54         7.10         5.69        14.47 
TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DI TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BA-A8YP 
        7.82         2.27        11.05        13.38        20.48        16.41 
TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 
        6.15       105.90         9.14         4.41        18.38        22.42 
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-A5HY TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO 
       71.05        20.52        10.55        27.19        12.92         8.81 
TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4726 TCGA-CN-4730 
        6.28        12.69        48.76        55.86         4.67        26.86 
TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 
       32.81        52.14        12.99        20.55        14.33        45.83 
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-5374 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 
        8.52        52.08        56.94        30.67        48.00        23.90 
TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6989 
       47.44        28.04        19.07        34.13         6.74        32.22 
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-A6V6 TCGA-CQ-5324 
       16.57        12.07         2.70        23.44        20.88        52.37 
TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 
       21.50         2.93        54.58        70.45        62.37        45.99 
TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6220 TCGA-CQ-6224 TCGA-CQ-6225 
       11.21         4.24        41.19        32.38        56.58        13.25 
TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7069 
        4.24        14.99        38.76        64.87        53.52        41.88 
TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE 
       43.10        77.56        44.48        29.36        33.60        29.49 
TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 
       14.14        12.46        31.23        84.23        11.77        54.67 
TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6473 
       37.87        26.27        58.42        50.01        39.52        36.99 
TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 
       18.54        16.90        11.90        10.22        11.34        11.64 
TCGA-CR-6487 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-7364 TCGA-CR-7367 TCGA-CR-7368 
        7.69        22.78        15.75        47.18        47.34        40.93 
TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7372 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 
       35.84         3.45        24.95         0.99        31.96         9.17 
TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 
       34.06        19.92        26.17        17.13        32.78        47.01 
TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 
       27.06        12.89        49.58        30.02        46.85        32.65 
TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7401 TCGA-CR-7402 
       44.25        30.58        24.79         5.13        35.41        29.95 
TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5435 TCGA-CV-5439 TCGA-CV-5440 
      139.43        17.16       129.21        76.24        17.95       107.51 
TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 
       94.88        76.50        17.92        13.35        23.05        86.83 
TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 
       48.59        60.49         7.07        43.23        54.74        21.07 
TCGA-CV-6436 TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6937 
       62.43        90.12         2.14         9.70         5.46        20.52 
TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 
        4.73        21.90        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-6961 TCGA-CV-7089 TCGA-CV-7090 
       10.98         7.13         8.42         2.50        64.83       172.67 
TCGA-CV-7091 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7102 TCGA-CV-7103 
      111.16        12.66         7.99         9.01         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-7250 
        4.73        89.65        36.00        31.36        26.20        95.34 
TCGA-CV-7252 TCGA-CV-7255 TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7407 TCGA-CV-7409 
        4.96         2.10        49.71        57.47        35.54        17.85 
TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7414 TCGA-CV-7415 TCGA-CV-7421 
      210.97        89.33         9.67         0.46        22.85         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-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-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 
        6.48         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-D6-6824 TCGA-D6-6825 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 
        9.60         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-A6ES TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7590 
       13.94        12.79        37.25        33.86        18.02        46.45 
TCGA-DQ-7592 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 
       37.58        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-A76A TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7831 
       15.06        20.94        33.76        28.47        25.74        21.93 
TCGA-HD-7832 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-A4C1 TCGA-HD-A633 
       27.48        27.48        14.66        22.03         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-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-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X 
       19.04        15.48        19.27        10.75        14.37         7.96 
TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-P3-A5Q5 
       30.05         1.84        12.62         7.13        16.08        29.92 
TCGA-P3-A5Q6 TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T2 
       15.78        51.25        10.85        36.82        47.01        75.55 
TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-P3-A6T8 
       18.97         2.04        29.00        12.99        16.01        13.15 
TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II 
       21.07        21.21        23.15         7.30        21.47         9.34 
TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z8 
       12.72        27.39        21.07        19.73        12.89         5.62 
TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-RS-A6TO 
       14.76        12.20        17.82        15.32         8.32        12.72 
TCGA-RS-A6TP TCGA-T2-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-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JH 
       49.51        44.65        74.47        17.95        24.30        29.46 
TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT TCGA-WA-A7GZ 
       18.05        13.94        20.75        22.36        32.65        20.55 
TCGA-WA-A7H4 TCGA-KU-A66S TCGA-KU-A66T 
       14.56        13.35        18.15 

  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 
            19.53             21.21 
[1] "0.1 - 109.0 (19.5)" "0.1 - 211.0 (21.2)"
[1] "hr=" "1.1"
D52V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  6P LOSS MUTATED         1        9        10        39         0         0
  6P LOSS WILD-TYPE      26       67        72       213        12         1
D52V3, multiclass
           clus
vv          6P LOSS MUTATED 6P LOSS WILD-TYPE
  STAGE I                 1                26
  STAGE II                9                67
  STAGE III              10                72
  STAGE IVA              39               213
  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  15  23
  6P LOSS WILD-TYPE    46 121  85 150
D52V4, multiclass
       clus
vv      6P LOSS MUTATED 6P LOSS WILD-TYPE
  T0+T1               4                46
  T2                 16               121
  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
  6P LOSS MUTATED    18   8  25   0
  6P LOSS WILD-TYPE 161  60 143   8
D52V5, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  N0              18               161
  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    16   0
  6P LOSS WILD-TYPE 174   1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     16    0
  6P LOSS WILD-TYPE  174    1
   clus
vv  6P LOSS MUTATED 6P LOSS WILD-TYPE
  0              16               174
  1               0                 1
[1] 2 2
[1] FALSE
D52V7, binary
                   cls
clus                  0   1
  6P LOSS MUTATED    14  53
  6P LOSS WILD-TYPE 126 329
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     14   53
  6P LOSS WILD-TYPE  126  329
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  FEMALE              14               126
  MALE                53               329
[1] 2 2
[1] FALSE
D52V8, binary
                   cls
clus                  0   1
  6P LOSS MUTATED    21  36
  6P LOSS WILD-TYPE 141 265
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     21   36
  6P LOSS WILD-TYPE  141  265
     clus
vv    6P LOSS MUTATED 6P LOSS WILD-TYPE
  NO               21               141
  YES              36               265
[1] 2 2
[1] FALSE
                   vv
clus                HEAD & NECK SQUAMOUS CELL CARCINOMA
  6P LOSS MUTATED                                    66
  6P LOSS WILD-TYPE                                 445
                   vv
clus                HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  6P LOSS MUTATED                                                   1
  6P LOSS WILD-TYPE                                                 9
                   vv
clus                HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  6P LOSS MUTATED                                                           0
  6P LOSS WILD-TYPE                                                         1
D52V9, multiclass
                                                           clus
vv                                                          6P LOSS MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                    66
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       1
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT               0
                                                           clus
vv                                                          6P LOSS WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                     445
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                         9
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                 1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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    52
  6P LOSS WILD-TYPE                        37   394
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                                         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"
D52V14, binary
                   cls
clus                  0   1
  6P LOSS MUTATED     6  53
  6P LOSS WILD-TYPE  20 406
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      6   53
  6P LOSS WILD-TYPE   20  406
                        clus
vv                       6P LOSS MUTATED 6P LOSS WILD-TYPE
  HISPANIC OR LATINO                   6                20
  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  28
  6Q LOSS WILD-TYPE 259 191
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               70               450 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               28               191 
$`6Q LOSS MUTATED`
TCGA-BA-5559 TCGA-CN-6024 TCGA-CQ-A4C7 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-BA-5152 
       68.48        11.08        11.61        14.04        46.32        42.35 
TCGA-BA-5555 TCGA-BB-4225 TCGA-CN-4725 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4740 
       17.10         4.80        38.04        56.68        12.89        27.58 
TCGA-CN-5359 TCGA-CN-6010 TCGA-CN-6020 TCGA-CN-6988 TCGA-CN-6994 TCGA-CN-A640 
       12.39        50.07         6.74        10.45        38.89         4.41 
TCGA-CN-A641 TCGA-CN-A6V7 TCGA-CQ-6223 TCGA-CQ-A4C9 TCGA-CR-5248 TCGA-CR-6473 
       12.07        19.53        46.95        23.24        54.67        36.99 
TCGA-CR-6491 TCGA-CR-7365 TCGA-CR-7373 TCGA-CR-7399 TCGA-CR-7404 TCGA-CV-5434 
       22.78        39.16        29.23         5.95        48.39       108.95 
TCGA-CV-5440 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-6441 TCGA-CV-6940 TCGA-CV-6953 
      107.51        91.53        80.12         9.60        26.43        53.95 
TCGA-CV-6954 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7101 TCGA-CV-7235 TCGA-CV-7247 
       65.82       111.16        18.81         5.26        77.16        18.97 
TCGA-CV-7248 TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7263 TCGA-CV-7416 TCGA-CV-A45U 
       17.13        11.87        47.97        18.41        25.08        35.47 
TCGA-D6-6823 TCGA-D6-6826 TCGA-DQ-5624 TCGA-DQ-5631 TCGA-DQ-7591 TCGA-F7-A50G 
       23.05        11.44        58.45        18.02        20.45        20.25 
TCGA-F7-A623 TCGA-HD-A633 TCGA-HD-A6HZ TCGA-IQ-A61G TCGA-IQ-A61I TCGA-MT-A67G 
       20.25        13.84         3.65        11.84         0.07         6.25 
TCGA-MZ-A7D7 TCGA-P3-A6SW TCGA-P3-A6T0 TCGA-RS-A6TP TCGA-T3-A92N TCGA-UF-A7JF 
       17.98        36.82        19.00        16.96         3.12        55.43 
TCGA-UF-A7JH TCGA-UF-A7JK TCGA-UP-A6WW TCGA-WA-A7GZ 
       29.46        13.94        17.03        20.55 

$`6Q LOSS WILD-TYPE`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-6871 TCGA-BA-A4IG TCGA-BA-A4II 
        9.30        37.28        20.48         3.55        28.11        30.18 
TCGA-BB-A5HU TCGA-CN-4727 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6992 
       25.71        51.29         9.07         9.24        52.08        35.05 
TCGA-CN-6997 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-6221 TCGA-CQ-7063 
       32.48        19.82        24.39        48.20        32.88        70.13 
TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CR-6472 TCGA-CR-6478 TCGA-CX-7082 TCGA-CX-7219 
       16.73        43.04        34.52         6.02         0.36        34.36 
TCGA-DQ-5629 TCGA-DQ-7593 TCGA-H7-A6C5 TCGA-HD-8634 TCGA-HD-8635 TCGA-UF-A71D 
       30.94        40.24        21.11        12.66        22.85        48.03 
TCGA-UF-A7JV TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-5149 
        2.96         3.35        15.19        13.64         9.07        26.50 
TCGA-BA-5151 TCGA-BA-5153 TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6869 
       23.74        57.93        23.84        65.59        15.52        21.17 
TCGA-BA-6870 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IH 
       14.83        12.62         4.01        41.85        29.42        20.45 
TCGA-BA-A6D8 TCGA-BA-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-7862 
      105.90         9.14         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-A5HY TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO 
       71.05        20.52        10.55        27.19        12.92         8.81 
TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4726 TCGA-CN-4730 
        6.28        12.69        48.76        55.86         4.67        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-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-6989 
       23.90        47.44        28.04        19.07        34.13        32.22 
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-A642 TCGA-CN-A6UY TCGA-CN-A6V6 TCGA-CQ-5324 
       12.39        16.57         2.70        23.44        20.88        52.37 
TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 
       21.50         2.93        54.58        70.45        62.37        45.99 
TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6220 TCGA-CQ-6224 
       10.42        11.21         4.24        41.19        32.38        56.58 
TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7065 
       13.25         4.24        14.99        38.76        64.87        53.52 
TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4CB TCGA-CQ-A4CD 
       41.88        43.10        77.56        44.48        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-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6474 
       37.87        26.27        58.42        50.01        39.52        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-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7367 TCGA-CR-7368 
       12.46        15.75         9.27        47.18        47.34        40.93 
TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7374 TCGA-CR-7376 
       35.84         3.45         3.09        24.95         0.99        31.96 
TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 
        9.17        34.06        19.92        26.17        17.13        32.78 
TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 
       47.01        27.06        12.89        49.58        30.02        46.85 
TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7401 
       32.65        44.25        30.58        24.79         5.13        35.41 
TCGA-CR-7402 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5435 TCGA-CV-5436 
       29.95       139.43        17.16       129.21        76.24        19.20 
TCGA-CV-5439 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 
       17.95        94.88        76.50        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-6941 TCGA-CV-6942 TCGA-CV-6943 
       20.52         4.73        21.90        11.24       140.78        19.79 
TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6955 
       12.03        42.38        15.09        30.08         6.08        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-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7102 TCGA-CV-7103 
      172.67        12.66         7.99         9.01         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-7250 TCGA-CV-7252 
       89.65        36.00        31.36        26.20        95.34         4.96 
TCGA-CV-7255 TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7407 TCGA-CV-7409 TCGA-CV-7410 
        2.10        49.71        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-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-A45R TCGA-CV-A45T TCGA-CV-A45V TCGA-CV-A45W TCGA-CV-A45X TCGA-CV-A45Y 
      180.16       159.65         1.05        45.96         6.51        88.87 
TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A463 TCGA-CV-A464 TCGA-CV-A465 
       48.20        60.43        67.86         0.76        56.61         7.07 
TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JM TCGA-CV-A6JN TCGA-CV-A6JO 
       15.25         5.98        35.34         6.38        29.79         6.48 
TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 
       28.01         3.62        21.24        23.47        19.92        22.52 
TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6516 
       10.42        10.55        18.84        51.12        13.25        25.41 
TCGA-D6-6517 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 
        9.60         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-5625 TCGA-DQ-5630 
       13.94        12.10        12.79        23.34        37.25        33.86 
TCGA-DQ-7590 TCGA-DQ-7592 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 
       46.45        37.58        40.04        39.12        41.59        37.18 
TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V 
       32.71        21.63         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-A76A TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7831 
       15.06        20.94        33.76        28.47        25.74        21.93 
TCGA-HD-7832 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-A4C1 TCGA-HD-A634 
       27.48        27.48        14.66        22.03         0.36         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-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A 
       15.48        19.27        10.75        14.37         7.96        30.05 
TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-P3-A5Q5 
        1.84        12.62        15.42         7.13        16.08        29.92 
TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SX TCGA-P3-A6T2 
       15.78        71.74        51.25        10.85        47.01        75.55 
TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-P3-A6T8 
       18.97         2.04        29.00        12.99        16.01        13.15 
TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II 
       21.07        21.21        23.15         7.30        21.47         9.34 
TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z8 
       12.72        27.39        21.07        19.73        12.89         5.62 
TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-RS-A6TO 
       14.76        12.20        17.82        15.32         8.32        12.72 
TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-T3-A92M TCGA-TN-A7HI 
        6.87        15.91         7.10        32.45        13.71        13.55 
TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B 
       13.25        20.35        64.80        54.67         2.83        49.51 
TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JJ 
       49.45        44.65        74.47        17.95        24.30        18.05 
TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT TCGA-WA-A7H4 TCGA-KU-A66S TCGA-KU-A66T 
       20.75        22.36        32.65        14.56        13.35        18.15 

  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 
            20.35             21.19 
[1] "0.1 - 111.2 (20.4)" "0.1 - 211.0 (21.2)"
[1] "hr=" "1.1"
D53V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  6Q LOSS MUTATED         1        9        11        36         1         0
  6Q LOSS WILD-TYPE      26       67        71       216        11         1
D53V3, multiclass
           clus
vv          6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  STAGE I                 1                26
  STAGE II                9                67
  STAGE III              11                71
  STAGE IVA              36               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
  6Q LOSS MUTATED       4  18  11  26
  6Q LOSS WILD-TYPE    46 119  89 147
D53V4, multiclass
       clus
vv      6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  T0+T1               4                46
  T2                 18               119
  T3                 11                89
  T4                 26               147
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  6Q LOSS MUTATED    19   9  24   1
  6Q LOSS WILD-TYPE 160  59 144   7
D53V5, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  N0              19               160
  N1               9                59
  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"
D53V6, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED    18   0
  6Q LOSS WILD-TYPE 172   1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     18    0
  6Q LOSS WILD-TYPE  172    1
   clus
vv  6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  0              18               172
  1               0                 1
[1] 2 2
[1] FALSE
D53V7, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED    13  57
  6Q LOSS WILD-TYPE 127 325
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     13   57
  6Q LOSS WILD-TYPE  127  325
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  FEMALE              13               127
  MALE                57               325
[1] 2 2
[1] FALSE
D53V8, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED    21  39
  6Q LOSS WILD-TYPE 141 262
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     21   39
  6Q LOSS WILD-TYPE  141  262
     clus
vv    6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  NO               21               141
  YES              39               262
[1] 2 2
[1] FALSE
                   vv
clus                HEAD & NECK SQUAMOUS CELL CARCINOMA
  6Q LOSS MUTATED                                    69
  6Q LOSS WILD-TYPE                                 442
                   vv
clus                HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  6Q LOSS MUTATED                                                   1
  6Q LOSS WILD-TYPE                                                 9
                   vv
clus                HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  6Q LOSS MUTATED                                                           0
  6Q LOSS WILD-TYPE                                                         1
D53V9, multiclass
                                                           clus
vv                                                          6Q LOSS MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                    69
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       1
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT               0
                                                           clus
vv                                                          6Q LOSS WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                     442
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                         9
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                 1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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                          13    54
  6Q LOSS WILD-TYPE                        35   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                     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"
D53V14, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED     4  59
  6Q LOSS WILD-TYPE  22 400
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      4   59
  6Q LOSS WILD-TYPE   22  400
                        clus
vv                       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   4                22
  NOT HISPANIC OR LATINO              59               400
[1] 2 2
[1] FALSE

Clustering(54) Variable = 7P LOSS MUTATION ANALYSIS
D54V1, survival
                   sevent
clus2                 0   1
  7P LOSS MUTATED    17  12
  7P LOSS WILD-TYPE 284 207
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               29               491 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               12               207 
$`7P LOSS MUTATED`
TCGA-BA-5559 TCGA-BA-A4IG TCGA-CN-6992 TCGA-CN-6997 TCGA-CX-7082 TCGA-BA-A6DE 
       68.48        28.11        35.05        32.48         0.36        14.47 
TCGA-CN-5374 TCGA-CN-6998 TCGA-CN-A49B TCGA-CN-A63U TCGA-CN-A63W TCGA-CN-A6V7 
       56.94        11.74        29.72        31.69        12.39        19.53 
TCGA-CR-6473 TCGA-CV-5435 TCGA-CV-6003 TCGA-CV-7242 TCGA-CV-7429 TCGA-CV-7430 
       36.99        76.24        54.74        36.00         3.52        16.27 
TCGA-CV-7433 TCGA-D6-A6EQ TCGA-F7-A50G TCGA-F7-A623 TCGA-HD-A6HZ TCGA-KU-A6H7 
       19.76        12.10        20.25        20.25         3.65        19.27 
TCGA-MZ-A5BI TCGA-QK-A6IH TCGA-QK-A8Z8 TCGA-QK-AA3J TCGA-UF-A719 
        7.13        21.47         5.62        15.32        54.67 

$`7P LOSS WILD-TYPE`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-6871 TCGA-BA-A4II TCGA-BB-A5HU 
        9.30        37.28        20.48         3.55        30.18        25.71 
TCGA-CN-4727 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-A6V1 
       51.29         9.07         9.24        52.08        11.08        19.82 
TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-6221 TCGA-CQ-7063 TCGA-CQ-7067 TCGA-CQ-7068 
       24.39        48.20        32.88        70.13        16.73        43.04 
TCGA-CQ-A4C7 TCGA-CR-6472 TCGA-CR-6478 TCGA-CX-7219 TCGA-DQ-5629 TCGA-DQ-7588 
       11.61        34.52         6.02        34.36        30.94        14.04 
TCGA-DQ-7589 TCGA-DQ-7593 TCGA-H7-A6C5 TCGA-HD-8634 TCGA-HD-8635 TCGA-UF-A71D 
       46.32        40.24        21.11        12.66        22.85        48.03 
TCGA-UF-A7JV TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-5149 
        2.96         3.35        15.19        13.64         9.07        26.50 
TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5558 
       23.74        42.35        57.93        17.10        23.84        65.59 
TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 
       15.52        21.17        14.83        12.62         4.01        41.85 
TCGA-BA-A4IF TCGA-BA-A4IH TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD 
       29.42        20.45        27.95        11.54         7.10         5.69 
TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DI TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BA-A8YP 
        7.82         2.27        11.05        13.38        20.48        16.41 
TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 
        6.15       105.90         9.14         4.80         4.41        18.38 
TCGA-BB-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-A5HY TCGA-BB-A5HZ 
       24.66        38.40        71.05        20.52        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-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 
       38.04         4.67        56.68        12.89        26.86        32.81 
TCGA-CN-4733 TCGA-CN-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-6988 TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 
        6.74        10.45        32.22        38.89         3.68        17.42 
TCGA-CN-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-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-A6V6 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 
       20.88        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-6223 TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 
       32.38        46.95        56.58        13.25         4.24        14.99 
TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 
       38.76        64.87        53.52        41.88        43.10        77.56 
TCGA-CQ-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-6474 TCGA-CR-6477 
       26.27        58.42        50.01        39.52        18.54        16.90 
TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 
       11.90        10.22        11.34        11.64         7.69        12.46 
TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 
       22.78        15.75         9.27        47.18        39.16        47.34 
TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 
       40.93        35.84         3.45         3.09        24.95        29.23 
TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7382 
        0.99        31.96         9.17        34.06        19.92        26.17 
TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 
       17.13        32.78        47.01        27.06        12.89        49.58 
TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 
       30.02        46.85        32.65        44.25        30.58        24.79 
TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 
        5.13         5.95        35.41        29.95        48.39       139.43 
TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 
       17.16       129.21       108.95        19.20        17.95       107.51 
TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 
       94.88        76.50        91.53        80.12        17.92        13.35 
TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 
       23.05        86.83        48.59        60.49         7.07        43.23 
TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6935 
       21.07        62.43         9.60        90.12         2.14         9.70 
TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6941 
        5.46        20.52         4.73        21.90        26.43        11.24 
TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-6951 
      140.78        19.79        12.03        42.38        15.09        30.08 
TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-6955 TCGA-CV-6956 TCGA-CV-6959 
        6.08        53.95        65.82        10.98         7.13         8.42 
TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7091 
       28.34         2.50         4.14        64.83       172.67       111.16 
TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 
       18.81        12.66         7.99         9.01         5.26         1.84 
TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-7178 TCGA-CV-7180 TCGA-CV-7183 
       52.31        12.92        21.80        71.21        10.75       130.88 
TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7247 
       77.16         4.73        89.65        31.36        26.20        18.97 
TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-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 
       49.71        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-7432 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7437 TCGA-CV-7438 
       54.94        84.49         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-7085 TCGA-CX-7086 TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 
       10.55        18.84        51.12        13.25        25.41         9.60 
TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 
       23.05         2.53        16.14        11.44        18.67        24.95 
TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EN 
       25.32        17.72        12.36        28.77         7.63        22.59 
TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 
       24.95        13.94        12.79        23.34        58.45        37.25 
TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7594 
       33.86        18.02        46.45        20.45        37.58        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-A76A TCGA-HD-7229 
       12.43        13.38        15.16        15.06        20.94        33.76 
TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-7917 TCGA-HD-8224 
       28.47        25.74        21.93        27.48        27.48        14.66 
TCGA-HD-8314 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6I0 TCGA-HL-7533 
       22.03         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-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D 
       15.48        10.75        14.37         7.96        30.05         1.84 
TCGA-MT-A67F TCGA-MT-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-A6SW TCGA-P3-A6SX 
       15.78        71.74        51.25        10.85        36.82        47.01 
TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T6 
       19.00        75.55        18.97         2.04        29.00        12.99 
TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG 
       16.01        13.15        21.07        21.21        23.15         7.30 
TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z7 
        9.34        12.72        27.39        21.07        19.73        12.89 
TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3K TCGA-RS-A6TO TCGA-RS-A6TP 
       14.76        12.20        17.82         8.32        12.72        16.96 
TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-T3-A92M TCGA-T3-A92N 
        6.87        15.91         7.10        32.45        13.71         3.12 
TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A71A TCGA-UF-A71B 
       13.55        13.25        20.35        64.80         2.83        49.51 
TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF 
       49.45        44.65        74.47        17.95        24.30        55.43 
TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT 
       29.46        18.05        13.94        20.75        22.36        32.65 
TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 TCGA-KU-A66S TCGA-KU-A66T 
       17.03        20.55        14.56        13.35        18.15 

  7P LOSS MUTATED 7P LOSS WILD-TYPE 
             0.36              0.07 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
            76.24            210.97 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
            20.25             21.17 
[1] "0.4 - 76.2 (20.2)"  "0.1 - 211.0 (21.2)"
[1] "hr=" "1.1"
D54V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  7P LOSS MUTATED         1        3         4        15         1         1
  7P LOSS WILD-TYPE      26       73        78       237        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              15               237
  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   7   7
  7P LOSS WILD-TYPE    47 128  93 166
D54V4, multiclass
       clus
vv      7P LOSS MUTATED 7P LOSS WILD-TYPE
  T0+T1               3                47
  T2                  9               128
  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
  7P LOSS MUTATED     5   6  14   0
  7P LOSS WILD-TYPE 174  62 154   8
D54V5, multiclass
    clus
vv   7P LOSS MUTATED 7P LOSS WILD-TYPE
  N0               5               174
  N1               6                62
  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"
D54V6, binary
                   cls
clus                  0   1
  7P LOSS MUTATED     9   1
  7P LOSS WILD-TYPE 181   0
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      9    1
  7P LOSS WILD-TYPE  181    0
   clus
vv  7P LOSS MUTATED 7P LOSS WILD-TYPE
  0               9               181
  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  19
  7P LOSS WILD-TYPE 155 282
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      7   19
  7P LOSS WILD-TYPE  155  282
     clus
vv    7P LOSS MUTATED 7P LOSS WILD-TYPE
  NO                7               155
  YES              19               282
[1] 2 2
[1] FALSE
                   vv
clus                HEAD & NECK SQUAMOUS CELL CARCINOMA
  7P LOSS MUTATED                                    28
  7P LOSS WILD-TYPE                                 483
                   vv
clus                HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  7P LOSS MUTATED                                                   1
  7P LOSS WILD-TYPE                                                 9
                   vv
clus                HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  7P LOSS MUTATED                                                           0
  7P LOSS WILD-TYPE                                                         1
D54V9, multiclass
                                                           clus
vv                                                          7P LOSS MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                    28
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       1
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT               0
                                                           clus
vv                                                          7P LOSS WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                     483
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                         9
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                 1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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    22  19
  7Q LOSS WILD-TYPE 279 200
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               41               479 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               19               200 
$`7Q LOSS MUTATED`
TCGA-BA-5559 TCGA-CN-6997 TCGA-CX-7082 TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-5152 
       68.48        32.48         0.36        15.19        13.64        42.35 
TCGA-BA-A4IH TCGA-BA-A6DE TCGA-BB-4224 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4737 
       20.45        14.47         9.14        26.86        32.81        20.55 
TCGA-CN-5359 TCGA-CN-5374 TCGA-CN-6998 TCGA-CN-A49B TCGA-CN-A63U TCGA-CN-A63W 
       12.39        56.94        11.74        29.72        31.69        12.39 
TCGA-CQ-6220 TCGA-CR-6474 TCGA-CR-7365 TCGA-CR-7374 TCGA-CR-7398 TCGA-CV-5444 
       32.38        18.54        39.16         0.99         5.13        80.12 
TCGA-CV-6003 TCGA-CV-6954 TCGA-CV-7180 TCGA-CV-7429 TCGA-CV-7433 TCGA-CV-7438 
       54.74        65.82        10.75         3.52        19.76         6.38 
TCGA-D6-6823 TCGA-D6-A6EM TCGA-F7-8489 TCGA-F7-A50G TCGA-HD-A6HZ TCGA-IQ-7632 
       23.05         7.63        21.63        20.25         3.65        14.50 
TCGA-KU-A6H7 TCGA-MZ-A5BI TCGA-P3-A5QE TCGA-QK-A8Z9 TCGA-KU-A66T 
       19.27         7.13        51.25        14.76        18.15 

$`7Q LOSS WILD-TYPE`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-6871 TCGA-BA-A4IG TCGA-BA-A4II 
        9.30        37.28        20.48         3.55        28.11        30.18 
TCGA-BB-A5HU TCGA-CN-4727 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 
       25.71        51.29         9.07         9.24        52.08        11.08 
TCGA-CN-6992 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-6221 TCGA-CQ-7063 
       35.05        19.82        24.39        48.20        32.88        70.13 
TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-A4C7 TCGA-CR-6472 TCGA-CR-6478 TCGA-CX-7219 
       16.73        43.04        11.61        34.52         6.02        34.36 
TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7593 TCGA-H7-A6C5 TCGA-HD-8634 
       30.94        14.04        46.32        40.24        21.11        12.66 
TCGA-HD-8635 TCGA-UF-A71D TCGA-UF-A7JV TCGA-4P-AA8J TCGA-BA-4078 TCGA-BA-5149 
       22.85        48.03         2.96         3.35         9.07        26.50 
TCGA-BA-5151 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-6868 
       23.74        57.93        17.10        23.84        65.59        15.52 
TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF 
       21.17        14.83        12.62         4.01        41.85        29.42 
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-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 
        4.80         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-A5HY TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO TCGA-C9-A47Z 
       20.52        10.55        27.19        12.92         8.81         6.28 
TCGA-C9-A480 TCGA-CN-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-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4738 TCGA-CN-4739 
       12.89        52.14        57.11        12.99        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-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-6012 
       12.49         8.52        52.08        50.07        30.67        48.00 
TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 
       23.90        47.44        28.04        19.07        34.13         6.74 
TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-A497 
       10.45        32.22        38.89         3.68        17.42        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-A6V6 
       16.57         4.41        12.07         2.70        23.44        20.88 
TCGA-CN-A6V7 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 
       19.53        52.37        21.50         2.93        54.58        70.45 
TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 
       62.37        45.99        10.42        11.21         4.24        41.19 
TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 
       46.95        56.58        13.25         4.24        14.99        38.76 
TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 
       64.87        53.52        41.88        43.10        77.56        44.48 
TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH 
       23.24        29.36        33.60        29.49        14.14        12.46 
TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 
       31.23        84.23        11.77        54.67        37.87        26.27 
TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6477 TCGA-CR-6480 
       58.42        50.01        39.52        36.99        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-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7376 TCGA-CR-7377 
        3.45         3.09        24.95        29.23        31.96         9.17 
TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 
       34.06        19.92        26.17        17.13        32.78        47.01 
TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 
       27.06        12.89        49.58        30.02        46.85        32.65 
TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 
       44.25        30.58        24.79         5.95        35.41        29.95 
TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 
       48.39       139.43        17.16       129.21       108.95        76.24 
TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 
       19.20        17.95       107.51        94.88        76.50        91.53 
TCGA-CV-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-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       172.67 
TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 
      111.16        18.81        12.66         7.99         9.01         5.26 
TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-7178 TCGA-CV-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        89.65        36.00        31.36        26.20 
TCGA-CV-7247 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7254 
       18.97        17.13        95.34         4.96        11.87        47.97 
TCGA-CV-7255 TCGA-CV-7261 TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7407 TCGA-CV-7409 
        2.10        49.71        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-7430 TCGA-CV-7432 TCGA-CV-7434 TCGA-CV-7435 
      156.49        54.94        16.27        84.49         7.17       153.86 
TCGA-CV-7437 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45R 
       16.64        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-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-D6-6824 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-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        23.34        58.45        37.25 
TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7594 
       33.86        18.02        46.45        20.45        37.58        40.04 
TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-A50I TCGA-F7-A50J 
       39.12        41.59        37.18        32.71         3.02        31.13 
TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A623 
       18.94        24.95         0.46        17.85        11.80        20.25 
TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A76A TCGA-HD-7229 
       12.43        13.38        15.16        15.06        20.94        33.76 
TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-7917 TCGA-HD-8224 
       28.47        25.74        21.93        27.48        27.48        14.66 
TCGA-HD-8314 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6I0 TCGA-HL-7533 
       22.03         0.36        13.84         4.27         6.90        34.75 
TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I 
       15.95        38.53        37.71        11.84        37.41         0.07 
TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O TCGA-IQ-A6SG TCGA-IQ-A6SH 
       33.57         5.29        13.68        13.84        19.04        15.48 
TCGA-KU-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-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5Q6 
        6.25        15.42        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-A6IG TCGA-QK-A6IH TCGA-QK-A6II 
       21.07        21.21        23.15         7.30        21.47         9.34 
TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z8 
       12.72        27.39        21.07        19.73        12.89         5.62 
TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-RS-A6TO TCGA-RS-A6TP 
       12.20        17.82        15.32         8.32        12.72        16.96 
TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-T3-A92M TCGA-T3-A92N 
        6.87        15.91         7.10        32.45        13.71         3.12 
TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A 
       13.55        13.25        20.35        64.80        54.67         2.83 
TCGA-UF-A71B TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD 
       49.51        49.45        44.65        74.47        17.95        24.30 
TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS 
       55.43        29.46        18.05        13.94        20.75        22.36 
TCGA-UF-A7JT TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 TCGA-KU-A66S 
       32.65        17.03        20.55        14.56        13.35 

  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
             0.36              0.07 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
            80.12            210.97 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
            19.27             21.24 
[1] "0.4 - 80.1 (19.3)"  "0.1 - 211.0 (21.2)"
[1] "hr=" "1.3"
D55V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  7Q LOSS MUTATED         1        5         7        23         0         0
  7Q LOSS WILD-TYPE      26       71        75       229        12         1
D55V3, multiclass
           clus
vv          7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  STAGE I                 1                26
  STAGE II                5                71
  STAGE III               7                75
  STAGE IVA              23               229
  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  17   6  13
  7Q LOSS WILD-TYPE    49 120  94 160
D55V4, multiclass
       clus
vv      7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  T0+T1               1                49
  T2                 17               120
  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
  7Q LOSS MUTATED     9   9  16   0
  7Q LOSS WILD-TYPE 170  59 152   8
D55V5, multiclass
    clus
vv   7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  N0               9               170
  N1               9                59
  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    14   0
  7Q LOSS WILD-TYPE 176   1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED     14    0
  7Q LOSS WILD-TYPE  176    1
   clus
vv  7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  0              14               176
  1               0                 1
[1] 2 2
[1] FALSE
D55V7, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED    13  28
  7Q LOSS WILD-TYPE 127 354
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED     13   28
  7Q LOSS WILD-TYPE  127  354
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  FEMALE              13               127
  MALE                28               354
[1] 2 2
[1] FALSE
D55V8, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED    13  26
  7Q LOSS WILD-TYPE 149 275
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED     13   26
  7Q LOSS WILD-TYPE  149  275
     clus
vv    7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  NO               13               149
  YES              26               275
[1] 2 2
[1] FALSE
                   vv
clus                HEAD & NECK SQUAMOUS CELL CARCINOMA
  7Q LOSS MUTATED                                    39
  7Q LOSS WILD-TYPE                                 472
                   vv
clus                HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  7Q LOSS MUTATED                                                   2
  7Q LOSS WILD-TYPE                                                 8
                   vv
clus                HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  7Q LOSS MUTATED                                                           0
  7Q LOSS WILD-TYPE                                                         1
D55V9, multiclass
                                                           clus
vv                                                          7Q LOSS MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                    39
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       2
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT               0
                                                           clus
vv                                                          7Q LOSS WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                     472
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                         8
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                 1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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    38
  7Q LOSS WILD-TYPE                        45   408
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                                         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"
D55V14, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED     1  39
  7Q LOSS WILD-TYPE  25 420
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      1   39
  7Q LOSS WILD-TYPE   25  420
                        clus
vv                       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                25
  NOT HISPANIC OR LATINO              39               420
[1] 2 2
[1] FALSE

Clustering(56) Variable = 8P LOSS MUTATION ANALYSIS
D56V1, survival
                   sevent
clus2                 0   1
  8P LOSS MUTATED    96  89
  8P LOSS WILD-TYPE 205 130
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
              185               335 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               89               130 
$`8P LOSS MUTATED`
TCGA-BB-A5HU TCGA-CN-6992 TCGA-CN-6997 TCGA-CQ-7063 TCGA-CQ-7067 TCGA-CX-7219 
       25.71        35.05        32.48        70.13        16.73        34.36 
TCGA-HD-8635 TCGA-UF-A71D TCGA-UF-A7JV TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-5149 
       22.85        48.03         2.96        15.19        13.64        26.50 
TCGA-BA-5151 TCGA-BA-5558 TCGA-BA-6870 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 
       23.74        65.59        14.83        12.62         4.01        41.85 
TCGA-BA-A6D8 TCGA-BA-A6DE TCGA-BA-A6DI TCGA-BA-A8YP TCGA-BB-4227 TCGA-BB-7862 
       27.95        14.47        11.05        16.41         4.41        36.72 
TCGA-BB-7863 TCGA-BB-7871 TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-BB-A6UO TCGA-C9-A47Z 
       33.70        24.66        10.55        27.19         8.81         6.28 
TCGA-C9-A480 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4736 TCGA-CN-4742 TCGA-CN-5360 
       12.69        38.04         4.67        12.99        13.05        71.31 
TCGA-CN-5363 TCGA-CN-5365 TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 
        8.32        11.54        11.57         8.52        52.08        56.94 
TCGA-CN-6011 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6020 TCGA-CN-6996 TCGA-CN-A498 
       30.67        23.90        47.44         6.74        17.42        25.41 
TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A640 TCGA-CN-A641 TCGA-CQ-5326 TCGA-CQ-5332 
       17.29        29.72         4.41        12.07         2.93        10.42 
TCGA-CQ-5334 TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7064 
        4.24        13.25         4.24        14.99        38.76        64.87 
TCGA-CQ-7065 TCGA-CQ-7069 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4CB TCGA-CR-5247 
       53.52        41.88        77.56        44.48        29.36        11.77 
TCGA-CR-6471 TCGA-CR-6474 TCGA-CR-6484 TCGA-CR-7364 TCGA-CR-7369 TCGA-CR-7372 
       39.52        18.54        11.64        47.18        35.84        24.95 
TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7377 TCGA-CR-7380 TCGA-CR-7388 TCGA-CR-7399 
       29.23         0.99         9.17        19.92        27.06         5.95 
TCGA-CR-7401 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5441 TCGA-CV-5444 TCGA-CV-5966 
       35.41       129.21       108.95        94.88        80.12        17.92 
TCGA-CV-5973 TCGA-CV-6436 TCGA-CV-6933 TCGA-CV-6935 TCGA-CV-6940 TCGA-CV-6952 
       86.83        62.43        90.12         9.70        26.43         6.08 
TCGA-CV-6954 TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-6962 TCGA-CV-7089 
       65.82         7.13         8.42        28.34         4.14        64.83 
TCGA-CV-7090 TCGA-CV-7100 TCGA-CV-7102 TCGA-CV-7104 TCGA-CV-7235 TCGA-CV-7236 
      172.67         9.01         1.84        12.92        77.16         4.73 
TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7247 TCGA-CV-7248 TCGA-CV-7255 TCGA-CV-7261 
       89.65        36.00        18.97        17.13         2.10        49.71 
TCGA-CV-7414 TCGA-CV-7416 TCGA-CV-7421 TCGA-CV-7422 TCGA-CV-7423 TCGA-CV-7427 
        0.46        25.08         0.07        34.09       100.57       156.49 
TCGA-CV-7434 TCGA-CV-7438 TCGA-CV-7440 TCGA-CV-A45U TCGA-CV-A45W TCGA-CV-A460 
        7.17         6.38        22.19        35.47        45.96        60.43 
TCGA-CV-A464 TCGA-CV-A465 TCGA-CV-A6JD TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JZ 
       56.61         7.07         5.98         6.48        28.01        23.47 
TCGA-D6-6517 TCGA-D6-6825 TCGA-D6-A4Z9 TCGA-D6-A6EM TCGA-D6-A6EN TCGA-D6-A6ES 
        9.60        16.14        17.72         7.63        22.59        12.79 
TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7592 TCGA-F7-8298 
       58.45        37.25        33.86        18.02        37.58        32.71 
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-A633 TCGA-IQ-7630 TCGA-IQ-A61E TCGA-IQ-A61G 
       28.47        14.66        13.84        15.95        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-MT-A51X TCGA-MT-A7BN TCGA-MZ-A6I9 TCGA-P3-A5Q6 TCGA-P3-A5QA 
       15.48         7.96        15.42        16.08        15.78        71.74 
TCGA-P3-A6SX TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IH 
       47.01        16.01        13.15        21.07        21.21        21.47 
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-QK-AA3K TCGA-T2-A6WZ TCGA-TN-A7HJ TCGA-UF-A71A TCGA-UF-A71E 
       15.32         8.32        15.91        13.25         2.83        49.45 
TCGA-UF-A7J9 TCGA-UF-A7JD TCGA-UF-A7JJ TCGA-WA-A7H4 TCGA-KU-A66T 
       44.65        24.30        18.05        14.56        18.15 

$`8P LOSS WILD-TYPE`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4IG 
        9.30        37.28        20.48        68.48         3.55        28.11 
TCGA-BA-A4II TCGA-CN-4727 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 
       30.18        51.29         9.07         9.24        52.08        11.08 
TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-6221 TCGA-CQ-7068 TCGA-CQ-A4C7 
       19.82        24.39        48.20        32.88        43.04        11.61 
TCGA-CR-6472 TCGA-CR-6478 TCGA-CX-7082 TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7589 
       34.52         6.02         0.36        30.94        14.04        46.32 
TCGA-DQ-7593 TCGA-H7-A6C5 TCGA-HD-8634 TCGA-4P-AA8J TCGA-BA-4078 TCGA-BA-5152 
       40.24        21.11        12.66         3.35         9.07        42.35 
TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-A4IF 
       57.93        17.10        23.84        15.52        21.17        29.42 
TCGA-BA-A4IH TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DF TCGA-BA-A6DG 
       20.45        11.54         7.10         5.69         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         4.80 
TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7872 
       18.38        22.42        50.20        44.98        66.28        38.40 
TCGA-BB-8596 TCGA-BB-8601 TCGA-BB-A6UM TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4728 
       71.05        20.52        12.92        48.76        55.86        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-6988 TCGA-CN-6989 
       48.00        28.04        19.07        34.13        10.45        32.22 
TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A499 TCGA-CN-A49C 
       38.89         3.68        11.74        35.01        23.57        21.21 
TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A642 
        7.40        31.69        22.32        12.39        16.57         2.70 
TCGA-CN-A6UY TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 
       23.44        20.88        19.53        52.37        21.50        54.58 
TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5333 TCGA-CQ-6218 TCGA-CQ-6220 
       70.45        62.37        45.99        11.21        41.19        32.38 
TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-7071 TCGA-CQ-A4C9 TCGA-CQ-A4CD TCGA-CQ-A4CE 
       46.95        56.58        43.10        23.24        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-6473 TCGA-CR-6477 TCGA-CR-6480 
       26.27        58.42        50.01        36.99        16.90        11.90 
TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 
       10.22        11.34         7.69        12.46        22.78        15.75 
TCGA-CR-6493 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7370 TCGA-CR-7371 
        9.27        39.16        47.34        40.93         3.45         3.09 
TCGA-CR-7376 TCGA-CR-7379 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 
       31.96        34.06        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        49.58        30.02        46.85        32.65        44.25 
TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 
       30.58        24.79         5.13        29.95        48.39       139.43 
TCGA-CV-5431 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5442 
       17.16        76.24        19.20        17.95       107.51        76.50 
TCGA-CV-5443 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 
       91.53        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-6942 TCGA-CV-6943 
       20.52         4.73        21.90        11.24       140.78        19.79 
TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6953 TCGA-CV-6955 
       12.03        42.38        15.09        30.08        53.95        10.98 
TCGA-CV-6961 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7101 
        2.50       111.16        18.81        12.66         7.99         5.26 
TCGA-CV-7103 TCGA-CV-7177 TCGA-CV-7178 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7243 
       52.31        21.80        71.21        10.75       130.88        31.36 
TCGA-CV-7245 TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7263 
       26.20        95.34         4.96        11.87        47.97        18.41 
TCGA-CV-7406 TCGA-CV-7407 TCGA-CV-7409 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 
       57.47        35.54        17.85       210.97        89.33         9.67 
TCGA-CV-7415 TCGA-CV-7418 TCGA-CV-7424 TCGA-CV-7425 TCGA-CV-7428 TCGA-CV-7429 
       22.85        25.94        14.89        56.48        54.94         3.52 
TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7435 TCGA-CV-7437 TCGA-CV-A45O 
       16.27        84.49        19.76       153.86        16.64        27.98 
TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45V TCGA-CV-A45X 
       21.01       169.38       180.16       159.65         1.05         6.51 
TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A461 TCGA-CV-A463 TCGA-CV-A468 TCGA-CV-A6JE 
       88.87        48.20        67.86         0.76        15.25        35.34 
TCGA-CV-A6JM TCGA-CV-A6JN TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6K0 TCGA-CV-A6K1 
        6.38        29.79         3.62        21.24        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-D6-6823 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-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A74Q 
       12.36        28.77        24.95        13.94        12.10        23.34 
TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 
       46.45        20.45        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-A623 
       21.63        20.25         3.02        18.94        24.95        20.25 
TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7754 TCGA-HD-7831 
       12.43        13.38        20.94        33.76        25.74        21.93 
TCGA-HD-7832 TCGA-HD-7917 TCGA-HD-8314 TCGA-HD-A4C1 TCGA-HD-A634 TCGA-HD-A6HZ 
       27.48        27.48        22.03         0.36         4.27         3.65 
TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61O TCGA-KU-A6H7 
        6.90        34.75        38.53        14.50        13.84        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-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW 
        7.13        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-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A8Z7 
       23.15         7.30         9.34        12.72        27.39        12.89 
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-A71B 
        3.12        13.55        20.35        64.80        54.67        49.51 
TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JK TCGA-UF-A7JO 
       74.47        17.95        55.43        29.46        13.94        20.75 
TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-KU-A66S 
       22.36        32.65        17.03        20.55        13.35 

  8P LOSS MUTATED 8P LOSS WILD-TYPE 
             0.07              0.36 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
           172.67            210.97 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
            18.05             21.93 
[1] "0.1 - 172.7 (18.1)" "0.4 - 211.0 (21.9)"
[1] "hr=" "1.4"
D56V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  8P LOSS MUTATED        11       22        36        91         6         1
  8P LOSS WILD-TYPE      16       54        46       161         6         0
D56V3, multiclass
           clus
vv          8P LOSS MUTATED 8P LOSS WILD-TYPE
  STAGE I                11                16
  STAGE II               22                54
  STAGE III              36                46
  STAGE IVA              91               161
  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
  8P LOSS MUTATED      19  40  45  65
  8P LOSS WILD-TYPE    31  97  55 108
D56V4, multiclass
       clus
vv      8P LOSS MUTATED 8P LOSS WILD-TYPE
  T0+T1              19                31
  T2                 40                97
  T3                 45                55
  T4                 65               108
[1] 4 2
[1] TRUE
[1] "dimension of 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    59  30  64   3
  8P LOSS WILD-TYPE 120  38 104   5
D56V5, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  N0              59               120
  N1              30                38
  N2              64               104
  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"
D56V6, binary
                   cls
clus                  0   1
  8P LOSS MUTATED    74   1
  8P LOSS WILD-TYPE 116   0
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     74    1
  8P LOSS WILD-TYPE  116    0
   clus
vv  8P LOSS MUTATED 8P LOSS WILD-TYPE
  0              74               116
  1               1                 0
[1] 2 2
[1] FALSE
D56V7, binary
                   cls
clus                  0   1
  8P LOSS MUTATED    56 129
  8P LOSS WILD-TYPE  84 253
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     56  129
  8P LOSS WILD-TYPE   84  253
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  FEMALE              56                84
  MALE               129               253
[1] 2 2
[1] FALSE
D56V8, binary
                   cls
clus                  0   1
  8P LOSS MUTATED    57 113
  8P LOSS WILD-TYPE 105 188
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     57  113
  8P LOSS WILD-TYPE  105  188
     clus
vv    8P LOSS MUTATED 8P LOSS WILD-TYPE
  NO               57               105
  YES             113               188
[1] 2 2
[1] FALSE
                   vv
clus                HEAD & NECK SQUAMOUS CELL CARCINOMA
  8P LOSS MUTATED                                   183
  8P LOSS WILD-TYPE                                 328
                   vv
clus                HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  8P LOSS MUTATED                                                   2
  8P LOSS WILD-TYPE                                                 8
                   vv
clus                HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  8P LOSS MUTATED                                                           0
  8P LOSS WILD-TYPE                                                         1
D56V9, multiclass
                                                           clus
vv                                                          8P LOSS MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                   183
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       2
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT               0
                                                           clus
vv                                                          8P LOSS WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                     328
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                         8
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                 1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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                          23   151
  8P LOSS WILD-TYPE                        25   295
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                     23                25
  WHITE                                        151               295
[1] 4 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    10 161
  8P LOSS WILD-TYPE  16 298
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     10  161
  8P LOSS WILD-TYPE   16  298
                        clus
vv                       8P LOSS MUTATED 8P LOSS WILD-TYPE
  HISPANIC OR LATINO                  10                16
  NOT HISPANIC OR LATINO             161               298
[1] 2 2
[1] FALSE

Clustering(57) Variable = 8Q LOSS MUTATION ANALYSIS
D57V1, survival
                   sevent
clus2                 0   1
  8Q LOSS MUTATED    13  12
  8Q LOSS WILD-TYPE 288 207
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               25               495 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               12               207 
$`8Q LOSS MUTATED`
TCGA-CQ-7063 TCGA-BA-4076 TCGA-BA-A6D8 TCGA-BB-A6UO TCGA-CN-4726 TCGA-CN-5360 
       70.13        13.64        27.95         8.81         4.67        71.31 
TCGA-CN-5367 TCGA-CN-6011 TCGA-CN-A641 TCGA-CQ-6225 TCGA-CQ-7064 TCGA-CV-6956 
       11.57        30.67        12.07        13.25        64.87         7.13 
TCGA-CV-7242 TCGA-CV-7261 TCGA-CV-7440 TCGA-CV-A45W TCGA-CV-A6JD TCGA-CV-A6JT 
       36.00        49.71        22.19        45.96         5.98        28.01 
TCGA-D6-A6EM TCGA-F7-A622 TCGA-H7-8502 TCGA-MZ-A6I9 TCGA-P3-A6T7 TCGA-QK-A6VB 
        7.63        11.80        15.06        16.08        16.01        21.07 
TCGA-QK-AA3J 
       15.32 

$`8Q LOSS WILD-TYPE`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4IG 
        9.30        37.28        20.48        68.48         3.55        28.11 
TCGA-BA-A4II TCGA-BB-A5HU TCGA-CN-4727 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 
       30.18        25.71        51.29         9.07         9.24        52.08 
TCGA-CN-6024 TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 
       11.08        35.05        32.48        19.82        24.39        48.20 
TCGA-CQ-6221 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-A4C7 TCGA-CR-6472 TCGA-CR-6478 
       32.88        16.73        43.04        11.61        34.52         6.02 
TCGA-CX-7082 TCGA-CX-7219 TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7593 
        0.36        34.36        30.94        14.04        46.32        40.24 
TCGA-H7-A6C5 TCGA-HD-8634 TCGA-HD-8635 TCGA-UF-A71D TCGA-UF-A7JV TCGA-4P-AA8J 
       21.11        12.66        22.85        48.03         2.96         3.35 
TCGA-BA-4074 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 
       15.19         9.07        26.50        23.74        42.35        57.93 
TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 
       17.10        23.84        65.59        15.52        21.17        14.83 
TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IH TCGA-BA-A6DA 
       12.62         4.01        41.85        29.42        20.45        11.54 
TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DI 
        7.10         5.69        14.47         7.82         2.27        11.05 
TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 
       13.38        20.48        16.41         6.15       105.90         9.14 
TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 
        4.80         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-A5HY TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-C9-A47Z TCGA-C9-A480 
       20.52        10.55        27.19        12.92         6.28        12.69 
TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 
       48.76        55.86        38.04        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-5356 
       45.83        27.58        73.61        13.05        42.02        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-5369 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6012 
       12.49         8.52        52.08        56.94        50.07        48.00 
TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 
       23.90        47.44        28.04        19.07        34.13         6.74 
TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6998 
       10.45        32.22        38.89         3.68        17.42        11.74 
TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C 
       35.01        25.41        23.57        17.29        29.72        21.21 
TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 
        7.40        31.69        22.32        12.39        16.57         4.41 
TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5324 TCGA-CQ-5325 
        2.70        23.44        20.88        19.53        52.37        21.50 
TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 
        2.93        54.58        70.45        62.37        45.99        10.42 
TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6220 TCGA-CQ-6223 TCGA-CQ-6224 
       11.21         4.24        41.19        32.38        46.95        56.58 
TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7065 TCGA-CQ-7069 TCGA-CQ-7071 
        4.24        14.99        38.76        53.52        41.88        43.10 
TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE 
       77.56        44.48        23.24        29.36        33.60        29.49 
TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 
       14.14        12.46        31.23        84.23        11.77        54.67 
TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6473 
       37.87        26.27        58.42        50.01        39.52        36.99 
TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 
       18.54        16.90        11.90        10.22        11.34        11.64 
TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 
        7.69        12.46        22.78        15.75         9.27        47.18 
TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 
       39.16        47.34        40.93        35.84         3.45         3.09 
TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 
       24.95        29.23         0.99        31.96         9.17        34.06 
TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 
       19.92        26.17        17.13        32.78        47.01        27.06 
TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 
       12.89        49.58        30.02        46.85        32.65        44.25 
TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 
       30.58        24.79         5.13         5.95        35.41        29.95 
TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 
       48.39       139.43        17.16       129.21       108.95        76.24 
TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 
       19.20        17.95       107.51        94.88        76.50        91.53 
TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 
       80.12        17.92        13.35        23.05        86.83        48.59 
TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 
       60.49         7.07        43.23        54.74        21.07        62.43 
TCGA-CV-6441 TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6937 
        9.60        90.12         2.14         9.70         5.46        20.52 
TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 
        4.73        21.90        26.43        11.24       140.78        19.79 
TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6953 
       12.03        42.38        15.09        30.08         6.08        53.95 
TCGA-CV-6954 TCGA-CV-6955 TCGA-CV-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-7095 TCGA-CV-7097 TCGA-CV-7099 
       64.83       172.67       111.16        18.81        12.66         7.99 
TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7177 
        9.01         5.26         1.84        52.31        12.92        21.80 
TCGA-CV-7178 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7238 
       71.21        10.75       130.88        77.16         4.73        89.65 
TCGA-CV-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-7263 TCGA-CV-7406 TCGA-CV-7407 
       11.87        47.97         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-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-7434 TCGA-CV-7435 TCGA-CV-7437 TCGA-CV-7438 TCGA-CV-A45O 
       19.76         7.17       153.86        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-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-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 
        6.48         3.62        21.24        23.47        19.92        22.52 
TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6516 
       10.42        10.55        18.84        51.12        13.25        25.41 
TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 
        9.60        23.05         2.53        16.14        11.44        18.67 
TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EN 
       24.95        25.32        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        23.34        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-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-A623 TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-A76A 
       17.85        20.25        12.43        13.38        15.16        20.94 
TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-7917 
       33.76        28.47        25.74        21.93        27.48        27.48 
TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ 
       14.66        22.03         0.36        13.84         4.27         3.65 
TCGA-HD-A6I0 TCGA-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-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W 
       13.84        19.04        15.48        19.27        10.75        14.37 
TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G TCGA-MT-A7BN 
        7.96        30.05         1.84        12.62         6.25        15.42 
TCGA-MZ-A5BI TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QE 
        7.13        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-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 
       23.15         7.30        21.47         9.34        12.72        27.39 
TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB 
       19.73        12.89         5.62        14.76        12.20        17.82 
TCGA-QK-AA3K TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T2-A6X0 
        8.32        12.72        16.96         6.87        15.91         7.10 
TCGA-T2-A6X2 TCGA-T3-A92M TCGA-T3-A92N TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL 
       32.45        13.71         3.12        13.55        13.25        20.35 
TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71E TCGA-UF-A7J9 
       64.80        54.67         2.83        49.51        49.45        44.65 
TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ 
       74.47        17.95        24.30        55.43        29.46        18.05 
TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UP-A6WW TCGA-WA-A7GZ 
       13.94        20.75        22.36        32.65        17.03        20.55 
TCGA-WA-A7H4 TCGA-KU-A66S TCGA-KU-A66T 
       14.56        13.35        18.15 

  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 
            16.01             21.21 
[1] "4.7 - 71.3 (16.0)"  "0.1 - 211.0 (21.2)"
[1] "hr=" "1.3"
D57V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  8Q LOSS MUTATED         2        4         5        11         0         0
  8Q LOSS WILD-TYPE      25       72        77       241        12         1
D57V3, multiclass
           clus
vv          8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  STAGE I                 2                25
  STAGE II                4                72
  STAGE III               5                77
  STAGE IVA              11               241
  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   5   6   9
  8Q LOSS WILD-TYPE    48 132  94 164
D57V4, multiclass
       clus
vv      8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  T0+T1               2                48
  T2                  5               132
  T3                  6                94
  T4                  9               164
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  8Q LOSS MUTATED     9   3   7   0
  8Q LOSS WILD-TYPE 170  65 161   8
D57V5, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  N0               9               170
  N1               3                65
  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"
D57V6, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED    12   0
  8Q LOSS WILD-TYPE 178   1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED     12    0
  8Q LOSS WILD-TYPE  178    1
   clus
vv  8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  0              12               178
  1               0                 1
[1] 2 2
[1] FALSE
D57V7, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED     7  18
  8Q LOSS WILD-TYPE 133 364
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      7   18
  8Q LOSS WILD-TYPE  133  364
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  FEMALE               7               133
  MALE                18               364
[1] 2 2
[1] FALSE
D57V8, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED     7  16
  8Q LOSS WILD-TYPE 155 285
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      7   16
  8Q LOSS WILD-TYPE  155  285
     clus
vv    8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  NO                7               155
  YES              16               285
[1] 2 2
[1] FALSE
                   vv
clus                HEAD & NECK SQUAMOUS CELL CARCINOMA
  8Q LOSS MUTATED                                    24
  8Q LOSS WILD-TYPE                                 487
                   vv
clus                HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  8Q LOSS MUTATED                                                   1
  8Q LOSS WILD-TYPE                                                 9
                   vv
clus                HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  8Q LOSS MUTATED                                                           0
  8Q LOSS WILD-TYPE                                                         1
D57V9, multiclass
                                                           clus
vv                                                          8Q LOSS MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                    24
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       1
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT               0
                                                           clus
vv                                                          8Q LOSS WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                     487
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                         9
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                 1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V10, continuous
D57V11, continuous
D57V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  8Q LOSS MUTATED                                  0     0
  8Q LOSS WILD-TYPE                                2    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  8Q LOSS MUTATED                           2    23
  8Q LOSS WILD-TYPE                        46   423
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                                         23               423
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V14, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED     1  23
  8Q LOSS WILD-TYPE  25 436
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      1   23
  8Q LOSS WILD-TYPE   25  436
                        clus
vv                       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                25
  NOT HISPANIC OR LATINO              23               436
[1] 2 2
[1] FALSE

Clustering(58) Variable = 9P LOSS MUTATION ANALYSIS
D58V1, survival
                   sevent
clus2                 0   1
  9P LOSS MUTATED   106  80
  9P LOSS WILD-TYPE 195 139
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              186               334 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               80               139 
$`9P LOSS MUTATED`
TCGA-BA-6871 TCGA-BB-A5HU TCGA-CN-4727 TCGA-CN-6021 TCGA-CN-6024 TCGA-CN-6992 
        3.55        25.71        51.29         9.07        11.08        35.05 
TCGA-CN-6997 TCGA-CQ-6221 TCGA-CQ-7067 TCGA-CR-6472 TCGA-CX-7082 TCGA-DQ-5629 
       32.48        32.88        16.73        34.52         0.36        30.94 
TCGA-DQ-7588 TCGA-H7-A6C5 TCGA-HD-8635 TCGA-UF-A71D TCGA-BA-4074 TCGA-BA-4076 
       14.04        21.11        22.85        48.03        15.19        13.64 
TCGA-BA-4078 TCGA-BA-5555 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6872 
        9.07        17.10        15.52        21.17        14.83        12.62 
TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A6D8 TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DL 
       41.85        29.42        27.95         5.69        14.47        20.48 
TCGA-BA-A8YP TCGA-BB-4224 TCGA-BB-7862 TCGA-BB-7872 TCGA-BB-8601 TCGA-CN-4723 
       16.41         9.14        36.72        38.40        20.52        55.86 
TCGA-CN-4726 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4735 TCGA-CN-4737 
        4.67        12.89        26.86        32.81        57.11        20.55 
TCGA-CN-4740 TCGA-CN-5360 TCGA-CN-5373 TCGA-CN-6018 TCGA-CN-6020 TCGA-CN-6988 
       27.58        71.31        52.08        19.07         6.74        10.45 
TCGA-CN-6989 TCGA-CN-A497 TCGA-CN-A63W TCGA-CN-A641 TCGA-CQ-5325 TCGA-CQ-5326 
       32.22        35.01        12.39        12.07        21.50         2.93 
TCGA-CQ-5332 TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-7064 TCGA-CQ-7065 
       10.42        13.25         4.24        14.99        64.87        53.52 
TCGA-CQ-7069 TCGA-CQ-7072 TCGA-CQ-A4CB TCGA-CR-5247 TCGA-CR-6474 TCGA-CR-6477 
       41.88        77.56        29.36        11.77        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        49.58         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-7086 TCGA-CX-A4AQ 
       60.43        67.86        56.61         3.62        18.84        51.12 
TCGA-D6-6823 TCGA-D6-6826 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB 
       23.05        11.44        24.95        25.32        17.72        12.36 
TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5631 TCGA-DQ-7595 
       24.95        13.94        12.79        23.34        18.02        39.12 
TCGA-F7-7848 TCGA-F7-A50I TCGA-F7-A61W TCGA-F7-A623 TCGA-HD-7753 TCGA-HD-7754 
       37.18         3.02         0.46        20.25        28.47        25.74 
TCGA-HD-A633 TCGA-HD-A6HZ TCGA-IQ-7630 TCGA-IQ-A61G TCGA-IQ-A61J TCGA-IQ-A6SG 
       13.84         3.65        15.95        11.84        33.57        19.04 
TCGA-IQ-A6SH TCGA-MT-A51X TCGA-MT-A67D TCGA-MZ-A5BI TCGA-MZ-A7D7 TCGA-P3-A5Q6 
       15.48         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        12.89         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-A71E TCGA-UF-A7JA TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH 
       49.51        49.45        74.47        24.30        55.43        29.46 
TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JS TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-KU-A66T 
       18.05        13.94        22.36        17.03        20.55        18.15 

$`9P LOSS WILD-TYPE`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-A4IG TCGA-BA-A4II 
        9.30        37.28        20.48        68.48        28.11        30.18 
TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-7063 
        9.24        52.08        19.82        24.39        48.20        70.13 
TCGA-CQ-7068 TCGA-CQ-A4C7 TCGA-CR-6478 TCGA-CX-7219 TCGA-DQ-7589 TCGA-DQ-7593 
       43.04        11.61         6.02        34.36        46.32        40.24 
TCGA-HD-8634 TCGA-UF-A7JV TCGA-4P-AA8J TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 
       12.66         2.96         3.35        26.50        23.74        42.35 
TCGA-BA-5153 TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-6873 TCGA-BA-A4IH TCGA-BA-A6DA 
       57.93        23.84        65.59         4.01        20.45        11.54 
TCGA-BA-A6DB TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DI TCGA-BA-A6DJ TCGA-BB-4217 
        7.10         7.82         2.27        11.05        13.38         6.15 
TCGA-BB-4223 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7863 
      105.90         4.80         4.41        18.38        22.42        33.70 
TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-8596 TCGA-BB-A5HY 
       50.20        44.98        66.28        24.66        71.05        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-4725 TCGA-CN-4728 TCGA-CN-4733 TCGA-CN-4736 TCGA-CN-4738 TCGA-CN-4739 
       38.04        56.68        52.14        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-5363 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5369 
        8.32        16.21        11.54        11.84        11.57        12.49 
TCGA-CN-5370 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 
        8.52        56.94        50.07        30.67        48.00        23.90 
TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6019 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 
       47.44        28.04        34.13        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-A6V6 TCGA-CN-A6V7 TCGA-CQ-5324 TCGA-CQ-5327 TCGA-CQ-5329 
       23.44        20.88        19.53        52.37        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-6223 TCGA-CQ-6224 TCGA-CQ-6229 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C9 
       46.95        56.58        38.76        43.10        44.48        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-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 
       36.99        11.90        10.22        11.34        11.64         7.69 
TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7367 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 
       15.75         9.27        47.34        35.84         3.45         3.09 
TCGA-CR-7373 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7382 
       29.23        31.96         9.17        34.06        19.92        26.17 
TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7389 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 
       32.78        47.01        12.89        30.02        46.85        32.65 
TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7399 TCGA-CR-7402 TCGA-CR-7404 
       44.25        30.58        24.79         5.95        29.95        48.39 
TCGA-CV-5431 TCGA-CV-5434 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 
       17.16       108.95       107.51        94.88        76.50        91.53 
TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-6003 
       17.92        13.35        23.05        60.49         7.07        54.74 
TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6938 TCGA-CV-6939 
       21.07        62.43         9.70         5.46         4.73        21.90 
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-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-7095 TCGA-CV-7099 TCGA-CV-7100 
        4.14        64.83       172.67        18.81         7.99         9.01 
TCGA-CV-7102 TCGA-CV-7178 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7238 TCGA-CV-7247 
        1.84        71.21       130.88        77.16        89.65        18.97 
TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7406 
       17.13        95.34        11.87        47.97        49.71        57.47 
TCGA-CV-7407 TCGA-CV-7409 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7414 TCGA-CV-7416 
       35.54        17.85       210.97        89.33         0.46        25.08 
TCGA-CV-7418 TCGA-CV-7424 TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7429 
       25.94        14.89        56.48       156.49        54.94         3.52 
TCGA-CV-7433 TCGA-CV-7437 TCGA-CV-7438 TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45Q 
       19.76        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-A45Z TCGA-CV-A463 TCGA-CV-A465 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE 
       48.20         0.76         7.07        15.25         5.98        35.34 
TCGA-CV-A6JM TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JY TCGA-CV-A6JZ 
        6.38        29.79         6.48        28.01        21.24        23.47 
TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-D6-6515 TCGA-D6-6516 
       19.92        22.52        10.42        10.55        13.25        25.41 
TCGA-D6-6517 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6827 TCGA-D6-A6EK TCGA-D6-A6EM 
        9.60         2.53        16.14        18.67        28.77         7.63 
TCGA-D6-A6EN TCGA-D6-A6EQ TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-7590 
       22.59        12.10        58.45        37.25        33.86        46.45 
TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7594 TCGA-DQ-7596 TCGA-F7-8298 TCGA-F7-8489 
       20.45        37.58        40.04        41.59        32.71        21.63 
TCGA-F7-A50G TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A620 TCGA-F7-A622 
       20.25        31.13        18.94        24.95        17.85        11.80 
TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A76A TCGA-HD-7229 
       12.43        13.38        15.16        15.06        20.94        33.76 
TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-A4C1 
       21.93        27.48        27.48        14.66        22.03         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-A6H7 
       37.41         0.07         5.29        13.68        13.84        19.27 
TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A67A TCGA-MT-A67F TCGA-MT-A67G TCGA-MT-A7BN 
       10.75        14.37        30.05        12.62         6.25        15.42 
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-A6T6 TCGA-P3-A6T7 TCGA-QK-A652 
       19.00        75.55        29.00        12.99        16.01        21.21 
TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6II TCGA-QK-A6V9 TCGA-QK-A8Z9 TCGA-QK-AA3K 
       23.15         7.30         9.34        27.39        14.76         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-A92N TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A7J9 TCGA-UF-A7JC 
        3.12        13.55        13.25        20.35        44.65        17.95 
TCGA-UF-A7JO TCGA-UF-A7JT TCGA-WA-A7H4 TCGA-KU-A66S 
       20.75        32.65        14.56        13.35 

  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 
           20.520            21.915 
[1] "0.1 - 153.9 (20.5)" "0.1 - 211.0 (21.9)"
[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       158         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               158
  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 123   0
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     67    1
  9P LOSS WILD-TYPE  123    0
   clus
vv  9P LOSS MUTATED 9P LOSS WILD-TYPE
  0              67               123
  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    57 102
  9P LOSS WILD-TYPE 105 199
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     57  102
  9P LOSS WILD-TYPE  105  199
     clus
vv    9P LOSS MUTATED 9P LOSS WILD-TYPE
  NO               57               105
  YES             102               199
[1] 2 2
[1] FALSE
                   vv
clus                HEAD & NECK SQUAMOUS CELL CARCINOMA
  9P LOSS MUTATED                                   183
  9P LOSS WILD-TYPE                                 328
                   vv
clus                HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  9P LOSS MUTATED                                                   3
  9P LOSS WILD-TYPE                                                 7
                   vv
clus                HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  9P LOSS MUTATED                                                           0
  9P LOSS WILD-TYPE                                                         1
D58V9, multiclass
                                                           clus
vv                                                          9P LOSS MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                   183
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       3
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT               0
                                                           clus
vv                                                          9P LOSS WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                     328
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                         7
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                 1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V10, continuous
D58V11, continuous
D58V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  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    48  35
  9Q LOSS WILD-TYPE 253 184
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               83               437 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               35               184 
$`9Q LOSS MUTATED`
TCGA-BA-6871 TCGA-BB-A5HU TCGA-CN-6024 TCGA-CQ-6221 TCGA-CQ-7067 TCGA-CR-6472 
        3.55        25.71        11.08        32.88        16.73        34.52 
TCGA-CX-7082 TCGA-H7-A6C5 TCGA-HD-8635 TCGA-BA-4074 TCGA-BA-7269 TCGA-BA-A4IF 
        0.36        21.11        22.85        15.19        41.85        29.42 
TCGA-BA-A6D8 TCGA-BA-A8YP TCGA-BB-8601 TCGA-CN-4737 TCGA-CN-4740 TCGA-CN-6018 
       27.95        16.41        20.52        20.55        27.58        19.07 
TCGA-CN-6020 TCGA-CN-A63W TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-7069 TCGA-CQ-7072 
        6.74        12.39         4.24        14.99        41.88        77.56 
TCGA-CR-5247 TCGA-CR-6474 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7372 TCGA-CR-7374 
       11.77        18.54        47.18        39.16        24.95         0.99 
TCGA-CR-7390 TCGA-CV-5430 TCGA-CV-5435 TCGA-CV-5973 TCGA-CV-5979 TCGA-CV-6441 
       49.58       139.43        76.24        86.83        43.23         9.60 
TCGA-CV-6933 TCGA-CV-6937 TCGA-CV-6940 TCGA-CV-6945 TCGA-CV-7091 TCGA-CV-7095 
       90.12        20.52        26.43        12.03       111.16        18.81 
TCGA-CV-7097 TCGA-CV-7101 TCGA-CV-7180 TCGA-CV-7243 TCGA-CV-7252 TCGA-CV-7255 
       12.66         5.26        10.75        31.36         4.96         2.10 
TCGA-CV-7413 TCGA-CV-7423 TCGA-CV-7435 TCGA-CV-7440 TCGA-CV-A464 TCGA-CV-A6JU 
        9.67       100.57       153.86        22.19        56.61         3.62 
TCGA-D6-6823 TCGA-D6-A6EP TCGA-DQ-5631 TCGA-F7-7848 TCGA-F7-A50I TCGA-F7-A623 
       23.05        13.94        18.02        37.18         3.02        20.25 
TCGA-HD-7753 TCGA-HD-A6HZ TCGA-IQ-A61G TCGA-IQ-A61J TCGA-IQ-A6SG TCGA-IQ-A6SH 
       28.47         3.65        11.84        33.57        19.04        15.48 
TCGA-MT-A67D TCGA-MZ-A5BI TCGA-P3-A5Q6 TCGA-P3-A6T3 TCGA-QK-A6IJ TCGA-QK-A6VB 
        1.84         7.13        15.78        18.97        12.72        21.07 
TCGA-QK-A6VC TCGA-QK-A8Z8 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-UF-A719 TCGA-UF-A71B 
       19.73         5.62        12.20        17.82        54.67        49.51 
TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-KU-A66T 
       24.30        55.43        18.05        13.94        18.15 

$`9Q LOSS WILD-TYPE`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-A4IG TCGA-BA-A4II 
        9.30        37.28        20.48        68.48        28.11        30.18 
TCGA-CN-4727 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6992 TCGA-CN-6997 
       51.29         9.07         9.24        52.08        35.05        32.48 
TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CQ-A4C7 
       19.82        24.39        48.20        70.13        43.04        11.61 
TCGA-CR-6478 TCGA-CX-7219 TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7593 
        6.02        34.36        30.94        14.04        46.32        40.24 
TCGA-HD-8634 TCGA-UF-A71D TCGA-UF-A7JV TCGA-4P-AA8J TCGA-BA-4076 TCGA-BA-4078 
       12.66        48.03         2.96         3.35        13.64         9.07 
TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 
       26.50        23.74        42.35        57.93        17.10        23.84 
TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6872 TCGA-BA-6873 
       65.59        15.52        21.17        14.83        12.62         4.01 
TCGA-BA-A4IH TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF 
       20.45        11.54         7.10         5.69        14.47         7.82 
TCGA-BA-A6DG TCGA-BA-A6DI TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BB-4217 TCGA-BB-4223 
        2.27        11.05        13.38        20.48         6.15       105.90 
TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 
        9.14         4.80         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-A5HY TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO TCGA-C9-A47Z 
       71.05        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-6019 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 
       34.13        10.45        32.22        38.89         3.68        17.42 
TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B 
       11.74        35.01        25.41        23.57        17.29        29.72 
TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A640 
       21.21         7.40        31.69        22.32        16.57         4.41 
TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5324 
       12.07         2.70        23.44        20.88        19.53        52.37 
TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 
       21.50         2.93        54.58        70.45        62.37        45.99 
TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-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-7064 TCGA-CQ-7065 TCGA-CQ-7071 
       56.58        13.25        38.76        64.87        53.52        43.10 
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-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-6473 TCGA-CR-6477 TCGA-CR-6480 
       58.42        50.01        39.52        36.99        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-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 
       15.75         9.27        47.34        40.93        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-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        24.79 
TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5431 
        5.13         5.95        35.41        29.95        48.39        17.16 
TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 
      129.21       108.95        19.20        17.95       107.51        94.88 
TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 
       76.50        91.53        80.12        17.92        13.35        23.05 
TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 
       48.59        60.49         7.07        54.74        21.07        62.43 
TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6941 
        2.14         9.70         5.46         4.73        21.90        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-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-7099 TCGA-CV-7100 
        2.50         4.14        64.83       172.67         7.99         9.01 
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-7245 TCGA-CV-7247 
       77.16         4.73        89.65        36.00        26.20        18.97 
TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7263 
       17.13        95.34        11.87        47.97        49.71        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-7416 TCGA-CV-7418 TCGA-CV-7421 TCGA-CV-7422 TCGA-CV-7424 
       22.85        25.08        25.94         0.07        34.09        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-7437 TCGA-CV-7438 TCGA-CV-A45O TCGA-CV-A45P 
       19.76         7.17        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-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-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-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-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-D6-6824 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-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 
       24.95        12.10        12.79        23.34        58.45        37.25 
TCGA-DQ-5630 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7594 TCGA-DQ-7595 
       33.86        46.45        20.45        37.58        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-A76A TCGA-HD-7229 TCGA-HD-7754 TCGA-HD-7831 
       15.16        15.06        20.94        33.76        25.74        21.93 
TCGA-HD-7832 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-A4C1 TCGA-HD-A633 
       27.48        27.48        14.66        22.03         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-A61H TCGA-IQ-A61I TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O 
       37.71        37.41         0.07         5.29        13.68        13.84 
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-MT-A67G TCGA-MT-A7BN TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5QA 
        6.25        15.42        16.08        17.98        29.92        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-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A64Z 
        2.04        29.00        12.99        16.01        13.15        21.07 
TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6V9 
       21.21        23.15         7.30        21.47         9.34        27.39 
TCGA-QK-A8Z7 TCGA-QK-A8Z9 TCGA-QK-AA3J TCGA-QK-AA3K TCGA-RS-A6TO TCGA-RS-A6TP 
       12.89        14.76        15.32         8.32        12.72        16.96 
TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-T3-A92M TCGA-T3-A92N 
        6.87        15.91         7.10        32.45        13.71         3.12 
TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A71A TCGA-UF-A71E 
       13.55        13.25        20.35        64.80         2.83        49.45 
TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JH TCGA-UF-A7JO TCGA-UF-A7JS 
       44.65        74.47        17.95        29.46        20.75        22.36 
TCGA-UF-A7JT TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 TCGA-KU-A66S 
       32.65        17.03        20.55        14.56        13.35 

  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
             0.36              0.07 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
           153.86            210.97 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
            19.07             21.63 
[1] "0.4 - 153.9 (19.1)" "0.1 - 211.0 (21.6)"
[1] "hr=" "1.1"
D59V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  9Q LOSS MUTATED         4       14        16        37         2         1
  9Q LOSS WILD-TYPE      23       62        66       215        10         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              37               215
  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
  9Q LOSS MUTATED       7  29  12  28
  9Q LOSS WILD-TYPE    43 108  88 145
D59V4, multiclass
       clus
vv      9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  T0+T1               7                43
  T2                 29               108
  T3                 12                88
  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
  9Q LOSS MUTATED    29  14  25   1
  9Q LOSS WILD-TYPE 150  54 143   7
D59V5, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  N0              29               150
  N1              14                54
  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"
D59V6, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED    34   1
  9Q LOSS WILD-TYPE 156   0
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     34    1
  9Q LOSS WILD-TYPE  156    0
   clus
vv  9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  0              34               156
  1               1                 0
[1] 2 2
[1] FALSE
D59V7, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED    21  62
  9Q LOSS WILD-TYPE 119 320
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     21   62
  9Q LOSS WILD-TYPE  119  320
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  FEMALE              21               119
  MALE                62               320
[1] 2 2
[1] FALSE
D59V8, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED    24  47
  9Q LOSS WILD-TYPE 138 254
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     24   47
  9Q LOSS WILD-TYPE  138  254
     clus
vv    9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  NO               24               138
  YES              47               254
[1] 2 2
[1] FALSE
                   vv
clus                HEAD & NECK SQUAMOUS CELL CARCINOMA
  9Q LOSS MUTATED                                    83
  9Q LOSS WILD-TYPE                                 428
                   vv
clus                HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  9Q LOSS MUTATED                                                   0
  9Q LOSS WILD-TYPE                                                10
                   vv
clus                HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  9Q LOSS MUTATED                                                           0
  9Q LOSS WILD-TYPE                                                         1
D59V9, multiclass
                                                           clus
vv                                                          9Q LOSS MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                    83
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       0
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT               0
                                                           clus
vv                                                          9Q LOSS WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                     428
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        10
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                 1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V10, continuous
D59V11, continuous
D59V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  9Q LOSS MUTATED                                  0     0
  9Q LOSS WILD-TYPE                                2    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  9Q LOSS MUTATED                          12    66
  9Q LOSS WILD-TYPE                        36   380
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                     12                36
  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"
D59V14, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED     6  67
  9Q LOSS WILD-TYPE  20 392
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      6   67
  9Q LOSS WILD-TYPE   20  392
                        clus
vv                       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   6                20
  NOT HISPANIC OR LATINO              67               392
[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 220 144
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
               156                364 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                75                144 
$`10P LOSS MUTATED`
TCGA-BA-4075 TCGA-BA-5559 TCGA-BB-A5HU TCGA-CN-6024 TCGA-CQ-5323 TCGA-CQ-A4C7 
        9.30        68.48        25.71        11.08        48.20        11.61 
TCGA-CX-7219 TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7593 TCGA-HD-8635 TCGA-BA-4078 
       34.36        30.94        14.04        40.24        22.85         9.07 
TCGA-BA-5152 TCGA-BA-6868 TCGA-BA-6870 TCGA-BA-6873 TCGA-BA-A4IF TCGA-BA-A6D8 
       42.35        15.52        14.83         4.01        29.42        27.95 
TCGA-BA-A6DI TCGA-BA-A8YP TCGA-BB-7870 TCGA-BB-7872 TCGA-BB-8601 TCGA-BB-A5HY 
       11.05        16.41        66.28        38.40        20.52        10.55 
TCGA-C9-A47Z TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4737 TCGA-CN-5355 TCGA-CN-5359 
        6.28        55.86        38.04        20.55        42.02        12.39 
TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5374 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6018 
       71.31         8.32        56.94        30.67        48.00        19.07 
TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6988 TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A49A 
       34.13         6.74        10.45        17.42        11.74        17.29 
TCGA-CN-A63U TCGA-CN-A63W TCGA-CN-A6V7 TCGA-CQ-5326 TCGA-CQ-6223 TCGA-CQ-6224 
       31.69        12.39        19.53         2.93        46.95        56.58 
TCGA-CQ-6225 TCGA-CQ-6228 TCGA-CQ-7064 TCGA-CQ-7069 TCGA-CQ-7072 TCGA-CR-6474 
       13.25        14.99        64.87        41.88        77.56        18.54 
TCGA-CR-6484 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 
       11.64        39.16        47.34        40.93        35.84         3.45 
TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7386 
       24.95        29.23        19.92        26.17        17.13        47.01 
TCGA-CR-7389 TCGA-CR-7398 TCGA-CV-5435 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5977 
       12.89         5.13        76.24        80.12        17.92        60.49 
TCGA-CV-5979 TCGA-CV-6936 TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6950 
       43.23         5.46        26.43        11.24       140.78        15.09 
TCGA-CV-6952 TCGA-CV-6954 TCGA-CV-6961 TCGA-CV-6962 TCGA-CV-7090 TCGA-CV-7097 
        6.08        65.82         2.50         4.14       172.67        12.66 
TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7178 TCGA-CV-7242 TCGA-CV-7243 
        9.01         5.26         1.84        71.21        36.00        31.36 
TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7248 TCGA-CV-7252 TCGA-CV-7263 TCGA-CV-7406 
       26.20        18.97        17.13         4.96        18.41        57.47 
TCGA-CV-7414 TCGA-CV-7418 TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7428 TCGA-CV-7432 
        0.46        25.94       100.57        14.89        54.94        84.49 
TCGA-CV-7434 TCGA-CV-7438 TCGA-CV-A45W TCGA-CV-A45X TCGA-CV-A465 TCGA-CV-A6JD 
        7.17         6.38        45.96         6.51         7.07         5.98 
TCGA-CV-A6JT TCGA-CV-A6K1 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6826 TCGA-D6-A4ZB 
       28.01        22.52         9.60        23.05        11.44        12.36 
TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-DQ-5631 TCGA-DQ-7590 TCGA-F7-8489 TCGA-F7-A50G 
       13.94        12.10        18.02        46.45        21.63        20.25 
TCGA-F7-A50I TCGA-F7-A61V TCGA-F7-A620 TCGA-HD-7831 TCGA-HD-A633 TCGA-IQ-A61G 
        3.02        24.95        17.85        21.93        13.84        11.84 
TCGA-IQ-A61H TCGA-IQ-A61J TCGA-IQ-A61K TCGA-KU-A6H7 TCGA-MT-A51X TCGA-MZ-A6I9 
       37.41        33.57         5.29        19.27         7.96        16.08 
TCGA-P3-A6SX TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T8 
       47.01        75.55        18.97         2.04        29.00        13.15 
TCGA-QK-A64Z TCGA-QK-A6IF TCGA-QK-A6IH TCGA-QK-A6V9 TCGA-QK-A8Z9 TCGA-QK-A8ZA 
       21.07        23.15        21.47        27.39        14.76        12.20 
TCGA-QK-A8ZB TCGA-QK-AA3K TCGA-T2-A6X0 TCGA-TN-A7HJ TCGA-UF-A718 TCGA-UF-A71A 
       17.82         8.32         7.10        13.25        64.80         2.83 
TCGA-UF-A71B TCGA-UF-A7JC TCGA-UF-A7JD TCGA-WA-A7GZ TCGA-WA-A7H4 TCGA-KU-A66T 
       49.51        17.95        24.30        20.55        14.56        18.15 

$`10P LOSS WILD-TYPE`
TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-6871 TCGA-BA-A4IG TCGA-BA-A4II TCGA-CN-4727 
       37.28        20.48         3.55        28.11        30.18        51.29 
TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-A6V1 
        9.07         9.24        52.08        35.05        32.48        19.82 
TCGA-CN-A6V3 TCGA-CQ-6221 TCGA-CQ-7063 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CR-6472 
       24.39        32.88        70.13        16.73        43.04        34.52 
TCGA-CR-6478 TCGA-CX-7082 TCGA-DQ-7589 TCGA-H7-A6C5 TCGA-HD-8634 TCGA-UF-A71D 
        6.02         0.36        46.32        21.11        12.66        48.03 
TCGA-UF-A7JV TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-5149 TCGA-BA-5151 
        2.96         3.35        15.19        13.64        26.50        23.74 
TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-6869 TCGA-BA-6872 
       57.93        17.10        23.84        65.59        21.17        12.62 
TCGA-BA-7269 TCGA-BA-A4IH TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE 
       41.85        20.45        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         4.80         4.41        18.38        22.42        36.72 
TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7871 TCGA-BB-8596 TCGA-BB-A5HZ 
       33.70        50.20        44.98        24.66        71.05        27.19 
TCGA-BB-A6UM TCGA-BB-A6UO TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4726 TCGA-CN-4728 
       12.92         8.81        12.69        48.76         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-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-5364 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5369 
        8.58        16.21        11.54        11.84        11.57        12.49 
TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-6010 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 
        8.52        52.08        50.07        23.90        47.44        28.04 
TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 
       32.22        38.89         3.68        35.01        25.41        23.57 
TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A640 
       29.72        21.21         7.40        22.32        16.57         4.41 
TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V6 TCGA-CQ-5324 TCGA-CQ-5325 
       12.07         2.70        23.44        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-6227 TCGA-CQ-6229 TCGA-CQ-7065 
        4.24        41.19        32.38         4.24        38.76        53.52 
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-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-6477 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6487 TCGA-CR-6488 
       16.90        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        49.58 
TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 
       30.02        46.85        32.65        44.25        30.58        24.79 
TCGA-CR-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        94.88 
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        89.65        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 
       49.71        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-7085 
        3.62        21.24        23.47        19.92        10.42        10.55 
TCGA-CX-7086 TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6824 TCGA-D6-6825 
       18.84        51.12        13.25        25.41         2.53        16.14 
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-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 
       22.59        24.95        12.79        23.34        58.45        37.25 
TCGA-DQ-5630 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 
       33.86        20.45        37.58        40.04        39.12        41.59 
TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61W TCGA-F7-A622 
       37.18        32.71        31.13        18.94         0.46        11.80 
TCGA-F7-A623 TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A76A 
       20.25        12.43        13.38        15.16        15.06        20.94 
TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7832 TCGA-HD-7917 TCGA-HD-8224 
       33.76        28.47        25.74        27.48        27.48        14.66 
TCGA-HD-8314 TCGA-HD-A4C1 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-HL-7533 
       22.03         0.36         4.27         3.65         6.90        34.75 
TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61I TCGA-IQ-A61L 
       15.95        38.53        14.50        37.71         0.07        13.68 
TCGA-IQ-A61O TCGA-IQ-A6SG TCGA-IQ-A6SH TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A67A 
       13.84        19.04        15.48        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        12.89         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-A71E TCGA-UF-A7J9 
        3.12        13.55        20.35        54.67        49.45        44.65 
TCGA-UF-A7JA TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO 
       74.47        55.43        29.46        18.05        13.94        20.75 
TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UP-A6WW TCGA-KU-A66S 
       22.36        32.65        17.03        13.35 

  10P LOSS MUTATED 10P LOSS WILD-TYPE 
              0.46               0.07 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
            172.67             210.97 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
            19.170             21.965 
[1] "0.5 - 172.7 (19.2)" "0.1 - 211.0 (22.0)"
[1] "hr=" "1.3"
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       168         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                168
  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 135   1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     55    0
  10P LOSS WILD-TYPE  135    1
   clus
vv  10P LOSS MUTATED 10P LOSS WILD-TYPE
  0               55                135
  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  92
  10P LOSS WILD-TYPE 117 209
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     45   92
  10P LOSS WILD-TYPE  117  209
     clus
vv    10P LOSS MUTATED 10P LOSS WILD-TYPE
  NO                45                117
  YES               92                209
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD & NECK SQUAMOUS CELL CARCINOMA
  10P LOSS MUTATED                                   156
  10P LOSS WILD-TYPE                                 355
                    vv
clus                 HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  10P LOSS MUTATED                                                   0
  10P LOSS WILD-TYPE                                                10
                    vv
clus                 HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  10P LOSS MUTATED                                                           0
  10P LOSS WILD-TYPE                                                         1
D60V9, multiclass
                                                           clus
vv                                                          10P LOSS MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                    156
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        0
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                0
                                                           clus
vv                                                          10P LOSS WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                      355
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                         10
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                  1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V10, continuous
D60V11, continuous
D60V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  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    64  50
  10Q LOSS WILD-TYPE 237 169
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
               114                406 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                50                169 
$`10Q LOSS MUTATED`
TCGA-BA-4075 TCGA-BA-5559 TCGA-CN-6024 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7593 
        9.30        68.48        11.08        14.04        46.32        40.24 
TCGA-BA-4074 TCGA-BA-4078 TCGA-BA-5152 TCGA-BA-5555 TCGA-BA-A6D8 TCGA-BA-A6DI 
       15.19         9.07        42.35        17.10        27.95        11.05 
TCGA-BA-A8YP TCGA-BB-7870 TCGA-BB-8601 TCGA-C9-A47Z TCGA-CN-4725 TCGA-CN-5355 
       16.41        66.28        20.52         6.28        38.04        42.02 
TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5374 TCGA-CN-6012 TCGA-CN-6018 TCGA-CN-6019 
       12.39        71.31        56.94        48.00        19.07        34.13 
TCGA-CN-6020 TCGA-CN-6998 TCGA-CN-A49A TCGA-CN-A63U TCGA-CN-A6V7 TCGA-CQ-5332 
        6.74        11.74        17.29        31.69        19.53        10.42 
TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6228 TCGA-CQ-7064 TCGA-CQ-7072 TCGA-CR-6470 
       56.58        13.25        14.99        64.87        77.56        50.01 
TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6484 TCGA-CR-7365 TCGA-CR-7368 TCGA-CR-7369 
       18.54        16.90        11.64        39.16        40.93        35.84 
TCGA-CR-7370 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7383 TCGA-CR-7386 TCGA-CR-7389 
        3.45        24.95        29.23        17.13        47.01        12.89 
TCGA-CR-7398 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5977 
        5.13        17.16       129.21       108.95        76.24        60.49 
TCGA-CV-5979 TCGA-CV-6936 TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6950 TCGA-CV-6961 
       43.23         5.46        26.43        11.24        15.09         2.50 
TCGA-CV-6962 TCGA-CV-7090 TCGA-CV-7097 TCGA-CV-7101 TCGA-CV-7242 TCGA-CV-7245 
        4.14       172.67        12.66         5.26        36.00        26.20 
TCGA-CV-7248 TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7414 TCGA-CV-7418 TCGA-CV-7423 
       17.13        18.41        57.47         0.46        25.94       100.57 
TCGA-CV-7424 TCGA-CV-7432 TCGA-CV-7438 TCGA-CV-A45W TCGA-CV-A465 TCGA-CV-A6JY 
       14.89        84.49         6.38        45.96         7.07        21.24 
TCGA-D6-6823 TCGA-D6-A4ZB TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-DQ-5631 
       23.05        12.36        13.94        12.10        12.79        18.02 
TCGA-DQ-7590 TCGA-HD-7831 TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61J TCGA-IQ-A61K 
       46.45        21.93        11.84        37.41        33.57         5.29 
TCGA-IQ-A6SG TCGA-KU-A6H7 TCGA-MT-A51X TCGA-MT-A7BN TCGA-MZ-A6I9 TCGA-MZ-A7D7 
       19.04        19.27         7.96        15.42        16.08        17.98 
TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T5 TCGA-QK-A6IH TCGA-QK-A6V9 TCGA-QK-A6VB 
       19.00        75.55        29.00        21.47        27.39        21.07 
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 TCGA-KU-A66T 
       49.51        44.65        17.95        20.55        14.56        18.15 

$`10Q LOSS WILD-TYPE`
TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-6871 TCGA-BA-A4IG TCGA-BA-A4II TCGA-BB-A5HU 
       37.28        20.48         3.55        28.11        30.18        25.71 
TCGA-CN-4727 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6992 TCGA-CN-6997 
       51.29         9.07         9.24        52.08        35.05        32.48 
TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-6221 TCGA-CQ-7063 TCGA-CQ-7067 
       19.82        24.39        48.20        32.88        70.13        16.73 
TCGA-CQ-7068 TCGA-CQ-A4C7 TCGA-CR-6472 TCGA-CR-6478 TCGA-CX-7082 TCGA-CX-7219 
       43.04        11.61        34.52         6.02         0.36        34.36 
TCGA-DQ-5629 TCGA-H7-A6C5 TCGA-HD-8634 TCGA-HD-8635 TCGA-UF-A71D TCGA-UF-A7JV 
       30.94        21.11        12.66        22.85        48.03         2.96 
TCGA-4P-AA8J TCGA-BA-4076 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5153 TCGA-BA-5556 
        3.35        13.64        26.50        23.74        57.93        23.84 
TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6872 TCGA-BA-6873 
       65.59        15.52        21.17        14.83        12.62         4.01 
TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IH TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD 
       41.85        29.42        20.45        11.54         7.10         5.69 
TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BB-4217 
       14.47         7.82         2.27        13.38        20.48         6.15 
TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 
      105.90         9.14         4.80         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-8596 TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO TCGA-C9-A480 
       71.05        10.55        27.19        12.92         8.81        12.69 
TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 
       48.76        55.86         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-5356 TCGA-CN-5358 
       45.83        27.58        73.61        13.05        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-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-6988 TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 
       28.04        10.45        32.22        38.89         3.68        17.42 
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-A6V6 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 
       23.44        20.88        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-6227 TCGA-CQ-6229 TCGA-CQ-7065 TCGA-CQ-7069 
       32.38        46.95         4.24        38.76        53.52        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-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-6471 TCGA-CR-6473 TCGA-CR-6480 
       37.87        26.27        58.42        39.52        36.99        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-7367 TCGA-CR-7371 TCGA-CR-7374 TCGA-CR-7376 
        9.27        47.18        47.34         3.09         0.99        31.96 
TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7385 TCGA-CR-7388 
        9.17        34.06        19.92        26.17        32.78        27.06 
TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 
       49.58        30.02        46.85        32.65        44.25        30.58 
TCGA-CR-7397 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 
       24.79         5.95        35.41        29.95        48.39       139.43 
TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 
       19.20        17.95       107.51        94.88        76.50        91.53 
TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 
       80.12        17.92        13.35        23.05        86.83        48.59 
TCGA-CV-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-6942 
        2.14         9.70        20.52         4.73        21.90       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-7089 
       65.82        10.98         7.13         8.42        28.34        64.83 
TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7102 TCGA-CV-7103 
      111.16        18.81         7.99         9.01         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-7247 TCGA-CV-7250 TCGA-CV-7252 
        4.73        89.65        31.36        18.97        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        49.71        35.54        17.85 
TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7415 TCGA-CV-7416 TCGA-CV-7421 
      210.97        89.33         9.67        22.85        25.08         0.07 
TCGA-CV-7422 TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7429 TCGA-CV-7430 
       34.09        56.48       156.49        54.94         3.52        16.27 
TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7437 TCGA-CV-7440 TCGA-CV-A45O 
       19.76         7.17       153.86        16.64        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-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-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-D6-6824 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-A6EK TCGA-D6-A6EM TCGA-D6-A6EN TCGA-D6-A6EO 
       25.32        17.72        28.77         7.63        22.59        24.95 
TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-7591 TCGA-DQ-7592 
       23.34        58.45        37.25        33.86        20.45        37.58 
TCGA-DQ-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-A76A TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7832 
       15.06        20.94        33.76        28.47        25.74        27.48 
TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 
       27.48        14.66        22.03         0.36        13.84         4.27 
TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-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-A61L TCGA-IQ-A61O TCGA-IQ-A6SH TCGA-KU-A6H8 
       37.71         0.07        13.68        13.84        15.48        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-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-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-P3-A6T8 
       47.01        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-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-A8ZB TCGA-QK-AA3J 
       19.73        12.89         5.62        14.76        17.82        15.32 
TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6X2 TCGA-T3-A92M TCGA-T3-A92N 
       12.72        16.96         6.87        32.45        13.71         3.12 
TCGA-TN-A7HI TCGA-TN-A7HL TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71E TCGA-UF-A7JA 
       13.55        20.35        54.67         2.83        49.45        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-UP-A6WW TCGA-KU-A66S 
       22.36        32.65        17.03        13.35 

  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
              0.46               0.07 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
            172.67             210.97 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
             19.02              21.85 
[1] "0.5 - 172.7 (19.0)" "0.1 - 211.0 (21.9)"
[1] "hr=" "1"  
D61V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  10Q LOSS MUTATED         3       18        14        60         3         0
  10Q LOSS WILD-TYPE      24       58        68       192         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               60                192
  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  32  25  38
  10Q LOSS WILD-TYPE    45 105  75 135
D61V4, multiclass
       clus
vv      10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  T0+T1                5                 45
  T2                  32                105
  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    41   8  42   1
  10Q LOSS WILD-TYPE 138  60 126   7
D61V5, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  N0               41                138
  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 147   1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     43    0
  10Q LOSS WILD-TYPE  147    1
   clus
vv  10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  0               43                147
  1                0                  1
[1] 2 2
[1] FALSE
D61V7, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED    21  93
  10Q LOSS WILD-TYPE 119 289
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     21   93
  10Q LOSS WILD-TYPE  119  289
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  FEMALE               21                119
  MALE                 93                289
[1] 2 2
[1] FALSE
D61V8, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED    29  72
  10Q LOSS WILD-TYPE 133 229
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     29   72
  10Q LOSS WILD-TYPE  133  229
     clus
vv    10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  NO                29                133
  YES               72                229
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD & NECK SQUAMOUS CELL CARCINOMA
  10Q LOSS MUTATED                                   114
  10Q LOSS WILD-TYPE                                 397
                    vv
clus                 HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  10Q LOSS MUTATED                                                   0
  10Q LOSS WILD-TYPE                                                10
                    vv
clus                 HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  10Q LOSS MUTATED                                                           0
  10Q LOSS WILD-TYPE                                                         1
D61V9, multiclass
                                                           clus
vv                                                          10Q LOSS MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                    114
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        0
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                0
                                                           clus
vv                                                          10Q LOSS WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                      397
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                         10
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                  1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V10, continuous
D61V11, continuous
D61V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  10Q LOSS MUTATED                                  0     3
  10Q LOSS WILD-TYPE                                2     8
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  10Q LOSS MUTATED                          15    96
  10Q LOSS WILD-TYPE                        33   350
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                      15                 33
  WHITE                                          96                350
[1] 4 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  99
  10Q LOSS WILD-TYPE  19 360
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      7   99
  10Q LOSS WILD-TYPE   19  360
                        clus
vv                       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    7                 19
  NOT HISPANIC OR LATINO               99                360
[1] 2 2
[1] FALSE

Clustering(62) Variable = 11P LOSS MUTATION ANALYSIS
D62V1, survival
                    sevent
clus2                  0   1
  11P LOSS MUTATED    76  60
  11P LOSS WILD-TYPE 225 159
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
               136                384 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                60                159 
$`11P LOSS MUTATED`
TCGA-BA-6871 TCGA-BA-A4IG TCGA-BA-A4II TCGA-CN-6021 TCGA-CN-6992 TCGA-CR-6478 
        3.55        28.11        30.18         9.07        35.05         6.02 
TCGA-CX-7082 TCGA-DQ-5629 TCGA-DQ-7589 TCGA-HD-8635 TCGA-UF-A71D TCGA-BA-4074 
        0.36        30.94        46.32        22.85        48.03        15.19 
TCGA-BA-4078 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IH TCGA-BA-A6DD 
        9.07        12.62         4.01        41.85        20.45         5.69 
TCGA-BA-A6DE TCGA-BB-4227 TCGA-BB-7870 TCGA-BB-8596 TCGA-BB-A6UO TCGA-CN-4728 
       14.47         4.41        66.28        71.05         8.81        56.68 
TCGA-CN-4729 TCGA-CN-4735 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-5356 TCGA-CN-5359 
       12.89        57.11        45.83        27.58        46.32        12.39 
TCGA-CN-5363 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5374 TCGA-CN-6011 TCGA-CN-6012 
        8.32        11.54        11.84        56.94        30.67        48.00 
TCGA-CN-6020 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6998 
        6.74        10.45        32.22        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-6481 TCGA-CR-7374 TCGA-CR-7383 TCGA-CR-7385 
       54.67        16.90        10.22         0.99        17.13        32.78 
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-5977 TCGA-CV-5978 TCGA-CV-6441 TCGA-CV-6933 TCGA-CV-6936 
      107.51        60.49         7.07         9.60        90.12         5.46 
TCGA-CV-6940 TCGA-CV-6942 TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-7091 TCGA-CV-7095 
       26.43       140.78        12.03        42.38       111.16        18.81 
TCGA-CV-7097 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7235 TCGA-CV-7245 TCGA-CV-7253 
       12.66         5.26         1.84        77.16        26.20        11.87 
TCGA-CV-7263 TCGA-CV-7415 TCGA-CV-7421 TCGA-CV-7423 TCGA-CV-7430 TCGA-CV-7435 
       18.41        22.85         0.07       100.57        16.27       153.86 
TCGA-CV-A45R TCGA-CV-A45Y TCGA-CV-A6JU TCGA-D6-8568 TCGA-D6-A4Z9 TCGA-D6-A4ZB 
      180.16        88.87         3.62        24.95        17.72        12.36 
TCGA-D6-A6ES TCGA-DQ-5624 TCGA-DQ-7594 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 
       12.79        58.45        40.04        41.59        37.18        32.71 
TCGA-F7-A50I TCGA-F7-A623 TCGA-HD-7753 TCGA-HD-7831 TCGA-HD-7917 TCGA-HD-A6HZ 
        3.02        20.25        28.47        21.93        27.48         3.65 
TCGA-IQ-A61G TCGA-IQ-A61J TCGA-MT-A51W TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A5BI 
       11.84        33.57        14.37         6.25        15.42         7.13 
TCGA-MZ-A6I9 TCGA-P3-A5Q6 TCGA-P3-A6SW TCGA-P3-A6T8 TCGA-QK-A6IH TCGA-QK-A8Z7 
       16.08        15.78        36.82        13.15        21.47        12.89 
TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-AA3J TCGA-QK-AA3K TCGA-T2-A6WZ TCGA-T3-A92N 
       14.76        12.20        15.32         8.32        15.91         3.12 
TCGA-TN-A7HJ TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71E 
       13.25        64.80        54.67         2.83        49.51        49.45 
TCGA-UF-A7JA TCGA-UF-A7JH TCGA-UF-A7JS TCGA-KU-A66T 
       74.47        29.46        22.36        18.15 

$`11P LOSS WILD-TYPE`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-5559 TCGA-BB-A5HU TCGA-CN-4727 
        9.30        37.28        20.48        68.48        25.71        51.29 
TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6997 TCGA-CN-A6V1 TCGA-CN-A6V3 
        9.24        52.08        11.08        32.48        19.82        24.39 
TCGA-CQ-5323 TCGA-CQ-6221 TCGA-CQ-7063 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-A4C7 
       48.20        32.88        70.13        16.73        43.04        11.61 
TCGA-CR-6472 TCGA-CX-7219 TCGA-DQ-7588 TCGA-DQ-7593 TCGA-H7-A6C5 TCGA-HD-8634 
       34.52        34.36        14.04        40.24        21.11        12.66 
TCGA-UF-A7JV TCGA-4P-AA8J TCGA-BA-4076 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 
        2.96         3.35        13.64        26.50        23.74        42.35 
TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6869 
       57.93        17.10        23.84        65.59        15.52        21.17 
TCGA-BA-6870 TCGA-BA-A4IF TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DF 
       14.83        29.42        27.95        11.54         7.10         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-4228 TCGA-BB-7861 TCGA-BB-7862 
      105.90         9.14         4.80        18.38        22.42        36.72 
TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8601 
       33.70        50.20        44.98        24.66        38.40        20.52 
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-4730 TCGA-CN-4731 TCGA-CN-4733 
       55.86        38.04         4.67        26.86        32.81        52.14 
TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 
       12.99        20.55        14.33        73.61        13.05        42.02 
TCGA-CN-5358 TCGA-CN-5360 TCGA-CN-5364 TCGA-CN-5367 TCGA-CN-5369 TCGA-CN-5370 
        8.58        71.31        16.21        11.57        12.49         8.52 
TCGA-CN-5373 TCGA-CN-6010 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 
       52.08        50.07        23.90        47.44        28.04        19.07 
TCGA-CN-6019 TCGA-CN-6996 TCGA-CN-A497 TCGA-CN-A499 TCGA-CN-A49B TCGA-CN-A63T 
       34.13        17.42        35.01        23.57        29.72         7.40 
TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY 
       22.32        12.39         4.41        12.07         2.70        23.44 
TCGA-CN-A6V6 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 
       20.88        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-6223 TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7065 
       46.95        56.58        13.25        38.76        64.87        53.52 
TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CD 
       41.88        43.10        77.56        44.48        23.24        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-6480 
       58.42        50.01        39.52        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-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7376 TCGA-CR-7377 
        3.45         3.09        24.95        29.23        31.96         9.17 
TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7386 TCGA-CR-7389 TCGA-CR-7390 
       34.06        19.92        26.17        47.01        12.89        49.58 
TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 
       30.02        46.85        32.65        44.25        30.58        24.79 
TCGA-CR-7398 TCGA-CR-7401 TCGA-CR-7402 TCGA-CV-5430 TCGA-CV-5434 TCGA-CV-5435 
        5.13        35.41        29.95       139.43       108.95        76.24 
TCGA-CV-5436 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 
       19.20        94.88        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-6934 TCGA-CV-6935 TCGA-CV-6937 TCGA-CV-6938 
       21.07        62.43         2.14         9.70        20.52         4.73 
TCGA-CV-6939 TCGA-CV-6941 TCGA-CV-6943 TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6952 
       21.90        11.24        19.79        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-7099 TCGA-CV-7100 
        2.50         4.14        64.83       172.67         7.99         9.01 
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-7247 TCGA-CV-7248 
        4.73        89.65        36.00        31.36        18.97        17.13 
TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7254 TCGA-CV-7255 TCGA-CV-7261 TCGA-CV-7406 
       95.34         4.96        47.97         2.10        49.71        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-7422 TCGA-CV-7424 TCGA-CV-7425 TCGA-CV-7427 
       25.08        25.94        34.09        14.89        56.48       156.49 
TCGA-CV-7428 TCGA-CV-7429 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7437 
       54.94         3.52        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-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-A45Z TCGA-CV-A460 
       35.47         1.05        45.96         6.51        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-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-7086 
       23.47        19.92        22.52        10.42        10.55        18.84 
TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 
       51.12        13.25        25.41         9.60        23.05         2.53 
TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8569 TCGA-D6-A6EK TCGA-D6-A6EM 
       16.14        11.44        18.67        25.32        28.77         7.63 
TCGA-D6-A6EN TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A74Q TCGA-DQ-5625 
       22.59        24.95        13.94        12.10        23.34        37.25 
TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7595 
       33.86        18.02        46.45        20.45        37.58        39.12 
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-A624 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 
       17.85        11.80        12.43        13.38        15.16        15.06 
TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7754 TCGA-HD-7832 TCGA-HD-8224 TCGA-HD-8314 
       20.94        33.76        25.74        27.48        14.66        22.03 
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-IQ-A6SG TCGA-IQ-A6SH TCGA-KU-A6H7 TCGA-KU-A6H8 
       13.68        13.84        19.04        15.48        19.27        10.75 
TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MZ-A7D7 TCGA-P3-A5Q5 
        7.96        30.05         1.84        12.62        17.98        29.92 
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-A6T5 TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-QK-A64Z 
       18.97         2.04        29.00        12.99        16.01        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        27.39 
TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z8 TCGA-QK-A8ZB TCGA-RS-A6TO TCGA-RS-A6TP 
       21.07        19.73         5.62        17.82        12.72        16.96 
TCGA-T2-A6WX TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-T3-A92M TCGA-TN-A7HI TCGA-TN-A7HL 
        6.87         7.10        32.45        13.71        13.55        20.35 
TCGA-UF-A7J9 TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JJ TCGA-UF-A7JK 
       44.65        17.95        24.30        55.43        18.05        13.94 
TCGA-UF-A7JO TCGA-UF-A7JT TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 TCGA-KU-A66S 
       20.75        32.65        17.03        20.55        14.56        13.35 

  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 
            18.280             21.565 
[1] "0.1 - 180.2 (18.3)" "0.1 - 211.0 (21.6)"
[1] "hr=" "1.1"
D62V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  11P LOSS MUTATED         6       13        16        69         8         0
  11P LOSS WILD-TYPE      21       63        66       183         4         1
D62V3, multiclass
           clus
vv          11P LOSS MUTATED 11P LOSS WILD-TYPE
  STAGE I                  6                 21
  STAGE II                13                 63
  STAGE III               16                 66
  STAGE IVA               69                183
  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  32  24  47
  11P LOSS WILD-TYPE    37 105  76 126
D62V4, multiclass
       clus
vv      11P LOSS MUTATED 11P LOSS WILD-TYPE
  T0+T1               13                 37
  T2                  32                105
  T3                  24                 76
  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
  11P LOSS MUTATED    40  13  49   5
  11P LOSS WILD-TYPE 139  55 119   3
D62V5, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  N0               40                139
  N1               13                 55
  N2               49                119
  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    44   0
  11P LOSS WILD-TYPE 146   1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     44    0
  11P LOSS WILD-TYPE  146    1
   clus
vv  11P LOSS MUTATED 11P LOSS WILD-TYPE
  0               44                146
  1                0                  1
[1] 2 2
[1] FALSE
D62V7, binary
                    cls
clus                   0   1
  11P LOSS MUTATED    32 105
  11P LOSS WILD-TYPE 108 277
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     32  105
  11P LOSS WILD-TYPE  108  277
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  FEMALE               32                108
  MALE                105                277
[1] 2 2
[1] FALSE
D62V8, binary
                    cls
clus                   0   1
  11P LOSS MUTATED    32  85
  11P LOSS WILD-TYPE 130 216
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     32   85
  11P LOSS WILD-TYPE  130  216
     clus
vv    11P LOSS MUTATED 11P LOSS WILD-TYPE
  NO                32                130
  YES               85                216
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD & NECK SQUAMOUS CELL CARCINOMA
  11P LOSS MUTATED                                   131
  11P LOSS WILD-TYPE                                 380
                    vv
clus                 HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  11P LOSS MUTATED                                                   6
  11P LOSS WILD-TYPE                                                 4
                    vv
clus                 HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  11P LOSS MUTATED                                                           0
  11P LOSS WILD-TYPE                                                         1
D62V9, multiclass
                                                           clus
vv                                                          11P LOSS MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                    131
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        6
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                0
                                                           clus
vv                                                          11P LOSS WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                      380
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                          4
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                  1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V10, continuous
D62V11, continuous
D62V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  11P LOSS MUTATED                                  1     0
  11P LOSS WILD-TYPE                                1    11
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  11P LOSS MUTATED                          15   118
  11P LOSS WILD-TYPE                        33   328
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                                         118                328
[1] 4 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    10 112
  11P LOSS WILD-TYPE  16 347
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     10  112
  11P LOSS WILD-TYPE   16  347
                        clus
vv                       11P LOSS MUTATED 11P LOSS WILD-TYPE
  HISPANIC OR LATINO                   10                 16
  NOT HISPANIC OR LATINO              112                347
[1] 2 2
[1] FALSE

Clustering(63) Variable = 11Q LOSS MUTATION ANALYSIS
D63V1, survival
                    sevent
clus2                  0   1
  11Q LOSS MUTATED   100  71
  11Q LOSS WILD-TYPE 201 148
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
               171                349 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                71                148 
$`11Q LOSS MUTATED`
TCGA-BA-4077 TCGA-BA-A4IG TCGA-BA-A4II TCGA-BB-A5HU TCGA-CN-4727 TCGA-CN-6021 
       37.28        28.11        30.18        25.71        51.29         9.07 
TCGA-CN-6992 TCGA-CQ-5323 TCGA-CQ-6221 TCGA-CR-6478 TCGA-CX-7082 TCGA-DQ-7588 
       35.05        48.20        32.88         6.02         0.36        14.04 
TCGA-DQ-7589 TCGA-DQ-7593 TCGA-H7-A6C5 TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4078 
       46.32        40.24        21.11        15.19        13.64         9.07 
TCGA-BA-5149 TCGA-BA-6868 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IH 
       26.50        15.52        12.62         4.01        41.85        20.45 
TCGA-BA-A6DA TCGA-BA-A6DD TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-8596 TCGA-BB-A6UM 
       11.54         5.69        44.98        66.28        71.05        12.92 
TCGA-BB-A6UO TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4735 TCGA-CN-4739 TCGA-CN-4741 
        8.81        56.68        12.89        57.11        45.83        73.61 
TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5374 
       12.39        71.31         8.32        11.54        11.84        56.94 
TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6020 TCGA-CN-6989 TCGA-CN-6994 
       30.67        48.00        23.90         6.74        32.22        38.89 
TCGA-CN-6995 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C 
        3.68        11.74        25.41        17.29        29.72        21.21 
TCGA-CN-A63T TCGA-CN-A63Y TCGA-CN-A641 TCGA-CN-A6UY TCGA-CN-A6V6 TCGA-CN-A6V7 
        7.40        16.57        12.07        23.44        20.88        19.53 
TCGA-CQ-5332 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-A4CB 
       10.42        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-6481 
       84.23        54.67        37.87        50.01        16.90        10.22 
TCGA-CR-6487 TCGA-CR-7374 TCGA-CR-7377 TCGA-CR-7380 TCGA-CR-7388 TCGA-CR-7399 
        7.69         0.99         9.17        19.92        27.06         5.95 
TCGA-CR-7404 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 
       48.39        17.16       129.21        17.95       107.51        94.88 
TCGA-CV-5970 TCGA-CV-5977 TCGA-CV-6433 TCGA-CV-6441 TCGA-CV-6933 TCGA-CV-6935 
       13.35        60.49        21.07         9.60        90.12         9.70 
TCGA-CV-6936 TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6942 TCGA-CV-6945 TCGA-CV-6961 
        5.46        21.90        26.43       140.78        12.03         2.50 
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-7247 TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7414 TCGA-CV-7415 
       26.20        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-A4AQ TCGA-D6-6825 TCGA-D6-A4Z9 TCGA-D6-A6ES 
       60.43        35.34        51.12        16.14        17.72        12.79 
TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-7590 TCGA-DQ-7594 TCGA-DQ-7596 TCGA-F7-7848 
       23.34        58.45        46.45        40.04        41.59        37.18 
TCGA-F7-8298 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A623 TCGA-H7-8502 TCGA-H7-A76A 
       32.71        20.25         3.02        20.25        15.06        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-MT-A51W TCGA-MT-A51X TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A5BI 
       33.57        14.37         7.96         6.25        15.42         7.13 
TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T4 
       16.08        17.98        10.85        36.82        47.01         2.04 
TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A6IH TCGA-QK-A6V9 TCGA-QK-A8Z7 TCGA-QK-A8Z9 
       16.01        13.15        21.47        27.39        12.89        14.76 
TCGA-QK-A8ZA TCGA-QK-AA3J TCGA-QK-AA3K TCGA-T2-A6WZ TCGA-T3-A92M TCGA-T3-A92N 
       12.20        15.32         8.32        15.91        13.71         3.12 
TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71E TCGA-UF-A7JA TCGA-UF-A7JH 
       54.67         2.83        49.51        49.45        74.47        29.46 
TCGA-UF-A7JS TCGA-UP-A6WW TCGA-KU-A66T 
       22.36        17.03        18.15 

$`11Q LOSS WILD-TYPE`
TCGA-BA-4075 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6871 TCGA-CN-6022 TCGA-CN-6023 
        9.30        20.48        68.48         3.55         9.24        52.08 
TCGA-CN-6024 TCGA-CN-6997 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-7063 TCGA-CQ-7067 
       11.08        32.48        19.82        24.39        70.13        16.73 
TCGA-CQ-7068 TCGA-CQ-A4C7 TCGA-CR-6472 TCGA-CX-7219 TCGA-DQ-5629 TCGA-HD-8634 
       43.04        11.61        34.52        34.36        30.94        12.66 
TCGA-HD-8635 TCGA-UF-A71D TCGA-UF-A7JV TCGA-4P-AA8J TCGA-BA-5151 TCGA-BA-5152 
       22.85        48.03         2.96         3.35        23.74        42.35 
TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-6869 TCGA-BA-6870 
       57.93        17.10        23.84        65.59        21.17        14.83 
TCGA-BA-A4IF TCGA-BA-A6D8 TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG 
       29.42        27.95         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-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         4.80         4.41        18.38        22.42        36.72 
TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8601 TCGA-BB-A5HY 
       33.70        50.20        24.66        38.40        20.52        10.55 
TCGA-BB-A5HZ TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4725 
       27.19         6.28        12.69        48.76        55.86        38.04 
TCGA-CN-4726 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4736 TCGA-CN-4737 
        4.67        26.86        32.81        52.14        12.99        20.55 
TCGA-CN-4738 TCGA-CN-4740 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 
       14.33        27.58        13.05        42.02        46.32         8.58 
TCGA-CN-5364 TCGA-CN-5367 TCGA-CN-5369 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-6010 
       16.21        11.57        12.49         8.52        52.08        50.07 
TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6988 TCGA-CN-6996 
       47.44        28.04        19.07        34.13        10.45        17.42 
TCGA-CN-A497 TCGA-CN-A499 TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A640 
       35.01        23.57        31.69        22.32        12.39         4.41 
TCGA-CN-A642 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 
        2.70        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-6223 TCGA-CQ-6225 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7069 TCGA-CQ-7071 
       46.95        13.25        64.87        53.52        41.88        43.10 
TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG 
       77.56        44.48        23.24        33.60        29.49        14.14 
TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5247 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6471 
       12.46        31.23        11.77        26.27        58.42        39.52 
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-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 
       40.93        35.84         3.45         3.09        24.95        29.23 
TCGA-CR-7376 TCGA-CR-7379 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 
       31.96        34.06        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        49.58        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        24.79         5.13        35.41        29.95       139.43 
TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 
      108.95        76.24        19.20        76.50        91.53        80.12 
TCGA-CV-5966 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5978 TCGA-CV-5979 
       17.92        23.05        86.83        48.59         7.07        43.23 
TCGA-CV-6003 TCGA-CV-6436 TCGA-CV-6934 TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6941 
       54.74        62.43         2.14        20.52         4.73        11.24 
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-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-7099 TCGA-CV-7100 TCGA-CV-7103 TCGA-CV-7104 
       64.83       172.67         7.99         9.01        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        89.65 
TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 
       36.00        31.36        17.13        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        49.71        35.54        17.85       210.97 
TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7416 TCGA-CV-7418 TCGA-CV-7423 TCGA-CV-7424 
       89.33         9.67        25.08        25.94       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-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-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-A45Z TCGA-CV-A461 TCGA-CV-A463 TCGA-CV-A464 TCGA-CV-A465 TCGA-CV-A468 
       48.20        67.86         0.76        56.61         7.07        15.25 
TCGA-CV-A6JD TCGA-CV-A6JM TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU 
        5.98         6.38        29.79         6.48        28.01         3.62 
TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 
       21.24        23.47        19.92        22.52        10.42        10.55 
TCGA-CX-7086 TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 
       18.84        13.25        25.41         9.60        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-A6EM TCGA-D6-A6EN TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-DQ-5625 
        7.63        22.59        24.95        13.94        12.10        37.25 
TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7595 TCGA-F7-8489 
       33.86        18.02        20.45        37.58        39.12        21.63 
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-HD-7229 TCGA-HD-7754 TCGA-HD-7831 
       12.43        13.38        15.16        33.76        25.74        21.93 
TCGA-HD-7832 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 
       27.48        27.48        14.66         0.36        13.84         4.27 
TCGA-HD-A6I0 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61I 
        6.90        15.95        38.53        14.50        37.71         0.07 
TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O TCGA-IQ-A6SG TCGA-IQ-A6SH TCGA-KU-A6H7 
        5.29        13.68        13.84        19.04        15.48        19.27 
TCGA-KU-A6H8 TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-P3-A5Q5 TCGA-P3-A5Q6 
       10.75        30.05         1.84        12.62        29.92        15.78 
TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T5 
       71.74        51.25        19.00        75.55        18.97        29.00 
TCGA-P3-A6T6 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6II 
       12.99        21.07        21.21        23.15         7.30         9.34 
TCGA-QK-A6IJ TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z8 TCGA-QK-A8ZB TCGA-RS-A6TO 
       12.72        21.07        19.73         5.62        17.82        12.72 
TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-TN-A7HI TCGA-TN-A7HJ 
       16.96         6.87         7.10        32.45        13.55        13.25 
TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A7J9 TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF 
       20.35        64.80        44.65        17.95        24.30        55.43 
TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JT TCGA-WA-A7GZ TCGA-WA-A7H4 
       18.05        13.94        20.75        32.65        20.55        14.56 
TCGA-KU-A66S 
       13.35 

  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 
             20.45              21.50 
[1] "0.1 - 180.2 (20.4)" "0.1 - 211.0 (21.5)"
[1] "hr=" "1"  
D63V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  11Q LOSS MUTATED         8       19        18        88         6         0
  11Q LOSS WILD-TYPE      19       57        64       164         6         1
D63V3, multiclass
           clus
vv          11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  STAGE I                  8                 19
  STAGE II                19                 57
  STAGE III               18                 64
  STAGE IVA               88                164
  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  56
  11Q LOSS WILD-TYPE    33  97  70 117
D63V4, multiclass
       clus
vv      11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  T0+T1               17                 33
  T2                  40                 97
  T3                  30                 70
  T4                  56                117
[1] 4 2
[1] TRUE
[1] "dimension of 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    46  17  69   3
  11Q LOSS WILD-TYPE 133  51  99   5
D63V5, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  N0               46                133
  N1               17                 51
  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    50   0
  11Q LOSS WILD-TYPE 140   1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     50    0
  11Q LOSS WILD-TYPE  140    1
   clus
vv  11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  0               50                140
  1                0                  1
[1] 2 2
[1] FALSE
D63V7, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED    28 144
  11Q LOSS WILD-TYPE 112 238
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     28  144
  11Q LOSS WILD-TYPE  112  238
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  FEMALE               28                112
  MALE                144                238
[1] 2 2
[1] FALSE
D63V8, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED    36 116
  11Q LOSS WILD-TYPE 126 185
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     36  116
  11Q LOSS WILD-TYPE  126  185
     clus
vv    11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  NO                36                126
  YES              116                185
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD & NECK SQUAMOUS CELL CARCINOMA
  11Q LOSS MUTATED                                   166
  11Q LOSS WILD-TYPE                                 345
                    vv
clus                 HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  11Q LOSS MUTATED                                                   6
  11Q LOSS WILD-TYPE                                                 4
                    vv
clus                 HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  11Q LOSS MUTATED                                                           0
  11Q LOSS WILD-TYPE                                                         1
D63V9, multiclass
                                                           clus
vv                                                          11Q LOSS MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                    166
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        6
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                0
                                                           clus
vv                                                          11Q LOSS WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                      345
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                          4
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                  1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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   154
  11Q LOSS WILD-TYPE                        34   292
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                                         154                292
[1] 4 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    13 146
  11Q LOSS WILD-TYPE  13 313
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     13  146
  11Q LOSS WILD-TYPE   13  313
                        clus
vv                       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   13                 13
  NOT HISPANIC OR LATINO              146                313
[1] 2 2
[1] FALSE

Clustering(64) Variable = 12P LOSS MUTATION ANALYSIS
D64V1, survival
                    sevent
clus2                  0   1
  12P LOSS MUTATED    14  22
  12P LOSS WILD-TYPE 287 197
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                36                484 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                22                197 
$`12P LOSS MUTATED`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5149 TCGA-BA-6868 TCGA-BA-6870 TCGA-BA-6872 
        9.30        37.28        26.50        15.52        14.83        12.62 
TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A6DA TCGA-BA-A6DE TCGA-BB-8596 TCGA-CN-5355 
        4.01        41.85        11.54        14.47        71.05        42.02 
TCGA-CN-5365 TCGA-CN-5374 TCGA-CR-6484 TCGA-CR-7377 TCGA-CR-7389 TCGA-CV-6441 
       11.54        56.94        11.64         9.17        12.89         9.60 
TCGA-CV-7090 TCGA-CV-7100 TCGA-CV-7255 TCGA-CV-7263 TCGA-CV-7432 TCGA-CV-A460 
      172.67         9.01         2.10        18.41        84.49        60.43 
TCGA-CV-A6JY TCGA-D6-6826 TCGA-D6-A6EP TCGA-DQ-5631 TCGA-HD-8224 TCGA-IQ-A61E 
       21.24        11.44        13.94        18.02        14.66        37.71 
TCGA-MZ-A5BI TCGA-P3-A6T5 TCGA-RS-A6TP TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-WA-A7GZ 
        7.13        29.00        16.96        15.91         7.10        20.55 

$`12P LOSS WILD-TYPE`
TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4IG TCGA-BA-A4II TCGA-BB-A5HU 
       20.48        68.48         3.55        28.11        30.18        25.71 
TCGA-CN-4727 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6992 
       51.29         9.07         9.24        52.08        11.08        35.05 
TCGA-CN-6997 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-6221 TCGA-CQ-7063 
       32.48        19.82        24.39        48.20        32.88        70.13 
TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-A4C7 TCGA-CR-6472 TCGA-CR-6478 TCGA-CX-7082 
       16.73        43.04        11.61        34.52         6.02         0.36 
TCGA-CX-7219 TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7593 TCGA-H7-A6C5 
       34.36        30.94        14.04        46.32        40.24        21.11 
TCGA-HD-8634 TCGA-HD-8635 TCGA-UF-A71D TCGA-UF-A7JV TCGA-4P-AA8J TCGA-BA-4074 
       12.66        22.85        48.03         2.96         3.35        15.19 
TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 
       13.64         9.07        23.74        42.35        57.93        17.10 
TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-6869 TCGA-BA-A4IF TCGA-BA-A4IH TCGA-BA-A6D8 
       23.84        65.59        21.17        29.42        20.45        27.95 
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-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 
       20.48        16.41         6.15       105.90         9.14         4.80 
TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-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-8601 TCGA-BB-A5HY 
       44.98        66.28        24.66        38.40        20.52        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-4742 TCGA-CN-5356 TCGA-CN-5358 
       45.83        27.58        73.61        13.05        46.32         8.58 
TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5366 TCGA-CN-5367 
       12.39        71.31         8.32        16.21        11.84        11.57 
TCGA-CN-5369 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 
       12.49         8.52        52.08        50.07        30.67        48.00 
TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 
       23.90        47.44        28.04        19.07        34.13         6.74 
TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6998 
       10.45        32.22        38.89         3.68        17.42        11.74 
TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C 
       35.01        25.41        23.57        17.29        29.72        21.21 
TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 
        7.40        31.69        22.32        12.39        16.57         4.41 
TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5324 
       12.07         2.70        23.44        20.88        19.53        52.37 
TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 
       21.50         2.93        54.58        70.45        62.37        45.99 
TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6220 TCGA-CQ-6223 
       10.42        11.21         4.24        41.19        32.38        46.95 
TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7064 
       56.58        13.25         4.24        14.99        38.76        64.87 
TCGA-CQ-7065 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C9 
       53.52        41.88        43.10        77.56        44.48        23.24 
TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI 
       29.36        33.60        29.49        14.14        12.46        31.23 
TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 
       84.23        11.77        54.67        37.87        26.27        58.42 
TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6480 
       50.01        39.52        36.99        18.54        16.90        11.90 
TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 
       10.22        11.34         7.69        12.46        22.78        15.75 
TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 
        9.27        47.18        39.16        47.34        40.93        35.84 
TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 
        3.45         3.09        24.95        29.23         0.99        31.96 
TCGA-CR-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        49.58        30.02        46.85        32.65        44.25 
TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 
       30.58        24.79         5.13         5.95        35.41        29.95 
TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 
       48.39       139.43        17.16       129.21       108.95        76.24 
TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 
       19.20        17.95       107.51        94.88        76.50        91.53 
TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 
       80.12        17.92        13.35        23.05        86.83        48.59 
TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 
       60.49         7.07        43.23        54.74        21.07        62.43 
TCGA-CV-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-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7101 
       64.83       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        89.65        36.00        31.36 
TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 
       26.20        18.97        17.13        95.34         4.96        11.87 
TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7407 TCGA-CV-7409 TCGA-CV-7410 
       47.97        49.71        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-7433 TCGA-CV-7434 TCGA-CV-7435 
       54.94         3.52        16.27        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-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-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 
       28.01         3.62        23.47        19.92        22.52        10.42 
TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 
       10.55        18.84        51.12        13.25        25.41         9.60 
TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6827 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-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 
       12.10        12.79        23.34        58.45        37.25        33.86 
TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 
       46.45        20.45        37.58        40.04        39.12        41.59 
TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J 
       37.18        32.71        21.63        20.25         3.02        31.13 
TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A623 
       18.94        24.95         0.46        17.85        11.80        20.25 
TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A76A TCGA-HD-7229 
       12.43        13.38        15.16        15.06        20.94        33.76 
TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-7917 TCGA-HD-8314 
       28.47        25.74        21.93        27.48        27.48        22.03 
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-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-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-A6SW TCGA-P3-A6SX 
       15.78        71.74        51.25        10.85        36.82        47.01 
TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T6 TCGA-P3-A6T7 
       19.00        75.55        18.97         2.04        12.99        16.01 
TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH 
       13.15        21.07        21.21        23.15         7.30        21.47 
TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z7 
        9.34        12.72        27.39        21.07        19.73        12.89 
TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K 
        5.62        14.76        12.20        17.82        15.32         8.32 
TCGA-RS-A6TO TCGA-T2-A6WX TCGA-T2-A6X2 TCGA-T3-A92M TCGA-T3-A92N TCGA-TN-A7HI 
       12.72         6.87        32.45        13.71         3.12        13.55 
TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B 
       13.25        20.35        64.80        54.67         2.83        49.51 
TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF 
       49.45        44.65        74.47        17.95        24.30        55.43 
TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT 
       29.46        18.05        13.94        20.75        22.36        32.65 
TCGA-UP-A6WW TCGA-WA-A7H4 TCGA-KU-A66S TCGA-KU-A66T 
       17.03        14.56        13.35        18.15 

  12P LOSS MUTATED 12P LOSS WILD-TYPE 
              2.10               0.07 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
            172.67             210.97 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
            15.175             21.565 
[1] "2.1 - 172.7 (15.2)" "0.1 - 211.0 (21.6)"
[1] "hr=" "1.7"
D64V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  12P LOSS MUTATED         0        6         6        14         1         0
  12P LOSS WILD-TYPE      27       70        76       238        11         1
D64V3, multiclass
           clus
vv          12P LOSS MUTATED 12P LOSS WILD-TYPE
  STAGE I                  0                 27
  STAGE II                 6                 70
  STAGE III                6                 76
  STAGE IVA               14                238
  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  10   7  11
  12P LOSS WILD-TYPE    49 127  93 162
D64V4, multiclass
       clus
vv      12P LOSS MUTATED 12P LOSS WILD-TYPE
  T0+T1                1                 49
  T2                  10                127
  T3                   7                 93
  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 178   1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     12    0
  12P LOSS WILD-TYPE  178    1
   clus
vv  12P LOSS MUTATED 12P LOSS WILD-TYPE
  0               12                178
  1                0                  1
[1] 2 2
[1] FALSE
D64V7, binary
                    cls
clus                   0   1
  12P LOSS MUTATED    11  25
  12P LOSS WILD-TYPE 129 357
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     11   25
  12P LOSS WILD-TYPE  129  357
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  FEMALE               11                129
  MALE                 25                357
[1] 2 2
[1] FALSE
D64V8, binary
                    cls
clus                   0   1
  12P LOSS MUTATED    14  19
  12P LOSS WILD-TYPE 148 282
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     14   19
  12P LOSS WILD-TYPE  148  282
     clus
vv    12P LOSS MUTATED 12P LOSS WILD-TYPE
  NO                14                148
  YES               19                282
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD & NECK SQUAMOUS CELL CARCINOMA
  12P LOSS MUTATED                                    36
  12P LOSS WILD-TYPE                                 475
                    vv
clus                 HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  12P LOSS MUTATED                                                   0
  12P LOSS WILD-TYPE                                                10
                    vv
clus                 HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  12P LOSS MUTATED                                                           0
  12P LOSS WILD-TYPE                                                         1
D64V9, multiclass
                                                           clus
vv                                                          12P LOSS MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                     36
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        0
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                0
                                                           clus
vv                                                          12P LOSS WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                      475
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                         10
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                  1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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                           6    29
  12P LOSS WILD-TYPE                        42   417
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                       6                 42
  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"
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    17  14
  12Q LOSS WILD-TYPE 284 205
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                31                489 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                14                205 
$`12Q LOSS MUTATED`
TCGA-BA-4075 TCGA-CN-6024 TCGA-CX-7219 TCGA-BA-6868 TCGA-BA-6870 TCGA-BA-6873 
        9.30        11.08        34.36        15.52        14.83         4.01 
TCGA-BA-7269 TCGA-BA-A4IH TCGA-BA-A6DE TCGA-BB-8596 TCGA-CN-5355 TCGA-CN-5374 
       41.85        20.45        14.47        71.05        42.02        56.94 
TCGA-CN-6994 TCGA-CR-6493 TCGA-CR-7390 TCGA-CV-6003 TCGA-CV-7090 TCGA-CV-7254 
       38.89         9.27        49.58        54.74       172.67        47.97 
TCGA-CV-7255 TCGA-CV-7263 TCGA-CV-7432 TCGA-CV-A6JY TCGA-D6-A6EP TCGA-F7-7848 
        2.10        18.41        84.49        21.24        13.94        37.18 
TCGA-IQ-A61G TCGA-IQ-A6SG TCGA-MZ-A5BI TCGA-P3-A6T5 TCGA-T2-A6WZ TCGA-T2-A6X0 
       11.84        19.04         7.13        29.00        15.91         7.10 
TCGA-WA-A7GZ 
       20.55 

$`12Q LOSS WILD-TYPE`
TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4IG TCGA-BA-A4II 
       37.28        20.48        68.48         3.55        28.11        30.18 
TCGA-BB-A5HU TCGA-CN-4727 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6992 
       25.71        51.29         9.07         9.24        52.08        35.05 
TCGA-CN-6997 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-6221 TCGA-CQ-7063 
       32.48        19.82        24.39        48.20        32.88        70.13 
TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-A4C7 TCGA-CR-6472 TCGA-CR-6478 TCGA-CX-7082 
       16.73        43.04        11.61        34.52         6.02         0.36 
TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7593 TCGA-H7-A6C5 TCGA-HD-8634 
       30.94        14.04        46.32        40.24        21.11        12.66 
TCGA-HD-8635 TCGA-UF-A71D TCGA-UF-A7JV TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 
       22.85        48.03         2.96         3.35        15.19        13.64 
TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 
        9.07        26.50        23.74        42.35        57.93        17.10 
TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-6869 TCGA-BA-6872 TCGA-BA-A4IF TCGA-BA-A6D8 
       23.84        65.59        21.17        12.62        29.42        27.95 
TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DI 
       11.54         7.10         5.69         7.82         2.27        11.05 
TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 
       13.38        20.48        16.41         6.15       105.90         9.14 
TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 
        4.80         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-8601 
       50.20        44.98        66.28        24.66        38.40        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-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-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-6988 TCGA-CN-6989 TCGA-CN-6995 TCGA-CN-6996 
       34.13         6.74        10.45        32.22         3.68        17.42 
TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B 
       11.74        35.01        25.41        23.57        17.29        29.72 
TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y 
       21.21         7.40        31.69        22.32        12.39        16.57 
TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V6 TCGA-CN-A6V7 
        4.41        12.07         2.70        23.44        20.88        19.53 
TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 
       52.37        21.50         2.93        54.58        70.45        62.37 
TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6220 
       45.99        10.42        11.21         4.24        41.19        32.38 
TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 
       46.95        56.58        13.25         4.24        14.99        38.76 
TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 
       64.87        53.52        41.88        43.10        77.56        44.48 
TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH 
       23.24        29.36        33.60        29.49        14.14        12.46 
TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 
       31.23        84.23        11.77        54.67        37.87        26.27 
TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 
       58.42        50.01        39.52        36.99        18.54        16.90 
TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 
       11.90        10.22        11.34        11.64         7.69        12.46 
TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-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-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-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        24.79         5.13         5.95 
TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 
       35.41        29.95        48.39       139.43        17.16       129.21 
TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 
      108.95        76.24        19.20        17.95       107.51        94.88 
TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 
       76.50        91.53        80.12        17.92        13.35        23.05 
TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-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-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-7100 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7104 
        7.99         9.01         5.26         1.84        52.31        12.92 
TCGA-CV-7177 TCGA-CV-7178 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7236 
       21.80        71.21        10.75       130.88        77.16         4.73 
TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7248 
       89.65        36.00        31.36        26.20        18.97        17.13 
TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7407 
       95.34         4.96        11.87        49.71        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-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-A6JZ 
        6.38        29.79         6.48        28.01         3.62        23.47 
TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-A4AQ 
       19.92        22.52        10.42        10.55        18.84        51.12 
TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 
       13.25        25.41         9.60        23.05         2.53        16.14 
TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB 
       11.44        18.67        24.95        25.32        17.72        12.36 
TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EN TCGA-D6-A6EO TCGA-D6-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-5630 TCGA-DQ-5631 TCGA-DQ-7590 
       23.34        58.45        37.25        33.86        18.02        46.45 
TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-8298 
       20.45        37.58        40.04        39.12        41.59        32.71 
TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V 
       21.63        20.25         3.02        31.13        18.94        24.95 
TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A623 TCGA-F7-A624 TCGA-H7-7774 
        0.46        17.85        11.80        20.25        12.43        13.38 
TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 
       15.16        15.06        20.94        33.76        28.47        25.74 
TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-A4C1 
       21.93        27.48        27.48        14.66        22.03         0.36 
TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 
       13.84         4.27         3.65         6.90        34.75        15.95 
TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J 
       38.53        14.50        37.71        37.41         0.07        33.57 
TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O TCGA-IQ-A6SH TCGA-KU-A6H7 TCGA-KU-A6H8 
        5.29        13.68        13.84        15.48        19.27        10.75 
TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G 
       14.37         7.96        30.05         1.84        12.62         6.25 
TCGA-MT-A7BN TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5Q6 TCGA-P3-A5QA 
       15.42        16.08        17.98        29.92        15.78        71.74 
TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 
       51.25        10.85        36.82        47.01        19.00        75.55 
TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T6 TCGA-P3-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 
       27.39        21.07        19.73        12.89         5.62        14.76 
TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-RS-A6TO TCGA-RS-A6TP 
       12.20        17.82        15.32         8.32        12.72        16.96 
TCGA-T2-A6WX TCGA-T2-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-A719 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71E 
       20.35        64.80        54.67         2.83        49.51        49.45 
TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH 
       44.65        74.47        17.95        24.30        55.43        29.46 
TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UP-A6WW 
       18.05        13.94        20.75        22.36        32.65        17.03 
TCGA-WA-A7H4 TCGA-KU-A66S TCGA-KU-A66T 
       14.56        13.35        18.15 

  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
              2.10               0.07 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
            172.67             210.97 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
             20.45              21.17 
[1] "2.1 - 172.7 (20.4)" "0.1 - 211.0 (21.2)"
[1] "hr=" "1"  
D65V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  12Q LOSS MUTATED         0        5         5        14         0         0
  12Q LOSS WILD-TYPE      27       71        77       238        12         1
D65V3, multiclass
           clus
vv          12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  STAGE I                  0                 27
  STAGE II                 5                 71
  STAGE III                5                 77
  STAGE IVA               14                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       0  10   5  12
  12Q LOSS WILD-TYPE    50 127  95 161
D65V4, multiclass
       clus
vv      12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  T0+T1                0                 50
  T2                  10                127
  T3                   5                 95
  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    12   4   7   0
  12Q LOSS WILD-TYPE 167  64 161   8
D65V5, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  N0               12                167
  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 180   1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED     10    0
  12Q LOSS WILD-TYPE  180    1
   clus
vv  12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  0               10                180
  1                0                  1
[1] 2 2
[1] FALSE
D65V7, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED     8  23
  12Q LOSS WILD-TYPE 132 359
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      8   23
  12Q LOSS WILD-TYPE  132  359
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  FEMALE                8                132
  MALE                 23                359
[1] 2 2
[1] FALSE
D65V8, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED    11  17
  12Q LOSS WILD-TYPE 151 284
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED     11   17
  12Q LOSS WILD-TYPE  151  284
     clus
vv    12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  NO                11                151
  YES               17                284
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD & NECK SQUAMOUS CELL CARCINOMA
  12Q LOSS MUTATED                                    30
  12Q LOSS WILD-TYPE                                 481
                    vv
clus                 HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  12Q LOSS MUTATED                                                   1
  12Q LOSS WILD-TYPE                                                 9
                    vv
clus                 HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  12Q LOSS MUTATED                                                           0
  12Q LOSS WILD-TYPE                                                         1
D65V9, multiclass
                                                           clus
vv                                                          12Q LOSS MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                     30
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        1
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                0
                                                           clus
vv                                                          12Q LOSS WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                      481
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                          9
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                  1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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                           7    24
  12Q LOSS WILD-TYPE                        41   422
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                       7                 41
  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"
D65V14, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED     4  26
  12Q LOSS WILD-TYPE  22 433
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      4   26
  12Q LOSS WILD-TYPE   22  433
                        clus
vv                       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                 22
  NOT HISPANIC OR LATINO               26                433
[1] 2 2
[1] FALSE

Clustering(66) Variable = 13Q LOSS MUTATION ANALYSIS
D66V1, survival
                    sevent
clus2                  0   1
  13Q LOSS MUTATED    97  70
  13Q LOSS WILD-TYPE 204 149
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
               167                353 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                70                149 
$`13Q LOSS MUTATED`
TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4II TCGA-CN-6021 TCGA-CN-6024 TCGA-CQ-5323 
       68.48         3.55        30.18         9.07        11.08        48.20 
TCGA-CQ-7067 TCGA-CR-6472 TCGA-CR-6478 TCGA-CX-7082 TCGA-CX-7219 TCGA-DQ-7588 
       16.73        34.52         6.02         0.36        34.36        14.04 
TCGA-DQ-7589 TCGA-HD-8635 TCGA-UF-A71D TCGA-BA-4074 TCGA-BA-4078 TCGA-BA-5152 
       46.32        22.85        48.03        15.19         9.07        42.35 
TCGA-BA-5555 TCGA-BA-6869 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IH TCGA-BA-A6D8 
       17.10        21.17         4.01        41.85        20.45        27.95 
TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DI TCGA-BA-A6DL 
       11.54         7.10         5.69        14.47        11.05        20.48 
TCGA-BB-4224 TCGA-BB-4227 TCGA-BB-7862 TCGA-BB-7864 TCGA-BB-7870 TCGA-BB-7871 
        9.14         4.41        36.72        50.20        66.28        24.66 
TCGA-BB-8596 TCGA-BB-8601 TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-C9-A47Z TCGA-CN-4723 
       71.05        20.52        10.55        27.19         6.28        55.86 
TCGA-CN-4725 TCGA-CN-4730 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-5360 TCGA-CN-5363 
       38.04        26.86        45.83        27.58        71.31         8.32 
TCGA-CN-5367 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 
       11.57        52.08        56.94        50.07        30.67        48.00 
TCGA-CN-6018 TCGA-CN-6020 TCGA-CN-6988 TCGA-CN-6994 TCGA-CN-6998 TCGA-CN-A497 
       19.07         6.74        10.45        38.89        11.74        35.01 
TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A6V7 
       25.41        23.57        17.29        21.21         7.40        19.53 
TCGA-CQ-5330 TCGA-CQ-6220 TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-7064 TCGA-CQ-A4CE 
       62.37        32.38        56.58        13.25        64.87        29.49 
TCGA-CR-5249 TCGA-CR-6477 TCGA-CR-6481 TCGA-CR-6487 TCGA-CR-7364 TCGA-CR-7372 
       37.87        16.90        10.22         7.69        47.18        24.95 
TCGA-CR-7374 TCGA-CR-7379 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7397 TCGA-CR-7402 
        0.99        34.06        17.13        32.78        24.79        29.95 
TCGA-CR-7404 TCGA-CV-5434 TCGA-CV-5441 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-6940 
       48.39       108.95        94.88        60.49         7.07        26.43 
TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6950 TCGA-CV-6954 TCGA-CV-6962 TCGA-CV-7089 
       11.24       140.78        15.09        65.82         4.14        64.83 
TCGA-CV-7091 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7177 
      111.16         7.99         9.01        52.31        12.92        21.80 
TCGA-CV-7235 TCGA-CV-7242 TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7263 TCGA-CV-7406 
       77.16        36.00        26.20        17.13        18.41        57.47 
TCGA-CV-7415 TCGA-CV-7418 TCGA-CV-7421 TCGA-CV-7422 TCGA-CV-7429 TCGA-CV-7435 
       22.85        25.94         0.07        34.09         3.52       153.86 
TCGA-CV-7440 TCGA-CV-A45R TCGA-CV-A45W TCGA-CV-A45Y TCGA-CV-A461 TCGA-CV-A464 
       22.19       180.16        45.96        88.87        67.86        56.61 
TCGA-CV-A465 TCGA-CV-A6JE TCGA-D6-6825 TCGA-D6-8568 TCGA-D6-A4Z9 TCGA-D6-A6EP 
        7.07        35.34        16.14        24.95        17.72        13.94 
TCGA-DQ-5630 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-A50G TCGA-F7-A50I 
       33.86        39.12        41.59        37.18        20.25         3.02 
TCGA-F7-A623 TCGA-HD-7753 TCGA-HD-7831 TCGA-HD-7917 TCGA-HD-A6HZ TCGA-IQ-A61O 
       20.25        28.47        21.93        27.48         3.65        13.84 
TCGA-IQ-A6SG TCGA-IQ-A6SH TCGA-MT-A67G TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-P3-A5Q6 
       19.04        15.48         6.25         7.13        16.08        15.78 
TCGA-P3-A5QA TCGA-P3-A6SX TCGA-P3-A6T4 TCGA-P3-A6T7 TCGA-QK-A6IG TCGA-QK-A6V9 
       71.74        47.01         2.04        16.01         7.30        27.39 
TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-AA3K TCGA-T2-A6X0 TCGA-T3-A92M 
       12.89         5.62        14.76         8.32         7.10        13.71 
TCGA-T3-A92N TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A71A TCGA-UF-A71E TCGA-UF-A7J9 
        3.12        20.35        64.80         2.83        49.45        44.65 
TCGA-UF-A7JC TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UP-A6WW TCGA-KU-A66T 
       17.95        13.94        20.75        17.03        18.15 

$`13Q LOSS WILD-TYPE`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-A4IG TCGA-BB-A5HU TCGA-CN-4727 
        9.30        37.28        20.48        28.11        25.71        51.29 
TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-A6V1 TCGA-CN-A6V3 
        9.24        52.08        35.05        32.48        19.82        24.39 
TCGA-CQ-6221 TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CQ-A4C7 TCGA-DQ-5629 TCGA-DQ-7593 
       32.88        70.13        43.04        11.61        30.94        40.24 
TCGA-H7-A6C5 TCGA-HD-8634 TCGA-UF-A7JV TCGA-4P-AA8J TCGA-BA-4076 TCGA-BA-5149 
       21.11        12.66         2.96         3.35        13.64        26.50 
TCGA-BA-5151 TCGA-BA-5153 TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6870 
       23.74        57.93        23.84        65.59        15.52        14.83 
TCGA-BA-6872 TCGA-BA-A4IF TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BA-A8YP 
       12.62        29.42         7.82         2.27        13.38        16.41 
TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4225 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7863 
        6.15       105.90         4.80        18.38        22.42        33.70 
TCGA-BB-7866 TCGA-BB-7872 TCGA-BB-A6UM TCGA-BB-A6UO TCGA-C9-A480 TCGA-CN-4722 
       44.98        38.40        12.92         8.81        12.69        48.76 
TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 
        4.67        56.68        12.89        32.81        52.14        57.11 
TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 
       12.99        20.55        14.33        73.61        13.05        42.02 
TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 
       46.32         8.58        12.39        16.21        11.54        11.84 
TCGA-CN-5369 TCGA-CN-5370 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6019 
       12.49         8.52        23.90        47.44        28.04        34.13 
TCGA-CN-6989 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-A49B TCGA-CN-A63U TCGA-CN-A63V 
       32.22         3.68        17.42        29.72        31.69        22.32 
TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY 
       12.39        16.57         4.41        12.07         2.70        23.44 
TCGA-CN-A6V6 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 
       20.88        52.37        21.50         2.93        54.58        70.45 
TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6223 
       45.99        10.42        11.21         4.24        41.19        46.95 
TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7065 TCGA-CQ-7069 TCGA-CQ-7071 
        4.24        14.99        38.76        53.52        41.88        43.10 
TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CG 
       77.56        44.48        23.24        29.36        33.60        14.14 
TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5250 
       12.46        31.23        84.23        11.77        54.67        26.27 
TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6480 
       58.42        50.01        39.52        36.99        18.54        11.90 
TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 
       11.34        11.64        12.46        22.78        15.75         9.27 
TCGA-CR-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-7376 TCGA-CR-7377 TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7386 
       29.23        31.96         9.17        19.92        26.17        47.01 
TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 
       27.06        12.89        49.58        30.02        46.85        32.65 
TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CV-5430 
       44.25        30.58         5.13         5.95        35.41       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-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-5979 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 
       86.83        48.59        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-6943 TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6951 
        4.73        21.90        19.79        12.03        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-7090 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7101 TCGA-CV-7102 
        2.50       172.67        18.81        12.66         5.26         1.84 
TCGA-CV-7178 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7243 
       71.21        10.75       130.88         4.73        89.65        31.36 
TCGA-CV-7247 TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7255 
       18.97        95.34         4.96        11.87        47.97         2.10 
TCGA-CV-7261 TCGA-CV-7407 TCGA-CV-7409 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 
       49.71        35.54        17.85       210.97        89.33         9.67 
TCGA-CV-7414 TCGA-CV-7416 TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7425 TCGA-CV-7427 
        0.46        25.08       100.57        14.89        56.48       156.49 
TCGA-CV-7428 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7437 
       54.94        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-A45X TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A463 TCGA-CV-A468 
        1.05         6.51        48.20        60.43         0.76        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-A4AQ TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 
       18.84        51.12        13.25        25.41         9.60        23.05 
TCGA-D6-6824 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8569 TCGA-D6-A4ZB TCGA-D6-A6EK 
        2.53        11.44        18.67        25.32        12.36        28.77 
TCGA-D6-A6EM TCGA-D6-A6EN TCGA-D6-A6EO TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q 
        7.63        22.59        24.95        12.10        12.79        23.34 
TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5631 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 
       58.45        37.25        18.02        46.45        20.45        37.58 
TCGA-DQ-7594 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V 
       40.04        32.71        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-H7-8502 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7754 TCGA-HD-7832 TCGA-HD-8224 
       15.06        20.94        33.76        25.74        27.48        14.66 
TCGA-HD-8314 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6I0 TCGA-HL-7533 
       22.03         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-KU-A6H7 TCGA-KU-A6H8 
        0.07        33.57         5.29        13.68        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-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-A6T5 TCGA-P3-A6T6 TCGA-P3-A6T8 TCGA-QK-A64Z 
       75.55        18.97        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-A6VB 
       21.21        23.15        21.47         9.34        12.72        21.07 
TCGA-QK-A6VC TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-RS-A6TO TCGA-RS-A6TP 
       19.73        12.20        17.82        15.32        12.72        16.96 
TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T2-A6X2 TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-UF-A719 
        6.87        15.91        32.45        13.55        13.25        54.67 
TCGA-UF-A71B TCGA-UF-A7JA TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ 
       49.51        74.47        24.30        55.43        29.46        18.05 
TCGA-UF-A7JS TCGA-UF-A7JT TCGA-WA-A7GZ TCGA-WA-A7H4 TCGA-KU-A66S 
       22.36        32.65        20.55        14.56        13.35 

  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 
             21.80              21.07 
[1] "0.1 - 180.2 (21.8)" "0.1 - 211.0 (21.1)"
[1] "hr=" "1"  
D66V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  13Q LOSS MUTATED        11       19        25        82         3         1
  13Q LOSS WILD-TYPE      16       57        57       170         9         0
D66V3, multiclass
           clus
vv          13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  STAGE I                 11                 16
  STAGE II                19                 57
  STAGE III               25                 57
  STAGE IVA               82                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  43  29  55
  13Q LOSS WILD-TYPE    33  94  71 118
D66V4, multiclass
       clus
vv      13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  T0+T1               17                 33
  T2                  43                 94
  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    53  22  56   2
  13Q LOSS WILD-TYPE 126  46 112   6
D66V5, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  N0               53                126
  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    59   1
  13Q LOSS WILD-TYPE 131   0
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     59    1
  13Q LOSS WILD-TYPE  131    0
   clus
vv  13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  0               59                131
  1                1                  0
[1] 2 2
[1] FALSE
D66V7, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED    42 126
  13Q LOSS WILD-TYPE  98 256
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     42  126
  13Q LOSS WILD-TYPE   98  256
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  FEMALE               42                 98
  MALE                126                256
[1] 2 2
[1] FALSE
D66V8, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED    50  96
  13Q LOSS WILD-TYPE 112 205
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     50   96
  13Q LOSS WILD-TYPE  112  205
     clus
vv    13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  NO                50                112
  YES               96                205
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD & NECK SQUAMOUS CELL CARCINOMA
  13Q LOSS MUTATED                                   164
  13Q LOSS WILD-TYPE                                 347
                    vv
clus                 HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  13Q LOSS MUTATED                                                   3
  13Q LOSS WILD-TYPE                                                 7
                    vv
clus                 HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  13Q LOSS MUTATED                                                           1
  13Q LOSS WILD-TYPE                                                         0
D66V9, multiclass
                                                           clus
vv                                                          13Q LOSS MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                    164
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        3
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                1
                                                           clus
vv                                                          13Q LOSS WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                      347
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                          7
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                  0
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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   139
  13Q LOSS WILD-TYPE                        26   307
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                                         139                307
[1] 4 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    11 138
  13Q LOSS WILD-TYPE  15 321
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     11  138
  13Q LOSS WILD-TYPE   15  321
                        clus
vv                       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   11                 15
  NOT HISPANIC OR LATINO              138                321
[1] 2 2
[1] FALSE

Clustering(67) Variable = 14Q LOSS MUTATION ANALYSIS
D67V1, survival
                    sevent
clus2                  0   1
  14Q LOSS MUTATED    32  24
  14Q LOSS WILD-TYPE 269 195
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                56                464 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                24                195 
$`14Q LOSS MUTATED`
TCGA-BA-6871 TCGA-CN-6992 TCGA-CQ-6221 TCGA-CR-6472 TCGA-H7-A6C5 TCGA-UF-A71D 
        3.55        35.05        32.88        34.52        21.11        48.03 
TCGA-4P-AA8J TCGA-BA-4078 TCGA-BA-5152 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-A4IH 
        3.35         9.07        42.35        21.17        14.83        20.45 
TCGA-BA-A6D8 TCGA-BA-A8YP TCGA-BB-7862 TCGA-BB-A6UM TCGA-CN-6019 TCGA-CN-6020 
       27.95        16.41        36.72        12.92        34.13         6.74 
TCGA-CN-6995 TCGA-CN-A63U TCGA-CQ-5332 TCGA-CR-5247 TCGA-CR-6470 TCGA-CR-7398 
        3.68        31.69        10.42        11.77        50.01         5.13 
TCGA-CV-5966 TCGA-CV-6933 TCGA-CV-6935 TCGA-CV-6939 TCGA-CV-6962 TCGA-CV-7263 
       17.92        90.12         9.70        21.90         4.14        18.41 
TCGA-CV-7406 TCGA-CV-7422 TCGA-CV-7423 TCGA-CV-7435 TCGA-CV-A45Z TCGA-CV-A460 
       57.47        34.09       100.57       153.86        48.20        60.43 
TCGA-CV-A6JY TCGA-CV-A6K1 TCGA-CX-A4AQ TCGA-D6-6826 TCGA-D6-8569 TCGA-D6-A6EM 
       21.24        22.52        51.12        11.44        25.32         7.63 
TCGA-DQ-5631 TCGA-DQ-7590 TCGA-F7-7848 TCGA-H7-A76A TCGA-HD-8224 TCGA-MT-A7BN 
       18.02        46.45        37.18        20.94        14.66        15.42 
TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-P3-A6T0 TCGA-T2-A6X0 TCGA-TN-A7HL TCGA-UF-A71E 
        7.13        16.08        19.00         7.10        20.35        49.45 
TCGA-UF-A7J9 TCGA-UF-A7JA 
       44.65        74.47 

$`14Q LOSS WILD-TYPE`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-A4IG TCGA-BA-A4II 
        9.30        37.28        20.48        68.48        28.11        30.18 
TCGA-BB-A5HU TCGA-CN-4727 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 
       25.71        51.29         9.07         9.24        52.08        11.08 
TCGA-CN-6997 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-7063 TCGA-CQ-7067 
       32.48        19.82        24.39        48.20        70.13        16.73 
TCGA-CQ-7068 TCGA-CQ-A4C7 TCGA-CR-6478 TCGA-CX-7082 TCGA-CX-7219 TCGA-DQ-5629 
       43.04        11.61         6.02         0.36        34.36        30.94 
TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7593 TCGA-HD-8634 TCGA-HD-8635 TCGA-UF-A7JV 
       14.04        46.32        40.24        12.66        22.85         2.96 
TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5153 TCGA-BA-5555 
       15.19        13.64        26.50        23.74        57.93        17.10 
TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 
       23.84        65.59        15.52        12.62         4.01        41.85 
TCGA-BA-A4IF TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF 
       29.42        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         4.80         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-A5HY TCGA-BB-A5HZ TCGA-BB-A6UO TCGA-C9-A47Z TCGA-C9-A480 
       20.52        10.55        27.19         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-6013 TCGA-CN-6016 
       56.94        50.07        30.67        48.00        23.90        47.44 
TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-6996 
       28.04        19.07        10.45        32.22        38.89        17.42 
TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B 
       11.74        35.01        25.41        23.57        17.29        29.72 
TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-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-A6V6 TCGA-CN-A6V7 TCGA-CQ-5324 
       12.07         2.70        23.44        20.88        19.53        52.37 
TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 
       21.50         2.93        54.58        70.45        62.37        45.99 
TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6220 TCGA-CQ-6223 TCGA-CQ-6224 
       11.21         4.24        41.19        32.38        46.95        56.58 
TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7065 
       13.25         4.24        14.99        38.76        64.87        53.52 
TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CB 
       41.88        43.10        77.56        44.48        23.24        29.36 
TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 
       33.60        29.49        14.14        12.46        31.23        84.23 
TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6471 TCGA-CR-6473 
       54.67        37.87        26.27        58.42        39.52        36.99 
TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 
       18.54        16.90        11.90        10.22        11.34        11.64 
TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 
        7.69        12.46        22.78        15.75         9.27        47.18 
TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 
       39.16        47.34        40.93        35.84         3.45         3.09 
TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 
       24.95        29.23         0.99        31.96         9.17        34.06 
TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 
       19.92        26.17        17.13        32.78        47.01        27.06 
TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 
       12.89        49.58        30.02        46.85        32.65        44.25 
TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 
       30.58        24.79         5.95        35.41        29.95        48.39 
TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 
      139.43        17.16       129.21       108.95        76.24        19.20 
TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 
       17.95       107.51        94.88        76.50        91.53        80.12 
TCGA-CV-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-6934 
       43.23        54.74        21.07        62.43         9.60         2.14 
TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6942 
        5.46        20.52         4.73        26.43        11.24       140.78 
TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6952 
       19.79        12.03        42.38        15.09        30.08         6.08 
TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-6955 TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6960 
       53.95        65.82        10.98         7.13         8.42        28.34 
TCGA-CV-6961 TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 
        2.50        64.83       172.67       111.16        18.81        12.66 
TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7104 
        7.99         9.01         5.26         1.84        52.31        12.92 
TCGA-CV-7177 TCGA-CV-7178 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7236 
       21.80        71.21        10.75       130.88        77.16         4.73 
TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7248 
       89.65        36.00        31.36        26.20        18.97        17.13 
TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7255 TCGA-CV-7261 
       95.34         4.96        11.87        47.97         2.10        49.71 
TCGA-CV-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-7424 TCGA-CV-7425 
       22.85        25.08        25.94         0.07        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-A461 TCGA-CV-A463 TCGA-CV-A464 TCGA-CV-A465 
        6.51        88.87        67.86         0.76        56.61         7.07 
TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JM TCGA-CV-A6JN TCGA-CV-A6JO 
       15.25         5.98        35.34         6.38        29.79         6.48 
TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K2 TCGA-CX-7085 
       28.01         3.62        23.47        19.92        10.42        10.55 
TCGA-CX-7086 TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 
       18.84        13.25        25.41         9.60        23.05         2.53 
TCGA-D6-6825 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK 
       16.14        18.67        24.95        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        23.34 
TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7594 
       58.45        37.25        33.86        20.45        37.58        40.04 
TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I 
       39.12        41.59        32.71        21.63        20.25         3.02 
TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 
       31.13        18.94        24.95         0.46        17.85        11.80 
TCGA-F7-A623 TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-HD-7229 
       20.25        12.43        13.38        15.16        15.06        33.76 
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-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-HL-7533 
        0.36        13.84         4.27         3.65         6.90        34.75 
TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H 
       15.95        38.53        14.50        37.71        11.84        37.41 
TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O TCGA-IQ-A6SG 
        0.07        33.57         5.29        13.68        13.84        19.04 
TCGA-IQ-A6SH TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A 
       15.48        19.27        10.75        14.37         7.96        30.05 
TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5Q6 
        1.84        12.62         6.25        17.98        29.92        15.78 
TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T2 
       71.74        51.25        10.85        36.82        47.01        75.55 
TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-P3-A6T8 
       18.97         2.04        29.00        12.99        16.01        13.15 
TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II 
       21.07        21.21        23.15         7.30        21.47         9.34 
TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z8 
       12.72        27.39        21.07        19.73        12.89         5.62 
TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-RS-A6TO 
       14.76        12.20        17.82        15.32         8.32        12.72 
TCGA-RS-A6TP TCGA-T2-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-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 
       20.75        22.36        32.65        17.03        20.55        14.56 
TCGA-KU-A66S TCGA-KU-A66T 
       13.35        18.15 

  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              21.07 
[1] "3.4 - 153.9 (21.1)" "0.1 - 211.0 (21.1)"
[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        27         1         0
  14Q LOSS WILD-TYPE      27       67        76       225        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               27                225
  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  18
  14Q LOSS WILD-TYPE    47 124  90 155
D67V4, multiclass
       clus
vv      14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  T0+T1                3                 47
  T2                  13                124
  T3                  10                 90
  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
  14Q LOSS MUTATED    17   8  15   1
  14Q LOSS WILD-TYPE 162  60 153   7
D67V5, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  N0               17                162
  N1                8                 60
  N2               15                153
  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    20   0
  14Q LOSS WILD-TYPE 170   1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     20    0
  14Q LOSS WILD-TYPE  170    1
   clus
vv  14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  0               20                170
  1                0                  1
[1] 2 2
[1] FALSE
D67V7, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED    10  46
  14Q LOSS WILD-TYPE 130 336
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     10   46
  14Q LOSS WILD-TYPE  130  336
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  FEMALE               10                130
  MALE                 46                336
[1] 2 2
[1] FALSE
D67V8, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED    10  40
  14Q LOSS WILD-TYPE 152 261
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     10   40
  14Q LOSS WILD-TYPE  152  261
     clus
vv    14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  NO                10                152
  YES               40                261
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD & NECK SQUAMOUS CELL CARCINOMA
  14Q LOSS MUTATED                                    54
  14Q LOSS WILD-TYPE                                 457
                    vv
clus                 HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  14Q LOSS MUTATED                                                   2
  14Q LOSS WILD-TYPE                                                 8
                    vv
clus                 HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  14Q LOSS MUTATED                                                           0
  14Q LOSS WILD-TYPE                                                         1
D67V9, multiclass
                                                           clus
vv                                                          14Q LOSS MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                     54
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        2
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                0
                                                           clus
vv                                                          14Q LOSS WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                      457
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                          8
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                  1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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                           7    49
  14Q LOSS WILD-TYPE                        41   397
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                       7                 41
  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"
D67V14, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED     2  45
  14Q LOSS WILD-TYPE  24 414
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      2   45
  14Q LOSS WILD-TYPE   24  414
                        clus
vv                       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                 24
  NOT HISPANIC OR LATINO               45                414
[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 251 166
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
               103                417 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                53                166 
$`15Q LOSS MUTATED`
TCGA-BA-5559 TCGA-BA-A4IG TCGA-BA-A4II TCGA-CN-6021 TCGA-CN-6024 TCGA-CN-6997 
       68.48        28.11        30.18         9.07        11.08        32.48 
TCGA-CQ-7067 TCGA-CQ-A4C7 TCGA-CR-6478 TCGA-CX-7219 TCGA-BA-5152 TCGA-BA-5153 
       16.73        11.61         6.02        34.36        42.35        57.93 
TCGA-BA-5555 TCGA-BA-6868 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A6DE TCGA-BA-A6DI 
       17.10        15.52        41.85        29.42        14.47        11.05 
TCGA-BA-A8YP TCGA-BB-4225 TCGA-BB-7870 TCGA-CN-4725 TCGA-CN-4728 TCGA-CN-4730 
       16.41         4.80        66.28        38.04        56.68        26.86 
TCGA-CN-5359 TCGA-CN-5363 TCGA-CN-5370 TCGA-CN-6012 TCGA-CN-6996 TCGA-CN-6998 
       12.39         8.32         8.52        48.00        17.42        11.74 
TCGA-CN-A499 TCGA-CN-A63W TCGA-CN-A6UY TCGA-CQ-5326 TCGA-CQ-5330 TCGA-CQ-5332 
       23.57        12.39        23.44         2.93        62.37        10.42 
TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6229 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4CE 
       56.58         4.24        38.76        77.56        44.48        29.49 
TCGA-CR-7402 TCGA-CV-5435 TCGA-CV-5441 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5976 
       29.95        76.24        94.88        17.92        13.35        48.59 
TCGA-CV-5977 TCGA-CV-6441 TCGA-CV-6937 TCGA-CV-6940 TCGA-CV-6948 TCGA-CV-6954 
       60.49         9.60        20.52        26.43        42.38        65.82 
TCGA-CV-6962 TCGA-CV-7095 TCGA-CV-7104 TCGA-CV-7242 TCGA-CV-7247 TCGA-CV-7407 
        4.14        18.81        12.92        36.00        18.97        35.54 
TCGA-CV-7424 TCGA-CV-7432 TCGA-CV-7435 TCGA-CV-7438 TCGA-CV-A45R TCGA-CV-A460 
       14.89        84.49       153.86         6.38       180.16        60.43 
TCGA-CV-A465 TCGA-CV-A6JM TCGA-CV-A6JZ TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6826 
        7.07         6.38        23.47         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        23.34        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-MT-A7BN TCGA-MZ-A5BI TCGA-P3-A5QA TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T5 
       15.42         7.13        71.74        18.97         2.04        29.00 
TCGA-QK-A6IG TCGA-QK-A6VC TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-RS-A6TO TCGA-T2-A6WZ 
        7.30        19.73        14.76        12.20        12.72        15.91 
TCGA-T3-A92M TCGA-T3-A92N TCGA-UF-A718 TCGA-UF-A7JA TCGA-UF-A7JD TCGA-UF-A7JO 
       13.71         3.12        64.80        74.47        24.30        20.75 
TCGA-KU-A66T 
       18.15 

$`15Q LOSS WILD-TYPE`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-6871 TCGA-BB-A5HU TCGA-CN-4727 
        9.30        37.28        20.48         3.55        25.71        51.29 
TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6992 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 
        9.24        52.08        35.05        19.82        24.39        48.20 
TCGA-CQ-6221 TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CR-6472 TCGA-CX-7082 TCGA-DQ-5629 
       32.88        70.13        43.04        34.52         0.36        30.94 
TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7593 TCGA-H7-A6C5 TCGA-HD-8634 TCGA-HD-8635 
       14.04        46.32        40.24        21.11        12.66        22.85 
TCGA-UF-A71D TCGA-UF-A7JV TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4078 
       48.03         2.96         3.35        15.19        13.64         9.07 
TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-6869 TCGA-BA-6870 
       26.50        23.74        23.84        65.59        21.17        14.83 
TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-A4IH TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB 
       12.62         4.01        20.45        27.95        11.54         7.10 
TCGA-BA-A6DD TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BB-4217 
        5.69         7.82         2.27        13.38        20.48         6.15 
TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 
      105.90         9.14         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-A47Z 
       20.52        10.55        27.19        12.92         8.81         6.28 
TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4726 TCGA-CN-4729 TCGA-CN-4731 
       12.69        48.76        55.86         4.67        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-5355 TCGA-CN-5356 TCGA-CN-5358 
       27.58        73.61        13.05        42.02        46.32         8.58 
TCGA-CN-5360 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5369 
       71.31        16.21        11.54        11.84        11.57        12.49 
TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6013 TCGA-CN-6016 
       52.08        56.94        50.07        30.67        23.90        47.44 
TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6988 TCGA-CN-6989 
       28.04        19.07        34.13         6.74        10.45        32.22 
TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A49A TCGA-CN-A49B 
       38.89         3.68        35.01        25.41        17.29        29.72 
TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A640 
       21.21         7.40        31.69        22.32        16.57         4.41 
TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5324 TCGA-CQ-5325 
       12.07         2.70        20.88        19.53        52.37        21.50 
TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5331 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 
       54.58        70.45        45.99        11.21         4.24        41.19 
TCGA-CQ-6220 TCGA-CQ-6223 TCGA-CQ-6225 TCGA-CQ-6228 TCGA-CQ-7064 TCGA-CQ-7065 
       32.38        46.95        13.25        14.99        64.87        53.52 
TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CG 
       41.88        43.10        23.24        29.36        33.60        14.14 
TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 
       12.46        31.23        84.23        11.77        54.67        37.87 
TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6474 
       26.27        58.42        50.01        39.52        36.99        18.54 
TCGA-CR-6477 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 
       16.90        11.90        10.22        11.34        11.64         7.69 
TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 
       12.46        22.78        15.75         9.27        47.18        39.16 
TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 
       47.34        40.93        35.84         3.45         3.09        24.95 
TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 
       29.23         0.99        31.96         9.17        34.06        19.92 
TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 
       26.17        17.13        32.78        47.01        27.06        12.89 
TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 
       49.58        30.02        46.85        32.65        44.25        30.58 
TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7404 TCGA-CV-5430 
       24.79         5.13         5.95        35.41        48.39       139.43 
TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 
       17.16       129.21       108.95        19.20        17.95       107.51 
TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5978 
       76.50        91.53        80.12        23.05        86.83         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-6941 TCGA-CV-6942 
        9.70         5.46         4.73        21.90        11.24       140.78 
TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6953 
       19.79        12.03        15.09        30.08         6.08        53.95 
TCGA-CV-6955 TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7089 
       10.98         7.13         8.42        28.34         2.50        64.83 
TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 
      172.67       111.16        12.66         7.99         9.01         5.26 
TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7177 TCGA-CV-7178 TCGA-CV-7180 TCGA-CV-7183 
        1.84        52.31        21.80        71.21        10.75       130.88 
TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7248 
       77.16         4.73        89.65        31.36        26.20        17.13 
TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7255 TCGA-CV-7261 
       95.34         4.96        11.87        47.97         2.10        49.71 
TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-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-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-7428 TCGA-CV-7429 TCGA-CV-7430 
      100.57        56.48       156.49        54.94         3.52        16.27 
TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7437 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45P 
       19.76         7.17        16.64        22.19        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-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-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-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-7086 
       21.24        19.92        22.52        10.42        10.55        18.84 
TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6827 
       51.12        13.25        25.41         2.53        16.14        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-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-DQ-5625 TCGA-DQ-5630 
       22.59        13.94        12.10        12.79        37.25        33.86 
TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 
       46.45        20.45        40.04        39.12        41.59        37.18 
TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50J TCGA-F7-A61V TCGA-F7-A61W 
       32.71        21.63        20.25        31.13        24.95         0.46 
TCGA-F7-A620 TCGA-F7-A622 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-HD-7229 
       17.85        11.80        13.38        15.16        15.06        33.76 
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-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 
       22.03         0.36        13.84         4.27         3.65         6.90 
TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61G TCGA-IQ-A61H 
       34.75        15.95        38.53        14.50        11.84        37.41 
TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A6SG TCGA-IQ-A6SH 
        0.07        33.57         5.29        13.68        19.04        15.48 
TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D 
       19.27        10.75        14.37         7.96        30.05         1.84 
TCGA-MT-A67F TCGA-MT-A67G TCGA-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        27.39        21.07        12.89 
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-A71E TCGA-UF-A7J9 TCGA-UF-A7JC TCGA-UF-A7JF 
        2.83        49.51        49.45        44.65        17.95        55.43 
TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UP-A6WW 
       29.46        18.05        13.94        22.36        32.65        17.03 
TCGA-WA-A7GZ TCGA-WA-A7H4 TCGA-KU-A66S 
       20.55        14.56        13.35 

  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 
             20.25              21.21 
[1] "2.0 - 180.2 (20.2)" "0.1 - 211.0 (21.2)"
[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       203         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                203
  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 159   1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED     31    0
  15Q LOSS WILD-TYPE  159    1
   clus
vv  15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  0               31                159
  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    28  61
  15Q LOSS WILD-TYPE 134 240
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED     28   61
  15Q LOSS WILD-TYPE  134  240
     clus
vv    15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  NO                28                134
  YES               61                240
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD & NECK SQUAMOUS CELL CARCINOMA
  15Q LOSS MUTATED                                   102
  15Q LOSS WILD-TYPE                                 409
                    vv
clus                 HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  15Q LOSS MUTATED                                                   0
  15Q LOSS WILD-TYPE                                                10
                    vv
clus                 HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  15Q LOSS MUTATED                                                           1
  15Q LOSS WILD-TYPE                                                         0
D68V9, multiclass
                                                           clus
vv                                                          15Q LOSS MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                    102
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        0
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                1
                                                           clus
vv                                                          15Q LOSS WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                      409
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                         10
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                  0
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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    34  28
  16P LOSS WILD-TYPE 267 191
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                62                458 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                28                191 
$`16P LOSS MUTATED`
TCGA-CQ-A4C7 TCGA-CX-7082 TCGA-4P-AA8J TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-7269 
       11.61         0.36         3.35        13.64         9.07        41.85 
TCGA-BA-A4IH TCGA-BA-A6DE TCGA-BB-7870 TCGA-BB-8596 TCGA-BB-8601 TCGA-BB-A5HY 
       20.45        14.47        66.28        71.05        20.52        10.55 
TCGA-CN-4729 TCGA-CN-5363 TCGA-CN-5374 TCGA-CN-A499 TCGA-CN-A63T TCGA-CQ-5330 
       12.89         8.32        56.94        23.57         7.40        62.37 
TCGA-CQ-6224 TCGA-CR-6473 TCGA-CR-7368 TCGA-CR-7374 TCGA-CR-7383 TCGA-CR-7398 
       56.58        36.99        40.93         0.99        17.13         5.13 
TCGA-CR-7399 TCGA-CV-5431 TCGA-CV-5436 TCGA-CV-6940 TCGA-CV-6950 TCGA-CV-6962 
        5.95        17.16        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-D6-A4Z9 TCGA-D6-A6EM TCGA-F7-A50G 
        3.52        84.49         6.38        17.72         7.63        20.25 
TCGA-F7-A50I TCGA-HD-7753 TCGA-HD-8224 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H 
        3.02        28.47        14.66        37.71        11.84        37.41 
TCGA-IQ-A61K TCGA-IQ-A6SG TCGA-KU-A6H7 TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q6 
        5.29        19.04        19.27        16.08        17.98        15.78 
TCGA-P3-A6SW TCGA-QK-A6IG TCGA-QK-A8ZA TCGA-QK-AA3K TCGA-T3-A92N TCGA-TN-A7HJ 
       36.82         7.30        12.20         8.32         3.12        13.25 
TCGA-UF-A719 TCGA-UP-A6WW 
       54.67        17.03 

$`16P LOSS WILD-TYPE`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4IG 
        9.30        37.28        20.48        68.48         3.55        28.11 
TCGA-BA-A4II TCGA-BB-A5HU TCGA-CN-4727 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 
       30.18        25.71        51.29         9.07         9.24        52.08 
TCGA-CN-6024 TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 
       11.08        35.05        32.48        19.82        24.39        48.20 
TCGA-CQ-6221 TCGA-CQ-7063 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CR-6472 TCGA-CR-6478 
       32.88        70.13        16.73        43.04        34.52         6.02 
TCGA-CX-7219 TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7593 TCGA-H7-A6C5 
       34.36        30.94        14.04        46.32        40.24        21.11 
TCGA-HD-8634 TCGA-HD-8635 TCGA-UF-A71D TCGA-UF-A7JV TCGA-BA-4074 TCGA-BA-5149 
       12.66        22.85        48.03         2.96        15.19        26.50 
TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5558 
       23.74        42.35        57.93        17.10        23.84        65.59 
TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-A4IF 
       15.52        21.17        14.83        12.62         4.01        29.42 
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         4.80         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-A5HZ 
       33.70        50.20        44.98        24.66        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-4728 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 
       38.04         4.67        56.68        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-5360 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5369 
       71.31        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-6988 
       47.44        28.04        19.07        34.13         6.74        10.45 
TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A497 
       32.22        38.89         3.68        17.42        11.74        35.01 
TCGA-CN-A498 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63U TCGA-CN-A63V 
       25.41        17.29        29.72        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-A6V6 TCGA-CN-A6V7 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 
       20.88        19.53        52.37        21.50         2.93        54.58 
TCGA-CQ-5329 TCGA-CQ-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-6225 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 
       32.38        46.95        13.25         4.24        14.99        38.76 
TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 
       64.87        53.52        41.88        43.10        77.56        44.48 
TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH 
       23.24        29.36        33.60        29.49        14.14        12.46 
TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 
       31.23        84.23        11.77        54.67        37.87        26.27 
TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6480 
       58.42        50.01        39.52        18.54        16.90        11.90 
TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 
       10.22        11.34        11.64         7.69        12.46        22.78 
TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7369 
       15.75         9.27        47.18        39.16        47.34        35.84 
TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7376 TCGA-CR-7377 
        3.45         3.09        24.95        29.23        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        49.58        30.02        46.85        32.65        44.25 
TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 
       30.58        24.79        35.41        29.95        48.39       139.43 
TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 
      129.21       108.95        76.24        17.95       107.51        94.88 
TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 
       76.50        91.53        80.12        17.92        13.35        23.05 
TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 
       86.83        48.59        60.49         7.07        43.23        54.74 
TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6935 
       21.07        62.43         9.60        90.12         2.14         9.70 
TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6941 TCGA-CV-6942 
        5.46        20.52         4.73        21.90        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-7089 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 
       64.83       172.67       111.16        18.81        12.66         7.99 
TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7177 
        9.01         5.26         1.84        52.31        12.92        21.80 
TCGA-CV-7178 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 
       71.21        10.75       130.88        89.65        36.00        31.36 
TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 
       26.20        18.97        17.13        95.34         4.96        11.87 
TCGA-CV-7254 TCGA-CV-7255 TCGA-CV-7261 TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7409 
       47.97         2.10        49.71        18.41        57.47        17.85 
TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7414 TCGA-CV-7415 TCGA-CV-7421 
      210.97        89.33         9.67         0.46        22.85         0.07 
TCGA-CV-7422 TCGA-CV-7423 TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7430 
       34.09       100.57        56.48       156.49        54.94        16.27 
TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7437 TCGA-CV-7440 TCGA-CV-A45O 
       19.76         7.17       153.86        16.64        22.19        27.98 
TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45U TCGA-CV-A45V 
       21.01       169.38       180.16       159.65        35.47         1.05 
TCGA-CV-A45W TCGA-CV-A45X TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 
       45.96         6.51        88.87        48.20        60.43        67.86 
TCGA-CV-A463 TCGA-CV-A464 TCGA-CV-A465 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE 
        0.76        56.61         7.07        15.25         5.98        35.34 
TCGA-CV-A6JM TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY 
        6.38        29.79         6.48        28.01         3.62        21.24 
TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-7086 
       23.47        19.92        22.52        10.42        10.55        18.84 
TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 
       51.12        13.25        25.41         9.60        23.05         2.53 
TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4ZB 
       16.14        11.44        18.67        24.95        25.32        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-5624 TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7590 
       23.34        58.45        37.25        33.86        18.02        46.45 
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-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-A76A TCGA-HD-7229 TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 
       15.06        20.94        33.76        25.74        21.93        27.48 
TCGA-HD-7917 TCGA-HD-8314 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ 
       27.48        22.03         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-A61I 
        6.90        34.75        15.95        38.53        14.50         0.07 
TCGA-IQ-A61J TCGA-IQ-A61L TCGA-IQ-A61O TCGA-IQ-A6SH TCGA-KU-A6H8 TCGA-MT-A51W 
       33.57        13.68        13.84        15.48        10.75        14.37 
TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G TCGA-MT-A7BN 
        7.96        30.05         1.84        12.62         6.25        15.42 
TCGA-MZ-A5BI TCGA-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        27.39        21.07        19.73        12.89 
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-A71E TCGA-UF-A7J9 
       20.35        64.80         2.83        49.51        49.45        44.65 
TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ 
       74.47        17.95        24.30        55.43        29.46        18.05 
TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT TCGA-WA-A7GZ TCGA-WA-A7H4 
       13.94        20.75        22.36        32.65        20.55        14.56 
TCGA-KU-A66S TCGA-KU-A66T 
       13.35        18.15 

  16P LOSS MUTATED 16P LOSS WILD-TYPE 
              0.36               0.07 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
             84.49             210.97 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
            16.555             21.980 
[1] "0.4 - 84.5 (16.6)"  "0.1 - 211.0 (22.0)"
[1] "hr=" "1.4"
D69V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  16P LOSS MUTATED         3        8        10        31         2         0
  16P LOSS WILD-TYPE      24       68        72       221        10         1
D69V3, multiclass
           clus
vv          16P LOSS MUTATED 16P LOSS WILD-TYPE
  STAGE I                  3                 24
  STAGE II                 8                 68
  STAGE III               10                 72
  STAGE IVA               31                221
  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       3  22  19  12
  16P LOSS WILD-TYPE    47 115  81 161
D69V4, multiclass
       clus
vv      16P LOSS MUTATED 16P LOSS WILD-TYPE
  T0+T1                3                 47
  T2                  22                115
  T3                  19                 81
  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  10  26   2
  16P LOSS WILD-TYPE 166  58 142   6
D69V5, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  N0               13                166
  N1               10                 58
  N2               26                142
  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 170   1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED     20    0
  16P LOSS WILD-TYPE  170    1
   clus
vv  16P LOSS MUTATED 16P LOSS WILD-TYPE
  0               20                170
  1                0                  1
[1] 2 2
[1] FALSE
D69V7, binary
                    cls
clus                   0   1
  16P LOSS MUTATED    19  43
  16P LOSS WILD-TYPE 121 339
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED     19   43
  16P LOSS WILD-TYPE  121  339
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  FEMALE               19                121
  MALE                 43                339
[1] 2 2
[1] FALSE
D69V8, binary
                    cls
clus                   0   1
  16P LOSS MUTATED    16  40
  16P LOSS WILD-TYPE 146 261
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED     16   40
  16P LOSS WILD-TYPE  146  261
     clus
vv    16P LOSS MUTATED 16P LOSS WILD-TYPE
  NO                16                146
  YES               40                261
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD & NECK SQUAMOUS CELL CARCINOMA
  16P LOSS MUTATED                                    60
  16P LOSS WILD-TYPE                                 451
                    vv
clus                 HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  16P LOSS MUTATED                                                   2
  16P LOSS WILD-TYPE                                                 8
                    vv
clus                 HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  16P LOSS MUTATED                                                           0
  16P LOSS WILD-TYPE                                                         1
D69V9, multiclass
                                                           clus
vv                                                          16P LOSS MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                     60
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        2
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                0
                                                           clus
vv                                                          16P LOSS WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                      451
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                          8
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                  1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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     7  53
  16P LOSS WILD-TYPE  19 406
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      7   53
  16P LOSS WILD-TYPE   19  406
                        clus
vv                       16P LOSS MUTATED 16P LOSS WILD-TYPE
  HISPANIC OR LATINO                    7                 19
  NOT HISPANIC OR LATINO               53                406
[1] 2 2
[1] FALSE

Clustering(70) Variable = 16Q LOSS MUTATION ANALYSIS
D70V1, survival
                    sevent
clus2                  0   1
  16Q LOSS MUTATED    51  31
  16Q LOSS WILD-TYPE 250 188
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                82                438 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                31                188 
$`16Q LOSS MUTATED`
TCGA-BA-5559 TCGA-CQ-A4C7 TCGA-CX-7082 TCGA-DQ-7589 TCGA-BA-4076 TCGA-BA-4078 
       68.48        11.61         0.36        46.32        13.64         9.07 
TCGA-BA-5153 TCGA-BA-A4IH TCGA-BB-4225 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7866 
       57.93        20.45         4.80        22.42        36.72        44.98 
TCGA-BB-7870 TCGA-BB-8596 TCGA-BB-8601 TCGA-BB-A5HY TCGA-CN-4729 TCGA-CN-5356 
       66.28        71.05        20.52        10.55        12.89        46.32 
TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5374 TCGA-CN-6012 TCGA-CN-A497 TCGA-CN-A499 
       71.31         8.32        56.94        48.00        35.01        23.57 
TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A6UY TCGA-CQ-6224 TCGA-CR-5243 TCGA-CR-6467 
        7.40        31.69        23.44        56.58        84.23        58.42 
TCGA-CR-6473 TCGA-CR-6481 TCGA-CR-6484 TCGA-CR-7368 TCGA-CR-7370 TCGA-CR-7398 
       36.99        10.22        11.64        40.93         3.45         5.13 
TCGA-CR-7402 TCGA-CV-5431 TCGA-CV-5441 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-6940 
       29.95        17.16        94.88        91.53        80.12        26.43 
TCGA-CV-6962 TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7407 TCGA-CV-7414 TCGA-CV-7418 
        4.14        77.16         4.73        35.54         0.46        25.94 
TCGA-CV-7424 TCGA-CV-7428 TCGA-CV-7429 TCGA-CV-7432 TCGA-CV-7438 TCGA-CV-A45W 
       14.89        54.94         3.52        84.49         6.38        45.96 
TCGA-CV-A460 TCGA-CX-A4AQ TCGA-D6-6827 TCGA-D6-A4Z9 TCGA-D6-A6EM TCGA-DQ-7590 
       60.43        51.12        18.67        17.72         7.63        46.45 
TCGA-DQ-7591 TCGA-F7-A50I TCGA-HD-8224 TCGA-IQ-A61E TCGA-IQ-A61H TCGA-IQ-A61I 
       20.45         3.02        14.66        37.71        37.41         0.07 
TCGA-IQ-A6SG TCGA-KU-A6H7 TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-P3-A5QE TCGA-P3-A6SW 
       19.04        19.27         7.13        16.08        51.25        36.82 
TCGA-QK-A6IF TCGA-QK-A8ZA TCGA-QK-AA3K TCGA-RS-A6TO TCGA-T3-A92N TCGA-TN-A7HJ 
       23.15        12.20         8.32        12.72         3.12        13.25 
TCGA-UF-A719 TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UP-A6WW 
       54.67        49.45        44.65        17.03 

$`16Q LOSS WILD-TYPE`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-6871 TCGA-BA-A4IG TCGA-BA-A4II 
        9.30        37.28        20.48         3.55        28.11        30.18 
TCGA-BB-A5HU TCGA-CN-4727 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 
       25.71        51.29         9.07         9.24        52.08        11.08 
TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-6221 
       35.05        32.48        19.82        24.39        48.20        32.88 
TCGA-CQ-7063 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CR-6472 TCGA-CR-6478 TCGA-CX-7219 
       70.13        16.73        43.04        34.52         6.02        34.36 
TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7593 TCGA-H7-A6C5 TCGA-HD-8634 TCGA-HD-8635 
       30.94        14.04        40.24        21.11        12.66        22.85 
TCGA-UF-A71D TCGA-UF-A7JV TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-5149 TCGA-BA-5151 
       48.03         2.96         3.35        15.19        26.50        23.74 
TCGA-BA-5152 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6869 
       42.35        17.10        23.84        65.59        15.52        21.17 
TCGA-BA-6870 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A6D8 
       14.83        12.62         4.01        41.85        29.42        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-7863 TCGA-BB-7864 TCGA-BB-7871 
        9.14         4.41        18.38        33.70        50.20        24.66 
TCGA-BB-7872 TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO TCGA-C9-A47Z TCGA-C9-A480 
       38.40        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-4730 
       48.76        55.86        38.04         4.67        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-6988 TCGA-CN-6989 
       28.04        19.07        34.13         6.74        10.45        32.22 
TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A49A 
       38.89         3.68        17.42        11.74        25.41        17.29 
TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 
       29.72        21.21        22.32        12.39        16.57         4.41 
TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5324 TCGA-CQ-5325 
       12.07         2.70        20.88        19.53        52.37        21.50 
TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 
        2.93        54.58        70.45        62.37        45.99        10.42 
TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6220 TCGA-CQ-6223 TCGA-CQ-6225 
       11.21         4.24        41.19        32.38        46.95        13.25 
TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7069 
        4.24        14.99        38.76        64.87        53.52        41.88 
TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD 
       43.10        77.56        44.48        23.24        29.36        33.60 
TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-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-6474 TCGA-CR-6477 
       37.87        26.27        50.01        39.52        18.54        16.90 
TCGA-CR-6480 TCGA-CR-6482 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 
       11.90        11.34         7.69        12.46        22.78        15.75 
TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7369 TCGA-CR-7371 
        9.27        47.18        39.16        47.34        35.84         3.09 
TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 
       24.95        29.23         0.99        31.96         9.17        34.06 
TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 
       19.92        26.17        17.13        32.78        47.01        27.06 
TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 
       12.89        49.58        30.02        46.85        32.65        44.25 
TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7404 TCGA-CV-5430 
       30.58        24.79         5.95        35.41        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-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-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-6945 
        4.73        21.90        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-7089 
       10.98         7.13         8.42        28.34         2.50        64.83 
TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 
      172.67       111.16        18.81        12.66         7.99         9.01 
TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-7178 
        5.26         1.84        52.31        12.92        21.80        71.21 
TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 
       10.75       130.88        89.65        36.00        31.36        26.20 
TCGA-CV-7247 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7254 
       18.97        17.13        95.34         4.96        11.87        47.97 
TCGA-CV-7255 TCGA-CV-7261 TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7409 TCGA-CV-7410 
        2.10        49.71        18.41        57.47        17.85       210.97 
TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7415 TCGA-CV-7416 TCGA-CV-7421 TCGA-CV-7422 
       89.33         9.67        22.85        25.08         0.07        34.09 
TCGA-CV-7423 TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7430 TCGA-CV-7433 TCGA-CV-7434 
      100.57        56.48       156.49        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-A461 TCGA-CV-A463 TCGA-CV-A464 TCGA-CV-A465 TCGA-CV-A468 
       48.20        67.86         0.76        56.61         7.07        15.25 
TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JM TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT 
        5.98        35.34         6.38        29.79         6.48        28.01 
TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 
        3.62        21.24        23.47        19.92        22.52        10.42 
TCGA-CX-7085 TCGA-CX-7086 TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 
       10.55        18.84        13.25        25.41         9.60        23.05 
TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4ZB 
        2.53        16.14        11.44        24.95        25.32        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-5624 TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7592 
       23.34        58.45        37.25        33.86        18.02        37.58 
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-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 
       20.25        31.13        18.94        24.95         0.46        17.85 
TCGA-F7-A622 TCGA-F7-A623 TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 
       11.80        20.25        12.43        13.38        15.16        15.06 
TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 
       20.94        33.76        28.47        25.74        21.93        27.48 
TCGA-HD-7917 TCGA-HD-8314 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ 
       27.48        22.03         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-A6H8 
       33.57         5.29        13.68        13.84        15.48        10.75 
TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G 
       14.37         7.96        30.05         1.84        12.62         6.25 
TCGA-MT-A7BN TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QF 
       15.42        17.98        29.92        15.78        71.74        10.85 
TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T5 
       47.01        19.00        75.55        18.97         2.04        29.00 
TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IG 
       12.99        16.01        13.15        21.07        21.21         7.30 
TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC 
       21.47         9.34        12.72        27.39        21.07        19.73 
TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-RS-A6TP 
       12.89         5.62        14.76        17.82        15.32        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-A7JA TCGA-UF-A7JC 
       20.35        64.80         2.83        49.51        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-WA-A7GZ TCGA-WA-A7H4 TCGA-KU-A66S TCGA-KU-A66T 
       22.36        32.65        20.55        14.56        13.35        18.15 

  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
              0.07               0.07 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
             94.88             210.97 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
            23.295             21.070 
[1] "0.1 - 94.9 (23.3)"  "0.1 - 211.0 (21.1)"
[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        36         2         0
  16Q LOSS WILD-TYPE      25       67        69       216        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               36                216
  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  18  18
  16Q LOSS WILD-TYPE    44 114  82 155
D70V4, multiclass
       clus
vv      16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  T0+T1                6                 44
  T2                  23                114
  T3                  18                 82
  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
  16Q LOSS MUTATED    17  12  29   2
  16Q LOSS WILD-TYPE 162  56 139   6
D70V5, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  N0               17                162
  N1               12                 56
  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"
D70V6, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED    24   0
  16Q LOSS WILD-TYPE 166   1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED     24    0
  16Q LOSS WILD-TYPE  166    1
   clus
vv  16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  0               24                166
  1                0                  1
[1] 2 2
[1] FALSE
D70V7, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED    16  66
  16Q LOSS WILD-TYPE 124 316
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED     16   66
  16Q LOSS WILD-TYPE  124  316
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  FEMALE               16                124
  MALE                 66                316
[1] 2 2
[1] FALSE
D70V8, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED    22  53
  16Q LOSS WILD-TYPE 140 248
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED     22   53
  16Q LOSS WILD-TYPE  140  248
     clus
vv    16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  NO                22                140
  YES               53                248
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD & NECK SQUAMOUS CELL CARCINOMA
  16Q LOSS MUTATED                                    78
  16Q LOSS WILD-TYPE                                 433
                    vv
clus                 HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  16Q LOSS MUTATED                                                   4
  16Q LOSS WILD-TYPE                                                 6
                    vv
clus                 HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  16Q LOSS MUTATED                                                           0
  16Q LOSS WILD-TYPE                                                         1
D70V9, multiclass
                                                           clus
vv                                                          16Q LOSS MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                     78
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        4
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                0
                                                           clus
vv                                                          16Q LOSS WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                      433
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                          6
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                  1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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    69
  16Q LOSS WILD-TYPE                        39   377
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                                          69                377
[1] 4 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     6  72
  16Q LOSS WILD-TYPE  20 387
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      6   72
  16Q LOSS WILD-TYPE   20  387
                        clus
vv                       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    6                 20
  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 243 170
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               107                413 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                49                170 
$`17P LOSS MUTATED`
TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4II TCGA-CQ-6221 TCGA-CQ-7067 
       20.48        68.48         3.55        30.18        32.88        16.73 
TCGA-CQ-A4C7 TCGA-CR-6472 TCGA-CX-7219 TCGA-DQ-5629 TCGA-DQ-7588 TCGA-H7-A6C5 
       11.61        34.52        34.36        30.94        14.04        21.11 
TCGA-HD-8635 TCGA-BA-5149 TCGA-BA-5152 TCGA-BA-6868 TCGA-BA-6870 TCGA-BA-A4IH 
       22.85        26.50        42.35        15.52        14.83        20.45 
TCGA-BA-A6D8 TCGA-BA-A6DE TCGA-BA-A8YP TCGA-BB-4223 TCGA-BB-7862 TCGA-BB-7866 
       27.95        14.47        16.41       105.90        36.72        44.98 
TCGA-BB-7870 TCGA-BB-7871 TCGA-CN-4725 TCGA-CN-4730 TCGA-CN-4735 TCGA-CN-4739 
       66.28        24.66        38.04        26.86        57.11        45.83 
TCGA-CN-4742 TCGA-CN-5360 TCGA-CN-5364 TCGA-CN-5374 TCGA-CN-6988 TCGA-CN-A49A 
       13.05        71.31        16.21        56.94        10.45        17.29 
TCGA-CN-A63W TCGA-CQ-6220 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6228 
       12.39        32.38        46.95        56.58        13.25        14.99 
TCGA-CQ-7069 TCGA-CQ-A4C9 TCGA-CR-6481 TCGA-CR-6484 TCGA-CR-7364 TCGA-CR-7371 
       41.88        23.24        10.22        11.64        47.18         3.09 
TCGA-CR-7390 TCGA-CR-7398 TCGA-CV-5431 TCGA-CV-5439 TCGA-CV-5444 TCGA-CV-5966 
       49.58         5.13        17.16        17.95        80.12        17.92 
TCGA-CV-5970 TCGA-CV-5978 TCGA-CV-6441 TCGA-CV-6953 TCGA-CV-6961 TCGA-CV-7102 
       13.35         7.07         9.60        53.95         2.50         1.84 
TCGA-CV-7180 TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7253 TCGA-CV-7263 TCGA-CV-7406 
       10.75        26.20        18.97        11.87        18.41        57.47 
TCGA-CV-7421 TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7428 TCGA-CV-7435 TCGA-CV-7440 
        0.07       100.57        14.89        54.94       153.86        22.19 
TCGA-CV-A460 TCGA-CV-A465 TCGA-CV-A6JU TCGA-CX-7086 TCGA-CX-A4AQ TCGA-D6-6823 
       60.43         7.07         3.62        18.84        51.12        23.05 
TCGA-D6-6826 TCGA-D6-8569 TCGA-D6-A6EM TCGA-DQ-7591 TCGA-DQ-7595 TCGA-F7-A50G 
       11.44        25.32         7.63        20.45        39.12        20.25 
TCGA-F7-A50J TCGA-F7-A620 TCGA-F7-A623 TCGA-HD-7831 TCGA-IQ-7630 TCGA-IQ-A61G 
       31.13        17.85        20.25        21.93        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-BA-4075 TCGA-BA-4077 TCGA-BA-A4IG TCGA-BB-A5HU TCGA-CN-4727 TCGA-CN-6021 
        9.30        37.28        28.11        25.71        51.29         9.07 
TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-A6V1 
        9.24        52.08        11.08        35.05        32.48        19.82 
TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CR-6478 TCGA-CX-7082 
       24.39        48.20        70.13        43.04         6.02         0.36 
TCGA-DQ-7589 TCGA-DQ-7593 TCGA-HD-8634 TCGA-UF-A71D TCGA-UF-A7JV TCGA-4P-AA8J 
       46.32        40.24        12.66        48.03         2.96         3.35 
TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-5151 TCGA-BA-5153 TCGA-BA-5555 
       15.19        13.64         9.07        23.74        57.93        17.10 
TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-6869 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 
       23.84        65.59        21.17        12.62         4.01        41.85 
TCGA-BA-A4IF TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DF TCGA-BA-A6DG 
       29.42        11.54         7.10         5.69         7.82         2.27 
TCGA-BA-A6DI TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BB-4217 TCGA-BB-4224 TCGA-BB-4225 
       11.05        13.38        20.48         6.15         9.14         4.80 
TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7872 
        4.41        18.38        22.42        33.70        50.20        38.40 
TCGA-BB-8596 TCGA-BB-8601 TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO 
       71.05        20.52        10.55        27.19        12.92         8.81 
TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4726 TCGA-CN-4728 
        6.28        12.69        48.76        55.86         4.67        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-6989 TCGA-CN-6994 
       28.04        19.07        34.13         6.74        32.22        38.89 
TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 
        3.68        17.42        11.74        35.01        25.41        23.57 
TCGA-CN-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-A6V6 TCGA-CN-A6V7 
        4.41        12.07         2.70        23.44        20.88        19.53 
TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 
       52.37        21.50         2.93        54.58        70.45        62.37 
TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6227 
       45.99        10.42        11.21         4.24        41.19         4.24 
TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 
       38.76        64.87        53.52        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-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 
       84.23        11.77        54.67        37.87        26.27        58.42 
TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6480 
       50.01        39.52        36.99        18.54        16.90        11.90 
TCGA-CR-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        24.79 
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        94.88        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       172.67       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        89.65        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 
       49.71        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-7085 TCGA-D6-6515 
       23.47        19.92        22.52        10.42        10.55        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-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-5630 
       12.10        12.79        23.34        58.45        37.25        33.86 
TCGA-DQ-5631 TCGA-DQ-7590 TCGA-DQ-7592 TCGA-DQ-7594 TCGA-DQ-7596 TCGA-F7-7848 
       18.02        46.45        37.58        40.04        41.59        37.18 
TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50I TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W 
       32.71        21.63         3.02        18.94        24.95         0.46 
TCGA-F7-A622 TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A76A 
       11.80        12.43        13.38        15.16        15.06        20.94 
TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7832 TCGA-HD-7917 TCGA-HD-8224 
       33.76        28.47        25.74        27.48        27.48        14.66 
TCGA-HD-8314 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 
       22.03         0.36        13.84         4.27         3.65         6.90 
TCGA-HL-7533 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61I TCGA-IQ-A61J 
       34.75        38.53        14.50        37.71         0.07        33.57 
TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O TCGA-IQ-A6SG TCGA-IQ-A6SH TCGA-KU-A6H7 
        5.29        13.68        13.84        19.04        15.48        19.27 
TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67F TCGA-MZ-A5BI 
       10.75        14.37         7.96        30.05        12.62         7.13 
TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6T0 
       16.08        17.98        29.92        10.85        36.82        19.00 
TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T6 TCGA-QK-A652 
       75.55        18.97         2.04        29.00        12.99        21.21 
TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 
       23.15         7.30        21.47         9.34        12.72        27.39 
TCGA-QK-A6VB TCGA-QK-A8Z7 TCGA-QK-A8Z9 TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K 
       21.07        12.89        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-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-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF 
       49.45        44.65        74.47        17.95        24.30        55.43 
TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT 
       29.46        18.05        13.94        20.75        22.36        32.65 
TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 TCGA-KU-A66S TCGA-KU-A66T 
       17.03        20.55        14.56        13.35        18.15 

  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              21.50 
[1] "0.1 - 153.9 (20.2)" "0.1 - 211.0 (21.5)"
[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        47         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               47                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 156   0
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     34    1
  17P LOSS WILD-TYPE  156    0
   clus
vv  17P LOSS MUTATED 17P LOSS WILD-TYPE
  0               34                156
  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  60
  17P LOSS WILD-TYPE 128 241
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     34   60
  17P LOSS WILD-TYPE  128  241
     clus
vv    17P LOSS MUTATED 17P LOSS WILD-TYPE
  NO                34                128
  YES               60                241
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD & NECK SQUAMOUS CELL CARCINOMA
  17P LOSS MUTATED                                   105
  17P LOSS WILD-TYPE                                 406
                    vv
clus                 HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  17P LOSS MUTATED                                                   2
  17P LOSS WILD-TYPE                                                 8
                    vv
clus                 HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  17P LOSS MUTATED                                                           0
  17P LOSS WILD-TYPE                                                         1
D71V9, multiclass
                                                           clus
vv                                                          17P LOSS MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                    105
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        2
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                0
                                                           clus
vv                                                          17P LOSS WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                      406
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                          8
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                  1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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    19  13
  17Q LOSS WILD-TYPE 282 206
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                32                488 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                13                206 
$`17Q LOSS MUTATED`
TCGA-BA-4075 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4II TCGA-CQ-6221 TCGA-CQ-7067 
        9.30        68.48         3.55        30.18        32.88        16.73 
TCGA-CQ-A4C7 TCGA-HD-8635 TCGA-BA-6868 TCGA-BA-6870 TCGA-BB-4223 TCGA-CN-4739 
       11.61        22.85        15.52        14.83       105.90        45.83 
TCGA-CN-5374 TCGA-CN-6011 TCGA-CQ-6224 TCGA-CR-6484 TCGA-CV-5966 TCGA-D6-6823 
       56.94        30.67        56.58        11.64        17.92        23.05 
TCGA-D6-6826 TCGA-F7-A50G TCGA-F7-A620 TCGA-HD-7831 TCGA-IQ-7630 TCGA-IQ-A61G 
       11.44        20.25        17.85        21.93        15.95        11.84 
TCGA-IQ-A61H TCGA-MT-A67G TCGA-MT-A7BN TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QE 
       37.41         6.25        15.42        15.78        71.74        51.25 
TCGA-P3-A6SX TCGA-T2-A6WZ 
       47.01        15.91 

$`17Q LOSS WILD-TYPE`
TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-A4IG TCGA-BB-A5HU TCGA-CN-4727 TCGA-CN-6021 
       37.28        20.48        28.11        25.71        51.29         9.07 
TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-A6V1 
        9.24        52.08        11.08        35.05        32.48        19.82 
TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CR-6472 TCGA-CR-6478 
       24.39        48.20        70.13        43.04        34.52         6.02 
TCGA-CX-7082 TCGA-CX-7219 TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7593 
        0.36        34.36        30.94        14.04        46.32        40.24 
TCGA-H7-A6C5 TCGA-HD-8634 TCGA-UF-A71D TCGA-UF-A7JV TCGA-4P-AA8J TCGA-BA-4074 
       21.11        12.66        48.03         2.96         3.35        15.19 
TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 
       13.64         9.07        26.50        23.74        42.35        57.93 
TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-6869 TCGA-BA-6872 TCGA-BA-6873 
       17.10        23.84        65.59        21.17        12.62         4.01 
TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IH TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB 
       41.85        29.42        20.45        27.95        11.54         7.10 
TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DI TCGA-BA-A6DJ 
        5.69        14.47         7.82         2.27        11.05        13.38 
TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 
       20.48        16.41         6.15         9.14         4.80         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-A5HY 
       66.28        24.66        38.40        71.05        20.52        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-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-6012 
       11.57        12.49         8.52        52.08        50.07        48.00 
TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 
       23.90        47.44        28.04        19.07        34.13         6.74 
TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6998 
       10.45        32.22        38.89         3.68        17.42        11.74 
TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C 
       35.01        25.41        23.57        17.29        29.72        21.21 
TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 
        7.40        31.69        22.32        12.39        16.57         4.41 
TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5324 
       12.07         2.70        23.44        20.88        19.53        52.37 
TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 
       21.50         2.93        54.58        70.45        62.37        45.99 
TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6220 TCGA-CQ-6223 
       10.42        11.21         4.24        41.19        32.38        46.95 
TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7065 
       13.25         4.24        14.99        38.76        64.87        53.52 
TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CB 
       41.88        43.10        77.56        44.48        23.24        29.36 
TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 
       33.60        29.49        14.14        12.46        31.23        84.23 
TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 
       11.77        54.67        37.87        26.27        58.42        50.01 
TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6480 TCGA-CR-6481 
       39.52        36.99        18.54        16.90        11.90        10.22 
TCGA-CR-6482 TCGA-CR-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-7364 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 
       47.18        39.16        47.34        40.93        35.84         3.45 
TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 
        3.09        24.95        29.23         0.99        31.96         9.17 
TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 
       34.06        19.92        26.17        17.13        32.78        47.01 
TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 
       27.06        12.89        49.58        30.02        46.85        32.65 
TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 
       44.25        30.58        24.79         5.13         5.95        35.41 
TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 
       29.95        48.39       139.43        17.16       129.21       108.95 
TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 
       76.24        19.20        17.95       107.51        94.88        76.50 
TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-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-6933 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6937 
        9.60        90.12         2.14         9.70         5.46        20.52 
TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 
        4.73        21.90        26.43        11.24       140.78        19.79 
TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6953 
       12.03        42.38        15.09        30.08         6.08        53.95 
TCGA-CV-6954 TCGA-CV-6955 TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-6961 
       65.82        10.98         7.13         8.42        28.34         2.50 
TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 
        4.14        64.83       172.67       111.16        18.81        12.66 
TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7104 
        7.99         9.01         5.26         1.84        52.31        12.92 
TCGA-CV-7177 TCGA-CV-7178 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7236 
       21.80        71.21        10.75       130.88        77.16         4.73 
TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7248 
       89.65        36.00        31.36        26.20        18.97        17.13 
TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7255 TCGA-CV-7261 
       95.34         4.96        11.87        47.97         2.10        49.71 
TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7407 TCGA-CV-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-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-A45R TCGA-CV-A45T TCGA-CV-A45U TCGA-CV-A45V TCGA-CV-A45W TCGA-CV-A45X 
      180.16       159.65        35.47         1.05        45.96         6.51 
TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A463 TCGA-CV-A464 
       88.87        48.20        60.43        67.86         0.76        56.61 
TCGA-CV-A465 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JM TCGA-CV-A6JN 
        7.07        15.25         5.98        35.34         6.38        29.79 
TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 
        6.48        28.01         3.62        21.24        23.47        19.92 
TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-A4AQ TCGA-D6-6515 
       22.52        10.42        10.55        18.84        51.12        13.25 
TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6824 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-5624 
       24.95        13.94        12.10        12.79        23.34        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-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-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A622 
        3.02        31.13        18.94        24.95         0.46        11.80 
TCGA-F7-A623 TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A76A 
       20.25        12.43        13.38        15.16        15.06        20.94 
TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7832 TCGA-HD-7917 TCGA-HD-8224 
       33.76        28.47        25.74        27.48        27.48        14.66 
TCGA-HD-8314 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 
       22.03         0.36        13.84         4.27         3.65         6.90 
TCGA-HL-7533 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61I TCGA-IQ-A61J 
       34.75        38.53        14.50        37.71         0.07        33.57 
TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O TCGA-IQ-A6SG TCGA-IQ-A6SH TCGA-KU-A6H7 
        5.29        13.68        13.84        19.04        15.48        19.27 
TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F 
       10.75        14.37         7.96        30.05         1.84        12.62 
TCGA-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-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG 
       16.01        13.15        21.07        21.21        23.15         7.30 
TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC 
       21.47         9.34        12.72        27.39        21.07        19.73 
TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J 
       12.89         5.62        14.76        12.20        17.82        15.32 
TCGA-QK-AA3K TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-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-A719 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA 
       54.67         2.83        49.51        49.45        44.65        74.47 
TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK 
       17.95        24.30        55.43        29.46        18.05        13.94 
TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 
       20.75        22.36        32.65        17.03        20.55        14.56 
TCGA-KU-A66S TCGA-KU-A66T 
       13.35        18.15 

  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 
            19.085             21.140 
[1] "3.5 - 105.9 (19.1)" "0.1 - 211.0 (21.1)"
[1] "hr=" "1"  
D72V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  17Q LOSS MUTATED         2        4         7        13         0         0
  17Q LOSS WILD-TYPE      25       72        75       239        12         1
D72V3, multiclass
           clus
vv          17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  STAGE I                  2                 25
  STAGE II                 4                 72
  STAGE III                7                 75
  STAGE IVA               13                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   5   7
  17Q LOSS WILD-TYPE    46 126  95 166
D72V4, multiclass
       clus
vv      17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  T0+T1                4                 46
  T2                  11                126
  T3                   5                 95
  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     8   7  10   0
  17Q LOSS WILD-TYPE 171  61 158   8
D72V5, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  N0                8                171
  N1                7                 61
  N2               10                158
  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 180   1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     10    0
  17Q LOSS WILD-TYPE  180    1
   clus
vv  17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  0               10                180
  1                0                  1
[1] 2 2
[1] FALSE
D72V7, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED     8  24
  17Q LOSS WILD-TYPE 132 358
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      8   24
  17Q LOSS WILD-TYPE  132  358
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  FEMALE                8                132
  MALE                 24                358
[1] 2 2
[1] FALSE
D72V8, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED    12  20
  17Q LOSS WILD-TYPE 150 281
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     12   20
  17Q LOSS WILD-TYPE  150  281
     clus
vv    17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  NO                12                150
  YES               20                281
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD & NECK SQUAMOUS CELL CARCINOMA
  17Q LOSS MUTATED                                    31
  17Q LOSS WILD-TYPE                                 480
                    vv
clus                 HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  17Q LOSS MUTATED                                                   1
  17Q LOSS WILD-TYPE                                                 9
                    vv
clus                 HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  17Q LOSS MUTATED                                                           0
  17Q LOSS WILD-TYPE                                                         1
D72V9, multiclass
                                                           clus
vv                                                          17Q LOSS MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                     31
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        1
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                0
                                                           clus
vv                                                          17Q LOSS WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                      480
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                          9
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                  1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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    27
  17Q LOSS WILD-TYPE                        45   419
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                                          27                419
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V14, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED     3  26
  17Q LOSS WILD-TYPE  23 433
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      3   26
  17Q LOSS WILD-TYPE   23  433
                        clus
vv                       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                 23
  NOT HISPANIC OR LATINO               26                433
[1] 2 2
[1] FALSE

Clustering(73) Variable = 18P LOSS MUTATION ANALYSIS
D73V1, survival
                    sevent
clus2                  0   1
  18P LOSS MUTATED    49  53
  18P LOSS WILD-TYPE 252 166
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
               102                418 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                53                166 
$`18P LOSS MUTATED`
TCGA-BA-4075 TCGA-BA-5557 TCGA-CN-4727 TCGA-CQ-A4C7 TCGA-CX-7219 TCGA-DQ-5629 
        9.30        20.48        51.29        11.61        34.36        30.94 
TCGA-DQ-7588 TCGA-UF-A71D TCGA-BA-6868 TCGA-BA-6870 TCGA-BA-A4IF TCGA-BA-A6D8 
       14.04        48.03        15.52        14.83        29.42        27.95 
TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DI TCGA-BB-8601 TCGA-CN-4735 TCGA-CN-4739 
        7.10         5.69        11.05        20.52        57.11        45.83 
TCGA-CN-4740 TCGA-CN-5370 TCGA-CN-6010 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6994 
       27.58         8.52        50.07        19.07        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-6225 TCGA-CQ-7072 TCGA-CQ-A4CG TCGA-CR-6484 
       32.38        46.95        13.25        77.56        14.14        11.64 
TCGA-CR-7367 TCGA-CR-7373 TCGA-CR-7374 TCGA-CV-5435 TCGA-CV-5439 TCGA-CV-5444 
       47.34        29.23         0.99        76.24        17.95        80.12 
TCGA-CV-5966 TCGA-CV-6003 TCGA-CV-6933 TCGA-CV-6937 TCGA-CV-6940 TCGA-CV-6942 
       17.92        54.74        90.12        20.52        26.43       140.78 
TCGA-CV-6948 TCGA-CV-6953 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7091 TCGA-CV-7095 
       42.38        53.95        28.34         2.50       111.16        18.81 
TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7245 TCGA-CV-7261 
       52.31        12.92        77.16         4.73        26.20        49.71 
TCGA-CV-7263 TCGA-CV-7407 TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7429 TCGA-CV-7432 
       18.41        35.54       100.57        14.89         3.52        84.49 
TCGA-CV-7433 TCGA-CV-7438 TCGA-CV-A45U TCGA-CV-A460 TCGA-CV-A465 TCGA-DQ-5624 
       19.76         6.38        35.47        60.43         7.07        58.45 
TCGA-DQ-5630 TCGA-F7-8489 TCGA-F7-A50I TCGA-F7-A620 TCGA-F7-A623 TCGA-HD-7229 
       33.86        21.63         3.02        17.85        20.25        33.76 
TCGA-IQ-7630 TCGA-IQ-A61E TCGA-IQ-A61H TCGA-IQ-A61L TCGA-IQ-A61O TCGA-IQ-A6SG 
       15.95        37.71        37.41        13.68        13.84        19.04 
TCGA-MT-A51W TCGA-MT-A67D TCGA-P3-A6T0 TCGA-P3-A6T5 TCGA-P3-A6T8 TCGA-QK-A6IH 
       14.37         1.84        19.00        29.00        13.15        21.47 
TCGA-QK-A6VC TCGA-QK-A8Z9 TCGA-T3-A92M TCGA-T3-A92N TCGA-TN-A7HJ TCGA-UF-A7JF 
       19.73        14.76        13.71         3.12        13.25        55.43 
TCGA-UF-A7JO TCGA-UF-A7JS TCGA-WA-A7GZ TCGA-WA-A7H4 TCGA-KU-A66S TCGA-KU-A66T 
       20.75        22.36        20.55        14.56        13.35        18.15 

$`18P LOSS WILD-TYPE`
TCGA-BA-4077 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4IG TCGA-BA-A4II TCGA-BB-A5HU 
       37.28        68.48         3.55        28.11        30.18        25.71 
TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6992 TCGA-CN-6997 
        9.07         9.24        52.08        11.08        35.05        32.48 
TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-6221 TCGA-CQ-7063 TCGA-CQ-7067 
       19.82        24.39        48.20        32.88        70.13        16.73 
TCGA-CQ-7068 TCGA-CR-6472 TCGA-CR-6478 TCGA-CX-7082 TCGA-DQ-7589 TCGA-DQ-7593 
       43.04        34.52         6.02         0.36        46.32        40.24 
TCGA-H7-A6C5 TCGA-HD-8634 TCGA-HD-8635 TCGA-UF-A7JV TCGA-4P-AA8J TCGA-BA-4074 
       21.11        12.66        22.85         2.96         3.35        15.19 
TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 
       13.64         9.07        26.50        23.74        42.35        57.93 
TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-6869 TCGA-BA-6872 TCGA-BA-6873 
       17.10        23.84        65.59        21.17        12.62         4.01 
TCGA-BA-7269 TCGA-BA-A4IH TCGA-BA-A6DA TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG 
       41.85        20.45        11.54        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-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 
        4.80         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-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-4736 TCGA-CN-4737 TCGA-CN-4738 
       26.86        32.81        52.14        12.99        20.55        14.33 
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-5373 TCGA-CN-5374 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 
       12.49        52.08        56.94        30.67        48.00        23.90 
TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6020 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-A497 
       47.44        28.04         6.74        10.45        32.22        35.01 
TCGA-CN-A498 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U 
       25.41        17.29        29.72        21.21         7.40        31.69 
TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY 
       22.32        12.39        16.57        12.07         2.70        23.44 
TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5324 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 
       20.88        19.53        52.37         2.93        54.58        70.45 
TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 
       62.37        45.99        10.42        11.21         4.24        41.19 
TCGA-CQ-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-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-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 
       29.49        12.46        31.23        84.23        11.77        54.67 
TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6473 
       37.87        26.27        58.42        50.01        39.52        36.99 
TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6487 
       18.54        16.90        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-7365 
       12.46        22.78        15.75         9.27        47.18        39.16 
TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7376 
       40.93        35.84         3.45         3.09        24.95        31.96 
TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 
        9.17        34.06        19.92        26.17        17.13        32.78 
TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 
       47.01        27.06        12.89        49.58        30.02        46.85 
TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 
       32.65        44.25        30.58        24.79         5.13         5.95 
TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 
       35.41        29.95        48.39       139.43        17.16       129.21 
TCGA-CV-5434 TCGA-CV-5436 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 
      108.95        19.20       107.51        94.88        76.50        91.53 
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-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-6941 TCGA-CV-6943 TCGA-CV-6945 
        5.46         4.73        21.90        11.24        19.79        12.03 
TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6954 TCGA-CV-6955 TCGA-CV-6956 
       15.09        30.08         6.08        65.82        10.98         7.13 
TCGA-CV-6959 TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7097 TCGA-CV-7099 
        8.42         4.14        64.83       172.67        12.66         7.99 
TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7177 TCGA-CV-7178 TCGA-CV-7180 
        9.01         5.26         1.84        21.80        71.21        10.75 
TCGA-CV-7183 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7247 TCGA-CV-7248 
      130.88        89.65        36.00        31.36        18.97        17.13 
TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7255 TCGA-CV-7406 
       95.34         4.96        11.87        47.97         2.10        57.47 
TCGA-CV-7409 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7414 TCGA-CV-7415 
       17.85       210.97        89.33         9.67         0.46        22.85 
TCGA-CV-7416 TCGA-CV-7418 TCGA-CV-7421 TCGA-CV-7422 TCGA-CV-7425 TCGA-CV-7427 
       25.08        25.94         0.07        34.09        56.48       156.49 
TCGA-CV-7428 TCGA-CV-7430 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7437 TCGA-CV-7440 
       54.94        16.27         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-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-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-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-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 
        6.48        28.01         3.62        21.24        23.47        19.92 
TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-A4AQ TCGA-D6-6515 
       22.52        10.42        10.55        18.84        51.12        13.25 
TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 
       25.41         9.60        23.05         2.53        16.14        11.44 
TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK 
       18.67        24.95        25.32        17.72        12.36        28.77 
TCGA-D6-A6EM TCGA-D6-A6EN TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES 
        7.63        22.59        24.95        13.94        12.10        12.79 
TCGA-D6-A74Q TCGA-DQ-5625 TCGA-DQ-5631 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 
       23.34        37.25        18.02        46.45        20.45        37.58 
TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-A50G 
       40.04        39.12        41.59        37.18        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-A76A TCGA-HD-7753 TCGA-HD-7754 
       13.38        15.16        15.06        20.94        28.47        25.74 
TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-A4C1 
       21.93        27.48        27.48        14.66        22.03         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-A61G TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A6SH 
       14.50        11.84         0.07        33.57         5.29        15.48 
TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67F TCGA-MT-A67G 
       19.27        10.75         7.96        30.05        12.62         6.25 
TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5Q6 
       15.42         7.13        16.08        17.98        29.92        15.78 
TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T2 
       71.74        51.25        10.85        36.82        47.01        75.55 
TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-QK-A64Z TCGA-QK-A652 
       18.97         2.04        12.99        16.01        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        27.39        21.07 
TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K 
       12.89         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-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-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JH 
       49.45        44.65        74.47        17.95        24.30        29.46 
TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JT TCGA-UP-A6WW 
       18.05        13.94        32.65        17.03 

  18P LOSS MUTATED 18P LOSS WILD-TYPE 
              0.99               0.07 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
            140.78             210.97 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
             20.52              21.21 
[1] "1.0 - 140.8 (20.5)" "0.1 - 211.0 (21.2)"
[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        49         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               49                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  27  20  38
  18P LOSS WILD-TYPE    41 110  80 135
D73V4, multiclass
       clus
vv      18P LOSS MUTATED 18P LOSS WILD-TYPE
  T0+T1                9                 41
  T2                  27                110
  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    42  14  31   1
  18P LOSS WILD-TYPE 137  54 137   7
D73V5, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  N0               42                137
  N1               14                 54
  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    35   0
  18P LOSS WILD-TYPE 155   1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     35    0
  18P LOSS WILD-TYPE  155    1
   clus
vv  18P LOSS MUTATED 18P LOSS WILD-TYPE
  0               35                155
  1                0                  1
[1] 2 2
[1] FALSE
D73V7, binary
                    cls
clus                   0   1
  18P LOSS MUTATED    36  67
  18P LOSS WILD-TYPE 104 315
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     36   67
  18P LOSS WILD-TYPE  104  315
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  FEMALE               36                104
  MALE                 67                315
[1] 2 2
[1] FALSE
D73V8, binary
                    cls
clus                   0   1
  18P LOSS MUTATED    34  58
  18P LOSS WILD-TYPE 128 243
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     34   58
  18P LOSS WILD-TYPE  128  243
     clus
vv    18P LOSS MUTATED 18P LOSS WILD-TYPE
  NO                34                128
  YES               58                243
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD & NECK SQUAMOUS CELL CARCINOMA
  18P LOSS MUTATED                                   101
  18P LOSS WILD-TYPE                                 410
                    vv
clus                 HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  18P LOSS MUTATED                                                   1
  18P LOSS WILD-TYPE                                                 9
                    vv
clus                 HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  18P LOSS MUTATED                                                           1
  18P LOSS WILD-TYPE                                                         0
D73V9, multiclass
                                                           clus
vv                                                          18P LOSS MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                    101
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        1
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                1
                                                           clus
vv                                                          18P LOSS WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                      410
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                          9
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                  0
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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    84
  18P LOSS WILD-TYPE                        33   362
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                                          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"
D73V14, binary
                    cls
clus                   0   1
  18P LOSS MUTATED    10  84
  18P LOSS WILD-TYPE  16 375
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     10   84
  18P LOSS WILD-TYPE   16  375
                        clus
vv                       18P LOSS MUTATED 18P LOSS WILD-TYPE
  HISPANIC OR LATINO                   10                 16
  NOT HISPANIC OR LATINO               84                375
[1] 2 2
[1] FALSE

Clustering(74) Variable = 18Q LOSS MUTATION ANALYSIS
D74V1, survival
                    sevent
clus2                  0   1
  18Q LOSS MUTATED   115  95
  18Q LOSS WILD-TYPE 186 124
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               210                310 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                95                124 
$`18Q LOSS MUTATED`
TCGA-BA-4075 TCGA-BA-5557 TCGA-BA-A4II TCGA-CN-4727 TCGA-CN-6022 TCGA-CQ-7067 
        9.30        20.48        30.18        51.29         9.24        16.73 
TCGA-CQ-A4C7 TCGA-CX-7219 TCGA-DQ-5629 TCGA-DQ-7588 TCGA-H7-A6C5 TCGA-HD-8635 
       11.61        34.36        30.94        14.04        21.11        22.85 
TCGA-UF-A71D TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6870 
       48.03         3.35        15.19        65.59        15.52        14.83 
TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A6D8 TCGA-BA-A6DB 
       12.62         4.01        41.85        29.42        27.95         7.10 
TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DI TCGA-BA-A6DL TCGA-BB-4224 TCGA-BB-7862 
        5.69        14.47        11.05        20.48         9.14        36.72 
TCGA-BB-7872 TCGA-BB-8601 TCGA-BB-A5HY TCGA-BB-A6UO TCGA-C9-A47Z TCGA-CN-4723 
       38.40        20.52        10.55         8.81         6.28        55.86 
TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4730 TCGA-CN-4735 TCGA-CN-4737 
       38.04         4.67        56.68        26.86        57.11        20.55 
TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-5355 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5366 
       45.83        27.58        42.02         8.32        16.21        11.84 
TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6018 
       11.57         8.52        52.08        50.07        30.67        19.07 
TCGA-CN-6019 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A499 
       34.13        38.89         3.68        17.42        11.74        23.57 
TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63W TCGA-CN-A640 TCGA-CN-A641 TCGA-CQ-5325 
        7.40        31.69        12.39         4.41        12.07        21.50 
TCGA-CQ-5326 TCGA-CQ-5332 TCGA-CQ-6218 TCGA-CQ-6220 TCGA-CQ-6223 TCGA-CQ-6225 
        2.93        10.42        41.19        32.38        46.95        13.25 
TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7072 
        4.24        14.99        38.76        64.87        53.52        77.56 
TCGA-CQ-A4C6 TCGA-CQ-A4CB TCGA-CQ-A4CG TCGA-CR-5247 TCGA-CR-6474 TCGA-CR-6484 
       44.48        29.36        14.14        11.77        18.54        11.64 
TCGA-CR-6493 TCGA-CR-7365 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7377 TCGA-CR-7386 
        9.27        39.16        29.23         0.99         9.17        47.01 
TCGA-CR-7399 TCGA-CR-7402 TCGA-CV-5435 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 
        5.95        29.95        76.24        17.95       107.51        94.88 
TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 
       80.12        17.92        13.35        86.83        48.59        60.49 
TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6933 TCGA-CV-6935 TCGA-CV-6937 TCGA-CV-6940 
       43.23        54.74        90.12         9.70        20.52        26.43 
TCGA-CV-6942 TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-6960 
      140.78        12.03        42.38        53.95        65.82        28.34 
TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7101 
       64.83       172.67       111.16        18.81        12.66         5.26 
TCGA-CV-7104 TCGA-CV-7180 TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7243 TCGA-CV-7245 
       12.92        10.75        77.16         4.73        31.36        26.20 
TCGA-CV-7247 TCGA-CV-7248 TCGA-CV-7253 TCGA-CV-7255 TCGA-CV-7263 TCGA-CV-7407 
       18.97        17.13        11.87         2.10        18.41        35.54 
TCGA-CV-7409 TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7429 TCGA-CV-7430 TCGA-CV-7432 
       17.85       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-D6-6516 TCGA-D6-6823 TCGA-D6-6825 TCGA-D6-8568 TCGA-D6-A4Z9 TCGA-DQ-5624 
       25.41        23.05        16.14        24.95        17.72        58.45 
TCGA-DQ-5630 TCGA-DQ-7595 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A61W 
       33.86        39.12        21.63        20.25         3.02         0.46 
TCGA-F7-A620 TCGA-F7-A623 TCGA-H7-8501 TCGA-H7-8502 TCGA-HD-7229 TCGA-HD-7831 
       17.85        20.25        15.16        15.06        33.76        21.93 
TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-A6HZ TCGA-IQ-7630 TCGA-IQ-A61E TCGA-IQ-A61G 
       27.48        14.66         3.65        15.95        37.71        11.84 
TCGA-IQ-A61H TCGA-IQ-A61L TCGA-IQ-A61O TCGA-IQ-A6SG TCGA-IQ-A6SH TCGA-MT-A51W 
       37.41        13.68        13.84        19.04        15.48        14.37 
TCGA-MT-A51X TCGA-MT-A67D TCGA-MT-A7BN TCGA-P3-A5QA TCGA-P3-A6T0 TCGA-P3-A6T4 
        7.96         1.84        15.42        71.74        19.00         2.04 
TCGA-P3-A6T5 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IH TCGA-QK-A8Z9 
       29.00        13.15        21.07        21.21        21.47        14.76 
TCGA-QK-A8ZA TCGA-QK-AA3K TCGA-RS-A6TO TCGA-T2-A6WZ TCGA-T3-A92M TCGA-T3-A92N 
       12.20         8.32        12.72        15.91        13.71         3.12 
TCGA-TN-A7HJ TCGA-UF-A71B TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF 
       13.25        49.51        74.47        17.95        24.30        55.43 
TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS TCGA-WA-A7H4 TCGA-KU-A66S TCGA-KU-A66T 
       13.94        20.75        22.36        14.56        13.35        18.15 

$`18Q LOSS WILD-TYPE`
TCGA-BA-4077 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4IG TCGA-BB-A5HU TCGA-CN-6021 
       37.28        68.48         3.55        28.11        25.71         9.07 
TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-A6V1 TCGA-CN-A6V3 
       52.08        11.08        35.05        32.48        19.82        24.39 
TCGA-CQ-5323 TCGA-CQ-6221 TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CR-6472 TCGA-CR-6478 
       48.20        32.88        70.13        43.04        34.52         6.02 
TCGA-CX-7082 TCGA-DQ-7589 TCGA-DQ-7593 TCGA-HD-8634 TCGA-UF-A7JV TCGA-BA-4076 
        0.36        46.32        40.24        12.66         2.96        13.64 
TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 
        9.07        26.50        23.74        42.35        57.93        17.10 
TCGA-BA-5556 TCGA-BA-6869 TCGA-BA-A4IH TCGA-BA-A6DA TCGA-BA-A6DF TCGA-BA-A6DG 
       23.84        21.17        20.45        11.54         7.82         2.27 
TCGA-BA-A6DJ TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4225 TCGA-BB-4227 
       13.38        16.41         6.15       105.90         4.80         4.41 
TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7870 
       18.38        22.42        33.70        50.20        44.98        66.28 
TCGA-BB-7871 TCGA-BB-8596 TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-C9-A480 TCGA-CN-4722 
       24.66        71.05        27.19        12.92        12.69        48.76 
TCGA-CN-4729 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4736 TCGA-CN-4738 TCGA-CN-4741 
       12.89        32.81        52.14        12.99        14.33        73.61 
TCGA-CN-4742 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5365 
       13.05        46.32         8.58        12.39        71.31        11.54 
TCGA-CN-5369 TCGA-CN-5374 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 
       12.49        56.94        48.00        23.90        47.44        28.04 
TCGA-CN-6020 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A49A 
        6.74        10.45        32.22        35.01        25.41        17.29 
TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A642 TCGA-CN-A6UY 
       29.72        21.21        22.32        16.57         2.70        23.44 
TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5324 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 
       20.88        19.53        52.37        54.58        70.45        62.37 
TCGA-CQ-5331 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6224 TCGA-CQ-7069 TCGA-CQ-7071 
       45.99        11.21         4.24        56.58        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-6473 TCGA-CR-6477 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6487 
       36.99        16.90        11.90        10.22        11.34         7.69 
TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-7364 TCGA-CR-7367 TCGA-CR-7368 
       12.46        22.78        15.75        47.18        47.34        40.93 
TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7376 TCGA-CR-7379 
       35.84         3.45         3.09        24.95        31.96        34.06 
TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7388 TCGA-CR-7389 
       19.92        26.17        17.13        32.78        27.06        12.89 
TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 
       49.58        30.02        46.85        32.65        44.25        30.58 
TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7401 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 
       24.79         5.13        35.41        48.39       139.43        17.16 
TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5436 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5971 
      129.21       108.95        19.20        76.50        91.53        23.05 
TCGA-CV-5978 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6936 
        7.07        21.07        62.43         9.60         2.14         5.46 
TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6941 TCGA-CV-6943 TCGA-CV-6950 TCGA-CV-6951 
        4.73        21.90        11.24        19.79        15.09        30.08 
TCGA-CV-6952 TCGA-CV-6955 TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6961 TCGA-CV-6962 
        6.08        10.98         7.13         8.42         2.50         4.14 
TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7177 TCGA-CV-7178 
        7.99         9.01         1.84        52.31        21.80        71.21 
TCGA-CV-7183 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7254 
      130.88        89.65        36.00        95.34         4.96        47.97 
TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7414 
       49.71        57.47       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-7425 
       22.85        25.08        25.94         0.07        34.09        56.48 
TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7435 TCGA-CV-7437 TCGA-CV-A45O TCGA-CV-A45P 
      156.49        54.94       153.86        16.64        27.98        21.01 
TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45V TCGA-CV-A45W TCGA-CV-A45Y 
      169.38       180.16       159.65         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-A6JM TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JY 
        5.98        35.34         6.38        29.79         6.48        21.24 
TCGA-CV-A6K0 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6517 
       19.92        10.42        10.55        51.12        13.25         9.60 
TCGA-D6-6824 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8569 TCGA-D6-A4ZB TCGA-D6-A6EK 
        2.53        11.44        18.67        25.32        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-5625 TCGA-DQ-5631 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 
       23.34        37.25        18.02        46.45        20.45        37.58 
TCGA-DQ-7594 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-A50J TCGA-F7-A61S 
       40.04        41.59        37.18        32.71        31.13        18.94 
TCGA-F7-A61V TCGA-F7-A622 TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-A76A TCGA-HD-7753 
       24.95        11.80        12.43        13.38        20.94        28.47 
TCGA-HD-7754 TCGA-HD-7832 TCGA-HD-8314 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 
       25.74        27.48        22.03         0.36        13.84         4.27 
TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61I TCGA-IQ-A61J 
        6.90        34.75        38.53        14.50         0.07        33.57 
TCGA-IQ-A61K TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A67A TCGA-MT-A67F TCGA-MT-A67G 
        5.29        19.27        10.75        30.05        12.62         6.25 
TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5Q6 TCGA-P3-A5QE 
        7.13        16.08        17.98        29.92        15.78        51.25 
TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T6 
       10.85        36.82        47.01        75.55        18.97        12.99 
TCGA-P3-A6T7 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 
       16.01        23.15         7.30         9.34        12.72        27.39 
TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8ZB TCGA-QK-AA3J 
       21.07        19.73        12.89         5.62        17.82        15.32 
TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-TN-A7HI TCGA-TN-A7HL 
       16.96         6.87         7.10        32.45        13.55        20.35 
TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JH 
       64.80        54.67         2.83        49.45        44.65        29.46 
TCGA-UF-A7JJ TCGA-UF-A7JT TCGA-UP-A6WW TCGA-WA-A7GZ 
       18.05        32.65        17.03        20.55 

  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
              0.46               0.07 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
            172.67             210.97 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
             19.02              23.10 
[1] "0.5 - 172.7 (19.0)" "0.1 - 211.0 (23.1)"
[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       140         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                140
  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 57 42 77
  18Q LOSS WILD-TYPE    30 80 58 96
D74V4, multiclass
       clus
vv      18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  T0+T1               20                 30
  T2                  57                 80
  T3                  42                 58
  T4                  77                 96
[1] 4 2
[1] TRUE
[1] "dimension of 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  30  80   3
  18Q LOSS WILD-TYPE 110  38  88   5
D74V5, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  N0               69                110
  N1               30                 38
  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 118   1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     72    0
  18Q LOSS WILD-TYPE  118    1
   clus
vv  18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  0               72                118
  1                0                  1
[1] 2 2
[1] FALSE
D74V7, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED    55 156
  18Q LOSS WILD-TYPE  85 226
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     55  156
  18Q LOSS WILD-TYPE   85  226
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  FEMALE               55                 85
  MALE                156                226
[1] 2 2
[1] FALSE
D74V8, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED    63 121
  18Q LOSS WILD-TYPE  99 180
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     63  121
  18Q LOSS WILD-TYPE   99  180
     clus
vv    18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  NO                63                 99
  YES              121                180
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD & NECK SQUAMOUS CELL CARCINOMA
  18Q LOSS MUTATED                                   209
  18Q LOSS WILD-TYPE                                 302
                    vv
clus                 HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  18Q LOSS MUTATED                                                   1
  18Q LOSS WILD-TYPE                                                 9
                    vv
clus                 HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  18Q LOSS MUTATED                                                           1
  18Q LOSS WILD-TYPE                                                         0
D74V9, multiclass
                                                           clus
vv                                                          18Q LOSS MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                    209
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        1
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                1
                                                           clus
vv                                                          18Q LOSS WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                      302
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                          9
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                  0
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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    13 180
  18Q LOSS WILD-TYPE  13 279
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     13  180
  18Q LOSS WILD-TYPE   13  279
                        clus
vv                       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   13                 13
  NOT HISPANIC OR LATINO              180                279
[1] 2 2
[1] FALSE

Clustering(75) Variable = 19P LOSS MUTATION ANALYSIS
D75V1, survival
                    sevent
clus2                  0   1
  19P LOSS MUTATED    51  49
  19P LOSS WILD-TYPE 250 170
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
               100                420 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                49                170 
$`19P LOSS MUTATED`
TCGA-BA-4075 TCGA-CN-6022 TCGA-CN-6992 TCGA-CQ-A4C7 TCGA-DQ-7588 TCGA-BA-5149 
        9.30         9.24        35.05        11.61        14.04        26.50 
TCGA-BA-5153 TCGA-BA-6868 TCGA-BA-A4IF TCGA-BA-A6DA TCGA-BA-A6DL TCGA-BB-4227 
       57.93        15.52        29.42        11.54        20.48         4.41 
TCGA-BB-8596 TCGA-BB-A5HY TCGA-C9-A47Z TCGA-CN-4725 TCGA-CN-4729 TCGA-CN-4737 
       71.05        10.55         6.28        38.04        12.89        20.55 
TCGA-CN-4738 TCGA-CN-5356 TCGA-CN-5363 TCGA-CN-5370 TCGA-CN-5374 TCGA-CN-6012 
       14.33        46.32         8.32         8.52        56.94        48.00 
TCGA-CN-6018 TCGA-CN-6020 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-A6V7 
       19.07         6.74        38.89         3.68        17.42        19.53 
TCGA-CQ-5326 TCGA-CQ-5330 TCGA-CQ-6220 TCGA-CQ-6223 TCGA-CQ-6225 TCGA-CQ-7064 
        2.93        62.37        32.38        46.95        13.25        64.87 
TCGA-CQ-7069 TCGA-CQ-A4C9 TCGA-CR-6477 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7370 
       41.88        23.24        16.90        47.18        39.16         3.45 
TCGA-CR-7373 TCGA-CR-7377 TCGA-CR-7398 TCGA-CR-7399 TCGA-CV-5434 TCGA-CV-5435 
       29.23         9.17         5.13         5.95       108.95        76.24 
TCGA-CV-5439 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6441 TCGA-CV-6933 TCGA-CV-6937 
       17.95        43.23        54.74         9.60        90.12        20.52 
TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6945 TCGA-CV-6950 TCGA-CV-6956 TCGA-CV-7095 
       26.43        11.24        12.03        15.09         7.13        18.81 
TCGA-CV-7097 TCGA-CV-7180 TCGA-CV-7254 TCGA-CV-7416 TCGA-CV-7429 TCGA-CV-7430 
       12.66        10.75        47.97        25.08         3.52        16.27 
TCGA-CV-7440 TCGA-CV-A465 TCGA-CV-A6JN TCGA-CV-A6K1 TCGA-D6-6825 TCGA-D6-6826 
       22.19         7.07        29.79        22.52        16.14        11.44 
TCGA-D6-8569 TCGA-D6-A6EM TCGA-D6-A6EQ TCGA-DQ-5624 TCGA-DQ-7592 TCGA-F7-7848 
       25.32         7.63        12.10        58.45        37.58        37.18 
TCGA-F7-A50I TCGA-F7-A61W TCGA-HD-7753 TCGA-HL-7533 TCGA-IQ-A61G TCGA-IQ-A61I 
        3.02         0.46        28.47        34.75        11.84         0.07 
TCGA-IQ-A61L TCGA-IQ-A6SG TCGA-IQ-A6SH TCGA-MT-A51X TCGA-P3-A6SX TCGA-QK-A652 
       13.68        19.04        15.48         7.96        47.01        21.21 
TCGA-QK-A6IJ TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-T3-A92M TCGA-T3-A92N 
       12.72        14.76        12.20        17.82        13.71         3.12 
TCGA-UF-A719 TCGA-UF-A7JC TCGA-UF-A7JK TCGA-UP-A6WW 
       54.67        17.95        13.94        17.03 

$`19P LOSS WILD-TYPE`
TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4IG TCGA-BA-A4II 
       37.28        20.48        68.48         3.55        28.11        30.18 
TCGA-BB-A5HU TCGA-CN-4727 TCGA-CN-6021 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6997 
       25.71        51.29         9.07        52.08        11.08        32.48 
TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-6221 TCGA-CQ-7063 TCGA-CQ-7067 
       19.82        24.39        48.20        32.88        70.13        16.73 
TCGA-CQ-7068 TCGA-CR-6472 TCGA-CR-6478 TCGA-CX-7082 TCGA-CX-7219 TCGA-DQ-5629 
       43.04        34.52         6.02         0.36        34.36        30.94 
TCGA-DQ-7589 TCGA-DQ-7593 TCGA-H7-A6C5 TCGA-HD-8634 TCGA-HD-8635 TCGA-UF-A71D 
       46.32        40.24        21.11        12.66        22.85        48.03 
TCGA-UF-A7JV TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-5151 
        2.96         3.35        15.19        13.64         9.07        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-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IH TCGA-BA-A6D8 TCGA-BA-A6DB 
       12.62         4.01        41.85        20.45        27.95         7.10 
TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DI TCGA-BA-A6DJ 
        5.69        14.47         7.82         2.27        11.05        13.38 
TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4228 
       16.41         6.15       105.90         9.14         4.80        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-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO 
       24.66        38.40        20.52        27.19        12.92         8.81 
TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4730 
       12.69        48.76        55.86         4.67        56.68        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-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-5373 
       16.21        11.54        11.84        11.57        12.49        52.08 
TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6019 
       50.07        30.67        23.90        47.44        28.04        34.13 
TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 
       10.45        32.22        11.74        35.01        25.41        23.57 
TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V 
       17.29        29.72        21.21         7.40        31.69        22.32 
TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY 
       12.39        16.57         4.41        12.07         2.70        23.44 
TCGA-CN-A6V6 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5331 
       20.88        52.37        21.50        54.58        70.45        45.99 
TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6224 TCGA-CQ-6227 
       10.42        11.21         4.24        41.19        56.58         4.24 
TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7065 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 
       14.99        38.76        53.52        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-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 
       84.23        11.77        54.67        37.87        26.27        58.42 
TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6480 TCGA-CR-6481 
       50.01        39.52        36.99        18.54        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-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7371 TCGA-CR-7372 
        9.27        47.34        40.93        35.84         3.09        24.95 
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-7389 TCGA-CR-7390 TCGA-CR-7391 
       32.78        47.01        27.06        12.89        49.58        30.02 
TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7401 
       46.85        32.65        44.25        30.58        24.79        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-5440 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 
      107.51        94.88        76.50        91.53        80.12        17.92 
TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 
       13.35        23.05        86.83        48.59        60.49         7.07 
TCGA-CV-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-6942 TCGA-CV-6943 TCGA-CV-6948 TCGA-CV-6951 TCGA-CV-6952 
       21.90       140.78        19.79        42.38        30.08         6.08 
TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-6955 TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-6961 
       53.95        65.82        10.98         8.42        28.34         2.50 
TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7099 TCGA-CV-7100 
        4.14        64.83       172.67       111.16         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-7242 TCGA-CV-7243 
      130.88        77.16         4.73        89.65        36.00        31.36 
TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 
       26.20        18.97        17.13        95.34         4.96        11.87 
TCGA-CV-7255 TCGA-CV-7261 TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7407 TCGA-CV-7409 
        2.10        49.71        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-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7437 
       54.94        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-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-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY 
       35.34         6.38         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-A4AQ 
       23.47        19.92        10.42        10.55        18.84        51.12 
TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6827 
       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-5630 TCGA-DQ-5631 
       13.94        12.79        23.34        37.25        33.86        18.02 
TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-8298 
       46.45        20.45        40.04        39.12        41.59        32.71 
TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A620 
       21.63        20.25        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-A76A TCGA-HD-7229 TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-7917 
       20.94        33.76        25.74        21.93        27.48        27.48 
TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ 
       14.66        22.03         0.36        13.84         4.27         3.65 
TCGA-HD-A6I0 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61H 
        6.90        15.95        38.53        14.50        37.71        37.41 
TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61O TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W 
       33.57         5.29        13.84        19.27        10.75        14.37 
TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A5BI 
       30.05         1.84        12.62         6.25        15.42         7.13 
TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QE 
       16.08        17.98        29.92        15.78        71.74        51.25 
TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T4 
       10.85        36.82        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-A6IF 
       29.00        12.99        16.01        13.15        21.07        23.15 
TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC 
        7.30        21.47         9.34        27.39        21.07        19.73 
TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-AA3J TCGA-QK-AA3K TCGA-RS-A6TO TCGA-RS-A6TP 
       12.89         5.62        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-A7HJ 
        6.87        15.91         7.10        32.45        13.55        13.25 
TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71E TCGA-UF-A7J9 
       20.35        64.80         2.83        49.51        49.45        44.65 
TCGA-UF-A7JA TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JO 
       74.47        24.30        55.43        29.46        18.05        20.75 
TCGA-UF-A7JS TCGA-UF-A7JT TCGA-WA-A7GZ TCGA-WA-A7H4 TCGA-KU-A66S TCGA-KU-A66T 
       22.36        32.65        20.55        14.56        13.35        18.15 

  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 
            17.225             22.175 
[1] "0.1 - 109.0 (17.2)" "0.1 - 211.0 (22.2)"
[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       206        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                206
  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       6  31  24  29
  19P LOSS WILD-TYPE    44 106  76 144
D75V4, multiclass
       clus
vv      19P LOSS MUTATED 19P LOSS WILD-TYPE
  T0+T1                6                 44
  T2                  31                106
  T3                  24                 76
  T4                  29                144
[1] 4 2
[1] TRUE
[1] "dimension of 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    28  20  33   1
  19P LOSS WILD-TYPE 151  48 135   7
D75V5, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  N0               28                151
  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    38   0
  19P LOSS WILD-TYPE 152   1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED     38    0
  19P LOSS WILD-TYPE  152    1
   clus
vv  19P LOSS MUTATED 19P LOSS WILD-TYPE
  0               38                152
  1                0                  1
[1] 2 2
[1] FALSE
D75V7, binary
                    cls
clus                   0   1
  19P LOSS MUTATED    22  78
  19P LOSS WILD-TYPE 118 304
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED     22   78
  19P LOSS WILD-TYPE  118  304
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  FEMALE               22                118
  MALE                 78                304
[1] 2 2
[1] FALSE
D75V8, binary
                    cls
clus                   0   1
  19P LOSS MUTATED    34  52
  19P LOSS WILD-TYPE 128 249
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED     34   52
  19P LOSS WILD-TYPE  128  249
     clus
vv    19P LOSS MUTATED 19P LOSS WILD-TYPE
  NO                34                128
  YES               52                249
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD & NECK SQUAMOUS CELL CARCINOMA
  19P LOSS MUTATED                                   100
  19P LOSS WILD-TYPE                                 411
                    vv
clus                 HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  19P LOSS MUTATED                                                   0
  19P LOSS WILD-TYPE                                                10
                    vv
clus                 HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  19P LOSS MUTATED                                                           0
  19P LOSS WILD-TYPE                                                         1
D75V9, multiclass
                                                           clus
vv                                                          19P LOSS MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                    100
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        0
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                0
                                                           clus
vv                                                          19P LOSS WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                      411
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                         10
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                  1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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    80
  19P LOSS WILD-TYPE                        35   366
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                                          80                366
[1] 4 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  87
  19P LOSS WILD-TYPE  18 372
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      8   87
  19P LOSS WILD-TYPE   18  372
                        clus
vv                       19P LOSS MUTATED 19P LOSS WILD-TYPE
  HISPANIC OR LATINO                    8                 18
  NOT HISPANIC OR LATINO               87                372
[1] 2 2
[1] FALSE

Clustering(76) Variable = 19Q LOSS MUTATION ANALYSIS
D76V1, survival
                    sevent
clus2                  0   1
  19Q LOSS MUTATED    46  42
  19Q LOSS WILD-TYPE 255 177
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                88                432 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                42                177 
$`19Q LOSS MUTATED`
TCGA-BA-4075 TCGA-BA-6871 TCGA-CN-6992 TCGA-CN-6997 TCGA-CQ-A4C7 TCGA-DQ-7588 
        9.30         3.55        35.05        32.48        11.61        14.04 
TCGA-UF-A71D TCGA-BA-5149 TCGA-BA-5555 TCGA-BA-6868 TCGA-BA-6870 TCGA-BA-6873 
       48.03        26.50        17.10        15.52        14.83         4.01 
TCGA-BA-A4IF TCGA-BA-A6DA TCGA-BA-A6DL TCGA-BB-4227 TCGA-BB-8596 TCGA-BB-8601 
       29.42        11.54        20.48         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-6020 TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-6996 
       56.94        19.07         6.74        32.22        38.89        17.42 
TCGA-CN-A49A TCGA-CN-A6V7 TCGA-CQ-5326 TCGA-CQ-6220 TCGA-CQ-7064 TCGA-CQ-7069 
       17.29        19.53         2.93        32.38        64.87        41.88 
TCGA-CQ-A4C9 TCGA-CQ-A4CI TCGA-CR-6477 TCGA-CR-7365 TCGA-CR-7370 TCGA-CR-7373 
       23.24        31.23        16.90        39.16         3.45        29.23 
TCGA-CR-7377 TCGA-CR-7398 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5439 
        9.17         5.13       129.21       108.95        76.24        17.95 
TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6441 TCGA-CV-6933 TCGA-CV-6940 TCGA-CV-6941 
       43.23        54.74         9.60        90.12        26.43        11.24 
TCGA-CV-6956 TCGA-CV-6960 TCGA-CV-7097 TCGA-CV-7180 TCGA-CV-7254 TCGA-CV-7416 
        7.13        28.34        12.66        10.75        47.97        25.08 
TCGA-CV-7429 TCGA-CV-7430 TCGA-CV-A465 TCGA-CV-A6JN TCGA-CV-A6K1 TCGA-D6-6517 
        3.52        16.27         7.07        29.79        22.52         9.60 
TCGA-D6-6826 TCGA-D6-8569 TCGA-D6-A6EM TCGA-D6-A6EP TCGA-F7-A61W TCGA-HD-7753 
       11.44        25.32         7.63        13.94         0.46        28.47 
TCGA-IQ-A61I TCGA-IQ-A61L TCGA-IQ-A6SG TCGA-IQ-A6SH TCGA-MT-A51X TCGA-P3-A6T2 
        0.07        13.68        19.04        15.48         7.96        75.55 
TCGA-QK-A652 TCGA-QK-A6IJ TCGA-QK-A8Z7 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-T3-A92M 
       21.21        12.72        12.89        12.20        17.82        13.71 
TCGA-T3-A92N TCGA-UF-A719 TCGA-UF-A7JC TCGA-UF-A7JK 
        3.12        54.67        17.95        13.94 

$`19Q LOSS WILD-TYPE`
TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-A4IG TCGA-BA-A4II TCGA-BB-A5HU 
       37.28        20.48        68.48        28.11        30.18        25.71 
TCGA-CN-4727 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-A6V1 
       51.29         9.07         9.24        52.08        11.08        19.82 
TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-6221 TCGA-CQ-7063 TCGA-CQ-7067 TCGA-CQ-7068 
       24.39        48.20        32.88        70.13        16.73        43.04 
TCGA-CR-6472 TCGA-CR-6478 TCGA-CX-7082 TCGA-CX-7219 TCGA-DQ-5629 TCGA-DQ-7589 
       34.52         6.02         0.36        34.36        30.94        46.32 
TCGA-DQ-7593 TCGA-H7-A6C5 TCGA-HD-8634 TCGA-HD-8635 TCGA-UF-A7JV TCGA-4P-AA8J 
       40.24        21.11        12.66        22.85         2.96         3.35 
TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 
       15.19        13.64         9.07        23.74        42.35        57.93 
TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-6869 TCGA-BA-6872 TCGA-BA-7269 TCGA-BA-A4IH 
       23.84        65.59        21.17        12.62        41.85        20.45 
TCGA-BA-A6D8 TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG 
       27.95         7.10         5.69        14.47         7.82         2.27 
TCGA-BA-A6DI TCGA-BA-A6DJ TCGA-BA-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-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 
        4.80        18.38        22.42        36.72        33.70        50.20 
TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-A5HZ TCGA-BB-A6UM 
       44.98        66.28        24.66        38.40        27.19        12.92 
TCGA-BB-A6UO TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4726 TCGA-CN-4728 
        8.81        12.69        48.76        55.86         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-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-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-6019 TCGA-CN-6988 
       48.00        23.90        47.44        28.04        34.13        10.45 
TCGA-CN-6995 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49B 
        3.68        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-A6V6 TCGA-CQ-5324 
        4.41        12.07         2.70        23.44        20.88        52.37 
TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 
       21.50        54.58        70.45        62.37        45.99        10.42 
TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6225 
       11.21         4.24        41.19        46.95        56.58        13.25 
TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7065 TCGA-CQ-7071 TCGA-CQ-7072 
        4.24        14.99        38.76        53.52        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-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 
       84.23        11.77        54.67        37.87        26.27        58.42 
TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6480 TCGA-CR-6481 
       50.01        39.52        36.99        18.54        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-7371 
        9.27        47.18        47.34        40.93        35.84         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        49.58 
TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 
       30.02        46.85        32.65        44.25        30.58        24.79 
TCGA-CR-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        94.88        76.50        91.53        80.12 
TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 
       17.92        13.35        23.05        86.83        48.59        60.49 
TCGA-CV-5978 TCGA-CV-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       172.67 
TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 
      111.16        18.81         7.99         9.01         5.26         1.84 
TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-7178 TCGA-CV-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        89.65        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-7261 
       17.13        95.34         4.96        11.87         2.10        49.71 
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-7424 TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7432 
      100.57        14.89        56.48       156.49        54.94        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-A468 TCGA-CV-A6JD TCGA-CV-A6JE 
       67.86         0.76        56.61        15.25         5.98        35.34 
TCGA-CV-A6JM TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ 
        6.38         6.48        28.01         3.62        21.24        23.47 
TCGA-CV-A6K0 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-A4AQ TCGA-D6-6515 
       19.92        10.42        10.55        18.84        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-5630 TCGA-DQ-5631 
       12.79        23.34        58.45        37.25        33.86        18.02 
TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 
       46.45        20.45        37.58        40.04        39.12        41.59 
TCGA-F7-7848 TCGA-F7-8298 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-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-A76A TCGA-HD-7229 TCGA-HD-7754 
       13.38        15.16        15.06        20.94        33.76        25.74 
TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-A4C1 
       21.93        27.48        27.48        14.66        22.03         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-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A67A 
        5.29        13.84        19.27        10.75        14.37        30.05 
TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-MZ-A6I9 
        1.84        12.62         6.25        15.42         7.13        16.08 
TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF 
       17.98        29.92        15.78        71.74        51.25        10.85 
TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T5 
       36.82        47.01        19.00        18.97         2.04        29.00 
TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A6IF TCGA-QK-A6IG 
       12.99        16.01        13.15        21.07        23.15         7.30 
TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z8 
       21.47         9.34        27.39        21.07        19.73         5.62 
TCGA-QK-A8Z9 TCGA-QK-AA3J TCGA-QK-AA3K TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX 
       14.76        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-A71A TCGA-UF-A71B TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA 
       64.80         2.83        49.51        49.45        44.65        74.47 
TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JO TCGA-UF-A7JS 
       24.30        55.43        29.46        18.05        20.75        22.36 
TCGA-UF-A7JT TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 TCGA-KU-A66S TCGA-KU-A66T 
       32.65        17.03        20.55        14.56        13.35        18.15 

  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 
            17.620             21.915 
[1] "0.1 - 129.2 (17.6)" "0.1 - 211.0 (21.9)"
[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        26        40         2         0
  19Q LOSS WILD-TYPE      26       67        56       212        10         1
D76V3, multiclass
           clus
vv          19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  STAGE I                  1                 26
  STAGE II                 9                 67
  STAGE III               26                 56
  STAGE IVA               40                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       5  25  26  24
  19Q LOSS WILD-TYPE    45 112  74 149
D76V4, multiclass
       clus
vv      19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  T0+T1                5                 45
  T2                  25                112
  T3                  26                 74
  T4                  24                149
[1] 4 2
[1] TRUE
[1] "dimension of 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  16  32   1
  19Q LOSS WILD-TYPE 153  52 136   7
D76V5, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  N0               26                153
  N1               16                 52
  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    33   0
  19Q LOSS WILD-TYPE 157   1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED     33    0
  19Q LOSS WILD-TYPE  157    1
   clus
vv  19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  0               33                157
  1                0                  1
[1] 2 2
[1] FALSE
D76V7, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED    20  68
  19Q LOSS WILD-TYPE 120 314
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED     20   68
  19Q LOSS WILD-TYPE  120  314
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  FEMALE               20                120
  MALE                 68                314
[1] 2 2
[1] FALSE
D76V8, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED    33  47
  19Q LOSS WILD-TYPE 129 254
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED     33   47
  19Q LOSS WILD-TYPE  129  254
     clus
vv    19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  NO                33                129
  YES               47                254
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD & NECK SQUAMOUS CELL CARCINOMA
  19Q LOSS MUTATED                                    86
  19Q LOSS WILD-TYPE                                 425
                    vv
clus                 HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  19Q LOSS MUTATED                                                   2
  19Q LOSS WILD-TYPE                                                 8
                    vv
clus                 HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  19Q LOSS MUTATED                                                           0
  19Q LOSS WILD-TYPE                                                         1
D76V9, multiclass
                                                           clus
vv                                                          19Q LOSS MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                     86
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        2
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                0
                                                           clus
vv                                                          19Q LOSS WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                      425
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                          8
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                  1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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                          17    66
  19Q LOSS WILD-TYPE                        31   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                      17                 31
  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  75
  19Q LOSS WILD-TYPE  20 384
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      6   75
  19Q LOSS WILD-TYPE   20  384
                        clus
vv                       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    6                 20
  NOT HISPANIC OR LATINO               75                384
[1] 2 2
[1] FALSE

Clustering(77) Variable = 20P LOSS MUTATION ANALYSIS
D77V1, survival
                    sevent
clus2                  0   1
  20P LOSS MUTATED    24  22
  20P LOSS WILD-TYPE 277 197
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                46                474 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                22                197 
$`20P LOSS MUTATED`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-6871 TCGA-CN-6992 TCGA-CR-6478 TCGA-DQ-7589 
        9.30        37.28         3.55        35.05         6.02        46.32 
TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-5152 TCGA-BA-5555 TCGA-BA-6870 TCGA-BA-6873 
       15.19        13.64        42.35        17.10        14.83         4.01 
TCGA-BB-4227 TCGA-BB-7866 TCGA-BB-8601 TCGA-BB-A6UO TCGA-CN-6011 TCGA-CN-6994 
        4.41        44.98        20.52         8.81        30.67        38.89 
TCGA-CN-6995 TCGA-CN-A63W TCGA-CQ-A4CD TCGA-CQ-A4CG TCGA-CR-6474 TCGA-CR-7364 
        3.68        12.39        33.60        14.14        18.54        47.18 
TCGA-CR-7374 TCGA-CR-7379 TCGA-CR-7383 TCGA-CV-5440 TCGA-CV-7091 TCGA-CV-7101 
        0.99        34.06        17.13       107.51       111.16         5.26 
TCGA-CV-7104 TCGA-CV-7235 TCGA-CV-7247 TCGA-CV-7254 TCGA-CV-7407 TCGA-CV-7418 
       12.92        77.16        18.97        47.97        35.54        25.94 
TCGA-CV-7435 TCGA-CV-A460 TCGA-D6-6823 TCGA-DQ-7590 TCGA-F7-7848 TCGA-F7-8298 
      153.86        60.43        23.05        46.45        37.18        32.71 
TCGA-F7-A623 TCGA-HD-7917 TCGA-QK-A6V9 TCGA-UF-A719 
       20.25        27.48        27.39        54.67 

$`20P LOSS WILD-TYPE`
TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-A4IG TCGA-BA-A4II TCGA-BB-A5HU TCGA-CN-4727 
       20.48        68.48        28.11        30.18        25.71        51.29 
TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6997 TCGA-CN-A6V1 
        9.07         9.24        52.08        11.08        32.48        19.82 
TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-6221 TCGA-CQ-7063 TCGA-CQ-7067 TCGA-CQ-7068 
       24.39        48.20        32.88        70.13        16.73        43.04 
TCGA-CQ-A4C7 TCGA-CR-6472 TCGA-CX-7082 TCGA-CX-7219 TCGA-DQ-5629 TCGA-DQ-7588 
       11.61        34.52         0.36        34.36        30.94        14.04 
TCGA-DQ-7593 TCGA-H7-A6C5 TCGA-HD-8634 TCGA-HD-8635 TCGA-UF-A71D TCGA-UF-A7JV 
       40.24        21.11        12.66        22.85        48.03         2.96 
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-5558 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6872 TCGA-BA-7269 TCGA-BA-A4IF 
       65.59        15.52        21.17        12.62        41.85        29.42 
TCGA-BA-A4IH TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE 
       20.45        27.95        11.54         7.10         5.69        14.47 
TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DI TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BA-A8YP 
        7.82         2.27        11.05        13.38        20.48        16.41 
TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4228 TCGA-BB-7861 
        6.15       105.90         9.14         4.80        18.38        22.42 
TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 
       36.72        33.70        50.20        66.28        24.66        38.40 
TCGA-BB-8596 TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-C9-A47Z TCGA-C9-A480 
       71.05        10.55        27.19        12.92         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-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-6988 TCGA-CN-6989 TCGA-CN-6996 
       19.07        34.13         6.74        10.45        32.22        17.42 
TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B 
       11.74        35.01        25.41        23.57        17.29        29.72 
TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A640 
       21.21         7.40        31.69        22.32        16.57         4.41 
TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5324 
       12.07         2.70        23.44        20.88        19.53        52.37 
TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 
       21.50         2.93        54.58        70.45        62.37        45.99 
TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6220 TCGA-CQ-6223 
       10.42        11.21         4.24        41.19        32.38        46.95 
TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7064 
       56.58        13.25         4.24        14.99        38.76        64.87 
TCGA-CQ-7065 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C9 
       53.52        41.88        43.10        77.56        44.48        23.24 
TCGA-CQ-A4CB TCGA-CQ-A4CE TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 
       29.36        29.49        12.46        31.23        84.23        11.77 
TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 
       54.67        37.87        26.27        58.42        50.01        39.52 
TCGA-CR-6473 TCGA-CR-6477 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 
       36.99        16.90        11.90        10.22        11.34        11.64 
TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7365 
        7.69        12.46        22.78        15.75         9.27        39.16 
TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 
       47.34        40.93        35.84         3.45         3.09        24.95 
TCGA-CR-7373 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7385 
       29.23        31.96         9.17        19.92        26.17        32.78 
TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 
       47.01        27.06        12.89        49.58        30.02        46.85 
TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 
       32.65        44.25        30.58        24.79         5.13         5.95 
TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 
       35.41        29.95        48.39       139.43        17.16       129.21 
TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5441 TCGA-CV-5442 
      108.95        76.24        19.20        17.95        94.88        76.50 
TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 
       91.53        80.12        17.92        13.35        23.05        86.83 
TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 
       48.59        60.49         7.07        43.23        54.74        21.07 
TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 
       62.43         9.60        90.12         2.14         9.70         5.46 
TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6942 
       20.52         4.73        21.90        26.43        11.24       140.78 
TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6952 
       19.79        12.03        42.38        15.09        30.08         6.08 
TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-6955 TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6960 
       53.95        65.82        10.98         7.13         8.42        28.34 
TCGA-CV-6961 TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7095 TCGA-CV-7097 
        2.50         4.14        64.83       172.67        18.81        12.66 
TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7177 TCGA-CV-7178 
        7.99         9.01         1.84        52.31        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        89.65        36.00        31.36 
TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7255 
       26.20        17.13        95.34         4.96        11.87         2.10 
TCGA-CV-7261 TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7409 TCGA-CV-7410 TCGA-CV-7411 
       49.71        18.41        57.47        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-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-7437 TCGA-CV-7438 
       16.27        84.49        19.76         7.17        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-A461 TCGA-CV-A463 TCGA-CV-A464 TCGA-CV-A465 TCGA-CV-A468 TCGA-CV-A6JD 
       67.86         0.76        56.61         7.07        15.25         5.98 
TCGA-CV-A6JE TCGA-CV-A6JM TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU 
       35.34         6.38        29.79         6.48        28.01         3.62 
TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 
       21.24        23.47        19.92        22.52        10.42        10.55 
TCGA-CX-7086 TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6824 
       18.84        51.12        13.25        25.41         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-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 
       12.10        12.79        23.34        58.45        37.25        33.86 
TCGA-DQ-5631 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 
       18.02        20.45        37.58        40.04        39.12        41.59 
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-A76A TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7831 
       15.06        20.94        33.76        28.47        25.74        21.93 
TCGA-HD-7832 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 
       27.48        14.66        22.03         0.36        13.84         4.27 
TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 
        3.65         6.90        34.75        15.95        38.53        14.50 
TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K 
       37.71        11.84        37.41         0.07        33.57         5.29 
TCGA-IQ-A61L TCGA-IQ-A61O TCGA-IQ-A6SG TCGA-IQ-A6SH TCGA-KU-A6H7 TCGA-KU-A6H8 
       13.68        13.84        19.04        15.48        19.27        10.75 
TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G 
       14.37         7.96        30.05         1.84        12.62         6.25 
TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5Q6 
       15.42         7.13        16.08        17.98        29.92        15.78 
TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 
       71.74        51.25        10.85        36.82        47.01        19.00 
TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T6 TCGA-P3-A6T7 
       75.55        18.97         2.04        29.00        12.99        16.01 
TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH 
       13.15        21.07        21.21        23.15         7.30        21.47 
TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z8 
        9.34        12.72        21.07        19.73        12.89         5.62 
TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-RS-A6TO 
       14.76        12.20        17.82        15.32         8.32        12.72 
TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-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-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD 
       49.51        49.45        44.65        74.47        17.95        24.30 
TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS 
       55.43        29.46        18.05        13.94        20.75        22.36 
TCGA-UF-A7JT TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 TCGA-KU-A66S TCGA-KU-A66T 
       32.65        17.03        20.55        14.56        13.35        18.15 

  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 
            26.665             21.070 
[1] "1.0 - 153.9 (26.7)" "0.1 - 211.0 (21.1)"
[1] "hr=" "1.1"
D77V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  20P LOSS MUTATED         3        9         5        21         0         0
  20P LOSS WILD-TYPE      24       67        77       231        12         1
D77V3, multiclass
           clus
vv          20P LOSS MUTATED 20P LOSS WILD-TYPE
  STAGE I                  3                 24
  STAGE II                 9                 67
  STAGE III                5                 77
  STAGE IVA               21                231
  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  11   8  14
  20P LOSS WILD-TYPE    45 126  92 159
D77V4, multiclass
       clus
vv      20P LOSS MUTATED 20P LOSS WILD-TYPE
  T0+T1                5                 45
  T2                  11                126
  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    17   2  15   0
  20P LOSS WILD-TYPE 162  66 153   8
D77V5, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  N0               17                162
  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    16   0
  20P LOSS WILD-TYPE 174   1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED     16    0
  20P LOSS WILD-TYPE  174    1
   clus
vv  20P LOSS MUTATED 20P LOSS WILD-TYPE
  0               16                174
  1                0                  1
[1] 2 2
[1] FALSE
D77V7, binary
                    cls
clus                   0   1
  20P LOSS MUTATED    12  34
  20P LOSS WILD-TYPE 128 348
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED     12   34
  20P LOSS WILD-TYPE  128  348
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  FEMALE               12                128
  MALE                 34                348
[1] 2 2
[1] FALSE
D77V8, binary
                    cls
clus                   0   1
  20P LOSS MUTATED    18  23
  20P LOSS WILD-TYPE 144 278
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED     18   23
  20P LOSS WILD-TYPE  144  278
     clus
vv    20P LOSS MUTATED 20P LOSS WILD-TYPE
  NO                18                144
  YES               23                278
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD & NECK SQUAMOUS CELL CARCINOMA
  20P LOSS MUTATED                                    46
  20P LOSS WILD-TYPE                                 465
                    vv
clus                 HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  20P LOSS MUTATED                                                   0
  20P LOSS WILD-TYPE                                                10
                    vv
clus                 HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  20P LOSS MUTATED                                                           0
  20P LOSS WILD-TYPE                                                         1
D77V9, multiclass
                                                           clus
vv                                                          20P LOSS MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                     46
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        0
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                0
                                                           clus
vv                                                          20P LOSS WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                      465
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                         10
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                  1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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    40
  20P LOSS WILD-TYPE                        43   406
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                                          40                406
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V14, binary
                    cls
clus                   0   1
  20P LOSS MUTATED     1  43
  20P LOSS WILD-TYPE  25 416
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      1   43
  20P LOSS WILD-TYPE   25  416
                        clus
vv                       20P LOSS MUTATED 20P LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                 25
  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    16  11
  20Q LOSS WILD-TYPE 285 208
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                27                493 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                11                208 
$`20Q LOSS MUTATED`
TCGA-BA-6871 TCGA-BA-5152 TCGA-BA-6870 TCGA-BB-7866 TCGA-BB-8601 TCGA-CN-4729 
        3.55        42.35        14.83        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-KU-A6H7 TCGA-UF-A719 
       27.48        19.27        54.67 

$`20Q LOSS WILD-TYPE`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-A4IG TCGA-BA-A4II 
        9.30        37.28        20.48        68.48        28.11        30.18 
TCGA-BB-A5HU TCGA-CN-4727 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 
       25.71        51.29         9.07         9.24        52.08        11.08 
TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-6221 
       35.05        32.48        19.82        24.39        48.20        32.88 
TCGA-CQ-7063 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-A4C7 TCGA-CR-6472 TCGA-CR-6478 
       70.13        16.73        43.04        11.61        34.52         6.02 
TCGA-CX-7082 TCGA-CX-7219 TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7593 
        0.36        34.36        30.94        14.04        46.32        40.24 
TCGA-H7-A6C5 TCGA-HD-8634 TCGA-HD-8635 TCGA-UF-A71D TCGA-UF-A7JV TCGA-4P-AA8J 
       21.11        12.66        22.85        48.03         2.96         3.35 
TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5153 
       15.19        13.64         9.07        26.50        23.74        57.93 
TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6872 
       17.10        23.84        65.59        15.52        21.17        12.62 
TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IH TCGA-BA-A6D8 TCGA-BA-A6DA 
        4.01        41.85        29.42        20.45        27.95        11.54 
TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DI 
        7.10         5.69        14.47         7.82         2.27        11.05 
TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 
       13.38        20.48        16.41         6.15       105.90         9.14 
TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 
        4.80         4.41        18.38        22.42        36.72        33.70 
TCGA-BB-7864 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-A5HY 
       50.20        66.28        24.66        38.40        71.05        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-4730 TCGA-CN-4731 
       55.86        38.04         4.67        56.68        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-5363 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 
       12.39         8.32        16.21        11.54        11.84        11.57 
TCGA-CN-5369 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 
       12.49         8.52        52.08        56.94        50.07        30.67 
TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 
       48.00        23.90        47.44        28.04        19.07        34.13 
TCGA-CN-6020 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 
        6.74        10.45        32.22        38.89         3.68        17.42 
TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B 
       11.74        35.01        25.41        23.57        17.29        29.72 
TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y 
       21.21         7.40        31.69        22.32        12.39        16.57 
TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V6 TCGA-CN-A6V7 
        4.41        12.07         2.70        23.44        20.88        19.53 
TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 
       52.37        21.50         2.93        54.58        70.45        62.37 
TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6220 
       45.99        10.42        11.21         4.24        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-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 
       64.87        53.52        41.88        43.10        77.56        44.48 
TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH 
       23.24        29.36        33.60        29.49        14.14        12.46 
TCGA-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-6474 TCGA-CR-6477 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 
       39.52        18.54        16.90        11.90        10.22        11.34 
TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 
       11.64         7.69        12.46        22.78        15.75         9.27 
TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7371 
       47.18        39.16        47.34        40.93        35.84         3.09 
TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 
       24.95        29.23         0.99        31.96         9.17        34.06 
TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 
       19.92        26.17        17.13        32.78        47.01        27.06 
TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 
       12.89        49.58        30.02        46.85        32.65        44.25 
TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7404 
       30.58        24.79         5.13         5.95        35.41        48.39 
TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 
      139.43        17.16       129.21       108.95        76.24        19.20 
TCGA-CV-5439 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 
       17.95        94.88        76.50        91.53        80.12        17.92 
TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 
       13.35        23.05        86.83        48.59        60.49         7.07 
TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6933 
       43.23        54.74        21.07        62.43         9.60        90.12 
TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6939 
        2.14         9.70         5.46        20.52         4.73        21.90 
TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6948 
       26.43        11.24       140.78        19.79        12.03        42.38 
TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-6955 
       15.09        30.08         6.08        53.95        65.82        10.98 
TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-6962 TCGA-CV-7089 
        7.13         8.42        28.34         2.50         4.14        64.83 
TCGA-CV-7090 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7102 
      172.67        18.81        12.66         7.99         9.01         1.84 
TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-7178 TCGA-CV-7180 TCGA-CV-7183 
       52.31        12.92        21.80        71.21        10.75       130.88 
TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7248 
        4.73        89.65        36.00        31.36        26.20        17.13 
TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7255 TCGA-CV-7261 TCGA-CV-7263 
       95.34         4.96        11.87         2.10        49.71        18.41 
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-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-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-7437 TCGA-CV-7438 TCGA-CV-7440 TCGA-CV-A45O 
       19.76         7.17        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-A6JY TCGA-CV-A6JZ 
       29.79         6.48        28.01         3.62        21.24        23.47 
TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-A4AQ 
       19.92        22.52        10.42        10.55        18.84        51.12 
TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 
       13.25        25.41         9.60        23.05         2.53        16.14 
TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK 
       18.67        24.95        25.32        17.72        12.36        28.77 
TCGA-D6-A6EM TCGA-D6-A6EN TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES 
        7.63        22.59        24.95        13.94        12.10        12.79 
TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7591 
       23.34        58.45        37.25        33.86        18.02        20.45 
TCGA-DQ-7592 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 
       37.58        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-A76A TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 
       15.16        15.06        20.94        33.76        28.47        25.74 
TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-A4C1 TCGA-HD-A633 
       21.93        27.48        14.66        22.03         0.36        13.84 
TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-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-A6H8 
        5.29        13.68        13.84        19.04        15.48        10.75 
TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G 
       14.37         7.96        30.05         1.84        12.62         6.25 
TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5Q6 
       15.42         7.13        16.08        17.98        29.92        15.78 
TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 
       71.74        51.25        10.85        36.82        47.01        19.00 
TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T6 TCGA-P3-A6T7 
       75.55        18.97         2.04        29.00        12.99        16.01 
TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH 
       13.15        21.07        21.21        23.15         7.30        21.47 
TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z7 
        9.34        12.72        27.39        21.07        19.73        12.89 
TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K 
        5.62        14.76        12.20        17.82        15.32         8.32 
TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-T2-A6X2 
       12.72        16.96         6.87        15.91         7.10        32.45 
TCGA-T3-A92M TCGA-T3-A92N TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 
       13.71         3.12        13.55        13.25        20.35        64.80 
TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC 
        2.83        49.51        49.45        44.65        74.47        17.95 
TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO 
       24.30        55.43        29.46        18.05        13.94        20.75 
TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 TCGA-KU-A66S 
       22.36        32.65        17.03        20.55        14.56        13.35 
TCGA-KU-A66T 
       18.15 

  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 
             35.54              20.94 
[1] "3.5 - 153.9 (35.5)" "0.1 - 211.0 (20.9)"
[1] "hr=" "1.4"
D78V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  20Q LOSS MUTATED         1        7         4         7         0         0
  20Q LOSS WILD-TYPE      26       69        78       245        12         1
D78V3, multiclass
           clus
vv          20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  STAGE I                  1                 26
  STAGE II                 7                 69
  STAGE III                4                 78
  STAGE IVA                7                245
  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   9   3   5
  20Q LOSS WILD-TYPE    48 128  97 168
D78V4, multiclass
       clus
vv      20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  T0+T1                2                 48
  T2                   9                128
  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     7   3   6   0
  20Q LOSS WILD-TYPE 172  65 162   8
D78V5, multiclass
    clus
vv   20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  N0                7                172
  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     6   0
  20Q LOSS WILD-TYPE 184   1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      6    0
  20Q LOSS WILD-TYPE  184    1
   clus
vv  20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  0                6                184
  1                0                  1
[1] 2 2
[1] FALSE
D78V7, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     6  21
  20Q LOSS WILD-TYPE 134 361
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      6   21
  20Q LOSS WILD-TYPE  134  361
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  FEMALE                6                134
  MALE                 21                361
[1] 2 2
[1] FALSE
D78V8, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     6  16
  20Q LOSS WILD-TYPE 156 285
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      6   16
  20Q LOSS WILD-TYPE  156  285
     clus
vv    20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  NO                 6                156
  YES               16                285
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD & NECK SQUAMOUS CELL CARCINOMA
  20Q LOSS MUTATED                                    26
  20Q LOSS WILD-TYPE                                 485
                    vv
clus                 HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  20Q LOSS MUTATED                                                   1
  20Q LOSS WILD-TYPE                                                 9
                    vv
clus                 HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  20Q LOSS MUTATED                                                           0
  20Q LOSS WILD-TYPE                                                         1
D78V9, multiclass
                                                           clus
vv                                                          20Q LOSS MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                     26
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        1
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                0
                                                           clus
vv                                                          20Q LOSS WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                      485
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                          9
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                  1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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    23
  20Q LOSS WILD-TYPE                        45   423
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                                          23                423
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V14, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     0  25
  20Q LOSS WILD-TYPE  26 434
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      0   25
  20Q LOSS WILD-TYPE   26  434
                        clus
vv                       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                 26
  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   101  83
  21Q LOSS WILD-TYPE 200 136
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
               184                336 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                83                136 
$`21Q LOSS MUTATED`
TCGA-BA-4075 TCGA-BA-5559 TCGA-BA-6871 TCGA-BB-A5HU TCGA-CN-6021 TCGA-CN-6022 
        9.30        68.48         3.55        25.71         9.07         9.24 
TCGA-CN-6997 TCGA-CQ-5323 TCGA-CQ-7067 TCGA-CQ-A4C7 TCGA-CX-7082 TCGA-CX-7219 
       32.48        48.20        16.73        11.61         0.36        34.36 
TCGA-DQ-5629 TCGA-DQ-7588 TCGA-HD-8634 TCGA-4P-AA8J TCGA-BA-5558 TCGA-BA-6868 
       30.94        14.04        12.66         3.35        65.59        15.52 
TCGA-BA-6870 TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BB-7862 TCGA-BB-7864 TCGA-BB-8596 
       14.83        27.95        11.54        36.72        50.20        71.05 
TCGA-BB-8601 TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-C9-A47Z TCGA-CN-4725 TCGA-CN-4728 
       20.52        10.55        27.19         6.28        38.04        56.68 
TCGA-CN-4736 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5363 
       12.99        14.33        45.83        73.61        13.05         8.32 
TCGA-CN-5365 TCGA-CN-5370 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6012 TCGA-CN-6018 
       11.54         8.52        56.94        50.07        48.00        19.07 
TCGA-CN-6019 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A499 TCGA-CN-A49B 
       34.13        38.89        17.42        11.74        23.57        29.72 
TCGA-CN-A63T TCGA-CN-A63W TCGA-CQ-5326 TCGA-CQ-5330 TCGA-CQ-5332 TCGA-CQ-6220 
        7.40        12.39         2.93        62.37        10.42        32.38 
TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7065 
       46.95        56.58        13.25        38.76        64.87        53.52 
TCGA-CQ-7069 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CE TCGA-CQ-A4CH 
       41.88        77.56        44.48        23.24        29.49        12.46 
TCGA-CQ-A4CI TCGA-CR-5247 TCGA-CR-6477 TCGA-CR-6484 TCGA-CR-6491 TCGA-CR-7365 
       31.23        11.77        16.90        11.64        22.78        39.16 
TCGA-CR-7367 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7373 TCGA-CR-7388 
       47.34        35.84         3.45         3.09        29.23        27.06 
TCGA-CR-7399 TCGA-CV-5431 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5444 TCGA-CV-5966 
        5.95        17.16        17.95       107.51        80.12        17.92 
TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6934 
       48.59        60.49         7.07        43.23        54.74         2.14 
TCGA-CV-6937 TCGA-CV-6941 TCGA-CV-6954 TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6961 
       20.52        11.24        65.82         7.13         8.42         2.50 
TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7097 TCGA-CV-7101 
        4.14        64.83       172.67       111.16        12.66         5.26 
TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-7180 TCGA-CV-7235 TCGA-CV-7242 
       52.31        12.92        21.80        10.75        77.16        36.00 
TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7248 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7263 
       26.20        18.97        17.13        47.97        49.71        18.41 
TCGA-CV-7409 TCGA-CV-7416 TCGA-CV-7422 TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7432 
       17.85        25.08        34.09       100.57        14.89        84.49 
TCGA-CV-7435 TCGA-CV-7440 TCGA-CV-A45W TCGA-CV-A465 TCGA-CV-A6JM TCGA-CV-A6JN 
      153.86        22.19        45.96         7.07         6.38        29.79 
TCGA-CV-A6JU TCGA-CX-7086 TCGA-D6-6516 TCGA-D6-6823 TCGA-D6-6826 TCGA-D6-A4Z9 
        3.62        18.84        25.41        23.05        11.44        17.72 
TCGA-D6-A4ZB TCGA-D6-A6EM TCGA-D6-A6EQ TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-7592 
       12.36         7.63        12.10        23.34        58.45        37.58 
TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61W TCGA-F7-A620 TCGA-H7-8501 
       20.25         3.02        31.13         0.46        17.85        15.16 
TCGA-H7-8502 TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7831 TCGA-HD-A633 TCGA-HD-A6HZ 
       15.06        33.76        28.47        21.93        13.84         3.65 
TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61J TCGA-IQ-A61L TCGA-IQ-A6SH 
       37.71        11.84        37.41        33.57        13.68        15.48 
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        12.89        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 TCGA-KU-A66T 
       29.46        13.94        14.56        18.15 

$`21Q LOSS WILD-TYPE`
TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-A4IG TCGA-BA-A4II TCGA-CN-4727 TCGA-CN-6023 
       37.28        20.48        28.11        30.18        51.29        52.08 
TCGA-CN-6024 TCGA-CN-6992 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-6221 TCGA-CQ-7063 
       11.08        35.05        19.82        24.39        32.88        70.13 
TCGA-CQ-7068 TCGA-CR-6472 TCGA-CR-6478 TCGA-DQ-7589 TCGA-DQ-7593 TCGA-H7-A6C5 
       43.04        34.52         6.02        46.32        40.24        21.11 
TCGA-HD-8635 TCGA-UF-A71D TCGA-UF-A7JV TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4078 
       22.85        48.03         2.96        15.19        13.64         9.07 
TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 
       26.50        23.74        42.35        57.93        17.10        23.84 
TCGA-BA-6869 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IH 
       21.17        12.62         4.01        41.85        29.42        20.45 
TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DI 
        7.10         5.69        14.47         7.82         2.27        11.05 
TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 
       13.38        20.48        16.41         6.15       105.90         9.14 
TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7863 TCGA-BB-7866 
        4.80         4.41        18.38        22.42        33.70        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-4726 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 
       48.76        55.86         4.67        12.89        26.86        32.81 
TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4737 TCGA-CN-4740 TCGA-CN-5355 TCGA-CN-5356 
       52.14        57.11        20.55        27.58        42.02        46.32 
TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5364 TCGA-CN-5366 TCGA-CN-5367 
        8.58        12.39        71.31        16.21        11.84        11.57 
TCGA-CN-5369 TCGA-CN-5373 TCGA-CN-6011 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 
       12.49        52.08        30.67        23.90        47.44        28.04 
TCGA-CN-6020 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6995 TCGA-CN-A497 TCGA-CN-A498 
        6.74        10.45        32.22         3.68        35.01        25.41 
TCGA-CN-A49A TCGA-CN-A49C TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A640 
       17.29        21.21        31.69        22.32        16.57         4.41 
TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5324 
       12.07         2.70        23.44        20.88        19.53        52.37 
TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5331 TCGA-CQ-5333 TCGA-CQ-5334 
       21.50        54.58        70.45        45.99        11.21         4.24 
TCGA-CQ-6218 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-7071 TCGA-CQ-A4CB TCGA-CQ-A4CD 
       41.19         4.24        14.99        43.10        29.36        33.60 
TCGA-CQ-A4CG TCGA-CR-5243 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 
       14.14        84.23        54.67        37.87        26.27        58.42 
TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6480 TCGA-CR-6481 
       50.01        39.52        36.99        18.54        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 
       49.58        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 
       24.79         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        94.88        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 
       89.65        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-A6JO 
        0.76        56.61        15.25         5.98        35.34         6.48 
TCGA-CV-A6JT TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 
       28.01        21.24        23.47        19.92        22.52        10.42 
TCGA-CX-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-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A6EK TCGA-D6-A6EN TCGA-D6-A6EO 
       18.67        24.95        25.32        28.77        22.59        24.95 
TCGA-D6-A6EP TCGA-D6-A6ES TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7590 
       13.94        12.79        37.25        33.86        18.02        46.45 
TCGA-DQ-7591 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 
       20.45        40.04        39.12        41.59        37.18        32.71 
TCGA-F7-8489 TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A622 TCGA-F7-A623 TCGA-F7-A624 
       21.63        18.94        24.95        11.80        20.25        12.43 
TCGA-H7-7774 TCGA-H7-A76A TCGA-HD-7754 TCGA-HD-7832 TCGA-HD-7917 TCGA-HD-8224 
       13.38        20.94        25.74        27.48        27.48        14.66 
TCGA-HD-8314 TCGA-HD-A4C1 TCGA-HD-A634 TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 
       22.03         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-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-P3-A5Q5 TCGA-P3-A5QE 
        6.25        15.42         7.13        16.08        29.92        51.25 
TCGA-P3-A6SW TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF 
       36.82        12.99        16.01        21.07        21.21        23.15 
TCGA-QK-A6II TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z8 TCGA-QK-A8ZA 
        9.34        27.39        21.07        19.73         5.62        12.20 
TCGA-QK-A8ZB TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T2-A6X0 
       17.82        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-A71B TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JF TCGA-UF-A7JJ 
       54.67        49.51        74.47        17.95        55.43        18.05 
TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-KU-A66S 
       20.75        22.36        32.65        17.03        20.55        13.35 

  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
              0.36               0.07 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
            172.67             210.97 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
            19.035             21.225 
[1] "0.4 - 172.7 (19.0)" "0.1 - 211.0 (21.2)"
[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       159         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                159
  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 126   1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     64    0
  21Q LOSS WILD-TYPE  126    1
   clus
vv  21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  0               64                126
  1                0                  1
[1] 2 2
[1] FALSE
D79V7, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED    47 138
  21Q LOSS WILD-TYPE  93 244
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     47  138
  21Q LOSS WILD-TYPE   93  244
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  FEMALE               47                 93
  MALE                138                244
[1] 2 2
[1] FALSE
D79V8, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED    50 105
  21Q LOSS WILD-TYPE 112 196
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     50  105
  21Q LOSS WILD-TYPE  112  196
     clus
vv    21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  NO                50                112
  YES              105                196
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD & NECK SQUAMOUS CELL CARCINOMA
  21Q LOSS MUTATED                                   181
  21Q LOSS WILD-TYPE                                 330
                    vv
clus                 HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  21Q LOSS MUTATED                                                   4
  21Q LOSS WILD-TYPE                                                 6
                    vv
clus                 HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  21Q LOSS MUTATED                                                           0
  21Q LOSS WILD-TYPE                                                         1
D79V9, multiclass
                                                           clus
vv                                                          21Q LOSS MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                    181
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        4
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                0
                                                           clus
vv                                                          21Q LOSS WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                      330
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                          6
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                  1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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   146
  21Q LOSS WILD-TYPE                        23   300
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                                         146                300
[1] 4 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     8 162
  21Q LOSS WILD-TYPE  18 297
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      8  162
  21Q LOSS WILD-TYPE   18  297
                        clus
vv                       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    8                 18
  NOT HISPANIC OR LATINO              162                297
[1] 2 2
[1] FALSE

Clustering(80) Variable = 22Q LOSS MUTATION ANALYSIS
D80V1, survival
                    sevent
clus2                  0   1
  22Q LOSS MUTATED    48  25
  22Q LOSS WILD-TYPE 253 194
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                73                447 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                25                194 
$`22Q LOSS MUTATED`
TCGA-BA-4075 TCGA-BA-6871 TCGA-CN-6021 TCGA-CQ-A4C7 TCGA-DQ-7593 TCGA-4P-AA8J 
        9.30         3.55         9.07        11.61        40.24         3.35 
TCGA-BA-5149 TCGA-BA-5558 TCGA-BA-6870 TCGA-BA-A6DE TCGA-BB-4223 TCGA-BB-4224 
       26.50        65.59        14.83        14.47       105.90         9.14 
TCGA-BB-4225 TCGA-BB-7861 TCGA-BB-A5HY TCGA-C9-A47Z TCGA-CN-4725 TCGA-CN-4730 
        4.80        22.42        10.55         6.28        38.04        26.86 
TCGA-CN-5355 TCGA-CN-5370 TCGA-CN-6018 TCGA-CN-6995 TCGA-CN-6998 TCGA-CN-A63W 
       42.02         8.52        19.07         3.68        11.74        12.39 
TCGA-CN-A6V7 TCGA-CQ-5327 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-A4CE TCGA-CR-5248 
       19.53        54.58        64.87        53.52        29.49        54.67 
TCGA-CR-6488 TCGA-CR-6493 TCGA-CR-7373 TCGA-CR-7379 TCGA-CR-7398 TCGA-CR-7399 
       12.46         9.27        29.23        34.06         5.13         5.95 
TCGA-CV-5973 TCGA-CV-5977 TCGA-CV-6003 TCGA-CV-6441 TCGA-CV-6945 TCGA-CV-6962 
       86.83        60.49        54.74         9.60        12.03         4.14 
TCGA-CV-7091 TCGA-CV-7180 TCGA-CV-7413 TCGA-CV-7416 TCGA-CV-7421 TCGA-CV-7432 
      111.16        10.75         9.67        25.08         0.07        84.49 
TCGA-CV-A465 TCGA-CV-A6JY TCGA-CV-A6K1 TCGA-CX-7086 TCGA-D6-8569 TCGA-D6-A4Z9 
        7.07        21.24        22.52        18.84        25.32        17.72 
TCGA-D6-A6EM TCGA-DQ-5631 TCGA-DQ-7592 TCGA-F7-A50G TCGA-F7-A50J TCGA-F7-A623 
        7.63        18.02        37.58        20.25        31.13        20.25 
TCGA-HD-A633 TCGA-IQ-7630 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A6SG TCGA-MT-A67G 
       13.84        15.95        37.71        11.84        19.04         6.25 
TCGA-P3-A5QA TCGA-P3-A6T0 TCGA-QK-A6IH TCGA-QK-A6IJ TCGA-QK-A6VB TCGA-T3-A92M 
       71.74        19.00        21.47        12.72        21.07        13.71 
TCGA-T3-A92N 
        3.12 

$`22Q LOSS WILD-TYPE`
TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-A4IG TCGA-BA-A4II TCGA-BB-A5HU 
       37.28        20.48        68.48        28.11        30.18        25.71 
TCGA-CN-4727 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6992 TCGA-CN-6997 
       51.29         9.24        52.08        11.08        35.05        32.48 
TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-6221 TCGA-CQ-7063 TCGA-CQ-7067 
       19.82        24.39        48.20        32.88        70.13        16.73 
TCGA-CQ-7068 TCGA-CR-6472 TCGA-CR-6478 TCGA-CX-7082 TCGA-CX-7219 TCGA-DQ-5629 
       43.04        34.52         6.02         0.36        34.36        30.94 
TCGA-DQ-7588 TCGA-DQ-7589 TCGA-H7-A6C5 TCGA-HD-8634 TCGA-HD-8635 TCGA-UF-A71D 
       14.04        46.32        21.11        12.66        22.85        48.03 
TCGA-UF-A7JV TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-5151 TCGA-BA-5152 
        2.96        15.19        13.64         9.07        23.74        42.35 
TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6872 
       57.93        17.10        23.84        15.52        21.17        12.62 
TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IH TCGA-BA-A6D8 TCGA-BA-A6DA 
        4.01        41.85        29.42        20.45        27.95        11.54 
TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-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-BA-A8YP TCGA-BB-4217 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7862 
       20.48        16.41         6.15         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-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO TCGA-C9-A480 
       71.05        20.52        27.19        12.92         8.81        12.69 
TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4731 
       48.76        55.86         4.67        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-6988 
       23.90        47.44        28.04        34.13         6.74        10.45 
TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 
       32.22        38.89        17.42        35.01        25.41        23.57 
TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V 
       17.29        29.72        21.21         7.40        31.69        22.32 
TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V6 
       16.57         4.41        12.07         2.70        23.44        20.88 
TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 
       52.37        21.50         2.93        70.45        62.37        45.99 
TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6220 TCGA-CQ-6223 
       10.42        11.21         4.24        41.19        32.38        46.95 
TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7069 
       56.58        13.25         4.24        14.99        38.76        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-6473 TCGA-CR-6474 
       26.27        58.42        50.01        39.52        36.99        18.54 
TCGA-CR-6477 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 
       16.90        11.90        10.22        11.34        11.64         7.69 
TCGA-CR-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-7371 TCGA-CR-7372 TCGA-CR-7374 TCGA-CR-7376 
       35.84         3.45         3.09        24.95         0.99        31.96 
TCGA-CR-7377 TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 
        9.17        19.92        26.17        17.13        32.78        47.01 
TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 
       27.06        12.89        49.58        30.02        46.85        32.65 
TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 
       44.25        30.58        24.79        35.41        29.95        48.39 
TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 
      139.43        17.16       129.21       108.95        76.24        19.20 
TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 
       17.95       107.51        94.88        76.50        91.53        80.12 
TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-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-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-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-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-7095 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 
       64.83       172.67        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-7183 TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 
      130.88        77.16         4.73        89.65        36.00        31.36 
TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 
       26.20        18.97        17.13        95.34         4.96        11.87 
TCGA-CV-7254 TCGA-CV-7255 TCGA-CV-7261 TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7407 
       47.97         2.10        49.71        18.41        57.47        35.54 
TCGA-CV-7409 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7414 TCGA-CV-7415 TCGA-CV-7418 
       17.85       210.97        89.33         0.46        22.85        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-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-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-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-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-A4AQ 
        3.62        23.47        19.92        10.42        10.55        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-A4ZB TCGA-D6-A6EK TCGA-D6-A6EN 
       11.44        18.67        24.95        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        23.34        58.45 
TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7594 TCGA-DQ-7595 
       37.25        33.86        46.45        20.45        40.04        39.12 
TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50I TCGA-F7-A61S 
       41.59        37.18        32.71        21.63         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-A76A TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 
       15.16        15.06        20.94        33.76        28.47        25.74 
TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-A4C1 
       21.93        27.48        27.48        14.66        22.03         0.36 
TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7631 TCGA-IQ-7632 
        4.27         3.65         6.90        34.75        38.53        14.50 
TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O 
       37.41         0.07        33.57         5.29        13.68        13.84 
TCGA-IQ-A6SH TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A 
       15.48        19.27        10.75        14.37         7.96        30.05 
TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-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 
       27.39        19.73        12.89         5.62        14.76        12.20 
TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX 
       17.82        15.32         8.32        12.72        16.96         6.87 
TCGA-T2-A6WZ TCGA-T2-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-A71E TCGA-UF-A7J9 
       64.80        54.67         2.83        49.51        49.45        44.65 
TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ 
       74.47        17.95        24.30        55.43        29.46        18.05 
TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UP-A6WW TCGA-WA-A7GZ 
       13.94        20.75        22.36        32.65        17.03        20.55 
TCGA-WA-A7H4 TCGA-KU-A66S TCGA-KU-A66T 
       14.56        13.35        18.15 

  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 
             18.84              21.90 
[1] "0.1 - 111.2 (18.8)" "0.1 - 211.0 (21.9)"
[1] "hr=" "1.1"
D80V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  22Q LOSS MUTATED         2       12        17        33         1         0
  22Q LOSS WILD-TYPE      25       64        65       219        11         1
D80V3, multiclass
           clus
vv          22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  STAGE I                  2                 25
  STAGE II                12                 64
  STAGE III               17                 65
  STAGE IVA               33                219
  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       5  22  19  19
  22Q LOSS WILD-TYPE    45 115  81 154
D80V4, multiclass
       clus
vv      22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  T0+T1                5                 45
  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    26  13  22   0
  22Q LOSS WILD-TYPE 153  55 146   8
D80V5, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  N0               26                153
  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    27   0
  22Q LOSS WILD-TYPE 163   1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     27    0
  22Q LOSS WILD-TYPE  163    1
   clus
vv  22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  0               27                163
  1                0                  1
[1] 2 2
[1] FALSE
D80V7, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED    24  50
  22Q LOSS WILD-TYPE 116 332
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     24   50
  22Q LOSS WILD-TYPE  116  332
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  FEMALE               24                116
  MALE                 50                332
[1] 2 2
[1] FALSE
D80V8, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED    24  44
  22Q LOSS WILD-TYPE 138 257
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     24   44
  22Q LOSS WILD-TYPE  138  257
     clus
vv    22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  NO                24                138
  YES               44                257
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD & NECK SQUAMOUS CELL CARCINOMA
  22Q LOSS MUTATED                                    74
  22Q LOSS WILD-TYPE                                 437
                    vv
clus                 HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  22Q LOSS MUTATED                                                   0
  22Q LOSS WILD-TYPE                                                10
                    vv
clus                 HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  22Q LOSS MUTATED                                                           0
  22Q LOSS WILD-TYPE                                                         1
D80V9, multiclass
                                                           clus
vv                                                          22Q LOSS MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                     74
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        0
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                0
                                                           clus
vv                                                          22Q LOSS WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                      437
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                         10
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                  1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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    59
  22Q LOSS WILD-TYPE                        40   387
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                                          59                387
[1] 4 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  63
  22Q LOSS WILD-TYPE  20 396
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      6   63
  22Q LOSS WILD-TYPE   20  396
                        clus
vv                       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    6                 20
  NOT HISPANIC OR LATINO               63                396
[1] 2 2
[1] FALSE

Clustering(81) Variable = XP LOSS MUTATION ANALYSIS
D81V1, survival
                   sevent
clus2                 0   1
  XP LOSS MUTATED    70  66
  XP LOSS WILD-TYPE 231 153
  XP LOSS MUTATED XP LOSS WILD-TYPE 
              136               384 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               66               153 
$`XP LOSS MUTATED`
TCGA-BB-A5HU TCGA-CN-6024 TCGA-CN-6992 TCGA-CN-6997 TCGA-CQ-6221 TCGA-CQ-A4C7 
       25.71        11.08        35.05        32.48        32.88        11.61 
TCGA-CR-6472 TCGA-CX-7082 TCGA-DQ-5629 TCGA-DQ-7588 TCGA-H7-A6C5 TCGA-HD-8635 
       34.52         0.36        30.94        14.04        21.11        22.85 
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-A5HY TCGA-BB-A6UM TCGA-BB-A6UO TCGA-CN-4725 
       24.66        71.05        10.55        12.92         8.81        38.04 
TCGA-CN-4728 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-5359 TCGA-CN-5360 
       56.68        57.11        12.99        20.55        12.39        71.31 
TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6018 TCGA-CN-6988 TCGA-CN-6989 
       50.07        30.67        48.00        19.07        10.45        32.22 
TCGA-CN-6996 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A6V7 TCGA-CQ-5332 TCGA-CQ-6218 
       17.42        17.29        29.72        19.53        10.42        41.19 
TCGA-CQ-6220 TCGA-CQ-6227 TCGA-CQ-6229 TCGA-CQ-7072 TCGA-CQ-A4CI TCGA-CR-5247 
       32.38         4.24        38.76        77.56        31.23        11.77 
TCGA-CR-5248 TCGA-CR-6487 TCGA-CR-6493 TCGA-CR-7371 TCGA-CR-7374 TCGA-CR-7380 
       54.67         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        49.58        24.79         5.13         5.95 
TCGA-CV-5430 TCGA-CV-5435 TCGA-CV-5439 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-6441 
      139.43        76.24        17.95        48.59        60.49         9.60 
TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6940 TCGA-CV-6948 TCGA-CV-6959 TCGA-CV-6960 
        9.70         5.46        26.43        42.38         8.42        28.34 
TCGA-CV-7095 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7243 
       18.81         5.26         1.84        77.16         4.73        31.36 
TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7255 TCGA-CV-7418 TCGA-CV-7425 TCGA-CV-7430 
       26.20        18.97         2.10        25.94        56.48        16.27 
TCGA-CV-7432 TCGA-CV-7437 TCGA-CV-7438 TCGA-CV-A45Q TCGA-CV-A460 TCGA-CV-A465 
       84.49        16.64         6.38       169.38        60.43         7.07 
TCGA-CV-A6JY TCGA-CV-A6K1 TCGA-CX-7086 TCGA-D6-6516 TCGA-D6-6826 TCGA-D6-6827 
       21.24        22.52        18.84        25.41        11.44        18.67 
TCGA-D6-8568 TCGA-D6-A6EM TCGA-DQ-5625 TCGA-DQ-5631 TCGA-DQ-7592 TCGA-F7-7848 
       24.95         7.63        37.25        18.02        37.58        37.18 
TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A61W TCGA-F7-A620 TCGA-HD-7917 TCGA-IQ-A6SG 
       21.63        20.25         0.46        17.85        27.48        19.04 
TCGA-MT-A51X TCGA-MT-A7BN TCGA-P3-A5QE TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-QK-A6IH 
        7.96        15.42        51.25        18.97         2.04        21.47 
TCGA-QK-A8Z8 TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-T2-A6WZ TCGA-T3-A92M TCGA-UF-A719 
        5.62        17.82        15.32        15.91        13.71        54.67 
TCGA-UF-A71B TCGA-UF-A71E TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JH TCGA-UF-A7JO 
       49.51        49.45        17.95        24.30        29.46        20.75 
TCGA-UF-A7JS TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 
       22.36        17.03        20.55        14.56 

$`XP LOSS WILD-TYPE`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4IG 
        9.30        37.28        20.48        68.48         3.55        28.11 
TCGA-BA-A4II TCGA-CN-4727 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-A6V1 
       30.18        51.29         9.07         9.24        52.08        19.82 
TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-7063 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CR-6478 
       24.39        48.20        70.13        16.73        43.04         6.02 
TCGA-CX-7219 TCGA-DQ-7589 TCGA-DQ-7593 TCGA-HD-8634 TCGA-UF-A71D TCGA-UF-A7JV 
       34.36        46.32        40.24        12.66        48.03         2.96 
TCGA-4P-AA8J TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 
        3.35        23.74        42.35        57.93        17.10        23.84 
TCGA-BA-5558 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF 
       65.59        21.17        14.83         4.01        41.85        29.42 
TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DI 
       11.54         7.10         5.69         7.82         2.27        11.05 
TCGA-BA-A6DJ TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 
       13.38         6.15       105.90         9.14         4.80         4.41 
TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7870 
       18.38        22.42        33.70        50.20        44.98        66.28 
TCGA-BB-7872 TCGA-BB-8601 TCGA-BB-A5HZ TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4722 
       38.40        20.52        27.19         6.28        12.69        48.76 
TCGA-CN-4723 TCGA-CN-4726 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 
       55.86         4.67        12.89        26.86        32.81        52.14 
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-5363 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 
       46.32         8.58         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-6013 
       11.57        12.49         8.52        52.08        56.94        23.90 
TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6994 TCGA-CN-6995 
       47.44        28.04        34.13         6.74        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-A6V6 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 
        2.70        23.44        20.88        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-6223 TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6228 TCGA-CQ-7064 TCGA-CQ-7065 
       46.95        56.58        13.25        14.99        64.87        53.52 
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-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6488 TCGA-CR-6491 
       11.90        10.22        11.34        11.64        12.46        22.78 
TCGA-CR-6492 TCGA-CR-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-7372 TCGA-CR-7373 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 
        3.45        24.95        29.23        31.96         9.17        34.06 
TCGA-CR-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-7401 TCGA-CR-7402 TCGA-CR-7404 
       32.65        44.25        30.58        35.41        29.95        48.39 
TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5436 TCGA-CV-5440 TCGA-CV-5441 
       17.16       129.21       108.95        19.20       107.51        94.88 
TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 
       76.50        91.53        80.12        17.92        13.35        23.05 
TCGA-CV-5973 TCGA-CV-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-6937 TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6941 
       90.12         2.14        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-6961 TCGA-CV-6962 
       53.95        65.82        10.98         7.13         2.50         4.14 
TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 
       64.83       172.67       111.16        12.66         7.99         9.01 
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-7248 TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 
       89.65        36.00        17.13        95.34         4.96        11.87 
TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7407 TCGA-CV-7409 
       47.97        49.71        18.41        57.47        35.54        17.85 
TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7414 TCGA-CV-7415 TCGA-CV-7416 
      210.97        89.33         9.67         0.46        22.85        25.08 
TCGA-CV-7421 TCGA-CV-7422 TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7427 TCGA-CV-7428 
        0.07        34.09       100.57        14.89       156.49        54.94 
TCGA-CV-7429 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7440 TCGA-CV-A45O 
        3.52        19.76         7.17       153.86        22.19        27.98 
TCGA-CV-A45P TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45U TCGA-CV-A45V TCGA-CV-A45W 
       21.01       180.16       159.65        35.47         1.05        45.96 
TCGA-CV-A45X TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A461 TCGA-CV-A463 TCGA-CV-A464 
        6.51        88.87        48.20        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-A6JT TCGA-CV-A6JU TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K2 TCGA-CX-7085 
       28.01         3.62        23.47        19.92        10.42        10.55 
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-D6-8569 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-5630 
       13.94        12.10        12.79        23.34        58.45        33.86 
TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-8298 
       46.45        20.45        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-A76A TCGA-HD-7229 
       12.43        13.38        15.16        15.06        20.94        33.76 
TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-8224 TCGA-HD-8314 
       28.47        25.74        21.93        27.48        14.66        22.03 
TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-HL-7533 
        0.36        13.84         4.27         3.65         6.90        34.75 
TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H 
       15.95        38.53        14.50        37.71        11.84        37.41 
TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O TCGA-IQ-A6SH 
        0.07        33.57         5.29        13.68        13.84        15.48 
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-MZ-A5BI TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5Q6 
        6.25         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-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        27.39        21.07 
TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-AA3K TCGA-RS-A6TO 
       19.73        12.89        14.76        12.20         8.32        12.72 
TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-T3-A92N TCGA-TN-A7HI 
       16.96         6.87         7.10        32.45         3.12        13.55 
TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A71A TCGA-UF-A7J9 TCGA-UF-A7JA 
       13.25        20.35        64.80         2.83        44.65        74.47 
TCGA-UF-A7JF TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JT TCGA-KU-A66S TCGA-KU-A66T 
       55.43        18.05        13.94        32.65        13.35        18.15 

  XP LOSS MUTATED XP LOSS WILD-TYPE 
             0.36              0.07 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
           169.38            210.97 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
            20.35             21.85 
[1] "0.4 - 169.4 (20.4)" "0.1 - 211.0 (21.9)"
[1] "hr=" "1.3"
D81V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  XP LOSS MUTATED         6       17        22        63         5         1
  XP LOSS WILD-TYPE      21       59        60       189         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              63               189
  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  39  39
  XP LOSS WILD-TYPE    38 108  61 134
D81V4, multiclass
       clus
vv      XP LOSS MUTATED XP LOSS WILD-TYPE
  T0+T1              12                38
  T2                 29               108
  T3                 39                61
  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
  XP LOSS MUTATED    43  16  50   2
  XP LOSS WILD-TYPE 136  52 118   6
D81V5, multiclass
    clus
vv   XP LOSS MUTATED XP LOSS WILD-TYPE
  N0              43               136
  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"
D81V6, binary
                   cls
clus                  0   1
  XP LOSS MUTATED    45   1
  XP LOSS WILD-TYPE 145   0
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED     45    1
  XP LOSS WILD-TYPE  145    0
   clus
vv  XP LOSS MUTATED XP LOSS WILD-TYPE
  0              45               145
  1               1                 0
[1] 2 2
[1] FALSE
D81V7, binary
                   cls
clus                  0   1
  XP LOSS MUTATED    32 104
  XP LOSS WILD-TYPE 108 278
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED     32  104
  XP LOSS WILD-TYPE  108  278
        clus
vv       XP LOSS MUTATED XP LOSS WILD-TYPE
  FEMALE              32               108
  MALE               104               278
[1] 2 2
[1] FALSE
D81V8, binary
                   cls
clus                  0   1
  XP LOSS MUTATED    40  82
  XP LOSS WILD-TYPE 122 219
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED     40   82
  XP LOSS WILD-TYPE  122  219
     clus
vv    XP LOSS MUTATED XP LOSS WILD-TYPE
  NO               40               122
  YES              82               219
[1] 2 2
[1] FALSE
                   vv
clus                HEAD & NECK SQUAMOUS CELL CARCINOMA
  XP LOSS MUTATED                                   131
  XP LOSS WILD-TYPE                                 380
                   vv
clus                HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  XP LOSS MUTATED                                                   5
  XP LOSS WILD-TYPE                                                 5
                   vv
clus                HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  XP LOSS MUTATED                                                           0
  XP LOSS WILD-TYPE                                                         1
D81V9, multiclass
                                                           clus
vv                                                          XP LOSS MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                   131
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       5
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT               0
                                                           clus
vv                                                          XP LOSS WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                     380
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                         5
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                 1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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   117
  XP LOSS WILD-TYPE                        35   329
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                                        117               329
[1] 4 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     7 117
  XP LOSS WILD-TYPE  19 342
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED      7  117
  XP LOSS WILD-TYPE   19  342
                        clus
vv                       XP LOSS MUTATED XP LOSS WILD-TYPE
  HISPANIC OR LATINO                   7                19
  NOT HISPANIC OR LATINO             117               342
[1] 2 2
[1] FALSE

Clustering(82) Variable = XQ LOSS MUTATION ANALYSIS
D82V1, survival
                   sevent
clus2                 0   1
  XQ LOSS MUTATED    43  39
  XQ LOSS WILD-TYPE 258 180
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               82               438 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               39               180 
$`XQ LOSS MUTATED`
TCGA-CN-6992 TCGA-CN-6997 TCGA-CQ-6221 TCGA-CQ-7067 TCGA-CR-6472 TCGA-CX-7082 
       35.05        32.48        32.88        16.73        34.52         0.36 
TCGA-DQ-7588 TCGA-H7-A6C5 TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-6868 
       14.04        21.11        15.19        13.64         9.07        15.52 
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-A5HY TCGA-BB-A6UM TCGA-CN-4725 TCGA-CN-4735 
       24.66        71.05        10.55        12.92        38.04        57.11 
TCGA-CN-4736 TCGA-CN-5360 TCGA-CN-6011 TCGA-CN-A49A TCGA-CN-A6V7 TCGA-CQ-6218 
       12.99        71.31        30.67        17.29        19.53        41.19 
TCGA-CQ-6227 TCGA-CQ-7064 TCGA-CQ-A4CI TCGA-CR-5248 TCGA-CR-6487 TCGA-CR-7371 
        4.24        64.87        31.23        54.67         7.69         3.09 
TCGA-CR-7374 TCGA-CR-7388 TCGA-CR-7390 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 
        0.99        27.06        49.58        24.79         5.13         5.95 
TCGA-CV-5439 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-6441 TCGA-CV-6935 
       17.95        86.83        48.59        60.49         9.60         9.70 
TCGA-CV-6940 TCGA-CV-6948 TCGA-CV-6960 TCGA-CV-7095 TCGA-CV-7101 TCGA-CV-7236 
       26.43        42.38        28.34        18.81         5.26         4.73 
TCGA-CV-7416 TCGA-CV-7418 TCGA-CV-7421 TCGA-CV-7425 TCGA-CV-7430 TCGA-CV-7435 
       25.08        25.94         0.07        56.48        16.27       153.86 
TCGA-CV-A460 TCGA-CV-A6K1 TCGA-D6-6826 TCGA-D6-6827 TCGA-F7-7848 TCGA-F7-A50G 
       60.43        22.52        11.44        18.67        37.18        20.25 
TCGA-F7-A61W TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-QK-A6IH 
        0.46        71.74        51.25        18.97         2.04        21.47 
TCGA-QK-A8Z8 TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-T2-A6WZ TCGA-UF-A7JC TCGA-UF-A7JD 
        5.62        17.82        15.32        15.91        17.95        24.30 
TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UP-A6WW TCGA-WA-A7GZ 
       20.75        22.36        17.03        20.55 

$`XQ LOSS WILD-TYPE`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4IG 
        9.30        37.28        20.48        68.48         3.55        28.11 
TCGA-BA-A4II TCGA-BB-A5HU TCGA-CN-4727 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 
       30.18        25.71        51.29         9.07         9.24        52.08 
TCGA-CN-6024 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-7063 TCGA-CQ-7068 
       11.08        19.82        24.39        48.20        70.13        43.04 
TCGA-CQ-A4C7 TCGA-CR-6478 TCGA-CX-7219 TCGA-DQ-5629 TCGA-DQ-7589 TCGA-DQ-7593 
       11.61         6.02        34.36        30.94        46.32        40.24 
TCGA-HD-8634 TCGA-HD-8635 TCGA-UF-A71D TCGA-UF-A7JV TCGA-4P-AA8J TCGA-BA-5149 
       12.66        22.85        48.03         2.96         3.35        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-6869 TCGA-BA-6870 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF 
       21.17        14.83        12.62         4.01        41.85        29.42 
TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DI 
       11.54         7.10         5.69         7.82         2.27        11.05 
TCGA-BA-A6DJ TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 
       13.38         6.15       105.90         9.14         4.80         4.41 
TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7870 
       18.38        22.42        33.70        50.20        44.98        66.28 
TCGA-BB-7872 TCGA-BB-8601 TCGA-BB-A5HZ TCGA-BB-A6UO TCGA-C9-A47Z TCGA-C9-A480 
       38.40        20.52        27.19         8.81         6.28        12.69 
TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 
       48.76        55.86         4.67        56.68        12.89        26.86 
TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 
       32.81        52.14        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-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-6012 TCGA-CN-6013 
        8.52        52.08        56.94        50.07        48.00        23.90 
TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6988 
       47.44        28.04        19.07        34.13         6.74        10.45 
TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A497 
       32.22        38.89         3.68        17.42        11.74        35.01 
TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U 
       25.41        23.57        29.72        21.21         7.40        31.69 
TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 
       22.32        12.39        16.57         4.41        12.07         2.70 
TCGA-CN-A6UY TCGA-CN-A6V6 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 
       23.44        20.88        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-7065 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C9 
       53.52        41.88        43.10        77.56        44.48        23.24 
TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CR-5243 
       29.36        33.60        29.49        14.14        12.46        84.23 
TCGA-CR-5247 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 
       11.77        37.87        26.27        58.42        50.01        39.52 
TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 
       36.99        18.54        16.90        11.90        10.22        11.34 
TCGA-CR-6484 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 
       11.64        12.46        22.78        15.75         9.27        47.18 
TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7372 
       39.16        47.34        40.93        35.84         3.45        24.95 
TCGA-CR-7373 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7382 
       29.23        31.96         9.17        34.06        19.92        26.17 
TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7389 TCGA-CR-7391 TCGA-CR-7392 
       17.13        32.78        47.01        12.89        30.02        46.85 
TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 
       32.65        44.25        30.58        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-5440 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 
      107.51        94.88        76.50        91.53        80.12        17.92 
TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 
       13.35        23.05         7.07        43.23        54.74        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-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-6959 TCGA-CV-6961 TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7091 
        8.42         2.50         4.14        64.83       172.67       111.16 
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-7235 TCGA-CV-7238 
       21.80        71.21        10.75       130.88        77.16        89.65 
TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7248 TCGA-CV-7250 
       36.00        31.36        26.20        18.97        17.13        95.34 
TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7255 TCGA-CV-7261 TCGA-CV-7263 
        4.96        11.87        47.97         2.10        49.71        18.41 
TCGA-CV-7406 TCGA-CV-7407 TCGA-CV-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-7422 TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7427 
        0.46        22.85        34.09       100.57        14.89       156.49 
TCGA-CV-7428 TCGA-CV-7429 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7437 
       54.94         3.52        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-A45Z TCGA-CV-A461 TCGA-CV-A463 TCGA-CV-A464 TCGA-CV-A465 TCGA-CV-A468 
       48.20        67.86         0.76        56.61         7.07        15.25 
TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JM TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT 
        5.98        35.34         6.38        29.79         6.48        28.01 
TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K2 TCGA-CX-7085 
        3.62        21.24        23.47        19.92        10.42        10.55 
TCGA-CX-7086 TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 
       18.84        51.12        13.25        25.41         9.60        23.05 
TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB 
        2.53        16.14        24.95        25.32        17.72        12.36 
TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EN TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ 
       28.77         7.63        22.59        24.95        13.94        12.10 
TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 
       12.79        23.34        58.45        37.25        33.86        18.02 
TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 
       46.45        20.45        37.58        40.04        39.12        41.59 
TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V 
       32.71        21.63         3.02        31.13        18.94        24.95 
TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A623 TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 
       17.85        11.80        20.25        12.43        13.38        15.16 
TCGA-H7-8502 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7831 
       15.06        20.94        33.76        28.47        25.74        21.93 
TCGA-HD-7832 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-A4C1 TCGA-HD-A633 
       27.48        27.48        14.66        22.03         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-A6H7 
        5.29        13.68        13.84        19.04        15.48        19.27 
TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F 
       10.75        14.37         7.96        30.05         1.84        12.62 
TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 
        6.25        15.42         7.13        16.08        17.98        29.92 
TCGA-P3-A5Q6 TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 
       15.78        10.85        36.82        47.01        19.00        75.55 
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        27.39        21.07 
TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-AA3K TCGA-RS-A6TO 
       19.73        12.89        14.76        12.20         8.32        12.72 
TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-T3-A92M TCGA-T3-A92N 
       16.96         6.87         7.10        32.45        13.71         3.12 
TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A 
       13.55        13.25        20.35        64.80        54.67         2.83 
TCGA-UF-A71B TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JF TCGA-UF-A7JH 
       49.51        49.45        44.65        74.47        55.43        29.46 
TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JT TCGA-WA-A7H4 TCGA-KU-A66S TCGA-KU-A66T 
       18.05        13.94        32.65        14.56        13.35        18.15 

  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 
           20.465            21.225 
[1] "0.1 - 153.9 (20.5)" "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         5        7        11        39         4         1
  XQ LOSS WILD-TYPE      22       69        71       213         8         0
D82V3, multiclass
           clus
vv          XQ LOSS MUTATED XQ LOSS WILD-TYPE
  STAGE I                 5                22
  STAGE II                7                69
  STAGE III              11                71
  STAGE IVA              39               213
  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       9  16  25  23
  XQ LOSS WILD-TYPE    41 121  75 150
D82V4, multiclass
       clus
vv      XQ LOSS MUTATED XQ LOSS WILD-TYPE
  T0+T1               9                41
  T2                 16               121
  T3                 25                75
  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    28   1
  XQ LOSS WILD-TYPE 162   0
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     28    1
  XQ LOSS WILD-TYPE  162    0
   clus
vv  XQ LOSS MUTATED XQ LOSS WILD-TYPE
  0              28               162
  1               1                 0
[1] 2 2
[1] FALSE
D82V7, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED    25  57
  XQ LOSS WILD-TYPE 115 325
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     25   57
  XQ LOSS WILD-TYPE  115  325
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  FEMALE              25               115
  MALE                57               325
[1] 2 2
[1] FALSE
D82V8, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED    23  51
  XQ LOSS WILD-TYPE 139 250
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     23   51
  XQ LOSS WILD-TYPE  139  250
     clus
vv    XQ LOSS MUTATED XQ LOSS WILD-TYPE
  NO               23               139
  YES              51               250
[1] 2 2
[1] FALSE
                   vv
clus                HEAD & NECK SQUAMOUS CELL CARCINOMA
  XQ LOSS MUTATED                                    78
  XQ LOSS WILD-TYPE                                 433
                   vv
clus                HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  XQ LOSS MUTATED                                                   4
  XQ LOSS WILD-TYPE                                                 6
                   vv
clus                HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  XQ LOSS MUTATED                                                           0
  XQ LOSS WILD-TYPE                                                         1
D82V9, multiclass
                                                           clus
vv                                                          XQ LOSS MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                    78
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       4
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT               0
                                                           clus
vv                                                          XQ LOSS WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                     433
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                         6
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                 1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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    70
  XQ LOSS WILD-TYPE                        40   376
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                                         70               376
[1] 4 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  72
  XQ LOSS WILD-TYPE  23 387
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      3   72
  XQ LOSS WILD-TYPE   23  387
                        clus
vv                       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  HISPANIC OR LATINO                   3                23
  NOT HISPANIC OR LATINO              72               387
[1] 2 2
[1] FALSE
