[1] "ofn"        "-oTSKCM-TM"
[1] "opt"       "-OPMUTSIG"
[1] "tl" ""  
[1] "dx" ""  
[1] "opt"    "MUTSIG"
[1] "dx" ""  
[1] "cfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/SKCM-TM/15087681/SKCM-TM.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/SKCM-TM/15098586/transformed.cor.cli.txt"

nPatients in clinical file=359, in cluster file=366, common to both=358
[1]  82 358
[1] "1P GAIN MUTATION ANALYSIS"
[1] 3
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               85               273 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               85               273 
[1] "1Q GAIN MUTATION ANALYSIS"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              169               189 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              169               189 
[1] "2P GAIN MUTATION ANALYSIS"
[1] 3
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               66               292 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               66               292 
[1] "2Q GAIN MUTATION ANALYSIS"
[1] 3
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               64               294 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               64               294 
[1] "3P GAIN MUTATION ANALYSIS"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               62               296 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               62               296 
[1] "3Q GAIN MUTATION ANALYSIS"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               71               287 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               71               287 
[1] "4P GAIN MUTATION ANALYSIS"
[1] 3
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               55               303 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               55               303 
[1] "4Q GAIN MUTATION ANALYSIS"
[1] 3
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               47               311 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               47               311 
[1] "5P GAIN MUTATION ANALYSIS"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               75               283 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               75               283 
[1] "5Q GAIN MUTATION ANALYSIS"
[1] 3
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               50               308 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               50               308 
[1] "6P GAIN MUTATION ANALYSIS"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
              140               218 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
              140               218 
[1] "6Q GAIN MUTATION ANALYSIS"
[1] 3
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               48               310 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               48               310 
[1] "7P GAIN MUTATION ANALYSIS"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              197               161 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              197               161 
[1] "7Q GAIN MUTATION ANALYSIS"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              194               164 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              194               164 
[1] "8P GAIN MUTATION ANALYSIS"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
              118               240 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
              118               240 
[1] "8Q GAIN MUTATION ANALYSIS"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              165               193 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              165               193 
[1] "9P GAIN MUTATION ANALYSIS"
[1] 3
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               16               342 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               16               342 
[1] "9Q GAIN MUTATION ANALYSIS"
[1] 3
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               21               337 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               21               337 
[1] "10P GAIN MUTATION ANALYSIS"
[1] 3
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                12                346 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                12                346 
[1] "10Q GAIN MUTATION ANALYSIS"
[1] 3
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 3                355 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 3                355 
[1] "11P GAIN MUTATION ANALYSIS"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                35                323 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                35                323 
[1] "11Q GAIN MUTATION ANALYSIS"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                29                329 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                29                329 
[1] "12P GAIN MUTATION ANALYSIS"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                62                296 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                62                296 
[1] "12Q GAIN MUTATION ANALYSIS"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                36                322 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                36                322 
[1] "13Q GAIN MUTATION ANALYSIS"
[1] 3
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                93                265 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                93                265 
[1] "14Q GAIN MUTATION ANALYSIS"
[1] 3
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                41                317 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                41                317 
[1] "15Q GAIN MUTATION ANALYSIS"
[1] 3
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                84                274 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                84                274 
[1] "16P GAIN MUTATION ANALYSIS"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                55                303 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                55                303 
[1] "16Q GAIN MUTATION ANALYSIS"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                43                315 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                43                315 
[1] "17P GAIN MUTATION ANALYSIS"
[1] 3
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                37                321 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                37                321 
[1] "17Q GAIN MUTATION ANALYSIS"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                65                293 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                65                293 
[1] "18P GAIN MUTATION ANALYSIS"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                53                305 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                53                305 
[1] "18Q GAIN MUTATION ANALYSIS"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                44                314 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                44                314 
[1] "19P GAIN MUTATION ANALYSIS"
[1] 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                55                303 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                55                303 
[1] "19Q GAIN MUTATION ANALYSIS"
[1] 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                55                303 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                55                303 
[1] "20P GAIN MUTATION ANALYSIS"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               145                213 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               145                213 
[1] "20Q GAIN MUTATION ANALYSIS"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               177                181 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               177                181 
[1] "21Q GAIN MUTATION ANALYSIS"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                67                291 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                67                291 
[1] "22Q GAIN MUTATION ANALYSIS"
[1] 3
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
               124                234 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
               124                234 
[1] "XP GAIN MUTATION ANALYSIS"
[1] 3
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               39               319 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               39               319 
[1] "XQ GAIN MUTATION ANALYSIS"
[1] 3
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               41               317 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               41               317 
[1] "1P LOSS MUTATION ANALYSIS"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               52               306 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               52               306 
[1] "1Q LOSS MUTATION ANALYSIS"
[1] 3
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               27               331 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               27               331 
[1] "2P LOSS MUTATION ANALYSIS"
[1] 3
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               50               308 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               50               308 
[1] "2Q LOSS MUTATION ANALYSIS"
[1] 3
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               51               307 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               51               307 
[1] "3P LOSS MUTATION ANALYSIS"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               60               298 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               60               298 
[1] "3Q LOSS MUTATION ANALYSIS"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               51               307 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               51               307 
[1] "4P LOSS MUTATION ANALYSIS"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               78               280 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               78               280 
[1] "4Q LOSS MUTATION ANALYSIS"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               82               276 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               82               276 
[1] "5P LOSS MUTATION ANALYSIS"
[1] 3
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               78               280 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               78               280 
[1] "5Q LOSS MUTATION ANALYSIS"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               98               260 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               98               260 
[1] "6P LOSS MUTATION ANALYSIS"
[1] 3
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               66               292 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               66               292 
[1] "6Q LOSS MUTATION ANALYSIS"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
              167               191 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
              167               191 
[1] "7P LOSS MUTATION ANALYSIS"
[1] 3
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               18               340 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               18               340 
[1] "7Q LOSS MUTATION ANALYSIS"
[1] 3
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               17               341 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               17               341 
[1] "8P LOSS MUTATION ANALYSIS"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               67               291 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               67               291 
[1] "8Q LOSS MUTATION ANALYSIS"
[1] 3
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               27               331 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               27               331 
[1] "9P LOSS MUTATION ANALYSIS"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              232               126 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              232               126 
[1] "9Q LOSS MUTATION ANALYSIS"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
              183               175 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
              183               175 
[1] "10P LOSS MUTATION ANALYSIS"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
               199                159 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
               199                159 
[1] "10Q LOSS MUTATION ANALYSIS"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
               219                139 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
               219                139 
[1] "11P LOSS MUTATION ANALYSIS"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
               124                234 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
               124                234 
[1] "11Q LOSS MUTATION ANALYSIS"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
               146                212 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
               146                212 
[1] "12P LOSS MUTATION ANALYSIS"
[1] 3
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                58                300 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                58                300 
[1] "12Q LOSS MUTATION ANALYSIS"
[1] 3
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                66                292 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                66                292 
[1] "13Q LOSS MUTATION ANALYSIS"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                77                281 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                77                281 
[1] "14Q LOSS MUTATION ANALYSIS"
[1] 3
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               111                247 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               111                247 
[1] "15Q LOSS MUTATION ANALYSIS"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                50                308 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                50                308 
[1] "16P LOSS MUTATION ANALYSIS"
[1] 3
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                67                291 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                67                291 
[1] "16Q LOSS MUTATION ANALYSIS"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
               103                255 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
               103                255 
[1] "17P LOSS MUTATION ANALYSIS"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               126                232 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               126                232 
[1] "17Q LOSS MUTATION ANALYSIS"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                64                294 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                64                294 
[1] "18P LOSS MUTATION ANALYSIS"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
               103                255 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
               103                255 
[1] "18Q LOSS MUTATION ANALYSIS"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                98                260 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                98                260 
[1] "19P LOSS MUTATION ANALYSIS"
[1] 3
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                75                283 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                75                283 
[1] "19Q LOSS MUTATION ANALYSIS"
[1] 3
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                70                288 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                70                288 
[1] "20P LOSS MUTATION ANALYSIS"
[1] 3
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                25                333 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                25                333 
[1] "20Q LOSS MUTATION ANALYSIS"
[1] 3
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 9                349 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 9                349 
[1] "21Q LOSS MUTATION ANALYSIS"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                68                290 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                68                290 
[1] "22Q LOSS MUTATION ANALYSIS"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                38                320 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                38                320 
[1] "XP LOSS MUTATION ANALYSIS"
[1] 3
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               96               262 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               96               262 
[1] "XQ LOSS MUTATION ANALYSIS"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               92               266 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               92               266 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                        
 [2] "VITAL_STATUS"                          
 [3] "DAYS_TO_DEATH"                         
 [4] "DAYS_TO_LAST_FOLLOWUP"                 
 [5] "DAYS_TO_SUBMITTED_SPECIMEN_DX"         
 [6] "PRIMARY_SITE_OF_DISEASE"               
 [7] "NEOPLASM_DISEASESTAGE"                 
 [8] "PATHOLOGY_T_STAGE"                     
 [9] "PATHOLOGY_N_STAGE"                     
[10] "PATHOLOGY_M_STAGE"                     
[11] "MELANOMA_ULCERATION"                   
[12] "MELANOMA_PRIMARY_KNOWN"                
[13] "BRESLOW_THICKNESS"                     
[14] "DCC_UPLOAD_DATE"                       
[15] "GENDER"                                
[16] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"  
[17] "RADIATION_THERAPY"                     
[18] "RADIATIONS_RADIATION_REGIMENINDICATION"
[19] "RACE"                                  
[20] "ETHNICITY"                             
[21] "BATCH_NUMBER"                          

Input Data has 21 rows and 358 columns.

[1] "Batch" "21"   
[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=68,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=179,	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=194,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'DAYS_TO_SUBMITTED_SPECIMEN_DX':	nDistinctValues=281,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 6:'PRIMARY_SITE_OF_DISEASE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'NEOPLASM_DISEASESTAGE':	nDistinctValues=14,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY_T_STAGE':	nDistinctValues=15,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY_N_STAGE':	nDistinctValues=10,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'PATHOLOGY_M_STAGE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'MELANOMA_ULCERATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'MELANOMA_PRIMARY_KNOWN':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'BRESLOW_THICKNESS':	nDistinctValues=125,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 14:'DCC_UPLOAD_DATE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 15:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=31,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 17:'RADIATION_THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATION_THERAPY is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 18:'RADIATIONS_RADIATION_REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATIONS_RADIATION_REGIMENINDICATION excluded in the analysis because there is no case of (both >= 3) in the table below"
              NO      YES    
freq.values   "2"     "356"  
freq.contrast "356"   "2"    
both >= 3     "FALSE" "FALSE"
Variable 19:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 20:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 21:'BATCH_NUMBER':	nDistinctValues=17,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] NA
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "TIME_FROM_SPECIMEN_DX_TO_DEATH_OR_LAST_FUP"
[2] "VITAL_STATUS"                              
[3] "DAYS_TO_DEATH_OR_LAST_FUP"                 
[4] "VITAL_STATUS"                              
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "TIME_FROM_SPECIMEN_DX_TO_DEATH_OR_LAST_FUP"
[2] "VITAL_STATUS"                              
[3] "DAYS_TO_DEATH_OR_LAST_FUP"                 
[4] "VITAL_STATUS"                              
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "TIME_FROM_SPECIMEN_DX_TO_DEATH_OR_LAST_FUP"
[2] "VITAL_STATUS"                              
[3] "DAYS_TO_DEATH_OR_LAST_FUP"                 
[4] "VITAL_STATUS"                              
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "TIME_FROM_SPECIMEN_DX_TO_DEATH_OR_LAST_FUP"
[2] "VITAL_STATUS"                              
[3] "DAYS_TO_DEATH_OR_LAST_FUP"                 
[4] "VITAL_STATUS"                              
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "TIME_FROM_SPECIMEN_DX_TO_DEATH_OR_LAST_FUP"
[2] "VITAL_STATUS"                              
[3] "DAYS_TO_DEATH_OR_LAST_FUP"                 
[4] "VITAL_STATUS"                              
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "TIME_FROM_SPECIMEN_DX_TO_DEATH_OR_LAST_FUP"
[2] "VITAL_STATUS"                              
[3] "DAYS_TO_DEATH_OR_LAST_FUP"                 
[4] "VITAL_STATUS"                              
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "TIME_FROM_SPECIMEN_DX_TO_DEATH_OR_LAST_FUP"
[2] "VITAL_STATUS"                              
[3] "DAYS_TO_DEATH_OR_LAST_FUP"                 
[4] "VITAL_STATUS"                              
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "TIME_FROM_SPECIMEN_DX_TO_DEATH_OR_LAST_FUP"
[2] "VITAL_STATUS"                              
[3] "DAYS_TO_DEATH_OR_LAST_FUP"                 
[4] "VITAL_STATUS"                              
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "TIME_FROM_SPECIMEN_DX_TO_DEATH_OR_LAST_FUP"
[2] "VITAL_STATUS"                              
[3] "DAYS_TO_DEATH_OR_LAST_FUP"                 
[4] "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 358 columns, 2 survival variables, and 12 non-survival variables.
[1] "* survival variables: "
[1] "TIME_FROM_SPECIMEN_DX_TO_DEATH_OR_LAST_FUP"
[2] "VITAL_STATUS"                              
[3] "DAYS_TO_DEATH_OR_LAST_FUP"                 
[4] "VITAL_STATUS"                              
[1] "* non-survival variables: "
 [1] "YEARS_TO_BIRTH"          "PRIMARY_SITE_OF_DISEASE"
 [3] "NEOPLASM_DISEASESTAGE"   "PATHOLOGY_T_STAGE"      
 [5] "PATHOLOGY_N_STAGE"       "PATHOLOGY_M_STAGE"      
 [7] "MELANOMA_ULCERATION"     "MELANOMA_PRIMARY_KNOWN" 
 [9] "BRESLOW_THICKNESS"       "GENDER"                 
[11] "RACE"                    "ETHNICITY"              
YEARS_TO_BIRTH, nv=68, binary=FALSE, numeric=TRUE
PRIMARY_SITE_OF_DISEASE, nv=4, binary=FALSE, numeric=FALSE
NEOPLASM_DISEASESTAGE, nv=14, binary=FALSE, numeric=FALSE
PATHOLOGY_T_STAGE, nv=5, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
T0 T1 T2 T3 T4 
23 41 72 77 68 
[1] "table(vv)"
vv
T0+T1    T2    T3    T4 
   64    72    77    68 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
T0 T1 T2 T3 T4 
23 41 72 77 68 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


T0+T1    T2    T3    T4 
   64    72    77    68 
PATHOLOGY_N_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2  N3 
169  63  38  49 
[1] "table(vv)"
vv
 N0  N1  N2  N3 
169  63  38  49 
$ClinVariableName
[1] "PATHOLOGY_N_STAGE"

$Table
vv
 N0  N1  N2  N3 
169  63  38  49 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 N0  N1  N2  N3 
169  63  38  49 
PATHOLOGY_M_STAGE, nv=2, binary=FALSE, numeric=TRUE
MELANOMA_ULCERATION, nv=2, binary=FALSE, numeric=FALSE
MELANOMA_PRIMARY_KNOWN, nv=2, binary=FALSE, numeric=FALSE
BRESLOW_THICKNESS, nv=125, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
RACE, nv=3, 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   27 26
  1P GAIN WILD-TYPE 94 92
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               53               186 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               26                92 
$`1P GAIN MUTATED`
TCGA-3N-A9WD TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JL TCGA-D3-A2JN 
       12.99        15.75        86.30         7.27       171.58        64.83 
TCGA-D3-A3C6 TCGA-D3-A3MR TCGA-D3-A8GD TCGA-D3-A8GJ TCGA-D3-A8GM TCGA-D9-A3Z1 
       58.06        90.21        23.61       179.97        70.62        15.02 
TCGA-D9-A6EC TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A29D TCGA-EE-A29E 
       57.90        24.89        62.37        20.38        12.99         0.26 
TCGA-EE-A29G TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A2 TCGA-EE-A2GM TCGA-EE-A2GP 
       44.28       346.49       185.19         7.20        18.35         0.76 
TCGA-EE-A2GS TCGA-EE-A2M6 TCGA-EE-A2MJ TCGA-EE-A2MM TCGA-EE-A2MR TCGA-EE-A2MU 
       71.31       103.13        63.25       145.45        25.08        53.26 
TCGA-EE-A3AB TCGA-EE-A3J7 TCGA-ER-A199 TCGA-ER-A19G TCGA-ER-A3ET TCGA-ER-A3PL 
      122.73        45.90         7.82       151.46        55.82        32.05 
TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7UA TCGA-FS-A1Z0 TCGA-FS-A1ZQ TCGA-FS-A1ZU 
      174.21       209.23         5.65       195.98       130.95         4.47 
TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A8LK TCGA-W3-A828 TCGA-W3-AA1Q 
       17.06         7.59       120.53        43.23       120.07        44.05 
TCGA-W3-AA1W TCGA-WE-A8K1 TCGA-WE-A8ZY TCGA-WE-AAA0 TCGA-YG-AA3O 
      185.13         1.15        48.39        26.60        28.21 

$`1P GAIN WILD-TYPE`
TCGA-3N-A9WC TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 
       60.46        14.83         8.42        15.72        31.89       110.93 
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 
       49.35       133.25        19.04        76.41        62.60        25.64 
TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JB TCGA-D3-A2JE TCGA-D3-A2JG TCGA-D3-A2JH 
       45.99        62.86       168.00         9.76       107.61        36.30 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE 
       66.08        43.53        46.98       140.98        40.01        59.70 
TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51J 
       16.96        13.87         9.34        23.67       173.85       144.46 
TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR 
       31.76        62.70        11.34        42.05        45.70       177.86 
TCGA-D3-A5GU TCGA-D3-A8GC TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GP TCGA-D3-A8GR 
      124.08        78.21       120.00        69.53       135.12        36.53 
TCGA-D9-A1X3 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY 
       10.78        16.90        18.44        22.85        48.66       106.85 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC 
       31.96       150.61        82.85        32.42        64.83        58.85 
TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5SG TCGA-EB-A5SH 
       25.12       214.59        14.96         3.91        33.24        50.07 
TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A182 TCGA-EE-A184 TCGA-EE-A20C 
       45.50         6.64        13.15         0.00        67.50        75.55 
TCGA-EE-A20H TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P 
      155.90        75.22        76.14        63.12        47.74        27.16 
TCGA-EE-A29Q TCGA-EE-A2A1 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE 
       61.12       102.38        77.98        26.14       239.11         0.20 
TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GO 
      189.40        68.65        10.62        32.48        31.00       118.32 
TCGA-EE-A2GR TCGA-EE-A2GU TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MF 
        0.20        81.99        15.25         5.75        23.77       209.79 
TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MP TCGA-EE-A2MS 
       94.19       171.85        67.50       104.78       227.01       143.93 
TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
       23.51       124.31        51.62         4.41        54.51         6.28 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JI TCGA-ER-A193 
       67.89       111.85         3.35       201.80       152.81        14.56 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C 
       34.45         1.58        47.31         4.54        53.29        39.81 
TCGA-ER-A19D TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P 
       11.47       150.12        99.06        59.84        42.48       120.76 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
       49.71        34.95       146.63        47.97        22.36         4.70 
TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3EV TCGA-FR-A7U8 TCGA-FR-A8YC 
       16.87        10.95       173.29        15.48        26.20        10.06 
TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD 
      171.78        49.74         8.35        27.62       312.07        32.78 
TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZS 
       35.90        12.92         7.82        36.33        78.61       136.27 
TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 
       35.28        23.21         5.29         3.06        30.90        66.67 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
      173.19        13.28        80.68        55.59        11.54        19.30 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        9.90         6.05         1.91        53.29       117.93        84.72 
TCGA-GN-A268 TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-GN-A9SD TCGA-LH-A9QB TCGA-OD-A75X 
       42.48        34.49        46.92        59.41        85.05       297.01 
TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-AA1R 
        7.23        18.05         0.33       174.12         1.97        79.99 
TCGA-W3-AA1V TCGA-W3-AA21 TCGA-WE-A8K5 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO 
        8.09        92.84        59.64        62.99        12.69        19.00 
TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-AA9Y TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-Z2-AA3S 
       59.44        10.95         1.94        16.64        15.65        91.23 

  1P GAIN MUTATED 1P GAIN WILD-TYPE 
             0.26              0.00 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
           346.49            312.07 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
           48.390            45.845 
[1] "0.3 - 346.5 (48.4)" "0.0 - 312.1 (45.8)"
[1] "hr=" "1.2"
D1V2, survival
                   sevent
clus2                 0   1
  1P GAIN MUTATED    40  43
  1P GAIN WILD-TYPE 129 137
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               83               266 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               43               137 
$`1P GAIN MUTATED`
TCGA-3N-A9WD TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JL TCGA-D3-A2JN 
       12.99       115.53        86.76        11.87       171.58        66.48 
TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3MR TCGA-D3-A5GO TCGA-D3-A8GD TCGA-D3-A8GI 
      130.72        58.06       103.59       137.92        23.61        58.52 
TCGA-D3-A8GJ TCGA-D3-A8GM TCGA-D9-A1JW TCGA-D9-A3Z1 TCGA-D9-A6E9 TCGA-D9-A6EA 
      241.38       107.15         3.65        15.39         9.90        25.18 
TCGA-D9-A6EC TCGA-DA-A1I0 TCGA-EB-A5UL TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A181 
       66.25        20.38        17.29        27.22        94.98        33.73 
TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29L 
       26.89       133.81        13.97        63.78        72.07         2.60 
TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A2 TCGA-EE-A2GI TCGA-EE-A2GM 
      369.93       195.02        17.92        36.82        48.72        75.48 
TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2M6 TCGA-EE-A2MD TCGA-EE-A2MJ TCGA-EE-A2MM 
       13.91        81.21       129.27        47.28        96.23       167.90 
TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AG 
       47.54        43.23       134.40        53.26       122.73        41.59 
TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-ER-A199 TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A3ET 
       64.08        53.19         9.17        26.37       268.93        80.32 
TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7UA 
       33.21         6.77        92.98       174.21       220.80        38.27 
TCGA-FS-A1YX TCGA-FS-A1Z0 TCGA-FS-A1ZH TCGA-FS-A1ZQ TCGA-FS-A1ZU TCGA-FS-A4F5 
       48.59       202.65        32.75       133.55        26.56        28.73 
TCGA-GF-A6C9 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A8LK 
       15.78        10.13        64.44        32.48       121.91        50.10 
TCGA-HR-A2OG TCGA-HR-A2OH TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1Q TCGA-W3-AA1W 
        0.23        65.88       121.08         4.01        69.07       219.16 
TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8ZY TCGA-WE-AAA0 TCGA-YG-AA3O 
       24.03        49.05        49.51        35.01        37.94 

$`1P GAIN WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
       17.03        66.48        14.93        16.57        16.67       112.04 
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA 
      112.57        71.80       133.25        28.08        31.59        90.90 
TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JB 
       95.74        43.43       103.10        65.49        23.77       168.00 
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JO 
       27.65        62.07       113.52        42.08        12.10        66.08 
TCGA-D3-A2JP TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE 
       59.57        46.98        46.32       166.52        86.93        60.23 
TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E 
       24.53        13.87         9.34        39.75        45.30       174.84 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R 
       55.73        56.35       145.12        32.94        22.62        63.81 
TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU 
       26.89       125.79       135.75       178.32        18.18       125.19 
TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GE TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GN 
       30.84        79.59        26.43       170.20        89.13       161.00 
TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A148 TCGA-D9-A149 
      152.75        29.06       129.63       117.17       151.53        54.67 
TCGA-D9-A1JX TCGA-D9-A1X3 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6EG TCGA-DA-A1HV 
        7.10        18.12        22.29        18.44        22.95        48.89 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
       36.03       117.21       194.83       176.55        35.93       107.34 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
       61.18        53.92        65.92        23.44        68.09        28.60 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH 
       10.49       215.44        15.68        13.87        10.36        20.35 
TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X 
       68.25        54.02        52.01         7.04        24.89        29.82 
TCGA-EE-A17Z TCGA-EE-A182 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A20F 
        8.65        14.70        68.15         4.96       151.27        91.56 
TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29H 
      168.26        13.55        63.35        85.08        78.97        64.64 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
       56.84        18.61        56.42        66.74        14.47        61.28 
TCGA-EE-A29V TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
       25.87        46.82       102.90        39.29        86.14        59.28 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK 
       67.43       340.14       161.03       208.04       107.38        54.74 
TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GR TCGA-EE-A2GT TCGA-EE-A2GU 
       79.66       102.12       126.81        42.77        44.88        94.82 
TCGA-EE-A2M5 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2ME TCGA-EE-A2MF 
       21.67        28.83        19.76        61.51       103.27       268.73 
TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MP 
      103.20        16.96       204.66       158.63       216.66       248.65 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
      162.48        71.21       124.31        51.62        28.77        54.51 
TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J8 
       13.81       138.81       172.18       127.20        36.95        34.32 
TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 
      201.80        27.35        51.35       109.58       152.81        31.40 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C 
       35.44        13.94        50.76        77.75        98.40        48.89 
TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
       12.59        13.02       152.35         6.44       131.51        61.05 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W 
       44.05       162.08        50.89        37.25         8.88       148.18 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
       79.99        43.82        23.34        20.15        16.37        31.27 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3EV TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A7U9 
       32.05       247.04        46.98        15.72        27.85        18.77 
TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z3 
       34.82        36.26       104.42       216.92       228.59        20.91 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD 
       28.08         7.79        27.72        48.85       357.37        53.52 
TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM 
       40.27        15.45         9.70        47.38        23.93       101.26 
TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A1ZY 
       74.73        11.41       148.80        53.16        49.48        27.09 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 
       27.02        77.82        50.14        66.67       174.84        34.03 
TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU 
       26.73        54.41        80.68         0.20        22.92        55.59 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 
       13.51        19.30         9.90         7.23         2.04       139.89 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A268 TCGA-GN-A26D TCGA-GN-A4U4 TCGA-GN-A4U7 
      117.93        84.72        62.79        39.58        39.35        10.42 
TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LL TCGA-GN-A9SD TCGA-LH-A9QB TCGA-OD-A75X 
       48.89        22.13        21.37        59.41       368.78       297.90 
TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 
        7.23        18.05         0.33         0.69       228.16        63.02 
TCGA-W3-AA1R TCGA-W3-AA1V TCGA-W3-AA21 TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZM 
      111.09        42.08       105.04        61.15        15.98        98.89 
TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-AA9Y 
       58.98        67.63        59.77        11.80        32.58        12.16 
TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YD-A89C TCGA-YD-A9TA TCGA-YG-AA3P TCGA-Z2-A8RT 
       19.73        22.29         6.90        49.18        14.43        27.58 
TCGA-Z2-AA3S TCGA-Z2-AA3V 
       96.99        15.98 

  1P GAIN MUTATED 1P GAIN WILD-TYPE 
             0.23              0.20 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
           369.93            368.78 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
            50.10             51.12 
[1] "0.2 - 369.9 (50.1)" "0.2 - 368.8 (51.1)"
[1] "hr=" "1"  
D1V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  1P GAIN MUTATED                   14             3
  1P GAIN WILD-TYPE                 51             2
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  1P GAIN MUTATED                                          21
  1P GAIN WILD-TYPE                                        51
                   vv
clus                REGIONAL LYMPH NODE
  1P GAIN MUTATED                    47
  1P GAIN WILD-TYPE                 168
D1V4, multiclass
                                           clus
vv                                          1P GAIN MUTATED 1P GAIN WILD-TYPE
  DISTANT METASTASIS                                     14                51
  PRIMARY TUMOR                                           3                 2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE              21                51
  REGIONAL LYMPH NODE                                    47               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                I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  1P GAIN MUTATED             3       3       7        5        8        8
  1P GAIN WILD-TYPE           9       4      21       13       19       16
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  1P GAIN MUTATED           1         2         2        11          9
  1P GAIN WILD-TYPE        13        17        10        26          6
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  1P GAIN MUTATED            6         10        3
  1P GAIN WILD-TYPE         26         50       17
D1V5, multiclass
             clus
vv            1P GAIN MUTATED 1P GAIN WILD-TYPE
  I OR II NOS               3                 9
  STAGE 0                   3                 4
  STAGE I                   7                21
  STAGE IA                  5                13
  STAGE IB                  8                19
  STAGE II                  8                16
  STAGE IIA                 1                13
  STAGE IIB                 2                17
  STAGE IIC                 2                10
  STAGE III                11                26
  STAGE IIIA                9                 6
  STAGE IIIB                6                26
  STAGE IIIC               10                50
  STAGE IV                  3                17
[1] 14  2
[1] TRUE
[1] "dimension of contingency 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      14 15 22 18
  1P GAIN WILD-TYPE    50 57 55 50
D1V6, multiclass
       clus
vv      1P GAIN MUTATED 1P GAIN WILD-TYPE
  T0+T1              14                50
  T2                 15                57
  T3                 22                55
  T4                 18                50
[1] 4 2
[1] TRUE
[1] "dimension of 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    42  19   9   8
  1P GAIN WILD-TYPE 127  44  29  41
D1V7, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  N0              42               127
  N1              19                44
  N2               9                29
  N3               8                41
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V8, binary
                   cls
clus                  0   1
  1P GAIN MUTATED    77   3
  1P GAIN WILD-TYPE 236  18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     77    3
  1P GAIN WILD-TYPE  236   18
   clus
vv  1P GAIN MUTATED 1P GAIN WILD-TYPE
  0              77               236
  1               3                18
[1] 2 2
[1] FALSE
D1V9, binary
                   cls
clus                 0  1
  1P GAIN MUTATED   37 20
  1P GAIN WILD-TYPE 95 68
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     37   20
  1P GAIN WILD-TYPE   95   68
     clus
vv    1P GAIN MUTATED 1P GAIN WILD-TYPE
  NO               37                95
  YES              20                68
[1] 2 2
[1] FALSE
D1V10, binary
                   cls
clus                  0   1
  1P GAIN MUTATED     9  75
  1P GAIN WILD-TYPE  35 238
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      9   75
  1P GAIN WILD-TYPE   35  238
     clus
vv    1P GAIN MUTATED 1P GAIN WILD-TYPE
  NO                9                35
  YES              75               238
[1] 2 2
[1] FALSE
D1V11, continuous
D1V12, binary
                   cls
clus                  0   1
  1P GAIN MUTATED    29  56
  1P GAIN WILD-TYPE 106 167
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     29   56
  1P GAIN WILD-TYPE  106  167
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  FEMALE              29               106
  MALE                56               167
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  1P GAIN MUTATED       1                         0    80
  1P GAIN WILD-TYPE     4                         1   264
D1V13, multiclass
                           clus
vv                          1P GAIN MUTATED 1P GAIN WILD-TYPE
  ASIAN                                   1                 4
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  80               264
[1] 3 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     2  79
  1P GAIN WILD-TYPE   5 265
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      2   79
  1P GAIN WILD-TYPE    5  265
                        clus
vv                       1P GAIN MUTATED 1P GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 5
  NOT HISPANIC OR LATINO              79               265
[1] 2 2
[1] FALSE

Clustering(2) Variable = 1Q GAIN MUTATION ANALYSIS
D2V1, survival
                   sevent
clus2                0  1
  1Q GAIN MUTATED   58 58
  1Q GAIN WILD-TYPE 63 60
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              116               123 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               58                60 
$`1Q GAIN MUTATED`
TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1QB TCGA-D3-A2J8 TCGA-D3-A2JA 
       12.99         8.42        15.72        62.60        62.86        15.75 
TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JE TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A3C6 
       86.30         7.27         9.76       171.58        64.83        58.06 
TCGA-D3-A3CE TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51K 
       59.70        13.87         9.34        90.21        23.67        31.76 
TCGA-D3-A51R TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GU TCGA-D3-A8GD TCGA-D3-A8GJ 
       62.70        42.05        45.70       124.08        23.61       179.97 
TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GP TCGA-D3-A8GR TCGA-D9-A3Z1 
      120.00        69.53        70.62       135.12        36.53        15.02 
TCGA-D9-A3Z3 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1I1 TCGA-DA-A1I5 TCGA-DA-A1IA 
       16.90        57.90        22.85        31.96        82.85        64.83 
TCGA-DA-A1IC TCGA-DA-A3F5 TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EE-A17Y TCGA-EE-A180 
       58.85       214.59        50.07        45.50        24.89        62.37 
TCGA-EE-A181 TCGA-EE-A184 TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G 
       20.38        67.50        75.22        12.99         0.26        44.28 
TCGA-EE-A29M TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 
       47.74       346.49       185.19       102.38         7.20        77.98 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO 
      239.11         0.20       189.40        18.35        31.00       118.32 
TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M7 TCGA-EE-A2MJ TCGA-EE-A2MR TCGA-EE-A2MS 
       71.31        81.99        15.25        63.25        25.08       143.93 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3J7 
       23.51        53.26       122.73        51.62         4.41        45.90 
TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19P TCGA-ER-A19Q 
        1.58         7.82        11.47       151.46       120.76        49.71 
TCGA-ER-A2ND TCGA-ER-A3ET TCGA-ER-A3PL TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7UA 
        4.70        55.82        32.05       174.21       209.23         5.65 
TCGA-FR-A8YC TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1ZC TCGA-FS-A1ZF TCGA-FS-A1ZQ 
       10.06       195.98         8.35       312.07        12.92       130.95 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4FD TCGA-GN-A267 
       35.28         4.47         5.29         3.06        80.68        17.06 
TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-GN-A8LK TCGA-GN-A9SD 
        7.59       120.53        34.49        46.92        43.23        59.41 
TCGA-LH-A9QB TCGA-QB-A6FS TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1Q TCGA-W3-AA1R 
       85.05         7.23         1.97       120.07        44.05        79.99 
TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8ZO TCGA-WE-A8ZY TCGA-WE-AAA0 
      185.13        92.84         1.15        19.00        48.39        26.60 
TCGA-WE-AAA4 TCGA-YG-AA3O 
       15.65        28.21 

$`1Q GAIN WILD-TYPE`
TCGA-3N-A9WC TCGA-BF-AAP0 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       60.46        14.83        31.89       110.93        49.35       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2JB TCGA-D3-A2JG 
       19.04        76.41        25.64        45.99       168.00       107.61 
TCGA-D3-A2JH TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CC 
       36.30        66.08        43.53        46.98       140.98        40.01 
TCGA-D3-A3CF TCGA-D3-A51E TCGA-D3-A51J TCGA-D3-A51T TCGA-D3-A5GR TCGA-D3-A8GC 
       16.96       173.85       144.46        11.34       177.86        78.21 
TCGA-D9-A1X3 TCGA-D9-A4Z6 TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I2 TCGA-DA-A1I7 
       10.78        18.44        48.66       106.85       150.61        32.42 
TCGA-DA-A3F2 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5SG TCGA-EB-A6L9 TCGA-EE-A17X 
       25.12        14.96         3.91        33.24         6.64        13.15 
TCGA-EE-A182 TCGA-EE-A20C TCGA-EE-A20H TCGA-EE-A29C TCGA-EE-A29H TCGA-EE-A29P 
        0.00        75.55       155.90        76.14        63.12        27.16 
TCGA-EE-A29Q TCGA-EE-A2GB TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GP 
       61.12        26.14        68.65        10.62        32.48         0.76 
TCGA-EE-A2GR TCGA-EE-A2M6 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MG 
        0.20       103.13         5.75        23.77       209.79        94.19 
TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A3AA 
      171.85        67.50       104.78       145.45       227.01       124.31 
TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J8 TCGA-EE-A3JB 
       54.51         6.28        67.89       111.85         3.35       201.80 
TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19B 
      152.81        14.56        34.45        47.31         4.54        53.29 
TCGA-ER-A19C TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19S 
       39.81       150.12        99.06        59.84        42.48        34.95 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A3ES 
      146.63        47.97        22.36        16.87        10.95       173.29 
TCGA-ER-A3EV TCGA-FR-A7U8 TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z4 TCGA-FS-A1ZD 
       15.48        26.20       171.78        49.74        27.62        32.78 
TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZS TCGA-FS-A1ZW 
       35.90         7.82        36.33        78.61       136.27        23.21 
TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FW-A3TU TCGA-FW-A3TV 
       30.90        66.67       173.19        13.28        55.59        11.54 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 
       19.30         9.90         6.05         1.91        53.29       117.93 
TCGA-GN-A265 TCGA-GN-A268 TCGA-OD-A75X TCGA-QB-AA9O TCGA-RP-A693 TCGA-W3-A824 
       84.72        42.48       297.01        18.05         0.33       174.12 
TCGA-W3-AA1V TCGA-WE-A8K5 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZQ TCGA-WE-A8ZT 
        8.09        59.64        62.99        12.69        59.44        10.95 
TCGA-WE-AA9Y TCGA-WE-AAA3 TCGA-Z2-AA3S 
        1.94        16.64        91.23 

  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              0.2               0.0 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
           346.49            297.01 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
            46.41             45.99 
[1] "0.2 - 346.5 (46.4)" "0.0 - 297.0 (46.0)"
[1] "hr=" "1"  
D2V2, survival
                   sevent
clus2                0  1
  1Q GAIN MUTATED   79 86
  1Q GAIN WILD-TYPE 90 94
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              165               184 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               86                94 
$`1Q GAIN MUTATED`
TCGA-3N-A9WB TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1QB TCGA-D3-A2J8 
       17.03        12.99        16.57        16.67        95.74        65.49 
TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JE TCGA-D3-A2JL TCGA-D3-A2JN 
      115.53        86.76        11.87        27.65       171.58        66.48 
TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR 
      130.72        58.06        60.23        13.87         9.34       103.59 
TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A5GL TCGA-D3-A5GN 
       39.75        45.30        32.94        63.81       125.79       135.75 
TCGA-D3-A5GO TCGA-D3-A5GU TCGA-D3-A8GD TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GK 
      137.92       125.19        23.61        58.52       241.38       170.20 
TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D9-A1JW 
       89.13       107.15       152.75        29.06       129.63         3.65 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG 
       15.39        22.29         9.90        25.18        66.25        22.95 
TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1IA TCGA-DA-A1IC 
       20.38       194.83        35.93       107.34        65.92        68.09 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-EB-A44R TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN 
       10.49       215.44        10.36        54.02        17.29        52.01 
TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A184 TCGA-EE-A20B 
       27.22         8.65        94.98        33.73        68.15       133.81 
TCGA-EE-A20I TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29L 
       13.55        85.08        13.97        63.78        72.07         2.60 
TCGA-EE-A29M TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 
       56.84        14.47        61.28       369.93       195.02       102.90 
TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
       36.82        86.14       340.14       161.03       208.04        48.72 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M7 
       75.48       102.12       126.81        81.21        94.82        28.83 
TCGA-EE-A2MD TCGA-EE-A2MJ TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS 
       47.28        96.23        47.54        43.23       134.40       162.48 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AG 
       71.21        53.26       122.73        51.62        28.77        41.59 
TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-EE-A3JH TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19D 
       64.08        53.19       109.58        13.94         9.17        12.59 
TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A2ND TCGA-ER-A2NF 
       26.37       268.93       162.08        50.89        23.34        16.37 
TCGA-ER-A2NH TCGA-ER-A3ET TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A 
       32.05        80.32        33.21         6.77        92.98       174.21 
TCGA-FR-A729 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FS-A1YX TCGA-FS-A1Z0 TCGA-FS-A1Z3 
      220.80        38.27        34.82        48.59       202.65        20.91 
TCGA-FS-A1ZA TCGA-FS-A1ZC TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-FS-A1ZK TCGA-FS-A1ZP 
       27.72       357.37        15.45        32.75        23.93        74.73 
TCGA-FS-A1ZQ TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F5 
      133.55        53.16        26.56        27.09        27.02        28.73 
TCGA-FS-A4FD TCGA-GF-A6C9 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A26D 
       80.68        15.78        10.13        64.44        32.48        39.58 
TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK 
      121.91        39.35        10.42        48.89        22.13        50.10 
TCGA-GN-A9SD TCGA-HR-A2OG TCGA-HR-A2OH TCGA-LH-A9QB TCGA-QB-A6FS TCGA-W3-A825 
       59.41         0.23        65.88       368.78         7.23        63.02 
TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1W TCGA-W3-AA21 
      121.08         4.01        69.07       111.09       219.16       105.04 
TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8ZO TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AAA0 
       24.03        49.05        67.63        32.58        49.51        35.01 
TCGA-WE-AAA4 TCGA-YD-A9TA TCGA-YG-AA3O 
       22.29        49.18        37.94 

$`1Q GAIN WILD-TYPE`
TCGA-3N-A9WC TCGA-BF-AAP0 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       66.48        14.93       112.04       112.57        71.80       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J9 
       28.08        31.59        90.90        43.43       103.10        23.77 
TCGA-D3-A2JB TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JO 
      168.00        62.07       113.52        42.08        12.10        66.08 
TCGA-D3-A2JP TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CF 
       59.57        46.98        46.32       166.52        86.93        24.53 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51N TCGA-D3-A51T 
      174.84        55.73        56.35       145.12        22.62        26.89 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GE TCGA-D3-A8GN 
      178.32        18.18        30.84        79.59        26.43       161.00 
TCGA-D3-A8GS TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JX TCGA-D9-A1X3 TCGA-D9-A4Z6 
      117.17       151.53        54.67         7.10        18.12        18.44 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I2 TCGA-DA-A1I7 TCGA-DA-A1I8 
       48.89        36.03       117.21       176.55        61.18        53.92 
TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5SG 
       23.44        28.60        15.68        13.87        20.35        68.25 
TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 
        7.04        24.89        29.82        14.70        26.89         4.96 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29H 
      151.27        91.56       168.26        63.35        78.97        64.64 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A0 
       18.61        56.42        66.74        25.87        17.92        46.82 
TCGA-EE-A2A5 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
       39.29        59.28        67.43       107.38        54.74        79.66 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M8 
       13.91        42.77        44.88        21.67       129.27        19.76 
TCGA-EE-A2MC TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
       61.51       103.27       268.73       103.20        16.96       204.66 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A3AA TCGA-EE-A3AE 
      158.63       216.66       167.90       248.65       124.31        54.51 
TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J8 
       13.81       138.81       172.18       127.20        36.95        34.32 
TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 
      201.80        27.35        51.35       152.81        31.40        35.44 
TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19E TCGA-ER-A19H 
       50.76        77.75        98.40        48.89        13.02       152.35 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19S TCGA-ER-A19T 
        6.44       131.51        61.05        44.05        37.25         8.88 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A3ES 
      148.18        79.99        43.82        20.15        31.27       247.04 
TCGA-ER-A3EV TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A8YD TCGA-FR-A8YE 
       46.98        15.72        27.85        18.77        36.26       104.42 
TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZB TCGA-FS-A1ZD 
      216.92       228.59        28.08         7.79        48.85        53.52 
TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZR TCGA-FS-A1ZS 
       40.27         9.70        47.38       101.26        11.41       148.80 
TCGA-FS-A1ZW TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 
       49.48        77.82        50.14        66.67       174.84        34.03 
TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV 
       26.73        54.41         0.20        22.92        55.59        13.51 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 
       19.30         9.90         7.23         2.04       139.89       117.93 
TCGA-GN-A265 TCGA-GN-A268 TCGA-GN-A8LL TCGA-OD-A75X TCGA-QB-AA9O TCGA-RP-A693 
       84.72        62.79        21.37       297.90        18.05         0.33 
TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-AA1V TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZM 
        0.69       228.16        42.08        61.15        15.98        98.89 
TCGA-WE-A8ZN TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-AA9Y TCGA-WE-AAA3 TCGA-YD-A89C 
       58.98        59.77        11.80        12.16        19.73         6.90 
TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
       14.43        27.58        96.99        15.98 

  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
             0.23              0.20 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
           369.93            297.90 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
            52.01             49.81 
[1] "0.2 - 369.9 (52.0)" "0.2 - 297.9 (49.8)"
[1] "hr=" "1.1"
D2V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  1Q GAIN MUTATED                   39             4
  1Q GAIN WILD-TYPE                 26             1
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  1Q GAIN MUTATED                                          33
  1Q GAIN WILD-TYPE                                        39
                   vv
clus                REGIONAL LYMPH NODE
  1Q GAIN MUTATED                    92
  1Q GAIN WILD-TYPE                 123
D2V4, multiclass
                                           clus
vv                                          1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  DISTANT METASTASIS                                     39                26
  PRIMARY TUMOR                                           4                 1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE              33                39
  REGIONAL LYMPH NODE                                    92               123
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  1Q GAIN MUTATED             4       3       9        9       16       16
  1Q GAIN WILD-TYPE           8       4      19        9       11        8
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  1Q GAIN MUTATED           6         8         6        19         12
  1Q GAIN WILD-TYPE         8        11         6        18          3
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  1Q GAIN MUTATED           17         24        7
  1Q GAIN WILD-TYPE         15         36       13
D2V5, multiclass
             clus
vv            1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  I OR II NOS               4                 8
  STAGE 0                   3                 4
  STAGE I                   9                19
  STAGE IA                  9                 9
  STAGE IB                 16                11
  STAGE II                 16                 8
  STAGE IIA                 6                 8
  STAGE IIB                 8                11
  STAGE IIC                 6                 6
  STAGE III                19                18
  STAGE IIIA               12                 3
  STAGE IIIB               17                15
  STAGE IIIC               24                36
  STAGE IV                  7                13
[1] 14  2
[1] TRUE
[1] "dimension of contingency 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      30 35 43 30
  1Q GAIN WILD-TYPE    34 37 34 38
D2V6, multiclass
       clus
vv      1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  T0+T1              30                34
  T2                 35                37
  T3                 43                34
  T4                 30                38
[1] 4 2
[1] TRUE
[1] "dimension of 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   82 29 22 20
  1Q GAIN WILD-TYPE 87 34 16 29
D2V7, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  N0              82                87
  N1              29                34
  N2              22                16
  N3              20                29
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V8, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED   152   7
  1Q GAIN WILD-TYPE 161  14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED    152    7
  1Q GAIN WILD-TYPE  161   14
   clus
vv  1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  0             152               161
  1               7                14
[1] 2 2
[1] FALSE
D2V9, binary
                   cls
clus                 0  1
  1Q GAIN MUTATED   69 40
  1Q GAIN WILD-TYPE 63 48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     69   40
  1Q GAIN WILD-TYPE   63   48
     clus
vv    1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  NO               69                63
  YES              40                48
[1] 2 2
[1] FALSE
D2V10, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED    18 150
  1Q GAIN WILD-TYPE  26 163
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     18  150
  1Q GAIN WILD-TYPE   26  163
     clus
vv    1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  NO               18                26
  YES             150               163
[1] 2 2
[1] FALSE
D2V11, continuous
D2V12, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED    61 108
  1Q GAIN WILD-TYPE  74 115
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     61  108
  1Q GAIN WILD-TYPE   74  115
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  FEMALE              61                74
  MALE               108               115
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  1Q GAIN MUTATED       2                         0   162
  1Q GAIN WILD-TYPE     3                         1   182
D2V13, multiclass
                           clus
vv                          1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  ASIAN                                   2                 3
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                 162               182
[1] 3 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     5 160
  1Q GAIN WILD-TYPE   2 184
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      5  160
  1Q GAIN WILD-TYPE    2  184
                        clus
vv                       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   5                 2
  NOT HISPANIC OR LATINO             160               184
[1] 2 2
[1] FALSE

Clustering(3) Variable = 2P GAIN MUTATION ANALYSIS
D3V1, survival
                   sevent
clus2                0  1
  2P GAIN MUTATED   22 22
  2P GAIN WILD-TYPE 99 96
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               44               195 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               22                96 
$`2P GAIN MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q6 TCGA-D3-A2JA TCGA-D3-A2JD TCGA-D3-A2JE TCGA-D3-A2JN 
        8.42        49.35        15.75         7.27         9.76        64.83 
TCGA-D3-A2JO TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3ML TCGA-D3-A5GN TCGA-D3-A8GC 
       66.08       140.98        40.01        13.87        45.70        78.21 
TCGA-DA-A1HY TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A5SH TCGA-EE-A20H TCGA-EE-A29D 
      106.85       214.59        14.96        50.07       155.90        12.99 
TCGA-EE-A29M TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2GM 
       47.74        61.12       346.49       185.19       102.38        18.35 
TCGA-EE-A2GN TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MR TCGA-EE-A2MU TCGA-EE-A3AE 
       31.00       103.13        15.25        25.08        53.26        54.51 
TCGA-EE-A3JB TCGA-EE-A3JI TCGA-ER-A197 TCGA-ER-A19B TCGA-ER-A19G TCGA-ER-A19H 
      201.80       152.81         1.58        53.29       151.46       150.12 
TCGA-ER-A19N TCGA-ER-A2NC TCGA-FS-A1ZD TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-QB-AA9O 
       42.48        22.36        32.78        78.61       130.95        18.05 
TCGA-W3-A825 TCGA-WE-A8ZY 
        1.97        48.39 

$`2P GAIN WILD-TYPE`
TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 
       60.46        12.99        14.83        15.72        31.89       110.93 
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
      133.25        19.04        76.41        62.60        25.64        45.99 
TCGA-D3-A2J8 TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL 
       62.86       168.00        86.30       107.61        36.30       171.58 
TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO 
       43.53        58.06        46.98        59.70        16.96         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R 
       90.21        23.67       173.85       144.46        31.76        62.70 
TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D3-A8GD TCGA-D3-A8GJ 
       11.34        42.05       177.86       124.08        23.61       179.97 
TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GP TCGA-D3-A8GR TCGA-D9-A1X3 
      120.00        69.53        70.62       135.12        36.53        10.78 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV 
       15.02        16.90        18.44        57.90        22.85        48.66 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC 
       31.96       150.61        82.85        32.42        64.83        58.85 
TCGA-DA-A3F2 TCGA-EB-A44Q TCGA-EB-A5SG TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X 
       25.12         3.91        33.24        45.50         6.64        13.15 
TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A184 TCGA-EE-A20C 
       24.89        62.37        20.38         0.00        67.50        75.55 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29P 
       75.22        76.14         0.26        44.28        63.12        27.16 
TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
        7.20        77.98        26.14       239.11         0.20       189.40 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR 
       68.65        10.62        32.48       118.32         0.76         0.20 
TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MG 
       71.31        81.99         5.75        23.77       209.79        94.19 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP 
      171.85        63.25        67.50       104.78       145.45       227.01 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
      143.93        23.51       124.31       122.73        51.62         4.41 
TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-ER-A193 
        6.28        67.89       111.85        45.90         3.35        14.56 
TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19C TCGA-ER-A19D 
       34.45        47.31         7.82         4.54        39.81        11.47 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W 
       99.06        59.84       120.76        49.71        34.95       146.63 
TCGA-ER-A1A1 TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET 
       47.97         4.70        16.87        10.95       173.29        55.82 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7UA 
       15.48        32.05       174.21       209.23        26.20         5.65 
TCGA-FR-A8YC TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 
       10.06       171.78        49.74       195.98         8.35        27.62 
TCGA-FS-A1ZC TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZS 
      312.07        35.90        12.92         7.82        36.33       136.27 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 
       35.28         4.47        23.21         5.29         3.06        30.90 
TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV 
       66.67       173.19        13.28        80.68        55.59        11.54 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 
       19.30         9.90         6.05         1.91        53.29       117.93 
TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 
       84.72        17.06        42.48         7.59       120.53        34.49 
TCGA-GN-A4U8 TCGA-GN-A8LK TCGA-GN-A9SD TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS 
       46.92        43.23        59.41        85.05       297.01         7.23 
TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A828 TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1V 
        0.33       174.12       120.07        44.05        79.99         8.09 
TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8ZM TCGA-WE-A8ZN 
      185.13        92.84         1.15        59.64        62.99        12.69 
TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 
       19.00        59.44        10.95         1.94        26.60        16.64 
TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-Z2-AA3S 
       15.65        28.21        91.23 

  2P GAIN MUTATED 2P GAIN WILD-TYPE 
             1.58              0.00 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
           346.49            312.07 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
            49.71             44.28 
[1] "1.6 - 346.5 (49.7)" "0.0 - 312.1 (44.3)"
[1] "hr=" "1.1"
D3V2, survival
                   sevent
clus2                 0   1
  2P GAIN MUTATED    32  32
  2P GAIN WILD-TYPE 137 148
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               64               285 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               32               148 
$`2P GAIN MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q6 TCGA-D3-A1Q9 TCGA-D3-A2JA TCGA-D3-A2JD TCGA-D3-A2JE 
       16.57        71.80        31.59       115.53        11.87        27.65 
TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3ML TCGA-D3-A3MV 
       66.48        66.08       166.52        86.93        13.87        45.30 
TCGA-D3-A5GN TCGA-D3-A8GC TCGA-D3-A8GI TCGA-D3-A8GQ TCGA-D9-A148 TCGA-D9-A6E9 
      135.75        79.59        58.52        29.06       151.53         9.90 
TCGA-DA-A1HY TCGA-DA-A1I8 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A5SH TCGA-EE-A20H 
      117.21        53.92       215.44        15.68        54.02       168.26 
TCGA-EE-A29A TCGA-EE-A29D TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29Q TCGA-EE-A29R 
       63.35        13.97         2.60        56.84        66.74        14.47 
TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2M6 
      369.93       195.02       102.90        75.48       102.12       129.27 
TCGA-EE-A2M7 TCGA-EE-A2MR TCGA-EE-A2MU TCGA-EE-A3AE TCGA-EE-A3AG TCGA-EE-A3JB 
       28.83       134.40        53.26        54.51        41.59       201.80 
TCGA-EE-A3JI TCGA-ER-A197 TCGA-ER-A19B TCGA-ER-A19E TCGA-ER-A19G TCGA-ER-A19H 
      152.81        13.94        98.40        13.02       268.93       152.35 
TCGA-ER-A19N TCGA-ER-A2NC TCGA-FR-A3YN TCGA-FS-A1ZD TCGA-FS-A1ZK TCGA-FS-A1ZM 
       44.05        43.82        92.98        53.52        23.93       101.26 
TCGA-FS-A1ZQ TCGA-FW-A3I3 TCGA-QB-AA9O TCGA-W3-A825 TCGA-W3-AA1O TCGA-WE-A8JZ 
      133.55         0.20        18.05        63.02         4.01        24.03 
TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-YD-A89C TCGA-YD-A9TA 
       32.58        49.51         6.90        49.18 

$`2P GAIN WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
       17.03        66.48        12.99        14.93        16.67       112.04 
TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 
      112.57       133.25        28.08        90.90        95.74        43.43 
TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JF 
      103.10        65.49        23.77       168.00        86.76        62.07 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JP TCGA-D3-A3BZ 
      113.52        42.08        12.10       171.58        59.57       130.72 
TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO 
       58.06        46.98        46.32        60.23        24.53         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J 
      103.59        39.75       174.84        55.73        56.35       145.12 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GO 
       32.94        22.62        63.81        26.89       125.79       137.92 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GD TCGA-D3-A8GE 
      178.32        18.18       125.19        30.84        23.61        26.43 
TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GP 
      241.38       170.20        89.13       107.15       161.00       152.75 
TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A1X3 
      129.63       117.17        54.67         3.65         7.10        18.12 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG 
       15.39        22.29        18.44        25.18        66.25        22.95 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 
       48.89        36.03        20.38       194.83       176.55        35.93 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
      107.34        61.18        65.92        23.44        68.09        28.60 
TCGA-DA-A3F3 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5UL 
       10.49        13.87        10.36        20.35        68.25        17.29 
TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
       52.01         7.04        24.89        29.82        27.22         8.65 
TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 
       94.98        33.73        14.70        26.89        68.15         4.96 
TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29B TCGA-EE-A29C 
      133.81       151.27        91.56        13.55        85.08        78.97 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29S 
       63.78        72.07        64.64        18.61        56.42        61.28 
TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
       25.87        17.92        46.82        36.82        39.29        86.14 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
       59.28        67.43       340.14       161.03       208.04        48.72 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR 
      107.38        54.74        79.66       126.81        13.91        42.77 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M8 TCGA-EE-A2MC 
       81.21        44.88        94.82        21.67        19.76        61.51 
TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
       47.28       103.27       268.73       103.20        16.96       204.66 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP 
       96.23       158.63       216.66       167.90        47.54       248.65 
TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC 
       43.23       162.48        71.21       124.31       122.73        51.62 
TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 
       28.77        13.81       138.81       172.18       127.20        36.95 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH 
       64.08        34.32        53.19        27.35        51.35       109.58 
TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19C 
       31.40        35.44        50.76         9.17        77.75        48.89 
TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19P 
       12.59        26.37         6.44       131.51        61.05       162.08 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2ND 
       50.89        37.25         8.88       148.18        79.99        23.34 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET 
       20.15        16.37        31.27        32.05       247.04        80.32 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 
       46.98        33.21         6.77       174.21        15.72       220.80 
TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE 
       27.85        18.77        38.27        34.82        36.26       104.42 
TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 
      216.92        48.59       228.59       202.65        20.91        28.08 
TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZE TCGA-FS-A1ZF 
        7.79        27.72        48.85       357.37        40.27        15.45 
TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZS 
        9.70        32.75        47.38        74.73        11.41       148.80 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 
       53.16        26.56        49.48        27.09        27.02        77.82 
TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB 
       50.14        66.67        28.73       174.84        34.03        26.73 
TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
       54.41        80.68        22.92        55.59        13.51        19.30 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 
        9.90         7.23         2.04        15.78       139.89       117.93 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
       84.72        10.13        64.44        62.79        32.48        39.58 
TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK 
      121.91        39.35        10.42        48.89        22.13        50.10 
TCGA-GN-A8LL TCGA-GN-A9SD TCGA-HR-A2OG TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X 
       21.37        59.41         0.23        65.88       368.78       297.90 
TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A828 TCGA-W3-AA1Q 
        7.23         0.33         0.69       228.16       121.08        69.07 
TCGA-W3-AA1R TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8K5 
      111.09        42.08       219.16       105.04        49.05        61.15 
TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT 
       15.98        98.89        58.98        67.63        59.77        11.80 
TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-YG-AA3P 
       12.16        35.01        19.73        22.29        37.94        14.43 
TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
       27.58        96.99        15.98 

  2P GAIN MUTATED 2P GAIN WILD-TYPE 
             0.20              0.23 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
           369.93            368.78 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
           55.675            49.050 
[1] "0.2 - 369.9 (55.7)" "0.2 - 368.8 (49.0)"
[1] "hr=" "1.1"
D3V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  2P GAIN MUTATED                   11             1
  2P GAIN WILD-TYPE                 54             4
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  2P GAIN MUTATED                                          17
  2P GAIN WILD-TYPE                                        55
                   vv
clus                REGIONAL LYMPH NODE
  2P GAIN MUTATED                    36
  2P GAIN WILD-TYPE                 179
D3V4, multiclass
                                           clus
vv                                          2P GAIN MUTATED 2P GAIN WILD-TYPE
  DISTANT METASTASIS                                     11                54
  PRIMARY TUMOR                                           1                 4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE              17                55
  REGIONAL LYMPH NODE                                    36               179
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  2P GAIN MUTATED             3       2       5        4        5        4
  2P GAIN WILD-TYPE           9       5      23       14       22       20
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  2P GAIN MUTATED           3         1         2         7          4
  2P GAIN WILD-TYPE        11        18        10        30         11
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  2P GAIN MUTATED            6         12        1
  2P GAIN WILD-TYPE         26         48       19
D3V5, multiclass
             clus
vv            2P GAIN MUTATED 2P GAIN WILD-TYPE
  I OR II NOS               3                 9
  STAGE 0                   2                 5
  STAGE I                   5                23
  STAGE IA                  4                14
  STAGE IB                  5                22
  STAGE II                  4                20
  STAGE IIA                 3                11
  STAGE IIB                 1                18
  STAGE IIC                 2                10
  STAGE III                 7                30
  STAGE IIIA                4                11
  STAGE IIIB                6                26
  STAGE IIIC               12                48
  STAGE IV                  1                19
[1] 14  2
[1] TRUE
[1] "dimension of contingency 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      10 17 11 12
  2P GAIN WILD-TYPE    54 55 66 56
D3V6, multiclass
       clus
vv      2P GAIN MUTATED 2P GAIN WILD-TYPE
  T0+T1              10                54
  T2                 17                55
  T3                 11                66
  T4                 12                56
[1] 4 2
[1] TRUE
[1] "dimension of 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    32  12   7  10
  2P GAIN WILD-TYPE 137  51  31  39
D3V7, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  N0              32               137
  N1              12                51
  N2               7                31
  N3              10                39
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V8, binary
                   cls
clus                  0   1
  2P GAIN MUTATED    62   2
  2P GAIN WILD-TYPE 251  19
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     62    2
  2P GAIN WILD-TYPE  251   19
   clus
vv  2P GAIN MUTATED 2P GAIN WILD-TYPE
  0              62               251
  1               2                19
[1] 2 2
[1] FALSE
D3V9, binary
                   cls
clus                  0   1
  2P GAIN MUTATED    21  17
  2P GAIN WILD-TYPE 111  71
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     21   17
  2P GAIN WILD-TYPE  111   71
     clus
vv    2P GAIN MUTATED 2P GAIN WILD-TYPE
  NO               21               111
  YES              17                71
[1] 2 2
[1] FALSE
D3V10, binary
                   cls
clus                  0   1
  2P GAIN MUTATED     8  58
  2P GAIN WILD-TYPE  36 255
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      8   58
  2P GAIN WILD-TYPE   36  255
     clus
vv    2P GAIN MUTATED 2P GAIN WILD-TYPE
  NO                8                36
  YES              58               255
[1] 2 2
[1] FALSE
D3V11, continuous
D3V12, binary
                   cls
clus                  0   1
  2P GAIN MUTATED    24  42
  2P GAIN WILD-TYPE 111 181
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     24   42
  2P GAIN WILD-TYPE  111  181
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  FEMALE              24               111
  MALE                42               181
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  2P GAIN MUTATED       0                         0    65
  2P GAIN WILD-TYPE     5                         1   279
D3V13, multiclass
                           clus
vv                          2P GAIN MUTATED 2P GAIN WILD-TYPE
  ASIAN                                   0                 5
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  65               279
[1] 3 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     0  64
  2P GAIN WILD-TYPE   7 280
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      0   64
  2P GAIN WILD-TYPE    7  280
                        clus
vv                       2P GAIN MUTATED 2P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 7
  NOT HISPANIC OR LATINO              64               280
[1] 2 2
[1] FALSE

Clustering(4) Variable = 2Q GAIN MUTATION ANALYSIS
D4V1, survival
                   sevent
clus2                 0   1
  2Q GAIN MUTATED    23  18
  2Q GAIN WILD-TYPE  98 100
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               41               198 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               18               100 
$`2Q GAIN MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q6 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JE 
        8.42        49.35        15.75        86.30         7.27         9.76 
TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3ML TCGA-D3-A5GN 
       64.83        66.08       140.98        40.01        13.87        45.70 
TCGA-D3-A8GC TCGA-DA-A1HY TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A5SH TCGA-EE-A20H 
       78.21       106.85       214.59        14.96        50.07       155.90 
TCGA-EE-A29M TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2GM 
       47.74        61.12       346.49       185.19       102.38        18.35 
TCGA-EE-A2GN TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MR TCGA-EE-A2MU TCGA-EE-A3AE 
       31.00       103.13        15.25        25.08        53.26        54.51 
TCGA-EE-A3JB TCGA-EE-A3JI TCGA-ER-A19B TCGA-ER-A19G TCGA-ER-A19N TCGA-ER-A2NC 
      201.80       152.81        53.29       151.46        42.48        22.36 
TCGA-FS-A1ZD TCGA-FS-A1ZM TCGA-GN-A9SD TCGA-QB-AA9O TCGA-W3-A825 
       32.78        78.61        59.41        18.05         1.97 

$`2Q GAIN WILD-TYPE`
TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 
       60.46        12.99        14.83        15.72        31.89       110.93 
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
      133.25        19.04        76.41        62.60        25.64        45.99 
TCGA-D3-A2J8 TCGA-D3-A2JB TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JP 
       62.86       168.00       107.61        36.30       171.58        43.53 
TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR 
       58.06        46.98        59.70        16.96         9.34        90.21 
TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T 
       23.67       173.85       144.46        31.76        62.70        11.34 
TCGA-D3-A5GL TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D3-A8GD TCGA-D3-A8GJ TCGA-D3-A8GK 
       42.05       177.86       124.08        23.61       179.97       120.00 
TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GP TCGA-D3-A8GR TCGA-D9-A1X3 TCGA-D9-A3Z1 
       69.53        70.62       135.12        36.53        10.78        15.02 
TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1I1 
       16.90        18.44        57.90        22.85        48.66        31.96 
TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 
      150.61        82.85        32.42        64.83        58.85        25.12 
TCGA-EB-A44Q TCGA-EB-A5SG TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y 
        3.91        33.24        45.50         6.64        13.15        24.89 
TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A184 TCGA-EE-A20C TCGA-EE-A29B 
       62.37        20.38         0.00        67.50        75.55        75.22 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29P 
       76.14        12.99         0.26        44.28        63.12        27.16 
TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
        7.20        77.98        26.14       239.11         0.20       189.40 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR 
       68.65        10.62        32.48       118.32         0.76         0.20 
TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MG 
       71.31        81.99         5.75        23.77       209.79        94.19 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP 
      171.85        63.25        67.50       104.78       145.45       227.01 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
      143.93        23.51       124.31       122.73        51.62         4.41 
TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-ER-A193 
        6.28        67.89       111.85        45.90         3.35        14.56 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19C 
       34.45         1.58        47.31         7.82         4.54        39.81 
TCGA-ER-A19D TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19P TCGA-ER-A19Q 
       11.47       150.12        99.06        59.84       120.76        49.71 
TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NG 
       34.95       146.63        47.97         4.70        16.87        10.95 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A44A TCGA-FR-A729 
      173.29        55.82        15.48        32.05       174.21       209.23 
TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 
       26.20         5.65        10.06       171.78        49.74       195.98 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG 
        8.35        27.62       312.07        35.90        12.92         7.82 
TCGA-FS-A1ZJ TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW 
       36.33       130.95       136.27        35.28         4.47        23.21 
TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 
        5.29         3.06        30.90        66.67       173.19        13.28 
TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
       80.68        55.59        11.54        19.30         9.90         6.05 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 
        1.91        53.29       117.93        84.72        17.06        42.48 
TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-GN-A8LK TCGA-LH-A9QB 
        7.59       120.53        34.49        46.92        43.23        85.05 
TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A828 TCGA-W3-AA1Q 
      297.01         7.23         0.33       174.12       120.07        44.05 
TCGA-W3-AA1R TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8K5 
       79.99         8.09       185.13        92.84         1.15        59.64 
TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZY 
       62.99        12.69        19.00        59.44        10.95        48.39 
TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-Z2-AA3S 
        1.94        26.60        16.64        15.65        28.21        91.23 

  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
             1.97              0.00 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
           346.49            312.07 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
           53.260            44.165 
[1] "2.0 - 346.5 (53.3)" "0.0 - 312.1 (44.2)"
[1] "hr=" "1.4"
D4V2, survival
                   sevent
clus2                 0   1
  2Q GAIN MUTATED    33  28
  2Q GAIN WILD-TYPE 136 152
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               61               288 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               28               152 
$`2Q GAIN MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q6 TCGA-D3-A1Q9 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JD 
       16.57        71.80        31.59       115.53        86.76        11.87 
TCGA-D3-A2JE TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3ML 
       27.65        66.48        66.08       166.52        86.93        13.87 
TCGA-D3-A3MV TCGA-D3-A5GN TCGA-D3-A8GC TCGA-D3-A8GI TCGA-D3-A8GQ TCGA-D9-A6E9 
       45.30       135.75        79.59        58.52        29.06         9.90 
TCGA-DA-A1HY TCGA-DA-A1I8 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A5SH TCGA-EB-A5UL 
      117.21        53.92       215.44        15.68        54.02        17.29 
TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29Q TCGA-EE-A29R 
      168.26        63.35         2.60        56.84        66.74        14.47 
TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2M6 
      369.93       195.02       102.90        75.48       102.12       129.27 
TCGA-EE-A2M7 TCGA-EE-A2MR TCGA-EE-A2MU TCGA-EE-A3AE TCGA-EE-A3AG TCGA-EE-A3JB 
       28.83       134.40        53.26        54.51        41.59       201.80 
TCGA-EE-A3JI TCGA-ER-A19B TCGA-ER-A19E TCGA-ER-A19G TCGA-ER-A19N TCGA-ER-A2NC 
      152.81        98.40        13.02       268.93        44.05        43.82 
TCGA-FR-A3YN TCGA-FS-A1ZD TCGA-FS-A1ZM TCGA-FS-A4F5 TCGA-FW-A3I3 TCGA-GN-A9SD 
       92.98        53.52       101.26        28.73         0.20        59.41 
TCGA-QB-AA9O TCGA-W3-A825 TCGA-W3-AA1O TCGA-WE-A8JZ TCGA-WE-A8ZX TCGA-YD-A89C 
       18.05        63.02         4.01        24.03        32.58         6.90 
TCGA-YD-A9TA 
       49.18 

$`2Q GAIN WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
       17.03        66.48        12.99        14.93        16.67       112.04 
TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 
      112.57       133.25        28.08        90.90        95.74        43.43 
TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JF TCGA-D3-A2JG 
      103.10        65.49        23.77       168.00        62.07       113.52 
TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 
       42.08        12.10       171.58        59.57       130.72        58.06 
TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR 
       46.98        46.32        60.23        24.53         9.34       103.59 
TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K 
       39.75       174.84        55.73        56.35       145.12        32.94 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GO TCGA-D3-A5GR 
       22.62        63.81        26.89       125.79       137.92       178.32 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GJ 
       18.18       125.19        30.84        23.61        26.43       241.38 
TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GR 
      170.20        89.13       107.15       161.00       152.75       129.63 
TCGA-D3-A8GS TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A1X3 
      117.17       151.53        54.67         3.65         7.10        18.12 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG 
       15.39        22.29        18.44        25.18        66.25        22.95 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 
       48.89        36.03        20.38       194.83       176.55        35.93 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
      107.34        61.18        65.92        23.44        68.09        28.60 
TCGA-DA-A3F3 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5UN 
       10.49        13.87        10.36        20.35        68.25        52.01 
TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 
        7.04        24.89        29.82        27.22         8.65        94.98 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B 
       33.73        14.70        26.89        68.15         4.96       133.81 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D 
      151.27        91.56        13.55        85.08        78.97        13.97 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29S 
       63.78        72.07        64.64        18.61        56.42        61.28 
TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
       25.87        17.92        46.82        36.82        39.29        86.14 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
       59.28        67.43       340.14       161.03       208.04        48.72 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR 
      107.38        54.74        79.66       126.81        13.91        42.77 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M8 TCGA-EE-A2MC 
       81.21        44.88        94.82        21.67        19.76        61.51 
TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
       47.28       103.27       268.73       103.20        16.96       204.66 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP 
       96.23       158.63       216.66       167.90        47.54       248.65 
TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC 
       43.23       162.48        71.21       124.31       122.73        51.62 
TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 
       28.77        13.81       138.81       172.18       127.20        36.95 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH 
       64.08        34.32        53.19        27.35        51.35       109.58 
TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A 
       31.40        35.44        13.94        50.76         9.17        77.75 
TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L 
       48.89        12.59        26.37       152.35         6.44       131.51 
TCGA-ER-A19M TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W 
       61.05       162.08        50.89        37.25         8.88       148.18 
TCGA-ER-A1A1 TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH 
       79.99        23.34        20.15        16.37        31.27        32.05 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A44A 
      247.04        80.32        46.98        33.21         6.77       174.21 
TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC 
       15.72       220.80        27.85        18.77        38.27        34.82 
TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
       36.26       104.42       216.92        48.59       228.59       202.65 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC 
       20.91        28.08         7.79        27.72        48.85       357.37 
TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK 
       40.27        15.45         9.70        32.75        47.38        23.93 
TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU 
       74.73       133.55        11.41       148.80        53.16        26.56 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 
       49.48        27.09        27.02        77.82        50.14        66.67 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3R5 
      174.84        34.03        26.73        54.41        80.68        22.92 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 
       55.59        13.51        19.30         9.90         7.23         2.04 
TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 
       15.78       139.89       117.93        84.72        10.13        64.44 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 
       62.79        32.48        39.58       121.91        39.35        10.42 
TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A8LL TCGA-HR-A2OG TCGA-HR-A2OH 
       48.89        22.13        50.10        21.37         0.23        65.88 
TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 
      368.78       297.90         7.23         0.33         0.69       228.16 
TCGA-W3-A828 TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 
      121.08        69.07       111.09        42.08       219.16       105.04 
TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO 
       49.05        61.15        15.98        98.89        58.98        67.63 
TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 
       59.77        11.80        49.51        12.16        35.01        19.73 
TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
       22.29        37.94        14.43        27.58        96.99        15.98 

  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
             0.20              0.23 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
           369.93            368.78 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
           56.840            49.265 
[1] "0.2 - 369.9 (56.8)" "0.2 - 368.8 (49.3)"
[1] "hr=" "1.2"
D4V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  2Q GAIN MUTATED                    9             1
  2Q GAIN WILD-TYPE                 56             4
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  2Q GAIN MUTATED                                          16
  2Q GAIN WILD-TYPE                                        56
                   vv
clus                REGIONAL LYMPH NODE
  2Q GAIN MUTATED                    38
  2Q GAIN WILD-TYPE                 177
D4V4, multiclass
                                           clus
vv                                          2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  DISTANT METASTASIS                                      9                56
  PRIMARY TUMOR                                           1                 4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE              16                56
  REGIONAL LYMPH NODE                                    38               177
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  2Q GAIN MUTATED             3       2       5        5        6        3
  2Q GAIN WILD-TYPE           9       5      23       13       21       21
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  2Q GAIN MUTATED           2         1         2         9          4
  2Q GAIN WILD-TYPE        12        18        10        28         11
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  2Q GAIN MUTATED            5         11        1
  2Q GAIN WILD-TYPE         27         49       19
D4V5, multiclass
             clus
vv            2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  I OR II NOS               3                 9
  STAGE 0                   2                 5
  STAGE I                   5                23
  STAGE IA                  5                13
  STAGE IB                  6                21
  STAGE II                  3                21
  STAGE IIA                 2                12
  STAGE IIB                 1                18
  STAGE IIC                 2                10
  STAGE III                 9                28
  STAGE IIIA                4                11
  STAGE IIIB                5                27
  STAGE IIIC               11                49
  STAGE IV                  1                19
[1] 14  2
[1] TRUE
[1] "dimension of contingency 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      12 18  9 10
  2Q GAIN WILD-TYPE    52 54 68 58
D4V6, multiclass
       clus
vv      2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  T0+T1              12                52
  T2                 18                54
  T3                  9                68
  T4                 10                58
[1] 4 2
[1] TRUE
[1] "dimension of 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  11   8   9
  2Q GAIN WILD-TYPE 138  52  30  40
D4V7, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  N0              31               138
  N1              11                52
  N2               8                30
  N3               9                40
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V8, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED    61   1
  2Q GAIN WILD-TYPE 252  20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     61    1
  2Q GAIN WILD-TYPE  252   20
   clus
vv  2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  0              61               252
  1               1                20
[1] 2 2
[1] FALSE
D4V9, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED    21  15
  2Q GAIN WILD-TYPE 111  73
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     21   15
  2Q GAIN WILD-TYPE  111   73
     clus
vv    2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  NO               21               111
  YES              15                73
[1] 2 2
[1] FALSE
D4V10, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED     9  55
  2Q GAIN WILD-TYPE  35 258
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      9   55
  2Q GAIN WILD-TYPE   35  258
     clus
vv    2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  NO                9                35
  YES              55               258
[1] 2 2
[1] FALSE
D4V11, continuous
D4V12, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED    26  38
  2Q GAIN WILD-TYPE 109 185
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     26   38
  2Q GAIN WILD-TYPE  109  185
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  FEMALE              26               109
  MALE                38               185
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  2Q GAIN MUTATED       0                         0    63
  2Q GAIN WILD-TYPE     5                         1   281
D4V13, multiclass
                           clus
vv                          2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  ASIAN                                   0                 5
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  63               281
[1] 3 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     0  62
  2Q GAIN WILD-TYPE   7 282
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      0   62
  2Q GAIN WILD-TYPE    7  282
                        clus
vv                       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 7
  NOT HISPANIC OR LATINO              62               282
[1] 2 2
[1] FALSE

Clustering(5) Variable = 3P GAIN MUTATION ANALYSIS
D5V1, survival
                   sevent
clus2                 0   1
  3P GAIN MUTATED    23  11
  3P GAIN WILD-TYPE  98 107
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               34               205 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               11               107 
$`3P GAIN MUTATED`
TCGA-D3-A2J8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3MR TCGA-D3-A5GN TCGA-D3-A5GR 
       62.86       140.98        40.01        90.21        45.70       177.86 
TCGA-D3-A8GD TCGA-D3-A8GM TCGA-DA-A1IA TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A5SG 
       23.61        70.62        64.83       214.59        14.96        33.24 
TCGA-EB-A5SH TCGA-EE-A180 TCGA-EE-A184 TCGA-EE-A20H TCGA-EE-A29M TCGA-EE-A29T 
       50.07        62.37        67.50       155.90        47.74       346.49 
TCGA-EE-A29W TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2MP TCGA-EE-A2MU TCGA-EE-A3AE 
      185.19        31.00         0.76       227.01        53.26        54.51 
TCGA-EE-A3JI TCGA-ER-A19G TCGA-ER-A3ET TCGA-ER-A3PL TCGA-FR-A7UA TCGA-FS-A1Z0 
      152.81       151.46        55.82        32.05         5.65       195.98 
TCGA-W3-AA1W TCGA-WE-A8K1 TCGA-WE-A8ZY TCGA-WE-AAA3 
      185.13         1.15        48.39        16.64 

$`3P GAIN WILD-TYPE`
TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
       60.46        12.99        14.83         8.42        15.72        31.89 
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB 
      110.93        49.35       133.25        19.04        76.41        62.60 
TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
       25.64        45.99        15.75       168.00        86.30         7.27 
TCGA-D3-A2JE TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
        9.76       107.61        36.30       171.58        64.83        66.08 
TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML 
       43.53        58.06        46.98        59.70        16.96        13.87 
TCGA-D3-A3MO TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R 
        9.34        23.67       173.85       144.46        31.76        62.70 
TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GU TCGA-D3-A8GC TCGA-D3-A8GJ TCGA-D3-A8GK 
       11.34        42.05       124.08        78.21       179.97       120.00 
TCGA-D3-A8GL TCGA-D3-A8GP TCGA-D3-A8GR TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       69.53       135.12        36.53        10.78        15.02        16.90 
TCGA-D9-A4Z6 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 
       18.44        57.90        22.85        48.66       106.85        31.96 
TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-EB-A44Q 
      150.61        82.85        32.42        58.85        25.12         3.91 
TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A182 
       45.50         6.64        13.15        24.89        20.38         0.00 
TCGA-EE-A20C TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G 
       75.55        75.22        76.14        12.99         0.26        44.28 
TCGA-EE-A29H TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 
       63.12        27.16        61.12       102.38         7.20        77.98 
TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK 
       26.14       239.11         0.20       189.40        68.65        10.62 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GO TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU 
       32.48        18.35       118.32         0.20        71.31        81.99 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MG 
      103.13        15.25         5.75        23.77       209.79        94.19 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MR 
      171.85        63.25        67.50       104.78       145.45        25.08 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
      143.93        23.51       124.31       122.73        51.62         4.41 
TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB 
        6.28        67.89       111.85        45.90         3.35       201.80 
TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A 
       14.56        34.45         1.58        47.31         7.82         4.54 
TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M 
       53.29        39.81        11.47       150.12        99.06        59.84 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 
       42.48       120.76        49.71        34.95       146.63        47.97 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3EV 
       22.36         4.70        16.87        10.95       173.29        15.48 
TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A8YC TCGA-FS-A1YW TCGA-FS-A1YY 
      174.21       209.23        26.20        10.06       171.78        49.74 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF 
        8.35        27.62       312.07        32.78        35.90        12.92 
TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT 
        7.82        36.33        78.61       130.95       136.27        35.28 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 
        4.47        23.21         5.29         3.06        30.90        66.67 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
      173.19        13.28        80.68        55.59        11.54        19.30 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        9.90         6.05         1.91        53.29       117.93        84.72 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 
       17.06        42.48         7.59       120.53        34.49        46.92 
TCGA-GN-A8LK TCGA-GN-A9SD TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O 
       43.23        59.41        85.05       297.01         7.23        18.05 
TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1Q TCGA-W3-AA1R 
        0.33       174.12         1.97       120.07        44.05        79.99 
TCGA-W3-AA1V TCGA-W3-AA21 TCGA-WE-A8K5 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO 
        8.09        92.84        59.64        62.99        12.69        19.00 
TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-YG-AA3O 
       59.44        10.95         1.94        26.60        15.65        28.21 
TCGA-Z2-AA3S 
       91.23 

  3P GAIN MUTATED 3P GAIN WILD-TYPE 
             0.76              0.00 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
           346.49            312.07 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
           59.095            43.230 
[1] "0.8 - 346.5 (59.1)" "0.0 - 312.1 (43.2)"
[1] "hr=" "2.5"
D5V2, survival
                   sevent
clus2                 0   1
  3P GAIN MUTATED    36  24
  3P GAIN WILD-TYPE 133 156
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               60               289 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               24               156 
$`3P GAIN MUTATED`
TCGA-D3-A2J8 TCGA-D3-A2JF TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3MR TCGA-D3-A3MV 
       65.49        62.07       166.52        86.93       103.59        45.30 
TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A8GD TCGA-D3-A8GI TCGA-D3-A8GM TCGA-D3-A8GN 
      135.75       178.32        23.61        58.52       107.15       161.00 
TCGA-D3-A8GQ TCGA-DA-A1IA TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A5SG 
       29.06        65.92        10.49       215.44        15.68        68.25 
TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EE-A180 TCGA-EE-A184 TCGA-EE-A20B TCGA-EE-A20H 
       54.02        17.29        94.98        68.15       133.81       168.26 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29R TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2GI 
        2.60        56.84        14.47       369.93       195.02        48.72 
TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2M5 TCGA-EE-A2MP TCGA-EE-A2MU TCGA-EE-A3AE 
      102.12        13.91        21.67       248.65        53.26        54.51 
TCGA-EE-A3J5 TCGA-EE-A3JA TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A19G TCGA-ER-A3ET 
       36.95        53.19       109.58       152.81       268.93        80.32 
TCGA-ER-A3PL TCGA-FR-A7UA TCGA-FR-A8YD TCGA-FS-A1Z0 TCGA-FS-A1ZK TCGA-FS-A4F2 
       33.21        38.27        36.26       202.65        23.93        50.14 
TCGA-GF-A6C9 TCGA-GN-A266 TCGA-GN-A8LL TCGA-HR-A2OG TCGA-HR-A2OH TCGA-W3-AA1W 
       15.78        10.13        21.37         0.23        65.88       219.16 
TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K6 TCGA-WE-A8ZY TCGA-WE-AAA3 TCGA-Z2-AA3V 
       24.03        49.05        15.98        49.51        19.73        15.98 

$`3P GAIN WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q3 
       17.03        66.48        12.99        14.93        16.57        16.67 
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 
      112.04       112.57        71.80       133.25        28.08        31.59 
TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J9 TCGA-D3-A2JA 
       90.90        95.74        43.43       103.10        23.77       115.53 
TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JE TCGA-D3-A2JG TCGA-D3-A2JH 
      168.00        86.76        11.87        27.65       113.52        42.08 
TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ 
       12.10       171.58        66.48        66.08        59.57       130.72 
TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML 
       58.06        46.98        46.32        60.23        24.53        13.87 
TCGA-D3-A3MO TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J 
        9.34        39.75       174.84        55.73        56.35       145.12 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GO 
       32.94        22.62        63.81        26.89       125.79       137.92 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GE TCGA-D3-A8GJ 
       18.18       125.19        30.84        79.59        26.43       241.38 
TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GP TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A148 
      170.20        89.13       152.75       129.63       117.17       151.53 
TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       54.67         3.65         7.10        18.12        15.39        22.29 
TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV 
       18.44         9.90        25.18        66.25        22.95        48.89 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 
       36.03       117.21        20.38       194.83       176.55        35.93 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
      107.34        61.18        53.92        23.44        68.09        28.60 
TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 
       13.87        10.36        20.35        52.01         7.04        24.89 
TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
       29.82        27.22         8.65        33.73        14.70        26.89 
TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
        4.96       151.27        91.56        13.55        63.35        85.08 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29N 
       78.97        13.97        63.78        72.07        64.64        18.61 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A0 
       56.42        66.74        61.28        25.87        17.92        46.82 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC 
      102.90        36.82        39.29        86.14        59.28        67.43 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
      340.14       161.03       208.04       107.38        54.74        79.66 
TCGA-EE-A2GM TCGA-EE-A2GO TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU 
       75.48       126.81        42.77        81.21        44.88        94.82 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME 
      129.27        28.83        19.76        61.51        47.28       103.27 
TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK 
      268.73       103.20        16.96       204.66        96.23       158.63 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS 
      216.66       167.90        47.54        43.23       134.40       162.48 
TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AF 
       71.21       124.31       122.73        51.62        28.77        13.81 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 
       41.59       138.81       172.18       127.20        64.08        34.32 
TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
      201.80        27.35        51.35        31.40        35.44        13.94 
TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D 
       50.76         9.17        77.75        98.40        48.89        12.59 
TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
       13.02        26.37       152.35         6.44       131.51        61.05 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W 
       44.05       162.08        50.89        37.25         8.88       148.18 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
       79.99        43.82        23.34        20.15        16.37        31.27 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3EV TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A 
       32.05       247.04        46.98         6.77        92.98       174.21 
TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A8YC TCGA-FR-A8YE 
       15.72       220.80        27.85        18.77        34.82       104.42 
TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 
      216.92        48.59       228.59        20.91        28.08         7.79 
TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF 
       27.72        48.85       357.37        53.52        40.27        15.45 
TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ 
        9.70        32.75        47.38       101.26        74.73       133.55 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY 
       11.41       148.80        53.16        26.56        49.48        27.09 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 
       27.02        77.82        66.67        28.73       174.84        34.03 
TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU 
       26.73        54.41        80.68         0.20        22.92        55.59 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 
       13.51        19.30         9.90         7.23         2.04       139.89 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
      117.93        84.72        64.44        62.79        32.48        39.58 
TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK 
      121.91        39.35        10.42        48.89        22.13        50.10 
TCGA-GN-A9SD TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 
       59.41       368.78       297.90         7.23        18.05         0.33 
TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1Q 
        0.69       228.16        63.02       121.08         4.01        69.07 
TCGA-W3-AA1R TCGA-W3-AA1V TCGA-W3-AA21 TCGA-WE-A8K5 TCGA-WE-A8ZM TCGA-WE-A8ZN 
      111.09        42.08       105.04        61.15        98.89        58.98 
TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-AA9Y TCGA-WE-AAA0 
       67.63        59.77        11.80        32.58        12.16        35.01 
TCGA-WE-AAA4 TCGA-YD-A89C TCGA-YD-A9TA TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-A8RT 
       22.29         6.90        49.18        37.94        14.43        27.58 
TCGA-Z2-AA3S 
       96.99 

  3P GAIN MUTATED 3P GAIN WILD-TYPE 
             0.23              0.20 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
           369.93            368.78 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
           54.265            49.480 
[1] "0.2 - 369.9 (54.3)" "0.2 - 368.8 (49.5)"
[1] "hr=" "1.6"
D5V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  3P GAIN MUTATED                   15             0
  3P GAIN WILD-TYPE                 50             5
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  3P GAIN MUTATED                                          14
  3P GAIN WILD-TYPE                                        58
                   vv
clus                REGIONAL LYMPH NODE
  3P GAIN MUTATED                    33
  3P GAIN WILD-TYPE                 182
D5V4, multiclass
                                           clus
vv                                          3P GAIN MUTATED 3P GAIN WILD-TYPE
  DISTANT METASTASIS                                     15                50
  PRIMARY TUMOR                                           0                 5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE              14                58
  REGIONAL LYMPH NODE                                    33               182
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  3P GAIN MUTATED             4       1       5        7        6        4
  3P GAIN WILD-TYPE           8       6      23       11       21       20
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  3P GAIN MUTATED           2         1         4         6          1
  3P GAIN WILD-TYPE        12        18         8        31         14
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  3P GAIN MUTATED            9          6        1
  3P GAIN WILD-TYPE         23         54       19
D5V5, multiclass
             clus
vv            3P GAIN MUTATED 3P GAIN WILD-TYPE
  I OR II NOS               4                 8
  STAGE 0                   1                 6
  STAGE I                   5                23
  STAGE IA                  7                11
  STAGE IB                  6                21
  STAGE II                  4                20
  STAGE IIA                 2                12
  STAGE IIB                 1                18
  STAGE IIC                 4                 8
  STAGE III                 6                31
  STAGE IIIA                1                14
  STAGE IIIB                9                23
  STAGE IIIC                6                54
  STAGE IV                  1                19
[1] 14  2
[1] TRUE
[1] "dimension of contingency 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      12 16 10 13
  3P GAIN WILD-TYPE    52 56 67 55
D5V6, multiclass
       clus
vv      3P GAIN MUTATED 3P GAIN WILD-TYPE
  T0+T1              12                52
  T2                 16                56
  T3                 10                67
  T4                 13                55
[1] 4 2
[1] TRUE
[1] "dimension of 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    36  10   5   4
  3P GAIN WILD-TYPE 133  53  33  45
D5V7, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  N0              36               133
  N1              10                53
  N2               5                33
  N3               4                45
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V8, binary
                   cls
clus                  0   1
  3P GAIN MUTATED    57   1
  3P GAIN WILD-TYPE 256  20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     57    1
  3P GAIN WILD-TYPE  256   20
   clus
vv  3P GAIN MUTATED 3P GAIN WILD-TYPE
  0              57               256
  1               1                20
[1] 2 2
[1] FALSE
D5V9, binary
                   cls
clus                  0   1
  3P GAIN MUTATED    22  17
  3P GAIN WILD-TYPE 110  71
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     22   17
  3P GAIN WILD-TYPE  110   71
     clus
vv    3P GAIN MUTATED 3P GAIN WILD-TYPE
  NO               22               110
  YES              17                71
[1] 2 2
[1] FALSE
D5V10, binary
                   cls
clus                  0   1
  3P GAIN MUTATED     5  57
  3P GAIN WILD-TYPE  39 256
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      5   57
  3P GAIN WILD-TYPE   39  256
     clus
vv    3P GAIN MUTATED 3P GAIN WILD-TYPE
  NO                5                39
  YES              57               256
[1] 2 2
[1] FALSE
D5V11, continuous
D5V12, binary
                   cls
clus                  0   1
  3P GAIN MUTATED    27  35
  3P GAIN WILD-TYPE 108 188
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     27   35
  3P GAIN WILD-TYPE  108  188
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  FEMALE              27               108
  MALE                35               188
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3P GAIN MUTATED       0                         0    59
  3P GAIN WILD-TYPE     5                         1   285
D5V13, multiclass
                           clus
vv                          3P GAIN MUTATED 3P GAIN WILD-TYPE
  ASIAN                                   0                 5
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  59               285
[1] 3 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     0  59
  3P GAIN WILD-TYPE   7 285
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      0   59
  3P GAIN WILD-TYPE    7  285
                        clus
vv                       3P GAIN MUTATED 3P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 7
  NOT HISPANIC OR LATINO              59               285
[1] 2 2
[1] FALSE

Clustering(6) Variable = 3Q GAIN MUTATION ANALYSIS
D6V1, survival
                   sevent
clus2                 0   1
  3Q GAIN MUTATED    27  16
  3Q GAIN WILD-TYPE  94 102
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               43               196 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               16               102 
$`3Q GAIN MUTATED`
TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A3CB TCGA-D3-A3MR 
       62.86        15.75       171.58        64.83       140.98        90.21 
TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A8GD TCGA-D3-A8GM TCGA-D9-A6EC TCGA-DA-A1IA 
       45.70       177.86        23.61        70.62        57.90        64.83 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A182 TCGA-EE-A184 
      214.59        14.96        33.24        62.37         0.00        67.50 
TCGA-EE-A20H TCGA-EE-A29M TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2GN TCGA-EE-A2GP 
      155.90        47.74       346.49       185.19        31.00         0.76 
TCGA-EE-A2M6 TCGA-EE-A2ML TCGA-EE-A2MP TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AE 
      103.13       104.78       227.01        53.26       124.31        54.51 
TCGA-EE-A3J7 TCGA-ER-A19G TCGA-ER-A19M TCGA-ER-A2ND TCGA-ER-A3ET TCGA-ER-A3PL 
       45.90       151.46        59.84         4.70        55.82        32.05 
TCGA-FR-A7UA TCGA-FS-A1Z0 TCGA-GN-A26A TCGA-W3-AA1W TCGA-WE-A8K1 TCGA-WE-A8ZY 
        5.65       195.98         7.59       185.13         1.15        48.39 
TCGA-WE-AAA3 
       16.64 

$`3Q GAIN WILD-TYPE`
TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
       60.46        12.99        14.83         8.42        15.72        31.89 
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB 
      110.93        49.35       133.25        19.04        76.41        62.60 
TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JE 
       25.64        45.99       168.00        86.30         7.27         9.76 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3C7 
      107.61        36.30        66.08        43.53        58.06        46.98 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MU 
       40.01        59.70        16.96        13.87         9.34        23.67 
TCGA-D3-A51E TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL 
      173.85       144.46        31.76        62.70        11.34        42.05 
TCGA-D3-A5GU TCGA-D3-A8GC TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GP 
      124.08        78.21       179.97       120.00        69.53       135.12 
TCGA-D3-A8GR TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6EG 
       36.53        10.78        15.02        16.90        18.44        22.85 
TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 
       48.66       106.85        31.96       150.61        82.85        32.42 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-EB-A44Q TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A6L9 
       58.85        25.12         3.91        50.07        45.50         6.64 
TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A20C TCGA-EE-A29B TCGA-EE-A29C 
       13.15        24.89        20.38        75.55        75.22        76.14 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29P TCGA-EE-A29Q 
       12.99         0.26        44.28        63.12        27.16        61.12 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE 
      102.38         7.20        77.98        26.14       239.11         0.20 
TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GO 
      189.40        68.65        10.62        32.48        18.35       118.32 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC 
        0.20        71.31        81.99        15.25         5.75        23.77 
TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2MM 
      209.79        94.19       171.85        63.25        67.50       145.45 
TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
       25.08       143.93        23.51       122.73        51.62         4.41 
TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JI 
        6.28        67.89       111.85         3.35       201.80       152.81 
TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A 
       14.56        34.45         1.58        47.31         7.82         4.54 
TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19N 
       53.29        39.81        11.47       150.12        99.06        42.48 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
      120.76        49.71        34.95       146.63        47.97        22.36 
TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3EV TCGA-FR-A44A TCGA-FR-A729 
       16.87        10.95       173.29        15.48       174.21       209.23 
TCGA-FR-A7U8 TCGA-FR-A8YC TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1Z4 
       26.20        10.06       171.78        49.74         8.35        27.62 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZJ 
      312.07        32.78        35.90        12.92         7.82        36.33 
TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW 
       78.61       130.95       136.27        35.28         4.47        23.21 
TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 
        5.29         3.06        30.90        66.67       173.19        13.28 
TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
       80.68        55.59        11.54        19.30         9.90         6.05 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 
        1.91        53.29       117.93        84.72        17.06        42.48 
TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-GN-A8LK TCGA-GN-A9SD TCGA-LH-A9QB 
      120.53        34.49        46.92        43.23        59.41        85.05 
TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A825 
      297.01         7.23        18.05         0.33       174.12         1.97 
TCGA-W3-A828 TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1V TCGA-W3-AA21 TCGA-WE-A8K5 
      120.07        44.05        79.99         8.09        92.84        59.64 
TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-AA9Y 
       62.99        12.69        19.00        59.44        10.95         1.94 
TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-Z2-AA3S 
       26.60        15.65        28.21        91.23 

  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
              0.0               0.2 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
           346.49            312.07 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
            59.84             42.48 
[1] "0.0 - 346.5 (59.8)" "0.2 - 312.1 (42.5)"
[1] "hr=" "1.9"
D6V2, survival
                   sevent
clus2                 0   1
  3Q GAIN MUTATED    41  28
  3Q GAIN WILD-TYPE 128 152
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               69               280 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               28               152 
$`3Q GAIN MUTATED`
TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JF TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A3CB 
       65.49       115.53        62.07       171.58        66.48       166.52 
TCGA-D3-A3MR TCGA-D3-A3MV TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A8GD TCGA-D3-A8GI 
      103.59        45.30       135.75       178.32        23.61        58.52 
TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GQ TCGA-D9-A6EC TCGA-DA-A1IA TCGA-DA-A3F3 
      107.15       161.00        29.06        66.25        65.92        10.49 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A5SG TCGA-EB-A5UL TCGA-EE-A180 TCGA-EE-A182 
      215.44        15.68        68.25        17.29        94.98        14.70 
TCGA-EE-A184 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29M TCGA-EE-A29R 
       68.15       133.81        91.56       168.26        56.84        14.47 
TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2GI TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2M5 
      369.93       195.02        48.72       102.12        13.91        21.67 
TCGA-EE-A2M6 TCGA-EE-A2ML TCGA-EE-A2MP TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AE 
      129.27       216.66       248.65        53.26       124.31        54.51 
TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-EE-A3JH TCGA-ER-A19G TCGA-ER-A19M 
       36.95        64.08        53.19       109.58       268.93        61.05 
TCGA-ER-A2ND TCGA-ER-A3ET TCGA-ER-A3PL TCGA-FR-A7UA TCGA-FR-A8YD TCGA-FS-A1Z0 
       23.34        80.32        33.21        38.27        36.26       202.65 
TCGA-FS-A1ZK TCGA-FS-A4F2 TCGA-GF-A6C9 TCGA-GN-A266 TCGA-GN-A26A TCGA-HR-A2OG 
       23.93        50.14        15.78        10.13        32.48         0.23 
TCGA-HR-A2OH TCGA-W3-AA1O TCGA-W3-AA1W TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K6 
       65.88         4.01       219.16        24.03        49.05        15.98 
TCGA-WE-A8ZY TCGA-WE-AAA3 TCGA-Z2-AA3V 
       49.51        19.73        15.98 

$`3Q GAIN WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q3 
       17.03        66.48        12.99        14.93        16.57        16.67 
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 
      112.04       112.57        71.80       133.25        28.08        31.59 
TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J9 TCGA-D3-A2JB 
       90.90        95.74        43.43       103.10        23.77       168.00 
TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JE TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK 
       86.76        11.87        27.65       113.52        42.08        12.10 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 
       66.08        59.57       130.72        58.06        46.98        46.32 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MU 
       86.93        60.23        24.53        13.87         9.34        39.75 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
      174.84        55.73        56.35       145.12        32.94        22.62 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GO TCGA-D3-A5GS TCGA-D3-A5GU 
       63.81        26.89       125.79       137.92        18.18       125.19 
TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL 
       30.84        79.59        26.43       241.38       170.20        89.13 
TCGA-D3-A8GP TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW 
      152.75       129.63       117.17       151.53        54.67         3.65 
TCGA-D9-A1JX TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 
        7.10        18.12        15.39        22.29        18.44         9.90 
TCGA-D9-A6EA TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 
       25.18        22.95        48.89        36.03       117.21        20.38 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
      194.83       176.55        35.93       107.34        61.18        53.92 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH 
       23.44        68.09        28.60        13.87        10.36        20.35 
TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y 
       54.02        52.01         7.04        24.89        29.82        27.22 
TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A20I 
        8.65        33.73        26.89         4.96       151.27        13.55 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G 
       63.35        85.08        78.97        13.97        63.78        72.07 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29S 
       64.64         2.60        18.61        56.42        66.74        61.28 
TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 
       25.87        17.92        46.82       102.90        36.82        39.29 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
       86.14        59.28        67.43       340.14       161.03       208.04 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GO TCGA-EE-A2GR 
      107.38        54.74        79.66        75.48       126.81        42.77 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC 
       81.21        44.88        94.82        28.83        19.76        61.51 
TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
       47.28       103.27       268.73       103.20        16.96       204.66 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MR 
       96.23       158.63       167.90        47.54        43.23       134.40 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AF 
      162.48        71.21       122.73        51.62        28.77        13.81 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J8 TCGA-EE-A3JB 
       41.59       138.81       172.18       127.20        34.32       201.80 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
       27.35        51.35       152.81        31.40        35.44        13.94 
TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D 
       50.76         9.17        77.75        98.40        48.89        12.59 
TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19N 
       13.02        26.37       152.35         6.44       131.51        44.05 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 
      162.08        50.89        37.25         8.88       148.18        79.99 
TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES 
       43.82        20.15        16.37        31.27        32.05       247.04 
TCGA-ER-A3EV TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 
       46.98         6.77        92.98       174.21        15.72       220.80 
TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A8YC TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YX 
       27.85        18.77        34.82       104.42       216.92        48.59 
TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB 
      228.59        20.91        28.08         7.79        27.72        48.85 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH 
      357.37        53.52        40.27        15.45         9.70        32.75 
TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS 
       47.38       101.26        74.73       133.55        11.41       148.80 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 
       53.16        26.56        49.48        27.09        27.02        77.82 
TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC 
       66.67        28.73       174.84        34.03        26.73        54.41 
TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
       80.68         0.20        22.92        55.59        13.51        19.30 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        9.90         7.23         2.04       139.89       117.93        84.72 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 
       64.44        62.79        39.58       121.91        39.35        10.42 
TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A8LL TCGA-GN-A9SD TCGA-LH-A9QB 
       48.89        22.13        50.10        21.37        59.41       368.78 
TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 
      297.90         7.23        18.05         0.33         0.69       228.16 
TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1V TCGA-W3-AA21 
       63.02       121.08        69.07       111.09        42.08       105.04 
TCGA-WE-A8K5 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT 
       61.15        98.89        58.98        67.63        59.77        11.80 
TCGA-WE-A8ZX TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-YD-A89C TCGA-YD-A9TA 
       32.58        12.16        35.01        22.29         6.90        49.18 
TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S 
       37.94        14.43        27.58        96.99 

  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
             0.23              0.20 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
           369.93            368.78 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
            61.05             48.89 
[1] "0.2 - 369.9 (61.0)" "0.2 - 368.8 (48.9)"
[1] "hr=" "1.6"
D6V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  3Q GAIN MUTATED                   17             1
  3Q GAIN WILD-TYPE                 48             4
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  3Q GAIN MUTATED                                          16
  3Q GAIN WILD-TYPE                                        56
                   vv
clus                REGIONAL LYMPH NODE
  3Q GAIN MUTATED                    37
  3Q GAIN WILD-TYPE                 178
D6V4, multiclass
                                           clus
vv                                          3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  DISTANT METASTASIS                                     17                48
  PRIMARY TUMOR                                           1                 4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE              16                56
  REGIONAL LYMPH NODE                                    37               178
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  3Q GAIN MUTATED             5       1       7        7        7        5
  3Q GAIN WILD-TYPE           7       6      21       11       20       19
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  3Q GAIN MUTATED           2         1         2         8          4
  3Q GAIN WILD-TYPE        12        18        10        29         11
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  3Q GAIN MUTATED            9          7        1
  3Q GAIN WILD-TYPE         23         53       19
D6V5, multiclass
             clus
vv            3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  I OR II NOS               5                 7
  STAGE 0                   1                 6
  STAGE I                   7                21
  STAGE IA                  7                11
  STAGE IB                  7                20
  STAGE II                  5                19
  STAGE IIA                 2                12
  STAGE IIB                 1                18
  STAGE IIC                 2                10
  STAGE III                 8                29
  STAGE IIIA                4                11
  STAGE IIIB                9                23
  STAGE IIIC                7                53
  STAGE IV                  1                19
[1] 14  2
[1] TRUE
[1] "dimension of contingency 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      17 18 13 10
  3Q GAIN WILD-TYPE    47 54 64 58
D6V6, multiclass
       clus
vv      3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  T0+T1              17                47
  T2                 18                54
  T3                 13                64
  T4                 10                58
[1] 4 2
[1] TRUE
[1] "dimension of 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    39  15   7   4
  3Q GAIN WILD-TYPE 130  48  31  45
D6V7, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  N0              39               130
  N1              15                48
  N2               7                31
  N3               4                45
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V8, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED    66   1
  3Q GAIN WILD-TYPE 247  20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     66    1
  3Q GAIN WILD-TYPE  247   20
   clus
vv  3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  0              66               247
  1               1                20
[1] 2 2
[1] FALSE
D6V9, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED    28  15
  3Q GAIN WILD-TYPE 104  73
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     28   15
  3Q GAIN WILD-TYPE  104   73
     clus
vv    3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  NO               28               104
  YES              15                73
[1] 2 2
[1] FALSE
D6V10, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED     8  63
  3Q GAIN WILD-TYPE  36 250
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      8   63
  3Q GAIN WILD-TYPE   36  250
     clus
vv    3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  NO                8                36
  YES              63               250
[1] 2 2
[1] FALSE
D6V11, continuous
D6V12, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED    29  42
  3Q GAIN WILD-TYPE 106 181
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     29   42
  3Q GAIN WILD-TYPE  106  181
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  FEMALE              29               106
  MALE                42               181
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3Q GAIN MUTATED       0                         0    68
  3Q GAIN WILD-TYPE     5                         1   276
D6V13, multiclass
                           clus
vv                          3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  ASIAN                                   0                 5
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  68               276
[1] 3 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     0  68
  3Q GAIN WILD-TYPE   7 276
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      0   68
  3Q GAIN WILD-TYPE    7  276
                        clus
vv                       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 7
  NOT HISPANIC OR LATINO              68               276
[1] 2 2
[1] FALSE

Clustering(7) Variable = 4P GAIN MUTATION ANALYSIS
D7V1, survival
                   sevent
clus2                 0   1
  4P GAIN MUTATED    22  18
  4P GAIN WILD-TYPE  99 100
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               40               199 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               18               100 
$`4P GAIN MUTATED`
TCGA-3N-A9WC TCGA-D3-A1Q3 TCGA-D3-A2JE TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CE 
       60.46        15.72         9.76        58.06        46.98        59.70 
TCGA-D3-A3MU TCGA-D3-A5GU TCGA-D3-A8GP TCGA-DA-A1HV TCGA-DA-A1I1 TCGA-DA-A3F5 
       23.67       124.08       135.12        48.66        31.96       214.59 
TCGA-EB-A5SH TCGA-EB-A6L9 TCGA-EE-A184 TCGA-EE-A29G TCGA-EE-A29P TCGA-EE-A2GB 
       50.07         6.64        67.50        44.28        27.16        26.14 
TCGA-EE-A2GP TCGA-EE-A2MJ TCGA-EE-A2MP TCGA-EE-A3AA TCGA-EE-A3J3 TCGA-EE-A3J7 
        0.76        63.25       227.01       124.31        67.89        45.90 
TCGA-EE-A3JB TCGA-ER-A19H TCGA-ER-A3ET TCGA-ER-A3PL TCGA-FR-A8YC TCGA-FS-A1ZJ 
      201.80       150.12        55.82        32.05        10.06        36.33 
TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZU TCGA-GF-A4EO TCGA-GN-A264 TCGA-GN-A268 
       78.61       130.95         4.47         6.05       117.93        42.48 
TCGA-GN-A8LK TCGA-QB-AA9O TCGA-WE-A8ZN TCGA-WE-A8ZQ 
       43.23        18.05        12.69        59.44 

$`4P GAIN WILD-TYPE`
TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 
       12.99        14.83         8.42        31.89       110.93        49.35 
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
      133.25        19.04        76.41        62.60        25.64        45.99 
TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG 
       62.86        15.75       168.00        86.30         7.27       107.61 
TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3CB 
       36.30       171.58        64.83        66.08        43.53       140.98 
TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A51E 
       40.01        16.96        13.87         9.34        90.21       173.85 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN 
      144.46        31.76        62.70        11.34        42.05        45.70 
TCGA-D3-A5GR TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL 
      177.86        78.21        23.61       179.97       120.00        69.53 
TCGA-D3-A8GM TCGA-D3-A8GR TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 
       70.62        36.53        10.78        15.02        16.90        18.44 
TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HY TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 
       57.90        22.85       106.85       150.61        82.85        32.42 
TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5SG 
       64.83        58.85        25.12        14.96         3.91        33.24 
TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 
       45.50        13.15        24.89        62.37        20.38         0.00 
TCGA-EE-A20C TCGA-EE-A20H TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
       75.55       155.90        75.22        76.14        12.99         0.26 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 
       63.12        47.74        61.12       346.49       185.19       102.38 
TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ 
        7.20        77.98       239.11         0.20       189.40        68.65 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GR 
       10.62        32.48        18.35        31.00       118.32         0.20 
TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC 
       71.31        81.99       103.13        15.25         5.75        23.77 
TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM 
      209.79        94.19       171.85        67.50       104.78       145.45 
TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC 
       25.08       143.93        23.51        53.26       122.73        51.62 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J4 TCGA-EE-A3J8 TCGA-EE-A3JI 
        4.41        54.51         6.28       111.85         3.35       152.81 
TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A 
       14.56        34.45         1.58        47.31         7.82         4.54 
TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19L TCGA-ER-A19M 
       53.29        39.81        11.47       151.46        99.06        59.84 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 
       42.48       120.76        49.71        34.95       146.63        47.97 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3EV 
       22.36         4.70        16.87        10.95       173.29        15.48 
TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FS-A1YW TCGA-FS-A1YY 
      174.21       209.23        26.20         5.65       171.78        49.74 
TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE 
      195.98         8.35        27.62       312.07        32.78        35.90 
TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A1ZY 
       12.92         7.82       136.27        35.28        23.21         5.29 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FD 
        3.06        30.90        66.67       173.19        13.28        80.68 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GN-A262 
       55.59        11.54        19.30         9.90         1.91        53.29 
TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 
       84.72        17.06         7.59       120.53        34.49        46.92 
TCGA-GN-A9SD TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A693 TCGA-W3-A824 
       59.41        85.05       297.01         7.23         0.33       174.12 
TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1V TCGA-W3-AA1W 
        1.97       120.07        44.05        79.99         8.09       185.13 
TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8ZM TCGA-WE-A8ZO TCGA-WE-A8ZT 
       92.84         1.15        59.64        62.99        19.00        10.95 
TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O 
       48.39         1.94        26.60        16.64        15.65        28.21 
TCGA-Z2-AA3S 
       91.23 

  4P GAIN MUTATED 4P GAIN WILD-TYPE 
             0.76              0.00 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
           227.01            346.49 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
            47.82             45.70 
[1] "0.8 - 227.0 (47.8)" "0.0 - 346.5 (45.7)"
[1] "hr=" "1.1"
D7V2, survival
                   sevent
clus2                 0   1
  4P GAIN MUTATED    28  25
  4P GAIN WILD-TYPE 141 155
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               53               296 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               25               155 
$`4P GAIN MUTATED`
TCGA-3N-A9WC TCGA-D3-A1Q3 TCGA-D3-A2JE TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CE 
       66.48        16.67        27.65        58.06        46.98        60.23 
TCGA-D3-A3MU TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GP TCGA-D3-A8GS TCGA-D9-A6EA 
       39.75       125.19        30.84       152.75       117.17        25.18 
TCGA-DA-A1HV TCGA-DA-A1I1 TCGA-DA-A1IB TCGA-DA-A3F5 TCGA-EB-A5SH TCGA-EB-A6L9 
       48.89       194.83        23.44       215.44        54.02        24.89 
TCGA-EE-A184 TCGA-EE-A20F TCGA-EE-A29G TCGA-EE-A29P TCGA-EE-A2GB TCGA-EE-A2GI 
       68.15        91.56        72.07        56.42        59.28        48.72 
TCGA-EE-A2GP TCGA-EE-A2MJ TCGA-EE-A2MP TCGA-EE-A3AA TCGA-EE-A3J3 TCGA-EE-A3J7 
       13.91        96.23       248.65       124.31       172.18        64.08 
TCGA-EE-A3JA TCGA-EE-A3JB TCGA-ER-A19H TCGA-ER-A3ET TCGA-ER-A3PL TCGA-FR-A3YN 
       53.19       201.80       152.35        80.32        33.21        92.98 
TCGA-FR-A8YC TCGA-FS-A1YX TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZQ 
       34.82        48.59        47.38        23.93       101.26       133.55 
TCGA-FS-A1ZU TCGA-FS-A4F2 TCGA-FS-A4F5 TCGA-GF-A4EO TCGA-GN-A264 TCGA-GN-A268 
       26.56        50.14        28.73         7.23       117.93        62.79 
TCGA-GN-A26D TCGA-GN-A8LK TCGA-QB-AA9O TCGA-WE-A8ZN TCGA-WE-A8ZQ 
       39.58        50.10        18.05        58.98        59.77 

$`4P GAIN WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 
       17.03        12.99        14.93        16.57       112.04       112.57 
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB 
       71.80       133.25        28.08        31.59        90.90        95.74 
TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB 
       43.43       103.10        65.49        23.77       115.53       168.00 
TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK 
       86.76        11.87        62.07       113.52        42.08        12.10 
TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C8 
      171.58        66.48        66.08        59.57       130.72        46.32 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR 
      166.52        86.93        24.53        13.87         9.34       103.59 
TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K 
       45.30       174.84        55.73        56.35       145.12        32.94 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO 
       22.62        63.81        26.89       125.79       135.75       137.92 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GI 
      178.32        18.18        79.59        23.61        26.43        58.52 
TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GQ 
      241.38       170.20        89.13       107.15       161.00        29.06 
TCGA-D3-A8GR TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A1X3 
      129.63       151.53        54.67         3.65         7.10        18.12 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-D9-A6EG 
       15.39        22.29        18.44         9.90        66.25        22.95 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
       36.03       117.21        20.38       176.55        35.93       107.34 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
       61.18        53.92        65.92        68.09        28.60        10.49 
TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5UL 
       15.68        13.87        10.36        20.35        68.25        17.29 
TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 
       52.01         7.04        29.82        27.22         8.65        94.98 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C 
       33.73        14.70        26.89         4.96       133.81       151.27 
TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D 
      168.26        13.55        63.35        85.08        78.97        13.97 
TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29Q 
       63.78        64.64         2.60        56.84        18.61        66.74 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X 
       14.47        61.28       369.93        25.87       195.02        17.92 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GC 
       46.82       102.90        36.82        39.29        86.14        67.43 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
      340.14       161.03       208.04       107.38        54.74        79.66 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT 
       75.48       102.12       126.81        42.77        81.21        44.88 
TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC 
       94.82        21.67       129.27        28.83        19.76        61.51 
TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
       47.28       103.27       268.73       103.20        16.96       204.66 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MR 
      158.63       216.66       167.90        47.54        43.23       134.40 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
      162.48        71.21        53.26       122.73        51.62        28.77 
TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J5 
       54.51        13.81        41.59       138.81       127.20        36.95 
TCGA-EE-A3J8 TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 
       34.32        27.35        51.35       109.58       152.81        31.40 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B 
       35.44        13.94        50.76         9.17        77.75        98.40 
TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19J 
       48.89        12.59        13.02        26.37       268.93         6.44 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S 
      131.51        61.05        44.05       162.08        50.89        37.25 
TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
        8.88       148.18        79.99        43.82        23.34        20.15 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3EV TCGA-ER-A42K 
       16.37        31.27        32.05       247.04        46.98         6.77 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA 
      174.21        15.72       220.80        27.85        18.77        38.27 
TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
       36.26       104.42       216.92       228.59       202.65        20.91 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD 
       28.08         7.79        27.72        48.85       357.37        53.52 
TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZP TCGA-FS-A1ZR 
       40.27        15.45         9.70        32.75        74.73        11.41 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 
      148.80        53.16        49.48        27.09        27.02        77.82 
TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD 
       66.67       174.84        34.03        26.73        54.41        80.68 
TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
        0.20        22.92        55.59        13.51        19.30         9.90 
TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 
        2.04        15.78       139.89        84.72        10.13        64.44 
TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A4U9 
       32.48       121.91        39.35        10.42        48.89        22.13 
TCGA-GN-A8LL TCGA-GN-A9SD TCGA-HR-A2OG TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X 
       21.37        59.41         0.23        65.88       368.78       297.90 
TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 
        7.23         0.33         0.69       228.16        63.02       121.08 
TCGA-W3-AA1O TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 
        4.01        69.07       111.09        42.08       219.16       105.04 
TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZO 
       24.03        49.05        61.15        15.98        98.89        67.63 
TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 
       11.80        32.58        49.51        12.16        35.01        19.73 
TCGA-WE-AAA4 TCGA-YD-A89C TCGA-YD-A9TA TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-A8RT 
       22.29         6.90        49.18        37.94        14.43        27.58 
TCGA-Z2-AA3S TCGA-Z2-AA3V 
       96.99        15.98 

  4P GAIN MUTATED 4P GAIN WILD-TYPE 
             7.23              0.20 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
           248.65            369.93 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
            58.06             49.33 
[1] "7.2 - 248.7 (58.1)" "0.2 - 369.9 (49.3)"
[1] "hr=" "1.2"
D7V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  4P GAIN MUTATED                    9             1
  4P GAIN WILD-TYPE                 56             4
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  4P GAIN MUTATED                                          14
  4P GAIN WILD-TYPE                                        58
                   vv
clus                REGIONAL LYMPH NODE
  4P GAIN MUTATED                    31
  4P GAIN WILD-TYPE                 184
D7V4, multiclass
                                           clus
vv                                          4P GAIN MUTATED 4P GAIN WILD-TYPE
  DISTANT METASTASIS                                      9                56
  PRIMARY TUMOR                                           1                 4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE              14                58
  REGIONAL LYMPH NODE                                    31               184
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  4P GAIN MUTATED             2       0       6        1        8        1
  4P GAIN WILD-TYPE          10       7      22       17       19       23
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  4P GAIN MUTATED           2         3         5         8          3
  4P GAIN WILD-TYPE        12        16         7        29         12
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  4P GAIN MUTATED            4          8        1
  4P GAIN WILD-TYPE         28         52       19
D7V5, multiclass
             clus
vv            4P GAIN MUTATED 4P GAIN WILD-TYPE
  I OR II NOS               2                10
  STAGE 0                   0                 7
  STAGE I                   6                22
  STAGE IA                  1                17
  STAGE IB                  8                19
  STAGE II                  1                23
  STAGE IIA                 2                12
  STAGE IIB                 3                16
  STAGE IIC                 5                 7
  STAGE III                 8                29
  STAGE IIIA                3                12
  STAGE IIIB                4                28
  STAGE IIIC                8                52
  STAGE IV                  1                19
[1] 14  2
[1] TRUE
[1] "dimension of contingency 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      12 16  7 13
  4P GAIN WILD-TYPE    52 56 70 55
D7V6, multiclass
       clus
vv      4P GAIN MUTATED 4P GAIN WILD-TYPE
  T0+T1              12                52
  T2                 16                56
  T3                  7                70
  T4                 13                55
[1] 4 2
[1] TRUE
[1] "dimension of 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    29   7   7   7
  4P GAIN WILD-TYPE 140  56  31  42
D7V7, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  N0              29               140
  N1               7                56
  N2               7                31
  N3               7                42
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V8, binary
                   cls
clus                  0   1
  4P GAIN MUTATED    50   1
  4P GAIN WILD-TYPE 263  20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED     50    1
  4P GAIN WILD-TYPE  263   20
   clus
vv  4P GAIN MUTATED 4P GAIN WILD-TYPE
  0              50               263
  1               1                20
[1] 2 2
[1] FALSE
D7V9, binary
                   cls
clus                  0   1
  4P GAIN MUTATED    20  14
  4P GAIN WILD-TYPE 112  74
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED     20   14
  4P GAIN WILD-TYPE  112   74
     clus
vv    4P GAIN MUTATED 4P GAIN WILD-TYPE
  NO               20               112
  YES              14                74
[1] 2 2
[1] FALSE
D7V10, binary
                   cls
clus                  0   1
  4P GAIN MUTATED     7  48
  4P GAIN WILD-TYPE  37 265
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      7   48
  4P GAIN WILD-TYPE   37  265
     clus
vv    4P GAIN MUTATED 4P GAIN WILD-TYPE
  NO                7                37
  YES              48               265
[1] 2 2
[1] FALSE
D7V11, continuous
D7V12, binary
                   cls
clus                  0   1
  4P GAIN MUTATED    21  34
  4P GAIN WILD-TYPE 114 189
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED     21   34
  4P GAIN WILD-TYPE  114  189
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  FEMALE              21               114
  MALE                34               189
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  4P GAIN MUTATED       1                         0    52
  4P GAIN WILD-TYPE     4                         1   292
D7V13, multiclass
                           clus
vv                          4P GAIN MUTATED 4P GAIN WILD-TYPE
  ASIAN                                   1                 4
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  52               292
[1] 3 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     1  54
  4P GAIN WILD-TYPE   6 290
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      1   54
  4P GAIN WILD-TYPE    6  290
                        clus
vv                       4P GAIN MUTATED 4P GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 6
  NOT HISPANIC OR LATINO              54               290
[1] 2 2
[1] FALSE

Clustering(8) Variable = 4Q GAIN MUTATION ANALYSIS
D8V1, survival
                   sevent
clus2                 0   1
  4Q GAIN MUTATED    18  17
  4Q GAIN WILD-TYPE 103 101
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               35               204 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               17               101 
$`4Q GAIN MUTATED`
TCGA-D3-A2JE TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3MU TCGA-D3-A5GU TCGA-D3-A8GP 
        9.76        58.06        59.70        23.67       124.08       135.12 
TCGA-DA-A1HV TCGA-DA-A1I1 TCGA-DA-A3F5 TCGA-EB-A5SH TCGA-EB-A6L9 TCGA-EE-A184 
       48.66        31.96       214.59        50.07         6.64        67.50 
TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29P TCGA-EE-A2GB TCGA-EE-A2GP TCGA-EE-A2MJ 
       12.99        44.28        27.16        26.14         0.76        63.25 
TCGA-EE-A2MP TCGA-EE-A2MR TCGA-EE-A3AD TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-EE-A3JB 
      227.01        25.08         4.41        67.89        45.90       201.80 
TCGA-ER-A19H TCGA-ER-A3PL TCGA-FR-A8YC TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZU 
      150.12        32.05        10.06        78.61       130.95         4.47 
TCGA-GF-A4EO TCGA-GN-A264 TCGA-GN-A268 TCGA-GN-A9SD TCGA-WE-A8ZQ 
        6.05       117.93        42.48        59.41        59.44 

$`4Q GAIN WILD-TYPE`
TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
       60.46        12.99        14.83         8.42        15.72        31.89 
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB 
      110.93        49.35       133.25        19.04        76.41        62.60 
TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC 
       25.64        45.99        62.86        15.75       168.00        86.30 
TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
        7.27       107.61        36.30       171.58        64.83        66.08 
TCGA-D3-A2JP TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3ML 
       43.53        46.98       140.98        40.01        16.96        13.87 
TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A51E TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R 
        9.34        90.21       173.85       144.46        31.76        62.70 
TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A8GC TCGA-D3-A8GD 
       11.34        42.05        45.70       177.86        78.21        23.61 
TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GR TCGA-D9-A1X3 
      179.97       120.00        69.53        70.62        36.53        10.78 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HY 
       15.02        16.90        18.44        57.90        22.85       106.85 
TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 
      150.61        82.85        32.42        64.83        58.85        25.12 
TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5SG TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y 
       14.96         3.91        33.24        45.50        13.15        24.89 
TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A20C TCGA-EE-A20H TCGA-EE-A29B 
       62.37        20.38         0.00        75.55       155.90        75.22 
TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29Q TCGA-EE-A29T 
       76.14         0.26        63.12        47.74        61.12       346.49 
TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GD TCGA-EE-A2GE 
      185.19       102.38         7.20        77.98       239.11         0.20 
TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN 
      189.40        68.65        10.62        32.48        18.35        31.00 
TCGA-EE-A2GO TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 
      118.32         0.20        71.31        81.99       103.13        15.25 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MK 
        5.75        23.77       209.79        94.19       171.85        67.50 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA 
      104.78       145.45       143.93        23.51        53.26       124.31 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J4 TCGA-EE-A3J8 
      122.73        51.62        54.51         6.28       111.85         3.35 
TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 
      152.81        14.56        34.45         1.58        47.31         7.82 
TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19L 
        4.54        53.29        39.81        11.47       151.46        99.06 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W 
       59.84        42.48       120.76        49.71        34.95       146.63 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A3ES 
       47.97        22.36         4.70        16.87        10.95       173.29 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7UA 
       55.82        15.48       174.21       209.23        26.20         5.65 
TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZC 
      171.78        49.74       195.98         8.35        27.62       312.07 
TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZS 
       32.78        35.90        12.92         7.82        36.33       136.27 
TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 
       35.28        23.21         5.29         3.06        30.90        66.67 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
      173.19        13.28        80.68        55.59        11.54        19.30 
TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A26A 
        9.90         1.91        53.29        84.72        17.06         7.59 
TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-GN-A8LK TCGA-LH-A9QB TCGA-OD-A75X 
      120.53        34.49        46.92        43.23        85.05       297.01 
TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 
        7.23        18.05         0.33       174.12         1.97       120.07 
TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 
       44.05        79.99         8.09       185.13        92.84         1.15 
TCGA-WE-A8K5 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-A8ZY 
       59.64        62.99        12.69        19.00        10.95        48.39 
TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-Z2-AA3S 
        1.94        26.60        16.64        15.65        28.21        91.23 

  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
             0.76              0.00 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
           227.01            346.49 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
           48.660            45.845 
[1] "0.8 - 227.0 (48.7)" "0.0 - 346.5 (45.8)"
[1] "hr=" "1"  
D8V2, survival
                   sevent
clus2                 0   1
  4Q GAIN MUTATED    23  22
  4Q GAIN WILD-TYPE 146 158
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               45               304 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               22               158 
$`4Q GAIN MUTATED`
TCGA-D3-A2JE TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3MU TCGA-D3-A5GU TCGA-D3-A8GB 
       27.65        58.06        60.23        39.75       125.19        30.84 
TCGA-D3-A8GP TCGA-D3-A8GS TCGA-D9-A6EA TCGA-DA-A1HV TCGA-DA-A1I1 TCGA-DA-A1IB 
      152.75       117.17        25.18        48.89       194.83        23.44 
TCGA-DA-A3F5 TCGA-EB-A5SH TCGA-EB-A6L9 TCGA-EE-A184 TCGA-EE-A20F TCGA-EE-A29D 
      215.44        54.02        24.89        68.15        91.56        13.97 
TCGA-EE-A29G TCGA-EE-A29P TCGA-EE-A2GB TCGA-EE-A2GP TCGA-EE-A2MJ TCGA-EE-A2MP 
       72.07        56.42        59.28        13.91        96.23       248.65 
TCGA-EE-A2MR TCGA-EE-A3AD TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-EE-A3JB 
      134.40        28.77       172.18        64.08        53.19       201.80 
TCGA-ER-A19H TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A8YC TCGA-FS-A1YX TCGA-FS-A1ZM 
      152.35        33.21        92.98        34.82        48.59       101.26 
TCGA-FS-A1ZQ TCGA-FS-A1ZU TCGA-FS-A4F5 TCGA-GF-A4EO TCGA-GN-A264 TCGA-GN-A268 
      133.55        26.56        28.73         7.23       117.93        62.79 
TCGA-GN-A26D TCGA-GN-A9SD TCGA-WE-A8ZQ 
       39.58        59.41        59.77 

$`4Q GAIN WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q3 
       17.03        66.48        12.99        14.93        16.57        16.67 
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 
      112.04       112.57        71.80       133.25        28.08        31.59 
TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 
       90.90        95.74        43.43       103.10        65.49        23.77 
TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG 
      115.53       168.00        86.76        11.87        62.07       113.52 
TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP 
       42.08        12.10       171.58        66.48        66.08        59.57 
TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CF 
      130.72        46.98        46.32       166.52        86.93        24.53 
TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F 
       13.87         9.34       103.59        45.30       174.84        55.73 
TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T 
       56.35       145.12        32.94        22.62        63.81        26.89 
TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A8GC 
      125.79       135.75       137.92       178.32        18.18        79.59 
TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL 
       23.61        26.43        58.52       241.38       170.20        89.13 
TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D9-A148 TCGA-D9-A149 
      107.15       161.00        29.06       129.63       151.53        54.67 
TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 
        3.65         7.10        18.12        15.39        22.29        18.44 
TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 
        9.90        66.25        22.95        36.03       117.21        20.38 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA 
      176.55        35.93       107.34        61.18        53.92        65.92 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R 
       68.09        28.60        10.49        15.68        13.87        10.36 
TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EE-A17X 
       20.35        68.25        17.29        52.01         7.04        29.82 
TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
       27.22         8.65        94.98        33.73        14.70        26.89 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A 
        4.96       133.81       151.27       168.26        13.55        63.35 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M 
       85.08        78.97        63.78        64.64         2.60        56.84 
TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V 
       18.61        66.74        14.47        61.28       369.93        25.87 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 
      195.02        17.92        46.82       102.90        36.82        39.29 
TCGA-EE-A2A6 TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
       86.14        67.43       340.14       161.03       208.04        48.72 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO 
      107.38        54.74        79.66        75.48       102.12       126.81 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 
       42.77        81.21        44.88        94.82        21.67       129.27 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF 
       28.83        19.76        61.51        47.28       103.27       268.73 
TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM 
      103.20        16.96       204.66       158.63       216.66       167.90 
TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA 
       47.54        43.23       162.48        71.21        53.26       124.31 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH 
      122.73        51.62        54.51        13.81        41.59       138.81 
TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J8 TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH 
      127.20        36.95        34.32        27.35        51.35       109.58 
TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 
      152.81        31.40        35.44        13.94        50.76         9.17 
TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F 
       77.75        98.40        48.89        12.59        13.02        26.37 
TCGA-ER-A19G TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P 
      268.93         6.44       131.51        61.05        44.05       162.08 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
       50.89        37.25         8.88       148.18        79.99        43.82 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES 
       23.34        20.15        16.37        31.27        32.05       247.04 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A42K TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 
       80.32        46.98         6.77       174.21        15.72       220.80 
TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW 
       27.85        18.77        38.27        36.26       104.42       216.92 
TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA 
      228.59       202.65        20.91        28.08         7.79        27.72 
TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG 
       48.85       357.37        53.52        40.27        15.45         9.70 
TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZS 
       32.75        47.38        23.93        74.73        11.41       148.80 
TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 
       53.16        49.48        27.09        27.02        77.82        50.14 
TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD 
       66.67       174.84        34.03        26.73        54.41        80.68 
TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
        0.20        22.92        55.59        13.51        19.30         9.90 
TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 
        2.04        15.78       139.89        84.72        10.13        64.44 
TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A4U9 
       32.48       121.91        39.35        10.42        48.89        22.13 
TCGA-GN-A8LK TCGA-GN-A8LL TCGA-HR-A2OG TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X 
       50.10        21.37         0.23        65.88       368.78       297.90 
TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 
        7.23        18.05         0.33         0.69       228.16        63.02 
TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1V TCGA-W3-AA1W 
      121.08         4.01        69.07       111.09        42.08       219.16 
TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZM 
      105.04        24.03        49.05        61.15        15.98        98.89 
TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AA9Y 
       58.98        67.63        11.80        32.58        49.51        12.16 
TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YD-A89C TCGA-YD-A9TA TCGA-YG-AA3O 
       35.01        19.73        22.29         6.90        49.18        37.94 
TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
       14.43        27.58        96.99        15.98 

  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
             7.23              0.20 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
           248.65            369.93 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
            59.41             49.33 
[1] "7.2 - 248.7 (59.4)" "0.2 - 369.9 (49.3)"
[1] "hr=" "1.2"
D8V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  4Q GAIN MUTATED                    7             1
  4Q GAIN WILD-TYPE                 58             4
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  4Q GAIN MUTATED                                          11
  4Q GAIN WILD-TYPE                                        61
                   vv
clus                REGIONAL LYMPH NODE
  4Q GAIN MUTATED                    28
  4Q GAIN WILD-TYPE                 187
D8V4, multiclass
                                           clus
vv                                          4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  DISTANT METASTASIS                                      7                58
  PRIMARY TUMOR                                           1                 4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE              11                61
  REGIONAL LYMPH NODE                                    28               187
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  4Q GAIN MUTATED             2       0       6        1        7        0
  4Q GAIN WILD-TYPE          10       7      22       17       20       24
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  4Q GAIN MUTATED           1         2         3         7          2
  4Q GAIN WILD-TYPE        13        17         9        30         13
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  4Q GAIN MUTATED            4          8        1
  4Q GAIN WILD-TYPE         28         52       19
D8V5, multiclass
             clus
vv            4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  I OR II NOS               2                10
  STAGE 0                   0                 7
  STAGE I                   6                22
  STAGE IA                  1                17
  STAGE IB                  7                20
  STAGE II                  0                24
  STAGE IIA                 1                13
  STAGE IIB                 2                17
  STAGE IIC                 3                 9
  STAGE III                 7                30
  STAGE IIIA                2                13
  STAGE IIIB                4                28
  STAGE IIIC                8                52
  STAGE IV                  1                19
[1] 14  2
[1] TRUE
[1] "dimension of contingency 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      10 15  7  9
  4Q GAIN WILD-TYPE    54 57 70 59
D8V6, multiclass
       clus
vv      4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  T0+T1              10                54
  T2                 15                57
  T3                  7                70
  T4                  9                59
[1] 4 2
[1] TRUE
[1] "dimension of 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    25   7   6   6
  4Q GAIN WILD-TYPE 144  56  32  43
D8V7, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  N0              25               144
  N1               7                56
  N2               6                32
  N3               6                43
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V8, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED    43   1
  4Q GAIN WILD-TYPE 270  20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED     43    1
  4Q GAIN WILD-TYPE  270   20
   clus
vv  4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  0              43               270
  1               1                20
[1] 2 2
[1] FALSE
D8V9, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED    18  12
  4Q GAIN WILD-TYPE 114  76
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED     18   12
  4Q GAIN WILD-TYPE  114   76
     clus
vv    4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  NO               18               114
  YES              12                76
[1] 2 2
[1] FALSE
D8V10, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     5  42
  4Q GAIN WILD-TYPE  39 271
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      5   42
  4Q GAIN WILD-TYPE   39  271
     clus
vv    4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  NO                5                39
  YES              42               271
[1] 2 2
[1] FALSE
D8V11, continuous
D8V12, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED    18  29
  4Q GAIN WILD-TYPE 117 194
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED     18   29
  4Q GAIN WILD-TYPE  117  194
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  FEMALE              18               117
  MALE                29               194
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  4Q GAIN MUTATED       1                         0    45
  4Q GAIN WILD-TYPE     4                         1   299
D8V13, multiclass
                           clus
vv                          4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  ASIAN                                   1                 4
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  45               299
[1] 3 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     1  46
  4Q GAIN WILD-TYPE   6 298
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      1   46
  4Q GAIN WILD-TYPE    6  298
                        clus
vv                       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 6
  NOT HISPANIC OR LATINO              46               298
[1] 2 2
[1] FALSE

Clustering(9) Variable = 5P GAIN MUTATION ANALYSIS
D9V1, survival
                   sevent
clus2                0  1
  5P GAIN MUTATED   24 21
  5P GAIN WILD-TYPE 97 97
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               45               194 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               21                97 
$`5P GAIN MUTATED`
TCGA-D3-A1Q3 TCGA-D3-A1Q5 TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3MU 
       15.72       110.93        64.83        43.53        58.06        23.67 
TCGA-D3-A51E TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D3-A8GM TCGA-D9-A6EC 
      173.85        45.70       177.86       124.08        70.62        57.90 
TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A20H TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2GM 
       62.37        20.38       155.90       346.49       185.19        18.35 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A3AA TCGA-EE-A3AB 
      103.13        15.25       227.01       143.93       124.31       122.73 
TCGA-EE-A3AE TCGA-EE-A3J3 TCGA-EE-A3JI TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19G 
       54.51        67.89       152.81        53.29        39.81       151.46 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A2ND TCGA-ER-A3PL TCGA-FR-A44A 
       59.84        42.48       120.76         4.70        32.05       174.21 
TCGA-FR-A8YC TCGA-FS-A1ZE TCGA-FS-A1ZQ TCGA-FW-A3TU TCGA-GF-A4EO TCGA-GN-A265 
       10.06        35.90       130.95        55.59         6.05        84.72 
TCGA-QB-AA9O TCGA-W3-AA1V TCGA-WE-A8ZQ 
       18.05         8.09        59.44 

$`5P GAIN WILD-TYPE`
TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q6 
       60.46        12.99        14.83         8.42        31.89        49.35 
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
      133.25        19.04        76.41        62.60        25.64        45.99 
TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JE 
       62.86        15.75       168.00        86.30         7.27         9.76 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JO TCGA-D3-A3C7 TCGA-D3-A3CB 
      107.61        36.30       171.58        66.08        46.98       140.98 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR 
       40.01        59.70        16.96        13.87         9.34        90.21 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A8GC 
      144.46        31.76        62.70        11.34        42.05        78.21 
TCGA-D3-A8GD TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GP TCGA-D3-A8GR 
       23.61       179.97       120.00        69.53       135.12        36.53 
TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6EG TCGA-DA-A1HV 
       10.78        15.02        16.90        18.44        22.85        48.66 
TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA 
      106.85        31.96       150.61        82.85        32.42        64.83 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5SG 
       58.85        25.12       214.59        14.96         3.91        33.24 
TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A182 
       50.07        45.50         6.64        13.15        24.89         0.00 
TCGA-EE-A184 TCGA-EE-A20C TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
       67.50        75.55        75.22        76.14        12.99         0.26 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A2A1 
       44.28        63.12        47.74        27.16        61.12       102.38 
TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
        7.20        77.98        26.14       239.11         0.20       189.40 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP 
       68.65        10.62        32.48        31.00       118.32         0.76 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MF 
        0.20        71.31        81.99         5.75        23.77       209.79 
TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM 
       94.19       171.85        63.25        67.50       104.78       145.45 
TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AF 
       25.08        23.51        53.26        51.62         4.41         6.28 
TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-ER-A193 TCGA-ER-A195 
      111.85        45.90         3.35       201.80        14.56        34.45 
TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19D TCGA-ER-A19H 
        1.58        47.31         7.82         4.54        11.47       150.12 
TCGA-ER-A19L TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
       99.06        49.71        34.95       146.63        47.97        22.36 
TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-FR-A729 
       16.87        10.95       173.29        55.82        15.48       209.23 
TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
       26.20         5.65       171.78        49.74       195.98         8.35 
TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZJ 
       27.62       312.07        32.78        12.92         7.82        36.33 
TCGA-FS-A1ZM TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY 
       78.61       136.27        35.28         4.47        23.21         5.29 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FD 
        3.06        30.90        66.67       173.19        13.28        80.68 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 
       11.54        19.30         9.90         1.91        53.29       117.93 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 
       17.06        42.48         7.59       120.53        34.49        46.92 
TCGA-GN-A8LK TCGA-GN-A9SD TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A693 
       43.23        59.41        85.05       297.01         7.23         0.33 
TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1W 
      174.12         1.97       120.07        44.05        79.99       185.13 
TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO 
       92.84         1.15        59.64        62.99        12.69        19.00 
TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 
       10.95        48.39         1.94        26.60        16.64        15.65 
TCGA-YG-AA3O TCGA-Z2-AA3S 
       28.21        91.23 

  5P GAIN MUTATED 5P GAIN WILD-TYPE 
              4.7               0.0 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
           346.49            312.07 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
           59.840            42.265 
[1] "4.7 - 346.5 (59.8)" "0.0 - 312.1 (42.3)"
[1] "hr=" "1.5"
D9V2, survival
                   sevent
clus2                 0   1
  5P GAIN MUTATED    38  34
  5P GAIN WILD-TYPE 131 146
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               72               277 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               34               146 
$`5P GAIN MUTATED`
TCGA-3N-A9WB TCGA-D3-A1Q3 TCGA-D3-A1Q5 TCGA-D3-A2JF TCGA-D3-A2JK TCGA-D3-A2JN 
       17.03        16.67       112.57        62.07        12.10        66.48 
TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51N TCGA-D3-A5GN 
       59.57        58.06        39.75       174.84        22.62       135.75 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GI TCGA-D3-A8GM TCGA-D9-A148 
      178.32        18.18       125.19        58.52       107.15       151.53 
TCGA-D9-A1JW TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-EB-A44R TCGA-EE-A180 
        3.65         9.90        25.18        66.25        10.36        94.98 
TCGA-EE-A181 TCGA-EE-A20B TCGA-EE-A20H TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A0 
       33.73       133.81       168.26       369.93       195.02        46.82 
TCGA-EE-A2GM TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A3AA 
       75.48       129.27        28.83       248.65       162.48       124.31 
TCGA-EE-A3AB TCGA-EE-A3AE TCGA-EE-A3J3 TCGA-EE-A3JA TCGA-EE-A3JI TCGA-ER-A19B 
      122.73        54.51       172.18        53.19       152.81        98.40 
TCGA-ER-A19C TCGA-ER-A19G TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19T 
       48.89       268.93        61.05        44.05       162.08         8.88 
TCGA-ER-A2ND TCGA-ER-A3PL TCGA-FR-A44A TCGA-FR-A7U9 TCGA-FR-A8YC TCGA-FR-A8YD 
       23.34        33.21       174.21        18.77        34.82        36.26 
TCGA-FR-A8YE TCGA-FS-A1YX TCGA-FS-A1ZE TCGA-FS-A1ZK TCGA-FS-A1ZQ TCGA-FS-A4F5 
      104.42        48.59        40.27        23.93       133.55        28.73 
TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-GF-A4EO TCGA-GN-A265 TCGA-GN-A4U9 TCGA-QB-AA9O 
        0.20        55.59         7.23        84.72        22.13        18.05 
TCGA-W3-AA1O TCGA-W3-AA1V TCGA-WE-A8JZ TCGA-WE-A8ZQ TCGA-YG-AA3P TCGA-Z2-A8RT 
        4.01        42.08        24.03        59.77        14.43        27.58 

$`5P GAIN WILD-TYPE`
TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q6 
       66.48        12.99        14.93        16.57       112.04        71.80 
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 
      133.25        28.08        31.59        90.90        95.74        43.43 
TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC 
      103.10        65.49        23.77       115.53       168.00        86.76 
TCGA-D3-A2JD TCGA-D3-A2JE TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JO 
       11.87        27.65       113.52        42.08       171.58        66.08 
TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE 
      130.72        46.98        46.32       166.52        86.93        60.23 
TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MV TCGA-D3-A51F 
       24.53        13.87         9.34       103.59        45.30        55.73 
TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL 
       56.35       145.12        32.94        63.81        26.89       125.79 
TCGA-D3-A5GO TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GJ 
      137.92        30.84        79.59        23.61        26.43       241.38 
TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR 
      170.20        89.13       161.00       152.75        29.06       129.63 
TCGA-D3-A8GS TCGA-D9-A149 TCGA-D9-A1JX TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 
      117.17        54.67         7.10        18.12        15.39        22.29 
TCGA-D9-A4Z6 TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 
       18.44        22.95        48.89        36.03       117.21        20.38 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
      194.83       176.55        35.93       107.34        61.18        53.92 
TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 
       65.92        23.44        68.09        28.60        10.49       215.44 
TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL 
       15.68        13.87        20.35        68.25        54.02        17.29 
TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
       52.01         7.04        24.89        29.82        27.22         8.65 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A20F 
       14.70        26.89        68.15         4.96       151.27        91.56 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
       13.55        63.35        85.08        78.97        13.97        63.78 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P 
       72.07        64.64         2.60        56.84        18.61        56.42 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A1 
       66.74        14.47        61.28        25.87        17.92       102.90 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD 
       36.82        39.29        86.14        59.28        67.43       340.14 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
      161.03       208.04        48.72       107.38        54.74        79.66 
TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT 
      102.12       126.81        13.91        42.77        81.21        44.88 
TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME 
       94.82        21.67        19.76        61.51        47.28       103.27 
TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK 
      268.73       103.20        16.96       204.66        96.23       158.63 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MT 
      216.66       167.90        47.54        43.23       134.40        71.21 
TCGA-EE-A2MU TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH 
       53.26        51.62        28.77        13.81        41.59       138.81 
TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JD 
      127.20        36.95        64.08        34.32       201.80        27.35 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
       51.35       109.58        31.40        35.44        13.94        50.76 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19H 
        9.17        77.75        12.59        13.02        26.37       152.35 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 
        6.44       131.51        50.89        37.25       148.18        79.99 
TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES 
       43.82        20.15        16.37        31.27        32.05       247.04 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A69P TCGA-FR-A729 
       80.32        46.98         6.77        92.98        15.72       220.80 
TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
       27.85        38.27       216.92       228.59       202.65        20.91 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD 
       28.08         7.79        27.72        48.85       357.37        53.52 
TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZP 
       15.45         9.70        32.75        47.38       101.26        74.73 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY 
       11.41       148.80        53.16        26.56        49.48        27.09 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 
       27.02        77.82        50.14        66.67       174.84        34.03 
TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3R5 TCGA-FW-A3TV TCGA-FW-A5DY 
       26.73        54.41        80.68        22.92        13.51        19.30 
TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A266 
        9.90         2.04        15.78       139.89       117.93        10.13 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A4U4 
       64.44        62.79        32.48        39.58       121.91        39.35 
TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A8LK TCGA-GN-A8LL TCGA-GN-A9SD TCGA-HR-A2OG 
       10.42        48.89        50.10        21.37        59.41         0.23 
TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 
       65.88       368.78       297.90         7.23         0.33         0.69 
TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1W 
      228.16        63.02       121.08        69.07       111.09       219.16 
TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN 
      105.04        49.05        61.15        15.98        98.89        58.98 
TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 
       67.63        11.80        32.58        49.51        12.16        35.01 
TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YD-A89C TCGA-YD-A9TA TCGA-YG-AA3O TCGA-Z2-AA3S 
       19.73        22.29         6.90        49.18        37.94        96.99 
TCGA-Z2-AA3V 
       15.98 

  5P GAIN MUTATED 5P GAIN WILD-TYPE 
             0.20              0.23 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
           369.93            368.78 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
            55.05             50.14 
[1] "0.2 - 369.9 (55.0)" "0.2 - 368.8 (50.1)"
[1] "hr=" "1.2"
D9V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  5P GAIN MUTATED                   13             4
  5P GAIN WILD-TYPE                 52             1
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  5P GAIN MUTATED                                          10
  5P GAIN WILD-TYPE                                        62
                   vv
clus                REGIONAL LYMPH NODE
  5P GAIN MUTATED                    48
  5P GAIN WILD-TYPE                 167
D9V4, multiclass
                                           clus
vv                                          5P GAIN MUTATED 5P GAIN WILD-TYPE
  DISTANT METASTASIS                                     13                52
  PRIMARY TUMOR                                           4                 1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE              10                62
  REGIONAL LYMPH NODE                                    48               167
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  5P GAIN MUTATED             4       2       7        5        6        7
  5P GAIN WILD-TYPE           8       5      21       13       21       17
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  5P GAIN MUTATED           2         4         4         6          3
  5P GAIN WILD-TYPE        12        15         8        31         12
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  5P GAIN MUTATED            3          8        5
  5P GAIN WILD-TYPE         29         52       15
D9V5, multiclass
             clus
vv            5P GAIN MUTATED 5P GAIN WILD-TYPE
  I OR II NOS               4                 8
  STAGE 0                   2                 5
  STAGE I                   7                21
  STAGE IA                  5                13
  STAGE IB                  6                21
  STAGE II                  7                17
  STAGE IIA                 2                12
  STAGE IIB                 4                15
  STAGE IIC                 4                 8
  STAGE III                 6                31
  STAGE IIIA                3                12
  STAGE IIIB                3                29
  STAGE IIIC                8                52
  STAGE IV                  5                15
[1] 14  2
[1] TRUE
[1] "dimension of contingency 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      18 13 17 12
  5P GAIN WILD-TYPE    46 59 60 56
D9V6, multiclass
       clus
vv      5P GAIN MUTATED 5P GAIN WILD-TYPE
  T0+T1              18                46
  T2                 13                59
  T3                 17                60
  T4                 12                56
[1] 4 2
[1] TRUE
[1] "dimension of 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    45   7   7  10
  5P GAIN WILD-TYPE 124  56  31  39
D9V7, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  N0              45               124
  N1               7                56
  N2               7                31
  N3              10                39
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V8, binary
                   cls
clus                  0   1
  5P GAIN MUTATED    66   6
  5P GAIN WILD-TYPE 247  15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     66    6
  5P GAIN WILD-TYPE  247   15
   clus
vv  5P GAIN MUTATED 5P GAIN WILD-TYPE
  0              66               247
  1               6                15
[1] 2 2
[1] FALSE
D9V9, binary
                   cls
clus                  0   1
  5P GAIN MUTATED    31  12
  5P GAIN WILD-TYPE 101  76
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     31   12
  5P GAIN WILD-TYPE  101   76
     clus
vv    5P GAIN MUTATED 5P GAIN WILD-TYPE
  NO               31               101
  YES              12                76
[1] 2 2
[1] FALSE
D9V10, binary
                   cls
clus                  0   1
  5P GAIN MUTATED    11  64
  5P GAIN WILD-TYPE  33 249
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     11   64
  5P GAIN WILD-TYPE   33  249
     clus
vv    5P GAIN MUTATED 5P GAIN WILD-TYPE
  NO               11                33
  YES              64               249
[1] 2 2
[1] FALSE
D9V11, continuous
D9V12, binary
                   cls
clus                  0   1
  5P GAIN MUTATED    28  47
  5P GAIN WILD-TYPE 107 176
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     28   47
  5P GAIN WILD-TYPE  107  176
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  FEMALE              28               107
  MALE                47               176
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  5P GAIN MUTATED       1                         0    71
  5P GAIN WILD-TYPE     4                         1   273
D9V13, multiclass
                           clus
vv                          5P GAIN MUTATED 5P GAIN WILD-TYPE
  ASIAN                                   1                 4
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  71               273
[1] 3 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     2  72
  5P GAIN WILD-TYPE   5 272
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      2   72
  5P GAIN WILD-TYPE    5  272
                        clus
vv                       5P GAIN MUTATED 5P GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 5
  NOT HISPANIC OR LATINO              72               272
[1] 2 2
[1] FALSE

Clustering(10) Variable = 5Q GAIN MUTATION ANALYSIS
D10V1, survival
                   sevent
clus2                 0   1
  5Q GAIN MUTATED    16  14
  5Q GAIN WILD-TYPE 105 104
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               30               209 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               14               104 
$`5Q GAIN MUTATED`
TCGA-3N-A9WC TCGA-D3-A1Q3 TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3MU TCGA-D3-A51K 
       60.46        15.72        64.83        43.53        23.67        31.76 
TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D3-A8GM TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A29W 
      177.86       124.08        70.62        62.37        20.38       185.19 
TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A3AA TCGA-EE-A3AE TCGA-EE-A3J3 TCGA-EE-A3JI 
      227.01       143.93       124.31        54.51        67.89       152.81 
TCGA-ER-A19C TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A2ND TCGA-ER-A3PL TCGA-FR-A8YC 
       39.81        42.48       120.76         4.70        32.05        10.06 
TCGA-FS-A1ZD TCGA-FW-A3TU TCGA-GF-A4EO TCGA-GN-A265 TCGA-QB-AA9O TCGA-WE-A8ZQ 
       32.78        55.59         6.05        84.72        18.05        59.44 

$`5Q GAIN WILD-TYPE`
TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 
       12.99        14.83         8.42        31.89       110.93        49.35 
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
      133.25        19.04        76.41        62.60        25.64        45.99 
TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JE 
       62.86        15.75       168.00        86.30         7.27         9.76 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JO TCGA-D3-A3C6 TCGA-D3-A3C7 
      107.61        36.30       171.58        66.08        58.06        46.98 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO 
      140.98        40.01        59.70        16.96        13.87         9.34 
TCGA-D3-A3MR TCGA-D3-A51E TCGA-D3-A51J TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL 
       90.21       173.85       144.46        62.70        11.34        42.05 
TCGA-D3-A5GN TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL 
       45.70        78.21        23.61       179.97       120.00        69.53 
TCGA-D3-A8GP TCGA-D3-A8GR TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 
      135.12        36.53        10.78        15.02        16.90        18.44 
TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 
       57.90        22.85        48.66       106.85        31.96       150.61 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 
       82.85        32.42        64.83        58.85        25.12       214.59 
TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A6L9 
       14.96         3.91        33.24        50.07        45.50         6.64 
TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A182 TCGA-EE-A184 TCGA-EE-A20C TCGA-EE-A20H 
       13.15        24.89         0.00        67.50        75.55       155.90 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H 
       75.22        76.14        12.99         0.26        44.28        63.12 
TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A2A1 TCGA-EE-A2A2 
       47.74        27.16        61.12       346.49       102.38         7.20 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ 
       77.98        26.14       239.11         0.20       189.40        68.65 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP 
       10.62        32.48        18.35        31.00       118.32         0.76 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 
        0.20        71.31        81.99       103.13        15.25         5.75 
TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK 
       23.77       209.79        94.19       171.85        63.25        67.50 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB 
      104.78       145.45        25.08        23.51        53.26       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 
       51.62         4.41         6.28       111.85        45.90         3.35 
TCGA-EE-A3JB TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 
      201.80        14.56        34.45         1.58        47.31         7.82 
TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L 
        4.54        53.29        11.47       151.46       150.12        99.06 
TCGA-ER-A19M TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
       59.84        49.71        34.95       146.63        47.97        22.36 
TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-FR-A44A 
       16.87        10.95       173.29        55.82        15.48       174.21 
TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 
      209.23        26.20         5.65       171.78        49.74       195.98 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG 
        8.35        27.62       312.07        35.90        12.92         7.82 
TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU 
       36.33        78.61       130.95       136.27        35.28         4.47 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 
       23.21         5.29         3.06        30.90        66.67       173.19 
TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 
       13.28        80.68        11.54        19.30         9.90         1.91 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 
       53.29       117.93        17.06        42.48         7.59       120.53 
TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-GN-A8LK TCGA-GN-A9SD TCGA-LH-A9QB TCGA-OD-A75X 
       34.49        46.92        43.23        59.41        85.05       297.01 
TCGA-QB-A6FS TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1Q 
        7.23         0.33       174.12         1.97       120.07        44.05 
TCGA-W3-AA1R TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8K5 
       79.99         8.09       185.13        92.84         1.15        59.64 
TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AA9Y 
       62.99        12.69        19.00        10.95        48.39         1.94 
TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-Z2-AA3S 
       26.60        16.64        15.65        28.21        91.23 

  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
              4.7               0.0 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
           227.01            346.49 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
           57.515            45.700 
[1] "4.7 - 227.0 (57.5)" "0.0 - 346.5 (45.7)"
[1] "hr=" "1.2"
D10V2, survival
                   sevent
clus2                 0   1
  5Q GAIN MUTATED    27  22
  5Q GAIN WILD-TYPE 142 158
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               49               300 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               22               158 
$`5Q GAIN MUTATED`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-D3-A1Q3 TCGA-D3-A2JF TCGA-D3-A2JN TCGA-D3-A2JP 
       17.03        66.48        16.67        62.07        66.48        59.57 
TCGA-D3-A3MU TCGA-D3-A51K TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GM 
       39.75        32.94       178.32        18.18       125.19       107.15 
TCGA-D9-A148 TCGA-D9-A1JW TCGA-D9-A6E9 TCGA-EB-A44R TCGA-EE-A180 TCGA-EE-A181 
      151.53         3.65         9.90        10.36        94.98        33.73 
TCGA-EE-A20B TCGA-EE-A29W TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A3AA TCGA-EE-A3AE 
      133.81       195.02       248.65       162.48       124.31        54.51 
TCGA-EE-A3J3 TCGA-EE-A3JA TCGA-EE-A3JI TCGA-ER-A19C TCGA-ER-A19N TCGA-ER-A19P 
      172.18        53.19       152.81        48.89        44.05       162.08 
TCGA-ER-A19T TCGA-ER-A2ND TCGA-ER-A3PL TCGA-FR-A7U9 TCGA-FR-A8YC TCGA-FR-A8YD 
        8.88        23.34        33.21        18.77        34.82        36.26 
TCGA-FR-A8YE TCGA-FS-A1ZD TCGA-FS-A1ZK TCGA-FS-A4F5 TCGA-FW-A3TU TCGA-GF-A4EO 
      104.42        53.52        23.93        28.73        55.59         7.23 
TCGA-GN-A265 TCGA-GN-A4U9 TCGA-QB-AA9O TCGA-WE-A8JZ TCGA-WE-A8ZQ TCGA-YG-AA3P 
       84.72        22.13        18.05        24.03        59.77        14.43 
TCGA-Z2-A8RT 
       27.58 

$`5Q GAIN WILD-TYPE`
TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 
       12.99        14.93        16.57       112.04       112.57        71.80 
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 
      133.25        28.08        31.59        90.90        95.74        43.43 
TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC 
      103.10        65.49        23.77       115.53       168.00        86.76 
TCGA-D3-A2JD TCGA-D3-A2JE TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL 
       11.87        27.65       113.52        42.08        12.10       171.58 
TCGA-D3-A2JO TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB 
       66.08       130.72        58.06        46.98        46.32       166.52 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR 
       86.93        60.23        24.53        13.87         9.34       103.59 
TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51N 
       45.30       174.84        55.73        56.35       145.12        22.62 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A8GB 
       63.81        26.89       125.79       135.75       137.92        30.84 
TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GK 
       79.59        23.61        26.43        58.52       241.38       170.20 
TCGA-D3-A8GL TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS 
       89.13       161.00       152.75        29.06       129.63       117.17 
TCGA-D9-A149 TCGA-D9-A1JX TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 
       54.67         7.10        18.12        15.39        22.29        18.44 
TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY 
       25.18        66.25        22.95        48.89        36.03       117.21 
TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 
       20.38       194.83       176.55        35.93       107.34        61.18 
TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
       53.92        65.92        23.44        68.09        28.60        10.49 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH 
      215.44        15.68        13.87        20.35        68.25        54.02 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y 
       17.29        52.01         7.04        24.89        29.82        27.22 
TCGA-EE-A17Z TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20C 
        8.65        14.70        26.89        68.15         4.96       151.27 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C 
       91.56       168.26        13.55        63.35        85.08        78.97 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M 
       13.97        63.78        72.07        64.64         2.60        56.84 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T 
       18.61        56.42        66.74        14.47        61.28       369.93 
TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 
       25.87        17.92        46.82       102.90        36.82        39.29 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
       86.14        59.28        67.43       340.14       161.03       208.04 
TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN 
       48.72       107.38        54.74        79.66        75.48       102.12 
TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU 
      126.81        13.91        42.77        81.21        44.88        94.82 
TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD 
       21.67       129.27        28.83        19.76        61.51        47.28 
TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ 
      103.27       268.73       103.20        16.96       204.66        96.23 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MR 
      158.63       216.66       167.90        47.54        43.23       134.40 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AF 
       71.21        53.26       122.73        51.62        28.77        13.81 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 
       41.59       138.81       127.20        36.95        64.08        34.32 
TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 
      201.80        27.35        51.35       109.58        31.40        35.44 
TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19D 
       13.94        50.76         9.17        77.75        98.40        12.59 
TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L 
       13.02        26.37       268.93       152.35         6.44       131.51 
TCGA-ER-A19M TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
       61.05        50.89        37.25       148.18        79.99        43.82 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET 
       20.15        16.37        31.27        32.05       247.04        80.32 
TCGA-ER-A3EV TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 
       46.98         6.77        92.98       174.21        15.72       220.80 
TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
       27.85        38.27       216.92        48.59       228.59       202.65 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC 
       20.91        28.08         7.79        27.72        48.85       357.37 
TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZM 
       40.27        15.45         9.70        32.75        47.38       101.26 
TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU 
       74.73       133.55        11.41       148.80        53.16        26.56 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 
       49.48        27.09        27.02        77.82        50.14        66.67 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 
      174.84        34.03        26.73        54.41        80.68         0.20 
TCGA-FW-A3R5 TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GF-A6C9 
       22.92        13.51        19.30         9.90         2.04        15.78 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
      139.89       117.93        10.13        64.44        62.79        32.48 
TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A8LK 
       39.58       121.91        39.35        10.42        48.89        50.10 
TCGA-GN-A8LL TCGA-GN-A9SD TCGA-HR-A2OG TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X 
       21.37        59.41         0.23        65.88       368.78       297.90 
TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 
        7.23         0.33         0.69       228.16        63.02       121.08 
TCGA-W3-AA1O TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 
        4.01        69.07       111.09        42.08       219.16       105.04 
TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO 
       49.05        61.15        15.98        98.89        58.98        67.63 
TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 
       11.80        32.58        49.51        12.16        35.01        19.73 
TCGA-WE-AAA4 TCGA-YD-A89C TCGA-YD-A9TA TCGA-YG-AA3O TCGA-Z2-AA3S TCGA-Z2-AA3V 
       22.29         6.90        49.18        37.94        96.99        15.98 

  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
             3.65              0.20 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
           248.65            369.93 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
            48.89             51.12 
[1] "3.6 - 248.7 (48.9)" "0.2 - 369.9 (51.1)"
[1] "hr=" "1.1"
D10V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  5Q GAIN MUTATED                    9             2
  5Q GAIN WILD-TYPE                 56             3
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  5Q GAIN MUTATED                                           5
  5Q GAIN WILD-TYPE                                        67
                   vv
clus                REGIONAL LYMPH NODE
  5Q GAIN MUTATED                    34
  5Q GAIN WILD-TYPE                 181
D10V4, multiclass
                                           clus
vv                                          5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  DISTANT METASTASIS                                      9                56
  PRIMARY TUMOR                                           2                 3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               5                67
  REGIONAL LYMPH NODE                                    34               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"
                   vv
clus                I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  5Q GAIN MUTATED             1       1       3        4        4        4
  5Q GAIN WILD-TYPE          11       6      25       14       23       20
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  5Q GAIN MUTATED           3         4         2         4          2
  5Q GAIN WILD-TYPE        11        15        10        33         13
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  5Q GAIN MUTATED            3          6        3
  5Q GAIN WILD-TYPE         29         54       17
D10V5, multiclass
             clus
vv            5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  I OR II NOS               1                11
  STAGE 0                   1                 6
  STAGE I                   3                25
  STAGE IA                  4                14
  STAGE IB                  4                23
  STAGE II                  4                20
  STAGE IIA                 3                11
  STAGE IIB                 4                15
  STAGE IIC                 2                10
  STAGE III                 4                33
  STAGE IIIA                2                13
  STAGE IIIB                3                29
  STAGE IIIC                6                54
  STAGE IV                  3                17
[1] 14  2
[1] TRUE
[1] "dimension of contingency 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      13 10 11  7
  5Q GAIN WILD-TYPE    51 62 66 61
D10V6, multiclass
       clus
vv      5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  T0+T1              13                51
  T2                 10                62
  T3                 11                66
  T4                  7                61
[1] 4 2
[1] TRUE
[1] "dimension of 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    26   5   5   8
  5Q GAIN WILD-TYPE 143  58  33  41
D10V7, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  N0              26               143
  N1               5                58
  N2               5                33
  N3               8                41
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V8, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED    43   4
  5Q GAIN WILD-TYPE 270  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     43    4
  5Q GAIN WILD-TYPE  270   17
   clus
vv  5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  0              43               270
  1               4                17
[1] 2 2
[1] FALSE
D10V9, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED    20  11
  5Q GAIN WILD-TYPE 112  77
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     20   11
  5Q GAIN WILD-TYPE  112   77
     clus
vv    5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  NO               20               112
  YES              11                77
[1] 2 2
[1] FALSE
D10V10, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED     7  43
  5Q GAIN WILD-TYPE  37 270
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      7   43
  5Q GAIN WILD-TYPE   37  270
     clus
vv    5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  NO                7                37
  YES              43               270
[1] 2 2
[1] FALSE
D10V11, continuous
D10V12, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED    17  33
  5Q GAIN WILD-TYPE 118 190
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     17   33
  5Q GAIN WILD-TYPE  118  190
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  FEMALE              17               118
  MALE                33               190
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  5Q GAIN MUTATED       1                         0    46
  5Q GAIN WILD-TYPE     4                         1   298
D10V13, multiclass
                           clus
vv                          5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  ASIAN                                   1                 4
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  46               298
[1] 3 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     3  46
  5Q GAIN WILD-TYPE   4 298
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      3   46
  5Q GAIN WILD-TYPE    4  298
                        clus
vv                       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                 4
  NOT HISPANIC OR LATINO              46               298
[1] 2 2
[1] FALSE

Clustering(11) Variable = 6P GAIN MUTATION ANALYSIS
D11V1, survival
                   sevent
clus2                0  1
  6P GAIN MUTATED   40 55
  6P GAIN WILD-TYPE 81 63
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               95               144 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               55                63 
$`6P GAIN MUTATED`
TCGA-3N-A9WC TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q7 TCGA-D3-A1QA TCGA-D3-A1QB 
       60.46         8.42        15.72       133.25        76.41        62.60 
TCGA-D3-A2J8 TCGA-D3-A2JE TCGA-D3-A2JO TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3MR 
       62.86         9.76        66.08        58.06        40.01        90.21 
TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GU TCGA-D3-A8GJ 
       23.67       173.85        11.34        45.70       124.08       179.97 
TCGA-D3-A8GL TCGA-D3-A8GP TCGA-D9-A1X3 TCGA-D9-A4Z6 TCGA-DA-A1HV TCGA-DA-A1I2 
       69.53       135.12        10.78        18.44        48.66       150.61 
TCGA-DA-A1IA TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A181 TCGA-EE-A184 TCGA-EE-A20H 
       64.83        33.24        50.07        20.38        67.50       155.90 
TCGA-EE-A29B TCGA-EE-A29P TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GH TCGA-EE-A2GN 
       75.22        27.16        26.14       239.11       189.40        31.00 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2MF TCGA-EE-A2MI 
        0.76         0.20        71.31        81.99       209.79       171.85 
TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AA 
       67.50       145.45       227.01       143.93        53.26       124.31 
TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JI 
        4.41         6.28        67.89        45.90         3.35       152.81 
TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19C TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P 
        1.58         7.82        39.81        59.84        42.48       120.76 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A2NC TCGA-ER-A3ES TCGA-ER-A3EV TCGA-ER-A3PL 
       49.71        34.95        22.36       173.29        15.48        32.05 
TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1ZC TCGA-FS-A1ZE TCGA-FS-A1ZJ TCGA-FS-A1ZM 
      195.98         8.35       312.07        35.90        36.33        78.61 
TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F8 TCGA-FS-A4FD TCGA-GF-A4EO 
        4.47         5.29         3.06       173.19        80.68         6.05 
TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A8LK TCGA-GN-A9SD TCGA-LH-A9QB 
      117.93        17.06         7.59        43.23        59.41        85.05 
TCGA-QB-AA9O TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1V TCGA-W3-AA21 TCGA-WE-A8ZO 
       18.05        44.05        79.99         8.09        92.84        19.00 
TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O 
       59.44        10.95        16.64        15.65        28.21 

$`6P GAIN WILD-TYPE`
TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q8 
       12.99        14.83        31.89       110.93        49.35        19.04 
TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
       25.64        45.99        15.75       168.00        86.30         7.27 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3C7 
      107.61        36.30       171.58        64.83        43.53        46.98 
TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A51J 
      140.98        59.70        16.96        13.87         9.34       144.46 
TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A5GL TCGA-D3-A5GR TCGA-D3-A8GC TCGA-D3-A8GD 
       31.76        62.70        42.05       177.86        78.21        23.61 
TCGA-D3-A8GK TCGA-D3-A8GM TCGA-D3-A8GR TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6EC 
      120.00        70.62        36.53        15.02        16.90        57.90 
TCGA-D9-A6EG TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IC 
       22.85       106.85        31.96        82.85        32.42        58.85 
TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5UN TCGA-EB-A6L9 
       25.12       214.59        14.96         3.91        45.50         6.64 
TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A182 TCGA-EE-A20C TCGA-EE-A29C 
       13.15        24.89        62.37         0.00        75.55        76.14 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29Q 
       12.99         0.26        44.28        63.12        47.74        61.12 
TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GE 
      346.49       185.19       102.38         7.20        77.98         0.20 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GO TCGA-EE-A2M6 
       68.65        10.62        32.48        18.35       118.32       103.13 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MG TCGA-EE-A2MJ TCGA-EE-A2ML 
       15.25         5.75        23.77        94.19        63.25       104.78 
TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3J4 
       25.08        23.51       122.73        51.62        54.51       111.85 
TCGA-EE-A3JB TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19B 
      201.80        14.56        34.45        47.31         4.54        53.29 
TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19W TCGA-ER-A1A1 
       11.47       151.46       150.12        99.06       146.63        47.97 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A3ET TCGA-FR-A44A TCGA-FR-A729 
        4.70        16.87        10.95        55.82       174.21       209.23 
TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z4 
       26.20         5.65        10.06       171.78        49.74        27.62 
TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT 
       32.78        12.92         7.82       130.95       136.27        35.28 
TCGA-FS-A1ZW TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F9 TCGA-FW-A3TU TCGA-FW-A3TV 
       23.21        30.90        66.67        13.28        55.59        11.54 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A268 
       19.30         9.90         1.91        53.29        84.72        42.48 
TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A693 
      120.53        34.49        46.92       297.01         7.23         0.33 
TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1W TCGA-WE-A8K1 TCGA-WE-A8K5 
      174.12         1.97       120.07       185.13         1.15        59.64 
TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-Z2-AA3S 
       62.99        12.69        48.39         1.94        26.60        91.23 

  6P GAIN MUTATED 6P GAIN WILD-TYPE 
              0.2               0.0 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
           312.07            346.49 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
            49.71             44.89 
[1] "0.2 - 312.1 (49.7)" "0.0 - 346.5 (44.9)"
[1] "hr=" "1.2"
D11V2, survival
                   sevent
clus2                 0   1
  6P GAIN MUTATED    55  81
  6P GAIN WILD-TYPE 114  99
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
              136               213 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               81                99 
$`6P GAIN MUTATED`
TCGA-3N-A9WC TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q7 TCGA-D3-A1QA TCGA-D3-A1QB 
       66.48        16.57        16.67       133.25        90.90        95.74 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A2JO TCGA-D3-A3C6 
       65.49        23.77        27.65        62.07        66.08        58.06 
TCGA-D3-A3CC TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51T TCGA-D3-A5GN 
       86.93       103.59        39.75       174.84        26.89       135.75 
TCGA-D3-A5GO TCGA-D3-A5GU TCGA-D3-A8GJ TCGA-D3-A8GL TCGA-D3-A8GP TCGA-D3-A8GQ 
      137.92       125.19       241.38        89.13       152.75        29.06 
TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1X3 TCGA-D9-A4Z6 TCGA-D9-A6E9 
      151.53        54.67         3.65        18.12        18.44         9.90 
TCGA-DA-A1HV TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1IA TCGA-DA-A3F3 TCGA-EB-A5KH 
       48.89        20.38       176.55        65.92        10.49        20.35 
TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A184 
       68.25        54.02         8.65        33.73        26.89        68.15 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20H TCGA-EE-A29B TCGA-EE-A29P TCGA-EE-A29R 
        4.96       133.81       168.26        85.08        56.42        14.47 
TCGA-EE-A29S TCGA-EE-A2A5 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GH TCGA-EE-A2GN 
       61.28        39.29        59.28       340.14       208.04       102.12 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2ME 
       13.91        42.77        81.21        44.88        94.82       103.27 
TCGA-EE-A2MF TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP 
      268.73       204.66       158.63       167.90        47.54       248.65 
TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AD TCGA-EE-A3AF 
       43.23       162.48        53.26       124.31        28.77        13.81 
TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA 
       41.59       172.18        36.95        64.08        34.32        53.19 
TCGA-EE-A3JI TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19C TCGA-ER-A19E TCGA-ER-A19F 
      152.81        13.94         9.17        48.89        13.02        26.37 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A2NC 
       61.05        44.05       162.08        50.89        37.25        43.82 
TCGA-ER-A2NF TCGA-ER-A3ES TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A8YD TCGA-FS-A1Z0 
       16.37       247.04        46.98        33.21        36.26       202.65 
TCGA-FS-A1Z3 TCGA-FS-A1ZC TCGA-FS-A1ZE TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM 
       20.91       357.37        40.27        47.38        23.93       101.26 
TCGA-FS-A1ZP TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F2 TCGA-FS-A4F5 
       74.73        26.56        27.09        27.02        50.14        28.73 
TCGA-FS-A4F8 TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-GF-A4EO TCGA-GF-A6C9 TCGA-GN-A264 
      174.84        80.68         0.20         7.23        15.78       117.93 
TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U9 TCGA-GN-A8LK 
       10.13        64.44        32.48        39.58        22.13        50.10 
TCGA-GN-A8LL TCGA-GN-A9SD TCGA-LH-A9QB TCGA-QB-AA9O TCGA-RP-A694 TCGA-W3-AA1Q 
       21.37        59.41       368.78        18.05         0.69        69.07 
TCGA-W3-AA1R TCGA-W3-AA1V TCGA-W3-AA21 TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT 
      111.09        42.08       105.04        67.63        59.77        11.80 
TCGA-WE-A8ZX TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O 
       32.58        19.73        22.29        37.94 

$`6P GAIN WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 
       17.03        12.99        14.93       112.04       112.57        71.80 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2JA TCGA-D3-A2JB 
       28.08        31.59        43.43       103.10       115.53       168.00 
TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL 
       86.76        11.87       113.52        42.08        12.10       171.58 
TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB 
       66.48        59.57       130.72        46.98        46.32       166.52 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MV TCGA-D3-A51F 
       60.23        24.53        13.87         9.34        45.30        55.73 
TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A5GL 
       56.35       145.12        32.94        22.62        63.81       125.79 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GE 
      178.32        18.18        30.84        79.59        23.61        26.43 
TCGA-D3-A8GI TCGA-D3-A8GK TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GR TCGA-D3-A8GS 
       58.52       170.20       107.15       161.00       129.63       117.17 
TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG 
        7.10        15.39        22.29        25.18        66.25        22.95 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 
       36.03       117.21       194.83        35.93       107.34        61.18 
TCGA-DA-A1I8 TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 
       53.92        23.44        68.09        28.60       215.44        15.68 
TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 
       13.87        10.36        17.29        52.01         7.04        24.89 
TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A182 TCGA-EE-A20C TCGA-EE-A20F 
       29.82        27.22        94.98        14.70       151.27        91.56 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G 
       13.55        63.35        78.97        13.97        63.78        72.07 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29T 
       64.64         2.60        56.84        18.61        66.74       369.93 
TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
       25.87       195.02        17.92        46.82       102.90        36.82 
TCGA-EE-A2A6 TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
       86.14        67.43       161.03        48.72       107.38        54.74 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GO TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 
       79.66        75.48       126.81        21.67       129.27        28.83 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MJ 
       19.76        61.51        47.28       103.20        16.96        96.23 
TCGA-EE-A2ML TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AE 
      216.66       134.40        71.21       122.73        51.62        54.51 
TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH 
      138.81       127.20       201.80        27.35        51.35       109.58 
TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19D 
       31.40        35.44        50.76        77.75        98.40        12.59 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19T TCGA-ER-A19W 
      268.93       152.35         6.44       131.51         8.88       148.18 
TCGA-ER-A1A1 TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ET 
       79.99        23.34        20.15        31.27        32.05        80.32 
TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 
        6.77        92.98       174.21        15.72       220.80        27.85 
TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YX 
       18.77        38.27        34.82       104.42       216.92        48.59 
TCGA-FS-A1YY TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZD 
      228.59        28.08         7.79        27.72        48.85        53.52 
TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS 
       15.45         9.70        32.75       133.55        11.41       148.80 
TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F9 TCGA-FS-A4FB 
       53.16        49.48        77.82        66.67        34.03        26.73 
TCGA-FS-A4FC TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
       54.41        22.92        55.59        13.51        19.30         9.90 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A268 TCGA-GN-A4U3 TCGA-GN-A4U4 
        2.04       139.89        84.72        62.79       121.91        39.35 
TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-HR-A2OG TCGA-HR-A2OH TCGA-OD-A75X TCGA-QB-A6FS 
       10.42        48.89         0.23        65.88       297.90         7.23 
TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1W 
        0.33       228.16        63.02       121.08         4.01       219.16 
TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN 
       24.03        49.05        61.15        15.98        98.89        58.98 
TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-YD-A89C TCGA-YD-A9TA TCGA-YG-AA3P 
       49.51        12.16        35.01         6.90        49.18        14.43 
TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
       27.58        96.99        15.98 

  6P GAIN MUTATED 6P GAIN WILD-TYPE 
             0.20              0.23 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
           368.78            369.93 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
            50.12             51.62 
[1] "0.2 - 368.8 (50.1)" "0.2 - 369.9 (51.6)"
[1] "hr=" "1.2"
D11V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  6P GAIN MUTATED                   29             2
  6P GAIN WILD-TYPE                 36             3
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  6P GAIN MUTATED                                          29
  6P GAIN WILD-TYPE                                        43
                   vv
clus                REGIONAL LYMPH NODE
  6P GAIN MUTATED                    79
  6P GAIN WILD-TYPE                 136
D11V4, multiclass
                                           clus
vv                                          6P GAIN MUTATED 6P GAIN WILD-TYPE
  DISTANT METASTASIS                                     29                36
  PRIMARY TUMOR                                           2                 3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE              29                43
  REGIONAL LYMPH NODE                                    79               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                I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  6P GAIN MUTATED             2       2      14        5       15       11
  6P GAIN WILD-TYPE          10       5      14       13       12       13
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  6P GAIN MUTATED           5         6         9        13          6
  6P GAIN WILD-TYPE         9        13         3        24          9
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  6P GAIN MUTATED           11         18        6
  6P GAIN WILD-TYPE         21         42       14
D11V5, multiclass
             clus
vv            6P GAIN MUTATED 6P GAIN WILD-TYPE
  I OR II NOS               2                10
  STAGE 0                   2                 5
  STAGE I                  14                14
  STAGE IA                  5                13
  STAGE IB                 15                12
  STAGE II                 11                13
  STAGE IIA                 5                 9
  STAGE IIB                 6                13
  STAGE IIC                 9                 3
  STAGE III                13                24
  STAGE IIIA                6                 9
  STAGE IIIB               11                21
  STAGE IIIC               18                42
  STAGE IV                  6                14
[1] 14  2
[1] TRUE
[1] "dimension of contingency 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      22 34 24 33
  6P GAIN WILD-TYPE    42 38 53 35
D11V6, multiclass
       clus
vv      6P GAIN MUTATED 6P GAIN WILD-TYPE
  T0+T1              22                42
  T2                 34                38
  T3                 24                53
  T4                 33                35
[1] 4 2
[1] TRUE
[1] "dimension of 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   73 22 13 15
  6P GAIN WILD-TYPE 96 41 25 34
D11V7, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  N0              73                96
  N1              22                41
  N2              13                25
  N3              15                34
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V8, binary
                   cls
clus                  0   1
  6P GAIN MUTATED   119   7
  6P GAIN WILD-TYPE 194  14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED    119    7
  6P GAIN WILD-TYPE  194   14
   clus
vv  6P GAIN MUTATED 6P GAIN WILD-TYPE
  0             119               194
  1               7                14
[1] 2 2
[1] FALSE
D11V9, binary
                   cls
clus                 0  1
  6P GAIN MUTATED   50 34
  6P GAIN WILD-TYPE 82 54
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     50   34
  6P GAIN WILD-TYPE   82   54
     clus
vv    6P GAIN MUTATED 6P GAIN WILD-TYPE
  NO               50                82
  YES              34                54
[1] 2 2
[1] FALSE
D11V10, binary
                   cls
clus                  0   1
  6P GAIN MUTATED    19 121
  6P GAIN WILD-TYPE  25 192
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     19  121
  6P GAIN WILD-TYPE   25  192
     clus
vv    6P GAIN MUTATED 6P GAIN WILD-TYPE
  NO               19                25
  YES             121               192
[1] 2 2
[1] FALSE
D11V11, continuous
D11V12, binary
                   cls
clus                  0   1
  6P GAIN MUTATED    57  83
  6P GAIN WILD-TYPE  78 140
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     57   83
  6P GAIN WILD-TYPE   78  140
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  FEMALE              57                78
  MALE                83               140
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  6P GAIN MUTATED       1                         0   136
  6P GAIN WILD-TYPE     4                         1   208
D11V13, multiclass
                           clus
vv                          6P GAIN MUTATED 6P GAIN WILD-TYPE
  ASIAN                                   1                 4
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                 136               208
[1] 3 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     2 138
  6P GAIN WILD-TYPE   5 206
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      2  138
  6P GAIN WILD-TYPE    5  206
                        clus
vv                       6P GAIN MUTATED 6P GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 5
  NOT HISPANIC OR LATINO             138               206
[1] 2 2
[1] FALSE

Clustering(12) Variable = 6Q GAIN MUTATION ANALYSIS
D12V1, survival
                   sevent
clus2                 0   1
  6Q GAIN MUTATED    10  21
  6Q GAIN WILD-TYPE 111  97
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               31               208 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               21                97 
$`6Q GAIN MUTATED`
TCGA-D3-A1Q3 TCGA-D3-A1Q7 TCGA-D3-A3CC TCGA-D3-A51E TCGA-D9-A1X3 TCGA-EB-A5SH 
       15.72       133.25        40.01       173.85        10.78        50.07 
TCGA-EE-A20H TCGA-EE-A29B TCGA-EE-A2GS TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2MS 
      155.90        75.22        71.31       171.85        67.50       143.93 
TCGA-EE-A2MU TCGA-EE-A3J3 TCGA-EE-A3J8 TCGA-EE-A3JI TCGA-ER-A197 TCGA-ER-A19C 
       53.26        67.89         3.35       152.81         1.58        39.81 
TCGA-ER-A19M TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A2NC TCGA-ER-A3EV TCGA-FS-A4F8 
       59.84        49.71        34.95        22.36        15.48       173.19 
TCGA-GN-A8LK TCGA-GN-A9SD TCGA-QB-AA9O TCGA-W3-AA1Q TCGA-W3-AA1V TCGA-W3-AA21 
       43.23        59.41        18.05        44.05         8.09        92.84 
TCGA-WE-A8ZT 
       10.95 

$`6Q GAIN WILD-TYPE`
TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 
       60.46        12.99        14.83         8.42        31.89       110.93 
TCGA-D3-A1Q6 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       49.35        19.04        76.41        62.60        25.64        45.99 
TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JE 
       62.86        15.75       168.00        86.30         7.27         9.76 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP 
      107.61        36.30       171.58        64.83        66.08        43.53 
TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML 
       58.06        46.98       140.98        59.70        16.96        13.87 
TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R 
        9.34        90.21        23.67       144.46        31.76        62.70 
TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D3-A8GC 
       11.34        42.05        45.70       177.86       124.08        78.21 
TCGA-D3-A8GD TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GP 
       23.61       179.97       120.00        69.53        70.62       135.12 
TCGA-D3-A8GR TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6EC TCGA-D9-A6EG 
       36.53        15.02        16.90        18.44        57.90        22.85 
TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 
       48.66       106.85        31.96       150.61        82.85        32.42 
TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q 
       64.83        58.85        25.12       214.59        14.96         3.91 
TCGA-EB-A5SG TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A180 
       33.24        45.50         6.64        13.15        24.89        62.37 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A184 TCGA-EE-A20C TCGA-EE-A29C TCGA-EE-A29D 
       20.38         0.00        67.50        75.55        76.14        12.99 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29Q 
        0.26        44.28        63.12        47.74        27.16        61.12 
TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB 
      346.49       185.19       102.38         7.20        77.98        26.14 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
      239.11         0.20       189.40        68.65        10.62        32.48 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GU 
       18.35        31.00       118.32         0.76         0.20        81.99 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MG 
      103.13        15.25         5.75        23.77       209.79        94.19 
TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MR TCGA-EE-A2MT 
       63.25       104.78       145.45       227.01        25.08        23.51 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
      124.31       122.73        51.62         4.41        54.51         6.28 
TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3JB TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A198 
      111.85        45.90       201.80        14.56        34.45        47.31 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19H 
        7.82         4.54        53.29        11.47       151.46       150.12 
TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2ND 
       99.06        42.48       120.76       146.63        47.97         4.70 
TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3PL TCGA-FR-A44A 
       16.87        10.95       173.29        55.82        32.05       174.21 
TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FS-A1YW TCGA-FS-A1YY 
      209.23        26.20         5.65        10.06       171.78        49.74 
TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE 
      195.98         8.35        27.62       312.07        32.78        35.90 
TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS 
       12.92         7.82        36.33        78.61       130.95       136.27 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 
       35.28         4.47        23.21         5.29         3.06        30.90 
TCGA-FS-A4F4 TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
       66.67        13.28        80.68        55.59        11.54        19.30 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        9.90         6.05         1.91        53.29       117.93        84.72 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 
       17.06        42.48         7.59       120.53        34.49        46.92 
TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A825 
       85.05       297.01         7.23         0.33       174.12         1.97 
TCGA-W3-A828 TCGA-W3-AA1R TCGA-W3-AA1W TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8ZM 
      120.07        79.99       185.13         1.15        59.64        62.99 
TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 
       12.69        19.00        59.44        48.39         1.94        26.60 
TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-Z2-AA3S 
       16.64        15.65        28.21        91.23 

  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
             1.58              0.00 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
           173.85            346.49 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
            50.07             45.80 
[1] "1.6 - 173.8 (50.1)" "0.0 - 346.5 (45.8)"
[1] "hr=" "1.4"
D12V2, survival
                   sevent
clus2                 0   1
  6Q GAIN MUTATED    18  30
  6Q GAIN WILD-TYPE 151 150
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               48               301 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               30               150 
$`6Q GAIN MUTATED`
TCGA-D3-A1Q3 TCGA-D3-A1Q7 TCGA-D3-A3CC TCGA-D3-A51E TCGA-D3-A5GO TCGA-D9-A149 
       16.67       133.25        86.93       174.84       137.92        54.67 
TCGA-D9-A1X3 TCGA-D9-A6E9 TCGA-DA-A1I0 TCGA-EB-A5SH TCGA-EE-A20H TCGA-EE-A29B 
       18.12         9.90        20.38        54.02       168.26        85.08 
TCGA-EE-A29R TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2ME TCGA-EE-A2MI TCGA-EE-A2MK 
       14.47        81.21        44.88       103.27       204.66       158.63 
TCGA-EE-A2MN TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3J3 TCGA-EE-A3J5 TCGA-EE-A3J8 
       47.54       162.48        53.26       172.18        36.95        34.32 
TCGA-EE-A3JA TCGA-EE-A3JI TCGA-ER-A197 TCGA-ER-A19C TCGA-ER-A19E TCGA-ER-A19M 
       53.19       152.81        13.94        48.89        13.02        61.05 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A2NC TCGA-ER-A3EV TCGA-FS-A1ZK TCGA-FS-A4F2 
       50.89        37.25        43.82        46.98        23.93        50.14 
TCGA-FS-A4F8 TCGA-FW-A3I3 TCGA-GF-A6C9 TCGA-GN-A266 TCGA-GN-A8LK TCGA-GN-A9SD 
      174.84         0.20        15.78        10.13        50.10        59.41 
TCGA-QB-AA9O TCGA-W3-AA1Q TCGA-W3-AA1V TCGA-W3-AA21 TCGA-WE-A8ZT TCGA-WE-A8ZX 
       18.05        69.07        42.08       105.04        11.80        32.58 

$`6Q GAIN WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q4 
       17.03        66.48        12.99        14.93        16.57       112.04 
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB 
      112.57        71.80        28.08        31.59        90.90        95.74 
TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB 
       43.43       103.10        65.49        23.77       115.53       168.00 
TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH 
       86.76        11.87        27.65        62.07       113.52        42.08 
TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ 
       12.10       171.58        66.48        66.08        59.57       130.72 
TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3CF 
       58.06        46.98        46.32       166.52        60.23        24.53 
TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51F 
       13.87         9.34       103.59        39.75        45.30        55.73 
TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T 
       56.35       145.12        32.94        22.62        63.81        26.89 
TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GB 
      125.79       135.75       178.32        18.18       125.19        30.84 
TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GK 
       79.59        23.61        26.43        58.52       241.38       170.20 
TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR 
       89.13       107.15       161.00       152.75        29.06       129.63 
TCGA-D3-A8GS TCGA-D9-A148 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 
      117.17       151.53         3.65         7.10        15.39        22.29 
TCGA-D9-A4Z6 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW 
       18.44        25.18        66.25        22.95        48.89        36.03 
TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 
      117.21       194.83       176.55        35.93       107.34        61.18 
TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
       53.92        65.92        23.44        68.09        28.60        10.49 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG 
      215.44        15.68        13.87        10.36        20.35        68.25 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y 
       17.29        52.01         7.04        24.89        29.82        27.22 
TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 
        8.65        94.98        33.73        14.70        26.89        68.15 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29A 
        4.96       133.81       151.27        91.56        13.55        63.35 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L 
       78.97        13.97        63.78        72.07        64.64         2.60 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29T 
       56.84        18.61        56.42        66.74        61.28       369.93 
TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
       25.87       195.02        17.92        46.82       102.90        36.82 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE 
       39.29        86.14        59.28        67.43       340.14       161.03 
TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
      208.04        48.72       107.38        54.74        79.66        75.48 
TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GU TCGA-EE-A2M5 
      102.12       126.81        13.91        42.77        94.82        21.67 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2MF 
      129.27        28.83        19.76        61.51        47.28       268.73 
TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP 
      103.20        16.96        96.23       216.66       167.90       248.65 
TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC 
       43.23       134.40        71.21       124.31       122.73        51.62 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J4 
       28.77        54.51        13.81        41.59       138.81       127.20 
TCGA-EE-A3J7 TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 
       64.08       201.80        27.35        51.35       109.58        31.40 
TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19D 
       35.44        50.76         9.17        77.75        98.40        12.59 
TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19N 
       26.37       268.93       152.35         6.44       131.51        44.05 
TCGA-ER-A19P TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2ND TCGA-ER-A2NE 
      162.08         8.88       148.18        79.99        23.34        20.15 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3PL 
       16.37        31.27        32.05       247.04        80.32        33.21 
TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 
        6.77        92.98       174.21        15.72       220.80        27.85 
TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW 
       18.77        38.27        34.82        36.26       104.42       216.92 
TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 
       48.59       228.59       202.65        20.91        28.08         7.79 
TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF 
       27.72        48.85       357.37        53.52        40.27        15.45 
TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ 
        9.70        32.75        47.38       101.26        74.73       133.55 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY 
       11.41       148.80        53.16        26.56        49.48        27.09 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F9 TCGA-FS-A4FB 
       27.02        77.82        66.67        28.73        34.03        26.73 
TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
       54.41        80.68        22.92        55.59        13.51        19.30 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        9.90         7.23         2.04       139.89       117.93        84.72 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A4U4 
       64.44        62.79        32.48        39.58       121.91        39.35 
TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LL TCGA-HR-A2OG TCGA-HR-A2OH 
       10.42        48.89        22.13        21.37         0.23        65.88 
TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 
      368.78       297.90         7.23         0.33         0.69       228.16 
TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1R TCGA-W3-AA1W TCGA-WE-A8JZ 
       63.02       121.08         4.01       111.09       219.16        24.03 
TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO 
       49.05        61.15        15.98        98.89        58.98        67.63 
TCGA-WE-A8ZQ TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 
       59.77        49.51        12.16        35.01        19.73        22.29 
TCGA-YD-A89C TCGA-YD-A9TA TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S 
        6.90        49.18        37.94        14.43        27.58        96.99 
TCGA-Z2-AA3V 
       15.98 

  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
             0.20              0.23 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
           204.66            369.93 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
            50.12             51.62 
[1] "0.2 - 204.7 (50.1)" "0.2 - 369.9 (51.6)"
[1] "hr=" "1.3"
D12V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  6Q GAIN MUTATED                   10             1
  6Q GAIN WILD-TYPE                 55             4
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  6Q GAIN MUTATED                                          12
  6Q GAIN WILD-TYPE                                        60
                   vv
clus                REGIONAL LYMPH NODE
  6Q GAIN MUTATED                    24
  6Q GAIN WILD-TYPE                 191
D12V4, multiclass
                                           clus
vv                                          6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  DISTANT METASTASIS                                     10                55
  PRIMARY TUMOR                                           1                 4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE              12                60
  REGIONAL LYMPH NODE                                    24               191
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  6Q GAIN MUTATED             1       0       7        2        8        4
  6Q GAIN WILD-TYPE          11       7      21       16       19       20
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  6Q GAIN MUTATED           1         2         3         5          2
  6Q GAIN WILD-TYPE        13        17         9        32         13
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  6Q GAIN MUTATED            3          2        3
  6Q GAIN WILD-TYPE         29         58       17
D12V5, multiclass
             clus
vv            6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  I OR II NOS               1                11
  STAGE 0                   0                 7
  STAGE I                   7                21
  STAGE IA                  2                16
  STAGE IB                  8                19
  STAGE II                  4                20
  STAGE IIA                 1                13
  STAGE IIB                 2                17
  STAGE IIC                 3                 9
  STAGE III                 5                32
  STAGE IIIA                2                13
  STAGE IIIB                3                29
  STAGE IIIC                2                58
  STAGE IV                  3                17
[1] 14  2
[1] TRUE
[1] "dimension of contingency 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       5 13  7 15
  6Q GAIN WILD-TYPE    59 59 70 53
D12V6, multiclass
       clus
vv      6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  T0+T1               5                59
  T2                 13                59
  T3                  7                70
  T4                 15                53
[1] 4 2
[1] TRUE
[1] "dimension of 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    30   9   1   2
  6Q GAIN WILD-TYPE 139  54  37  47
D12V7, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  N0              30               139
  N1               9                54
  N2               1                37
  N3               2                47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V8, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED    40   3
  6Q GAIN WILD-TYPE 273  18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED     40    3
  6Q GAIN WILD-TYPE  273   18
   clus
vv  6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  0              40               273
  1               3                18
[1] 2 2
[1] FALSE
D12V9, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED    23  10
  6Q GAIN WILD-TYPE 109  78
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED     23   10
  6Q GAIN WILD-TYPE  109   78
     clus
vv    6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  NO               23               109
  YES              10                78
[1] 2 2
[1] FALSE
D12V10, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED     7  41
  6Q GAIN WILD-TYPE  37 272
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      7   41
  6Q GAIN WILD-TYPE   37  272
     clus
vv    6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  NO                7                37
  YES              41               272
[1] 2 2
[1] FALSE
D12V11, continuous
D12V12, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED    17  31
  6Q GAIN WILD-TYPE 118 192
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED     17   31
  6Q GAIN WILD-TYPE  118  192
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  FEMALE              17               118
  MALE                31               192
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  6Q GAIN MUTATED       0                         0    48
  6Q GAIN WILD-TYPE     5                         1   296
D12V13, multiclass
                           clus
vv                          6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  ASIAN                                   0                 5
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  48               296
[1] 3 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     0  48
  6Q GAIN WILD-TYPE   7 296
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      0   48
  6Q GAIN WILD-TYPE    7  296
                        clus
vv                       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 7
  NOT HISPANIC OR LATINO              48               296
[1] 2 2
[1] FALSE

Clustering(13) Variable = 7P GAIN MUTATION ANALYSIS
D13V1, survival
                   sevent
clus2                0  1
  7P GAIN MUTATED   68 61
  7P GAIN WILD-TYPE 53 57
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              129               110 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               61                57 
$`7P GAIN MUTATED`
TCGA-3N-A9WC TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 
       60.46        14.83         8.42        15.72        31.89       110.93 
TCGA-D3-A1Q6 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JE TCGA-D3-A2JG 
       49.35        15.75        86.30         7.27         9.76       107.61 
TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CB 
      171.58        64.83        43.53        58.06        46.98       140.98 
TCGA-D3-A3CC TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51J 
       40.01        13.87         9.34        90.21        23.67       144.46 
TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D3-A8GC TCGA-D3-A8GD 
       62.70        45.70       177.86       124.08        78.21        23.61 
TCGA-D3-A8GK TCGA-D3-A8GP TCGA-D9-A3Z3 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV 
      120.00       135.12        16.90        57.90        22.85        48.66 
TCGA-DA-A1HY TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC 
      106.85       150.61        82.85        32.42        64.83        58.85 
TCGA-DA-A3F5 TCGA-EB-A44Q TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17Y TCGA-EE-A180 
      214.59         3.91        45.50         6.64        24.89        62.37 
TCGA-EE-A181 TCGA-EE-A20H TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29P 
       20.38       155.90        76.14        12.99         0.26        27.16 
TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH 
      346.49       185.19        77.98        26.14         0.20       189.40 
TCGA-EE-A2GJ TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP 
       68.65        32.48        18.35        31.00       118.32         0.76 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MP 
      103.13        15.25        63.25        67.50       145.45       227.01 
TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AD TCGA-EE-A3AE 
       25.08       143.93        53.26       124.31         4.41        54.51 
TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3JB TCGA-ER-A197 
        6.28        67.89       111.85        45.90       201.80         1.58 
TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19P 
        7.82        53.29        39.81       151.46       150.12       120.76 
TCGA-ER-A19S TCGA-ER-A2ND TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A44A TCGA-FR-A729 
       34.95         4.70        15.48        32.05       174.21       209.23 
TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD 
        5.65        10.06         8.35        27.62       312.07        32.78 
TCGA-FS-A1ZG TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F8 
        7.82        78.61       130.95         5.29         3.06       173.19 
TCGA-FW-A5DY TCGA-GF-A4EO TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 
       19.30         6.05       117.93        84.72        17.06        42.48 
TCGA-GN-A26A TCGA-GN-A4U8 TCGA-GN-A8LK TCGA-GN-A9SD TCGA-QB-A6FS TCGA-QB-AA9O 
        7.59        46.92        43.23        59.41         7.23        18.05 
TCGA-W3-AA1R TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K5 TCGA-WE-A8ZM TCGA-WE-A8ZQ 
       79.99       185.13        92.84        59.64        62.99        59.44 
TCGA-WE-AA9Y TCGA-WE-AAA3 TCGA-YG-AA3O 
        1.94        16.64        28.21 

$`7P GAIN WILD-TYPE`
TCGA-3N-A9WD TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 
       12.99       133.25        19.04        76.41        62.60        25.64 
TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JB TCGA-D3-A2JH TCGA-D3-A2JO TCGA-D3-A3CE 
       45.99        62.86       168.00        36.30        66.08        59.70 
TCGA-D3-A3CF TCGA-D3-A51E TCGA-D3-A51K TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A8GJ 
       16.96       173.85        31.76        11.34        42.05       179.97 
TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GR TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A4Z6 
       69.53        70.62        36.53        10.78        15.02        18.44 
TCGA-DA-A1I1 TCGA-DA-A3F2 TCGA-DA-A3F8 TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A17X 
       31.96        25.12        14.96        33.24        50.07        13.15 
TCGA-EE-A182 TCGA-EE-A184 TCGA-EE-A20C TCGA-EE-A29B TCGA-EE-A29G TCGA-EE-A29H 
        0.00        67.50        75.55        75.22        44.28        63.12 
TCGA-EE-A29M TCGA-EE-A29Q TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2GD TCGA-EE-A2GK 
       47.74        61.12       102.38         7.20       239.11        10.62 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MF 
        0.20        71.31        81.99         5.75        23.77       209.79 
TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2ML TCGA-EE-A2MT TCGA-EE-A3AB TCGA-EE-A3AC 
       94.19       171.85       104.78        23.51       122.73        51.62 
TCGA-EE-A3J8 TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A19A 
        3.35       152.81        14.56        34.45        47.31         4.54 
TCGA-ER-A19D TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A19W 
       11.47        99.06        59.84        42.48        49.71       146.63 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET 
       47.97        22.36        16.87        10.95       173.29        55.82 
TCGA-FR-A7U8 TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1ZE TCGA-FS-A1ZF 
       26.20       171.78        49.74       195.98        35.90        12.92 
TCGA-FS-A1ZJ TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A4F0 
       36.33       136.27        35.28         4.47        23.21        30.90 
TCGA-FS-A4F4 TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV TCGA-GF-A3OT 
       66.67        13.28        80.68        55.59        11.54         9.90 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-LH-A9QB TCGA-OD-A75X 
        1.91        53.29       120.53        34.49        85.05       297.01 
TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1Q TCGA-W3-AA1V 
        0.33       174.12         1.97       120.07        44.05         8.09 
TCGA-WE-A8K1 TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AAA0 
        1.15        12.69        19.00        10.95        48.39        26.60 
TCGA-WE-AAA4 TCGA-Z2-AA3S 
       15.65        91.23 

  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              0.2               0.0 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
           346.49            297.01 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
           48.660            43.265 
[1] "0.2 - 346.5 (48.7)" "0.0 - 297.0 (43.3)"
[1] "hr=" "1.2"
D13V2, survival
                   sevent
clus2                0  1
  7P GAIN MUTATED   95 97
  7P GAIN WILD-TYPE 74 83
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              192               157 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               97                83 
$`7P GAIN MUTATED`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
       17.03        66.48        14.93        16.57        16.67       112.04 
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JC 
      112.57        71.80        31.59        23.77       115.53        86.76 
TCGA-D3-A2JD TCGA-D3-A2JE TCGA-D3-A2JG TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JP 
       11.87        27.65       113.52       171.58        66.48        59.57 
TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC 
      130.72        58.06        46.98        46.32       166.52        86.93 
TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51J TCGA-D3-A51N 
       13.87         9.34       103.59        39.75       145.12        22.62 
TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GB 
       63.81       135.75       178.32        18.18       125.19        30.84 
TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GK TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GQ 
       79.59        23.61       170.20       161.00       152.75        29.06 
TCGA-D3-A8GS TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JX TCGA-D9-A3Z3 TCGA-D9-A6E9 
      117.17       151.53        54.67         7.10        22.29         9.90 
TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY 
       25.18        66.25        22.95        48.89        36.03       117.21 
TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
       20.38       176.55        35.93       107.34        61.18        53.92 
TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F5 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UL 
       65.92        68.09       215.44        13.87        20.35        17.29 
TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A20B 
       52.01        24.89        27.22        94.98        33.73       133.81 
TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29N 
      168.26        63.35        78.97        13.97        63.78        18.61 
TCGA-EE-A29P TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A0 TCGA-EE-A2A6 TCGA-EE-A2GB 
       56.42       369.93       195.02        46.82        86.14        59.28 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GL TCGA-EE-A2GM 
      161.03       208.04        48.72       107.38        79.66        75.48 
TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MH 
      102.12       126.81        13.91       129.27        28.83        16.96 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ 
       96.23       158.63       167.90        47.54       248.65        43.23 
TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AD TCGA-EE-A3AE 
      134.40       162.48        53.26       124.31        28.77        54.51 
TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 
       13.81        41.59       138.81       172.18       127.20        36.95 
TCGA-EE-A3J7 TCGA-EE-A3JB TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19C 
       64.08       201.80        13.94         9.17        98.40        48.89 
TCGA-ER-A19E TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19P TCGA-ER-A19S 
       13.02       268.93       152.35         6.44       162.08        37.25 
TCGA-ER-A19T TCGA-ER-A2ND TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN 
        8.88        23.34        46.98        33.21         6.77        92.98 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC 
      174.21        15.72       220.80        18.77        38.27        34.82 
TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YX TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 
       36.26       104.42        48.59        20.91        28.08         7.79 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZM TCGA-FS-A1ZQ 
      357.37        53.52         9.70        32.75       101.26       133.55 
TCGA-FS-A1ZR TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F2 TCGA-FS-A4F5 TCGA-FS-A4F8 
       11.41        27.09        27.02        50.14        28.73       174.84 
TCGA-FW-A3I3 TCGA-FW-A5DY TCGA-GF-A4EO TCGA-GF-A6C9 TCGA-GN-A264 TCGA-GN-A265 
        0.20        19.30         7.23        15.78       117.93        84.72 
TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U7 
       10.13        64.44        62.79        32.48        39.58        10.42 
TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A9SD TCGA-HR-A2OG TCGA-HR-A2OH 
       48.89        22.13        50.10        59.41         0.23        65.88 
TCGA-QB-A6FS TCGA-QB-AA9O TCGA-W3-AA1O TCGA-W3-AA1R TCGA-W3-AA1W TCGA-W3-AA21 
        7.23        18.05         4.01       111.09       219.16       105.04 
TCGA-WE-A8JZ TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZQ TCGA-WE-A8ZX 
       24.03        61.15        15.98        98.89        59.77        32.58 
TCGA-WE-AA9Y TCGA-WE-AAA3 TCGA-YD-A89C TCGA-YD-A9TA TCGA-YG-AA3O TCGA-YG-AA3P 
       12.16        19.73         6.90        49.18        37.94        14.43 

$`7P GAIN WILD-TYPE`
TCGA-3N-A9WD TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 
       12.99       133.25        28.08        90.90        95.74        43.43 
TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JB TCGA-D3-A2JF TCGA-D3-A2JH TCGA-D3-A2JK 
      103.10        65.49       168.00        62.07        42.08        12.10 
TCGA-D3-A2JO TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F 
       66.08        60.23        24.53        45.30       174.84        55.73 
TCGA-D3-A51H TCGA-D3-A51K TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GO TCGA-D3-A8GE 
       56.35        32.94        26.89       125.79       137.92        26.43 
TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GR TCGA-D9-A1JW 
       58.52       241.38        89.13       107.15       129.63         3.65 
TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A4Z6 TCGA-DA-A1I1 TCGA-DA-A1IB TCGA-DA-A3F2 
       18.12        15.39        18.44       194.83        23.44        28.60 
TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5VV 
       10.49        15.68        10.36        68.25        54.02         7.04 
TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 
       29.82         8.65        14.70        26.89        68.15         4.96 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29B TCGA-EE-A29G TCGA-EE-A29H 
      151.27        91.56        13.55        85.08        72.07        64.64 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V 
        2.60        56.84        66.74        14.47        61.28        25.87 
TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2GC TCGA-EE-A2GD 
       17.92       102.90        36.82        39.29        67.43       340.14 
TCGA-EE-A2GK TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 
       54.74        42.77        81.21        44.88        94.82        21.67 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG 
       19.76        61.51        47.28       103.27       268.73       103.20 
TCGA-EE-A2MI TCGA-EE-A2ML TCGA-EE-A2MT TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3J8 
      204.66       216.66        71.21       122.73        51.62        34.32 
TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 
       53.19        27.35        51.35       109.58       152.81        31.40 
TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19L 
       35.44        50.76        77.75        12.59        26.37       131.51 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
       61.05        44.05        50.89       148.18        79.99        43.82 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET 
       20.15        16.37        31.27        32.05       247.04        80.32 
TCGA-FR-A7U8 TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1ZA TCGA-FS-A1ZB 
       27.85       216.92       228.59       202.65        27.72        48.85 
TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZS 
       40.27        15.45        47.38        23.93        74.73       148.80 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F9 
       53.16        26.56        49.48        77.82        66.67        34.03 
TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV 
       26.73        54.41        80.68        22.92        55.59        13.51 
TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A8LL 
        9.90         2.04       139.89       121.91        39.35        21.37 
TCGA-LH-A9QB TCGA-OD-A75X TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 
      368.78       297.90         0.33         0.69       228.16        63.02 
TCGA-W3-A828 TCGA-W3-AA1Q TCGA-W3-AA1V TCGA-WE-A8K1 TCGA-WE-A8ZN TCGA-WE-A8ZO 
      121.08        69.07        42.08        49.05        58.98        67.63 
TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-Z2-A8RT TCGA-Z2-AA3S 
       11.80        49.51        35.01        22.29        27.58        96.99 
TCGA-Z2-AA3V 
       15.98 

  7P GAIN MUTATED 7P GAIN WILD-TYPE 
             0.20              0.33 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
           369.93            368.78 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
            50.12             51.35 
[1] "0.2 - 369.9 (50.1)" "0.3 - 368.8 (51.4)"
[1] "hr=" "1.1"
D13V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  7P GAIN MUTATED                   32             4
  7P GAIN WILD-TYPE                 33             1
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  7P GAIN MUTATED                                          39
  7P GAIN WILD-TYPE                                        33
                   vv
clus                REGIONAL LYMPH NODE
  7P GAIN MUTATED                   121
  7P GAIN WILD-TYPE                  94
D13V4, multiclass
                                           clus
vv                                          7P GAIN MUTATED 7P GAIN WILD-TYPE
  DISTANT METASTASIS                                     32                33
  PRIMARY TUMOR                                           4                 1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE              39                33
  REGIONAL LYMPH NODE                                   121                94
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  7P GAIN MUTATED            10       1      17        9        9       12
  7P GAIN WILD-TYPE           2       6      11        9       18       12
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  7P GAIN MUTATED           8         6         8        24         11
  7P GAIN WILD-TYPE         6        13         4        13          4
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  7P GAIN MUTATED           20         33       12
  7P GAIN WILD-TYPE         12         27        8
D13V5, multiclass
             clus
vv            7P GAIN MUTATED 7P GAIN WILD-TYPE
  I OR II NOS              10                 2
  STAGE 0                   1                 6
  STAGE I                  17                11
  STAGE IA                  9                 9
  STAGE IB                  9                18
  STAGE II                 12                12
  STAGE IIA                 8                 6
  STAGE IIB                 6                13
  STAGE IIC                 8                 4
  STAGE III                24                13
  STAGE IIIA               11                 4
  STAGE IIIB               20                12
  STAGE IIIC               33                27
  STAGE IV                 12                 8
[1] 14  2
[1] TRUE
[1] "dimension of contingency 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      40 36 41 39
  7P GAIN WILD-TYPE    24 36 36 29
D13V6, multiclass
       clus
vv      7P GAIN MUTATED 7P GAIN WILD-TYPE
  T0+T1              40                24
  T2                 36                36
  T3                 41                36
  T4                 39                29
[1] 4 2
[1] TRUE
[1] "dimension of 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   86 40 20 31
  7P GAIN WILD-TYPE 83 23 18 18
D13V7, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  N0              86                83
  N1              40                23
  N2              20                18
  N3              31                18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V8, binary
                   cls
clus                  0   1
  7P GAIN MUTATED   170  13
  7P GAIN WILD-TYPE 143   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED    170   13
  7P GAIN WILD-TYPE  143    8
   clus
vv  7P GAIN MUTATED 7P GAIN WILD-TYPE
  0             170               143
  1              13                 8
[1] 2 2
[1] FALSE
D13V9, binary
                   cls
clus                 0  1
  7P GAIN MUTATED   75 45
  7P GAIN WILD-TYPE 57 43
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     75   45
  7P GAIN WILD-TYPE   57   43
     clus
vv    7P GAIN MUTATED 7P GAIN WILD-TYPE
  NO               75                57
  YES              45                43
[1] 2 2
[1] FALSE
D13V10, binary
                   cls
clus                  0   1
  7P GAIN MUTATED    28 168
  7P GAIN WILD-TYPE  16 145
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     28  168
  7P GAIN WILD-TYPE   16  145
     clus
vv    7P GAIN MUTATED 7P GAIN WILD-TYPE
  NO               28                16
  YES             168               145
[1] 2 2
[1] FALSE
D13V11, continuous
D13V12, binary
                   cls
clus                  0   1
  7P GAIN MUTATED    80 117
  7P GAIN WILD-TYPE  55 106
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     80  117
  7P GAIN WILD-TYPE   55  106
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  FEMALE              80                55
  MALE               117               106
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  7P GAIN MUTATED       4                         0   187
  7P GAIN WILD-TYPE     1                         1   157
D13V13, multiclass
                           clus
vv                          7P GAIN MUTATED 7P GAIN WILD-TYPE
  ASIAN                                   4                 1
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                 187               157
[1] 3 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     5 187
  7P GAIN WILD-TYPE   2 157
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      5  187
  7P GAIN WILD-TYPE    2  157
                        clus
vv                       7P GAIN MUTATED 7P GAIN WILD-TYPE
  HISPANIC OR LATINO                   5                 2
  NOT HISPANIC OR LATINO             187               157
[1] 2 2
[1] FALSE

Clustering(14) Variable = 7Q GAIN MUTATION ANALYSIS
D14V1, survival
                   sevent
clus2                0  1
  7Q GAIN MUTATED   68 59
  7Q GAIN WILD-TYPE 53 59
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              127               112 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               59                59 
$`7Q GAIN MUTATED`
TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 
       14.83         8.42        15.72        31.89       110.93        49.35 
TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JE TCGA-D3-A2JG TCGA-D3-A2JL 
       15.75        86.30         7.27         9.76       107.61       171.58 
TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CC 
       64.83        43.53        58.06        46.98       140.98        40.01 
TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51J TCGA-D3-A51R 
       13.87         9.34        90.21        23.67       144.46        62.70 
TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GK 
       45.70       177.86       124.08        78.21        23.61       120.00 
TCGA-D3-A8GP TCGA-D9-A3Z3 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY 
      135.12        16.90        57.90        22.85        48.66       106.85 
TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F5 
      150.61        82.85        32.42        64.83        58.85       214.59 
TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17Y TCGA-EE-A180 
       14.96         3.91        45.50         6.64        24.89        62.37 
TCGA-EE-A181 TCGA-EE-A20H TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29P TCGA-EE-A29T 
       20.38       155.90        76.14         0.26        27.16       346.49 
TCGA-EE-A29W TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GL 
      185.19        77.98        26.14         0.20       189.40        32.48 
TCGA-EE-A2GM TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MJ 
       18.35       118.32         0.76       103.13        15.25        63.25 
TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MU 
       67.50       145.45       227.01        25.08       143.93        53.26 
TCGA-EE-A3AA TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 
      124.31        54.51         6.28        67.89       111.85        45.90 
TCGA-EE-A3JB TCGA-ER-A193 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19C 
      201.80        14.56         1.58         7.82        53.29        39.81 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19P TCGA-ER-A19S TCGA-ER-A2ND TCGA-ER-A3EV 
      151.46       150.12       120.76        34.95         4.70        15.48 
TCGA-ER-A3PL TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FS-A1Z3 
       32.05       174.21       209.23         5.65        10.06         8.35 
TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZM 
       27.62       312.07        32.78        12.92         7.82        78.61 
TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F8 TCGA-FW-A5DY 
      130.95       136.27         5.29         3.06       173.19        19.30 
TCGA-GF-A4EO TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
        6.05       117.93        84.72        17.06        42.48         7.59 
TCGA-GN-A8LK TCGA-GN-A9SD TCGA-LH-A9QB TCGA-QB-A6FS TCGA-QB-AA9O TCGA-W3-AA1R 
       43.23        59.41        85.05         7.23        18.05        79.99 
TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K5 TCGA-WE-A8ZQ TCGA-WE-AA9Y TCGA-WE-AAA3 
      185.13        92.84        59.64        59.44         1.94        16.64 
TCGA-YG-AA3O 
       28.21 

$`7Q GAIN WILD-TYPE`
TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB 
       60.46        12.99       133.25        19.04        76.41        62.60 
TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JB TCGA-D3-A2JH TCGA-D3-A2JO 
       25.64        45.99        62.86       168.00        36.30        66.08 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A51E TCGA-D3-A51K TCGA-D3-A51T TCGA-D3-A5GL 
       59.70        16.96       173.85        31.76        11.34        42.05 
TCGA-D3-A8GJ TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GR TCGA-D9-A1X3 TCGA-D9-A3Z1 
      179.97        69.53        70.62        36.53        10.78        15.02 
TCGA-D9-A4Z6 TCGA-DA-A1I1 TCGA-DA-A3F2 TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A17X 
       18.44        31.96        25.12        33.24        50.07        13.15 
TCGA-EE-A182 TCGA-EE-A184 TCGA-EE-A20C TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29G 
        0.00        67.50        75.55        75.22        12.99        44.28 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29Q TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2GD 
       63.12        47.74        61.12       102.38         7.20       239.11 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GN TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU 
       68.65        10.62        31.00         0.20        71.31        81.99 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2ML 
        5.75        23.77       209.79        94.19       171.85       104.78 
TCGA-EE-A2MT TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3J8 TCGA-EE-A3JI 
       23.51       122.73        51.62         4.41         3.35       152.81 
TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19D TCGA-ER-A19L TCGA-ER-A19M 
       34.45        47.31         4.54        11.47        99.06        59.84 
TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE 
       42.48        49.71       146.63        47.97        22.36        16.87 
TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-FR-A7U8 TCGA-FS-A1YW TCGA-FS-A1YY 
       10.95       173.29        55.82        26.20       171.78        49.74 
TCGA-FS-A1Z0 TCGA-FS-A1ZE TCGA-FS-A1ZJ TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW 
      195.98        35.90        36.33        35.28         4.47        23.21 
TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV 
       30.90        66.67        13.28        80.68        55.59        11.54 
TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 
        9.90         1.91        53.29       120.53        34.49        46.92 
TCGA-OD-A75X TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1Q 
      297.01         0.33       174.12         1.97       120.07        44.05 
TCGA-W3-AA1V TCGA-WE-A8K1 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT 
        8.09         1.15        62.99        12.69        19.00        10.95 
TCGA-WE-A8ZY TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-Z2-AA3S 
       48.39        26.60        15.65        91.23 

  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              0.2               0.0 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
           346.49            297.01 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
           48.660            44.165 
[1] "0.2 - 346.5 (48.7)" "0.0 - 297.0 (44.2)"
[1] "hr=" "1.3"
D14V2, survival
                   sevent
clus2                0  1
  7Q GAIN MUTATED   94 95
  7Q GAIN WILD-TYPE 75 85
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              189               160 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               95                85 
$`7Q GAIN MUTATED`
TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 
       14.93        16.57        16.67       112.04       112.57        71.80 
TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JE 
       31.59        23.77       115.53        86.76        11.87        27.65 
TCGA-D3-A2JG TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 
      113.52       171.58        66.48        59.57       130.72        58.06 
TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3ML TCGA-D3-A3MO 
       46.98        46.32       166.52        86.93        13.87         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51J TCGA-D3-A51R TCGA-D3-A5GN 
      103.59        39.75        45.30       145.12        63.81       135.75 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GD 
      178.32        18.18       125.19        30.84        79.59        23.61 
TCGA-D3-A8GI TCGA-D3-A8GK TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GS 
       58.52       170.20       161.00       152.75        29.06       117.17 
TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JX TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA 
      151.53        54.67         7.10        22.29         9.90        25.18 
TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 
       66.25        22.95        48.89        36.03       117.21        20.38 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA 
      176.55        35.93       107.34        61.18        53.92        65.92 
TCGA-DA-A1IC TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5UL TCGA-EB-A5UN 
       68.09       215.44        15.68        13.87        17.29        52.01 
TCGA-EB-A6L9 TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A20B 
       24.89        27.22        94.98        33.73        26.89       133.81 
TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29N TCGA-EE-A29P 
      168.26        63.35        78.97        63.78        18.61        56.42 
TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A0 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE 
      369.93       195.02        46.82        86.14        59.28       161.03 
TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GO TCGA-EE-A2GP 
      208.04        48.72        79.66        75.48       126.81        13.91 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MH TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2MM 
      129.27        28.83        16.96        96.23       158.63       167.90 
TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AA 
      248.65        43.23       134.40       162.48        53.26       124.31 
TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 
       54.51        13.81        41.59       138.81       172.18       127.20 
TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3JB TCGA-EE-A3JD TCGA-ER-A193 TCGA-ER-A197 
       36.95        64.08       201.80        27.35        31.40        13.94 
TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19E TCGA-ER-A19G TCGA-ER-A19H 
        9.17        98.40        48.89        13.02       268.93       152.35 
TCGA-ER-A19J TCGA-ER-A19P TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A2ND TCGA-ER-A3EV 
        6.44       162.08        37.25         8.88        23.34        46.98 
TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 
       33.21         6.77        92.98       174.21        15.72       220.80 
TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YX 
       18.77        38.27        34.82        36.26       104.42        48.59 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZF 
       20.91        28.08         7.79       357.37        53.52        15.45 
TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS 
        9.70        32.75       101.26       133.55        11.41       148.80 
TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F2 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FW-A3I3 
       27.09        27.02        50.14        28.73       174.84         0.20 
TCGA-FW-A5DY TCGA-GF-A4EO TCGA-GF-A6C9 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 
       19.30         7.23        15.78       117.93        84.72        10.13 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U7 TCGA-GN-A4U9 
       64.44        62.79        32.48        39.58        10.42        22.13 
TCGA-GN-A8LK TCGA-GN-A9SD TCGA-HR-A2OG TCGA-HR-A2OH TCGA-LH-A9QB TCGA-QB-A6FS 
       50.10        59.41         0.23        65.88       368.78         7.23 
TCGA-QB-AA9O TCGA-W3-AA1O TCGA-W3-AA1R TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8JZ 
       18.05         4.01       111.09       219.16       105.04        24.03 
TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZQ TCGA-WE-A8ZX TCGA-WE-AA9Y TCGA-WE-AAA3 
       61.15        15.98        59.77        32.58        12.16        19.73 
TCGA-YD-A89C TCGA-YG-AA3O TCGA-YG-AA3P 
        6.90        37.94        14.43 

$`7Q GAIN WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA 
       17.03        66.48        12.99       133.25        28.08        90.90 
TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JB TCGA-D3-A2JF 
       95.74        43.43       103.10        65.49       168.00        62.07 
TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JO TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A51E 
       42.08        12.10        66.08        60.23        24.53       174.84 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51T TCGA-D3-A5GL 
       55.73        56.35        32.94        22.62        26.89       125.79 
TCGA-D3-A5GO TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GR 
      137.92        26.43       241.38        89.13       107.15       129.63 
TCGA-D9-A1JW TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A4Z6 TCGA-DA-A1I1 TCGA-DA-A1IB 
        3.65        18.12        15.39        18.44       194.83        23.44 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH 
       28.60        10.49        10.36        20.35        68.25        54.02 
TCGA-EB-A5VV TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A182 TCGA-EE-A184 TCGA-EE-A185 
        7.04        29.82         8.65        14.70        68.15         4.96 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29G 
      151.27        91.56        13.55        85.08        13.97        72.07 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
       64.64         2.60        56.84        66.74        14.47        61.28 
TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2GC 
       25.87        17.92       102.90        36.82        39.29        67.43 
TCGA-EE-A2GD TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GN TCGA-EE-A2GR TCGA-EE-A2GS 
      340.14       107.38        54.74       102.12        42.77        81.21 
TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD 
       44.88        94.82        21.67        19.76        61.51        47.28 
TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2ML TCGA-EE-A2MN 
      103.27       268.73       103.20       204.66       216.66        47.54 
TCGA-EE-A2MT TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3J8 TCGA-EE-A3JA 
       71.21       122.73        51.62        28.77        34.32        53.19 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A19A 
       51.35       109.58       152.81        35.44        50.76        77.75 
TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19Q 
       12.59        26.37       131.51        61.05        44.05        50.89 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
      148.18        79.99        43.82        20.15        16.37        31.27 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-FR-A7U8 TCGA-FS-A1YW TCGA-FS-A1YY 
       32.05       247.04        80.32        27.85       216.92       228.59 
TCGA-FS-A1Z0 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZE TCGA-FS-A1ZJ TCGA-FS-A1ZK 
      202.65        27.72        48.85        40.27        47.38        23.93 
TCGA-FS-A1ZP TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A4F0 TCGA-FS-A4F4 
       74.73        53.16        26.56        49.48        77.82        66.67 
TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3R5 TCGA-FW-A3TU 
       34.03        26.73        54.41        80.68        22.92        55.59 
TCGA-FW-A3TV TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A4U3 TCGA-GN-A4U4 
       13.51         9.90         2.04       139.89       121.91        39.35 
TCGA-GN-A4U8 TCGA-GN-A8LL TCGA-OD-A75X TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 
       48.89        21.37       297.90         0.33         0.69       228.16 
TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1Q TCGA-W3-AA1V TCGA-WE-A8K1 TCGA-WE-A8ZM 
       63.02       121.08        69.07        42.08        49.05        98.89 
TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AAA0 TCGA-WE-AAA4 
       58.98        67.63        11.80        49.51        35.01        22.29 
TCGA-YD-A9TA TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
       49.18        27.58        96.99        15.98 

  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
             0.20              0.33 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
           369.93            340.14 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
            50.14             51.12 
[1] "0.2 - 369.9 (50.1)" "0.3 - 340.1 (51.1)"
[1] "hr=" "1.1"
D14V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  7Q GAIN MUTATED                   32             4
  7Q GAIN WILD-TYPE                 33             1
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  7Q GAIN MUTATED                                          38
  7Q GAIN WILD-TYPE                                        34
                   vv
clus                REGIONAL LYMPH NODE
  7Q GAIN MUTATED                   119
  7Q GAIN WILD-TYPE                  96
D14V4, multiclass
                                           clus
vv                                          7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  DISTANT METASTASIS                                     32                33
  PRIMARY TUMOR                                           4                 1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE              38                34
  REGIONAL LYMPH NODE                                   119                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                I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  7Q GAIN MUTATED            10       2      17        8        9       12
  7Q GAIN WILD-TYPE           2       5      11       10       18       12
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  7Q GAIN MUTATED           6         7         9        23         11
  7Q GAIN WILD-TYPE         8        12         3        14          4
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  7Q GAIN MUTATED           21         32       11
  7Q GAIN WILD-TYPE         11         28        9
D14V5, multiclass
             clus
vv            7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  I OR II NOS              10                 2
  STAGE 0                   2                 5
  STAGE I                  17                11
  STAGE IA                  8                10
  STAGE IB                  9                18
  STAGE II                 12                12
  STAGE IIA                 6                 8
  STAGE IIB                 7                12
  STAGE IIC                 9                 3
  STAGE III                23                14
  STAGE IIIA               11                 4
  STAGE IIIB               21                11
  STAGE IIIC               32                28
  STAGE IV                 11                 9
[1] 14  2
[1] TRUE
[1] "dimension of contingency 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      36 36 41 40
  7Q GAIN WILD-TYPE    28 36 36 28
D14V6, multiclass
       clus
vv      7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  T0+T1              36                28
  T2                 36                36
  T3                 41                36
  T4                 40                28
[1] 4 2
[1] TRUE
[1] "dimension of 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   88 36 23 30
  7Q GAIN WILD-TYPE 81 27 15 19
D14V7, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  N0              88                81
  N1              36                27
  N2              23                15
  N3              30                19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V8, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED   169  12
  7Q GAIN WILD-TYPE 144   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED    169   12
  7Q GAIN WILD-TYPE  144    9
   clus
vv  7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  0             169               144
  1              12                 9
[1] 2 2
[1] FALSE
D14V9, binary
                   cls
clus                 0  1
  7Q GAIN MUTATED   75 44
  7Q GAIN WILD-TYPE 57 44
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     75   44
  7Q GAIN WILD-TYPE   57   44
     clus
vv    7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  NO               75                57
  YES              44                44
[1] 2 2
[1] FALSE
D14V10, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED    27 166
  7Q GAIN WILD-TYPE  17 147
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     27  166
  7Q GAIN WILD-TYPE   17  147
     clus
vv    7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  NO               27                17
  YES             166               147
[1] 2 2
[1] FALSE
D14V11, continuous
D14V12, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED    82 112
  7Q GAIN WILD-TYPE  53 111
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     82  112
  7Q GAIN WILD-TYPE   53  111
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  FEMALE              82                53
  MALE               112               111
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  7Q GAIN MUTATED       3                         0   185
  7Q GAIN WILD-TYPE     2                         1   159
D14V13, multiclass
                           clus
vv                          7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  ASIAN                                   3                 2
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                 185               159
[1] 3 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     5 184
  7Q GAIN WILD-TYPE   2 160
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      5  184
  7Q GAIN WILD-TYPE    2  160
                        clus
vv                       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   5                 2
  NOT HISPANIC OR LATINO             184               160
[1] 2 2
[1] FALSE

Clustering(15) Variable = 8P GAIN MUTATION ANALYSIS
D15V1, survival
                   sevent
clus2                0  1
  8P GAIN MUTATED   42 37
  8P GAIN WILD-TYPE 79 81
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               79               160 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               37                81 
$`8P GAIN MUTATED`
TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q6 TCGA-D3-A2J7 TCGA-D3-A2JC TCGA-D3-A2JN 
       60.46        12.99        49.35        45.99        86.30        64.83 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3MR TCGA-D3-A3MU 
       66.08        43.53        40.01        59.70        90.21        23.67 
TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D3-A8GP TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HY 
      177.86       124.08       135.12        57.90        22.85       106.85 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A3F5 TCGA-EB-A44Q TCGA-EB-A5SH TCGA-EE-A17Y 
       31.96       150.61       214.59         3.91        50.07        24.89 
TCGA-EE-A181 TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
       20.38        12.99        44.28       239.11         0.20       189.40 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2M6 
       32.48        18.35        31.00       118.32         0.76       103.13 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MR TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE 
       15.25         5.75        25.08       122.73         4.41        54.51 
TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-ER-A19C TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L 
      111.85        45.90        39.81       151.46       150.12        99.06 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A2NC TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7U8 
       59.84        42.48        22.36       174.21       209.23        26.20 
TCGA-FR-A7UA TCGA-FS-A1YW TCGA-FS-A1Z4 TCGA-FS-A1ZD TCGA-FS-A1ZM TCGA-FS-A1ZQ 
        5.65       171.78        27.62        32.78        78.61       130.95 
TCGA-FS-A1ZY TCGA-FS-A4F4 TCGA-FS-A4FD TCGA-FW-A3TV TCGA-GF-A3OT TCGA-GN-A267 
        5.29        66.67        80.68        11.54         9.90        17.06 
TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A9SD TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A825 
        7.59       120.53        59.41         0.33       174.12         1.97 
TCGA-W3-AA1V TCGA-W3-AA21 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZQ TCGA-WE-A8ZT 
        8.09        92.84        62.99        12.69        59.44        10.95 
TCGA-YG-AA3O 
       28.21 

$`8P GAIN WILD-TYPE`
TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q7 
       14.83         8.42        15.72        31.89       110.93       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J8 TCGA-D3-A2JA 
       19.04        76.41        62.60        25.64        62.86        15.75 
TCGA-D3-A2JB TCGA-D3-A2JD TCGA-D3-A2JE TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL 
      168.00         7.27         9.76       107.61        36.30       171.58 
TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO 
       58.06        46.98       140.98        16.96        13.87         9.34 
TCGA-D3-A51E TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL 
      173.85       144.46        31.76        62.70        11.34        42.05 
TCGA-D3-A5GN TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL 
       45.70        78.21        23.61       179.97       120.00        69.53 
TCGA-D3-A8GM TCGA-D3-A8GR TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 
       70.62        36.53        10.78        15.02        16.90        18.44 
TCGA-DA-A1HV TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 
       48.66        82.85        32.42        64.83        58.85        25.12 
TCGA-DA-A3F8 TCGA-EB-A5SG TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A180 
       14.96        33.24        45.50         6.64        13.15        62.37 
TCGA-EE-A182 TCGA-EE-A184 TCGA-EE-A20C TCGA-EE-A20H TCGA-EE-A29B TCGA-EE-A29C 
        0.00        67.50        75.55       155.90        75.22        76.14 
TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T 
        0.26        63.12        47.74        27.16        61.12       346.49 
TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GJ 
      185.19       102.38         7.20        77.98        26.14        68.65 
TCGA-EE-A2GK TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2MC TCGA-EE-A2MF 
       10.62         0.20        71.31        81.99        23.77       209.79 
TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM 
       94.19       171.85        63.25        67.50       104.78       145.45 
TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AC 
      227.01       143.93        23.51        53.26       124.31        51.62 
TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JI TCGA-ER-A193 
        6.28        67.89         3.35       201.80       152.81        14.56 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B 
       34.45         1.58        47.31         7.82         4.54        53.29 
TCGA-ER-A19D TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 
       11.47       120.76        49.71        34.95       146.63        47.97 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
        4.70        16.87        10.95       173.29        55.82        15.48 
TCGA-ER-A3PL TCGA-FR-A8YC TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1ZC 
       32.05        10.06        49.74       195.98         8.35       312.07 
TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZS TCGA-FS-A1ZT 
       35.90        12.92         7.82        36.33       136.27        35.28 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F8 TCGA-FS-A4F9 
        4.47        23.21         3.06        30.90       173.19        13.28 
TCGA-FW-A3TU TCGA-FW-A5DY TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 
       55.59        19.30         6.05         1.91        53.29       117.93 
TCGA-GN-A265 TCGA-GN-A268 TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-GN-A8LK TCGA-LH-A9QB 
       84.72        42.48        34.49        46.92        43.23        85.05 
TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O TCGA-W3-A828 TCGA-W3-AA1Q TCGA-W3-AA1R 
      297.01         7.23        18.05       120.07        44.05        79.99 
TCGA-W3-AA1W TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8ZO TCGA-WE-A8ZY TCGA-WE-AA9Y 
      185.13         1.15        59.64        19.00        48.39         1.94 
TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-Z2-AA3S 
       26.60        16.64        15.65        91.23 

  8P GAIN MUTATED 8P GAIN WILD-TYPE 
              0.2               0.0 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
           239.11            346.49 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
            45.99             46.31 
[1] "0.2 - 239.1 (46.0)" "0.0 - 346.5 (46.3)"
[1] "hr=" "1.1"
D15V2, survival
                   sevent
clus2                 0   1
  8P GAIN MUTATED    55  59
  8P GAIN WILD-TYPE 114 121
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
              114               235 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               59               121 
$`8P GAIN MUTATED`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q6 TCGA-D3-A1Q9 TCGA-D3-A2J7 
       17.03        66.48        12.99        71.80        31.59       103.10 
TCGA-D3-A2JC TCGA-D3-A2JF TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3CC 
       86.76        62.07        66.48        66.08        59.57        86.93 
TCGA-D3-A3CE TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A5GR TCGA-D3-A5GS 
       60.23       103.59        39.75        45.30       178.32        18.18 
TCGA-D3-A5GU TCGA-D3-A8GI TCGA-D3-A8GP TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HW 
      125.19        58.52       152.75        66.25        22.95        36.03 
TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A3F5 TCGA-EB-A44Q 
      117.21       194.83       176.55        35.93       215.44        13.87 
TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SH TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A20B 
       10.36        20.35        54.02        27.22        33.73       133.81 
TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29R TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
       13.97        72.07        14.47       340.14       161.03       208.04 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2M6 
       79.66        75.48       102.12       126.81        13.91       129.27 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MH TCGA-EE-A2MR TCGA-EE-A3AB TCGA-EE-A3AD 
       28.83        19.76        16.96       134.40       122.73        28.77 
TCGA-EE-A3AE TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-ER-A19C 
       54.51       127.20        36.95        64.08        53.19        48.89 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
      268.93       152.35         6.44       131.51        61.05        44.05 
TCGA-ER-A2NC TCGA-ER-A2NF TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 
       43.82        16.37       174.21       220.80        27.85        18.77 
TCGA-FR-A7UA TCGA-FR-A8YD TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1Z4 TCGA-FS-A1Z7 
       38.27        36.26       216.92        48.59        28.08         7.79 
TCGA-FS-A1ZD TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR 
       53.52        23.93       101.26        74.73       133.55        11.41 
TCGA-FS-A1ZY TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4FD TCGA-FW-A3I3 
       27.09        50.14        66.67        28.73        80.68         0.20 
TCGA-FW-A3TV TCGA-GF-A3OT TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A26D 
       13.51         9.90        10.13        64.44        32.48        39.58 
TCGA-GN-A4U3 TCGA-GN-A8LL TCGA-GN-A9SD TCGA-HR-A2OH TCGA-RP-A693 TCGA-RP-A694 
      121.91        21.37        59.41        65.88         0.33         0.69 
TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-AA1V TCGA-W3-AA21 TCGA-WE-A8K6 TCGA-WE-A8ZM 
      228.16        63.02        42.08       105.04        15.98        98.89 
TCGA-WE-A8ZN TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-YG-AA3O TCGA-Z2-AA3V 
       58.98        59.77        11.80        32.58        37.94        15.98 

$`8P GAIN WILD-TYPE`
TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q7 
       14.93        16.57        16.67       112.04       112.57       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J8 TCGA-D3-A2J9 
       28.08        90.90        95.74        43.43        65.49        23.77 
TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JD TCGA-D3-A2JE TCGA-D3-A2JG TCGA-D3-A2JH 
      115.53       168.00        11.87        27.65       113.52        42.08 
TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 
       12.10       171.58       130.72        58.06        46.98        46.32 
TCGA-D3-A3CB TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A51E TCGA-D3-A51F 
      166.52        24.53        13.87         9.34       174.84        55.73 
TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T 
       56.35       145.12        32.94        22.62        63.81        26.89 
TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GD 
      125.79       135.75       137.92        30.84        79.59        23.61 
TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GN 
       26.43       241.38       170.20        89.13       107.15       161.00 
TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW 
       29.06       129.63       117.17       151.53        54.67         3.65 
TCGA-D9-A1JX TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 
        7.10        18.12        15.39        22.29        18.44         9.90 
TCGA-D9-A6EA TCGA-DA-A1HV TCGA-DA-A1I0 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
       25.18        48.89        20.38       107.34        61.18        53.92 
TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 
       65.92        23.44        68.09        28.60        10.49        15.68 
TCGA-EB-A5SG TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X 
       68.25        17.29        52.01         7.04        24.89        29.82 
TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 
        8.65        94.98        14.70        26.89        68.15         4.96 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
      151.27        91.56       168.26        13.55        63.35        85.08 
TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N 
       78.97        63.78        64.64         2.60        56.84        18.61 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W 
       56.42        66.74        61.28       369.93        25.87       195.02 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
       17.92        46.82       102.90        36.82        39.29        86.14 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GR 
       59.28        67.43        48.72       107.38        54.74        42.77 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2MC TCGA-EE-A2MD 
       81.21        44.88        94.82        21.67        61.51        47.28 
TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK 
      103.27       268.73       103.20       204.66        96.23       158.63 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MS 
      216.66       167.90        47.54       248.65        43.23       162.48 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AF TCGA-EE-A3AG 
       71.21        53.26       124.31        51.62        13.81        41.59 
TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE 
      138.81       172.18        34.32       201.80        27.35        51.35 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
      109.58       152.81        31.40        35.44        13.94        50.76 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F 
        9.17        77.75        98.40        12.59        13.02        26.37 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 
      162.08        50.89        37.25         8.88       148.18        79.99 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET 
       23.34        20.15        31.27        32.05       247.04        80.32 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A69P TCGA-FR-A8YC 
       46.98        33.21         6.77        92.98        15.72        34.82 
TCGA-FR-A8YE TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1ZA TCGA-FS-A1ZB 
      104.42       228.59       202.65        20.91        27.72        48.85 
TCGA-FS-A1ZC TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ 
      357.37        40.27        15.45         9.70        32.75        47.38 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZZ TCGA-FS-A4F0 
      148.80        53.16        26.56        49.48        27.02        77.82 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FW-A3R5 TCGA-FW-A3TU 
      174.84        34.03        26.73        54.41        22.92        55.59 
TCGA-FW-A5DY TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 
       19.30         7.23         2.04        15.78       139.89       117.93 
TCGA-GN-A265 TCGA-GN-A268 TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A4U9 
       84.72        62.79        39.35        10.42        48.89        22.13 
TCGA-GN-A8LK TCGA-HR-A2OG TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O 
       50.10         0.23       368.78       297.90         7.23        18.05 
TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1W TCGA-WE-A8JZ 
      121.08         4.01        69.07       111.09       219.16        24.03 
TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8ZO TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 
       49.05        61.15        67.63        49.51        12.16        35.01 
TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YD-A89C TCGA-YD-A9TA TCGA-YG-AA3P TCGA-Z2-A8RT 
       19.73        22.29         6.90        49.18        14.43        27.58 
TCGA-Z2-AA3S 
       96.99 

  8P GAIN MUTATED 8P GAIN WILD-TYPE 
             0.20              0.23 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
           340.14            369.93 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
           54.265            49.510 
[1] "0.2 - 340.1 (54.3)" "0.2 - 369.9 (49.5)"
[1] "hr=" "1"  
D15V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  8P GAIN MUTATED                   16             2
  8P GAIN WILD-TYPE                 49             3
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  8P GAIN MUTATED                                          31
  8P GAIN WILD-TYPE                                        41
                   vv
clus                REGIONAL LYMPH NODE
  8P GAIN MUTATED                    69
  8P GAIN WILD-TYPE                 146
D15V4, multiclass
                                           clus
vv                                          8P GAIN MUTATED 8P GAIN WILD-TYPE
  DISTANT METASTASIS                                     16                49
  PRIMARY TUMOR                                           2                 3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE              31                41
  REGIONAL LYMPH NODE                                    69               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                I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  8P GAIN MUTATED             3       1      11        6        7       12
  8P GAIN WILD-TYPE           9       6      17       12       20       12
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  8P GAIN MUTATED           5         3         6        17          7
  8P GAIN WILD-TYPE         9        16         6        20          8
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  8P GAIN MUTATED           10         17        6
  8P GAIN WILD-TYPE         22         43       14
D15V5, multiclass
             clus
vv            8P GAIN MUTATED 8P GAIN WILD-TYPE
  I OR II NOS               3                 9
  STAGE 0                   1                 6
  STAGE I                  11                17
  STAGE IA                  6                12
  STAGE IB                  7                20
  STAGE II                 12                12
  STAGE IIA                 5                 9
  STAGE IIB                 3                16
  STAGE IIC                 6                 6
  STAGE III                17                20
  STAGE IIIA                7                 8
  STAGE IIIB               10                22
  STAGE IIIC               17                43
  STAGE IV                  6                14
[1] 14  2
[1] TRUE
[1] "dimension of contingency 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      25 24 27 22
  8P GAIN WILD-TYPE    39 48 50 46
D15V6, multiclass
       clus
vv      8P GAIN MUTATED 8P GAIN WILD-TYPE
  T0+T1              25                39
  T2                 24                48
  T3                 27                50
  T4                 22                46
[1] 4 2
[1] TRUE
[1] "dimension of 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    53  27  13  12
  8P GAIN WILD-TYPE 116  36  25  37
D15V7, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  N0              53               116
  N1              27                36
  N2              13                25
  N3              12                37
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V8, binary
                   cls
clus                  0   1
  8P GAIN MUTATED   106   6
  8P GAIN WILD-TYPE 207  15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED    106    6
  8P GAIN WILD-TYPE  207   15
   clus
vv  8P GAIN MUTATED 8P GAIN WILD-TYPE
  0             106               207
  1               6                15
[1] 2 2
[1] FALSE
D15V9, binary
                   cls
clus                 0  1
  8P GAIN MUTATED   40 33
  8P GAIN WILD-TYPE 92 55
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     40   33
  8P GAIN WILD-TYPE   92   55
     clus
vv    8P GAIN MUTATED 8P GAIN WILD-TYPE
  NO               40                92
  YES              33                55
[1] 2 2
[1] FALSE
D15V10, binary
                   cls
clus                  0   1
  8P GAIN MUTATED    16 102
  8P GAIN WILD-TYPE  28 211
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     16  102
  8P GAIN WILD-TYPE   28  211
     clus
vv    8P GAIN MUTATED 8P GAIN WILD-TYPE
  NO               16                28
  YES             102               211
[1] 2 2
[1] FALSE
D15V11, continuous
D15V12, binary
                   cls
clus                  0   1
  8P GAIN MUTATED    41  77
  8P GAIN WILD-TYPE  94 146
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     41   77
  8P GAIN WILD-TYPE   94  146
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  FEMALE              41                94
  MALE                77               146
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  8P GAIN MUTATED       4                         0   110
  8P GAIN WILD-TYPE     1                         1   234
D15V13, multiclass
                           clus
vv                          8P GAIN MUTATED 8P GAIN WILD-TYPE
  ASIAN                                   4                 1
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                 110               234
[1] 3 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     2 113
  8P GAIN WILD-TYPE   5 231
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      2  113
  8P GAIN WILD-TYPE    5  231
                        clus
vv                       8P GAIN MUTATED 8P GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 5
  NOT HISPANIC OR LATINO             113               231
[1] 2 2
[1] FALSE

Clustering(16) Variable = 8Q GAIN MUTATION ANALYSIS
D16V1, survival
                   sevent
clus2                0  1
  8Q GAIN MUTATED   64 55
  8Q GAIN WILD-TYPE 57 63
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              119               120 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               55                63 
$`8Q GAIN MUTATED`
TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q6 TCGA-D3-A1QB 
       60.46        12.99         8.42        31.89        49.35        62.60 
TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JE TCGA-D3-A2JN 
       25.64        45.99        15.75        86.30         9.76        64.83 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE 
       66.08        43.53        58.06       140.98        40.01        59.70 
TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51J 
       13.87         9.34        90.21        23.67       173.85       144.46 
TCGA-D3-A51K TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D3-A8GJ TCGA-D3-A8GP 
       31.76        45.70       177.86       124.08       179.97       135.12 
TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A3F5 
       57.90        22.85       106.85        31.96       150.61       214.59 
TCGA-EB-A44Q TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A6L9 TCGA-EE-A17Y TCGA-EE-A181 
        3.91        33.24        50.07         6.64        24.89        20.38 
TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29T TCGA-EE-A2GD TCGA-EE-A2GE 
       76.14         0.26        44.28       346.49       239.11         0.20 
TCGA-EE-A2GH TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP 
      189.40        32.48        18.35        31.00       118.32         0.76 
TCGA-EE-A2GS TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MR TCGA-EE-A3AA 
       71.31       103.13        15.25         5.75        25.08       124.31 
TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 
      122.73         4.41        54.51        67.89       111.85        45.90 
TCGA-ER-A197 TCGA-ER-A19C TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M 
        1.58        39.81       151.46       150.12        99.06        59.84 
TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A3ET 
       42.48        49.71        34.95        22.36         4.70        55.82 
TCGA-ER-A3EV TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FS-A1YW 
       15.48       174.21       209.23        26.20         5.65       171.78 
TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1ZD TCGA-FS-A1ZM TCGA-FS-A1ZQ 
       49.74       195.98        27.62        32.78        78.61       130.95 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A4F4 TCGA-FS-A4F8 
      136.27        35.28         4.47         5.29        66.67       173.19 
TCGA-FS-A4FD TCGA-FW-A3TV TCGA-GF-A3OT TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A26A 
       80.68        11.54         9.90        84.72        17.06         7.59 
TCGA-GN-A4U3 TCGA-GN-A9SD TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 
      120.53        59.41       297.01         7.23        18.05         0.33 
TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-AA1V TCGA-W3-AA21 TCGA-WE-A8ZM TCGA-WE-A8ZN 
      174.12         1.97         8.09        92.84        62.99        12.69 
TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-AAA3 TCGA-YG-AA3O TCGA-Z2-AA3S 
       59.44        10.95        16.64        28.21        91.23 

$`8Q GAIN WILD-TYPE`
TCGA-BF-AAP0 TCGA-D3-A1Q3 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA 
       14.83        15.72       110.93       133.25        19.04        76.41 
TCGA-D3-A2J8 TCGA-D3-A2JB TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL 
       62.86       168.00         7.27       107.61        36.30       171.58 
TCGA-D3-A3C7 TCGA-D3-A3CF TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A8GC 
       46.98        16.96        62.70        11.34        42.05        78.21 
TCGA-D3-A8GD TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GR TCGA-D9-A1X3 
       23.61       120.00        69.53        70.62        36.53        10.78 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-DA-A1HV TCGA-DA-A1I5 TCGA-DA-A1I7 
       15.02        16.90        18.44        48.66        82.85        32.42 
TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F8 TCGA-EB-A5UN TCGA-EE-A17X 
       64.83        58.85        25.12        14.96        45.50        13.15 
TCGA-EE-A180 TCGA-EE-A182 TCGA-EE-A184 TCGA-EE-A20C TCGA-EE-A20H TCGA-EE-A29B 
       62.37         0.00        67.50        75.55       155.90        75.22 
TCGA-EE-A29D TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29W 
       12.99        63.12        47.74        27.16        61.12       185.19 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GJ TCGA-EE-A2GK 
      102.38         7.20        77.98        26.14        68.65        10.62 
TCGA-EE-A2GR TCGA-EE-A2GU TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI 
        0.20        81.99        23.77       209.79        94.19       171.85 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MS 
       63.25        67.50       104.78       145.45       227.01       143.93 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AC TCGA-EE-A3AF TCGA-EE-A3J8 TCGA-EE-A3JB 
       23.51        53.26        51.62         6.28         3.35       201.80 
TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A 
      152.81        14.56        34.45        47.31         7.82         4.54 
TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19P TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NE 
       53.29        11.47       120.76       146.63        47.97        16.87 
TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3PL TCGA-FR-A8YC TCGA-FS-A1Z3 TCGA-FS-A1ZC 
       10.95       173.29        32.05        10.06         8.35       312.07 
TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZW TCGA-FS-A1ZZ 
       35.90        12.92         7.82        36.33        23.21         3.06 
TCGA-FS-A4F0 TCGA-FS-A4F9 TCGA-FW-A3TU TCGA-FW-A5DY TCGA-GF-A4EO TCGA-GF-A6C8 
       30.90        13.28        55.59        19.30         6.05         1.91 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A268 TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-GN-A8LK 
       53.29       117.93        42.48        34.49        46.92        43.23 
TCGA-LH-A9QB TCGA-W3-A828 TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1W TCGA-WE-A8K1 
       85.05       120.07        44.05        79.99       185.13         1.15 
TCGA-WE-A8K5 TCGA-WE-A8ZO TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 
       59.64        19.00        48.39         1.94        26.60        15.65 

  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              0.2               0.0 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
           346.49            312.07 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
            45.99             46.21 
[1] "0.2 - 346.5 (46.0)" "0.0 - 312.1 (46.2)"
[1] "hr=" "1.3"
D16V2, survival
                   sevent
clus2                0  1
  8Q GAIN MUTATED   79 82
  8Q GAIN WILD-TYPE 90 98
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              161               188 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               82                98 
$`8Q GAIN MUTATED`
TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q6 TCGA-D3-A1Q9 
       66.48        12.99        16.57       112.04        71.80        31.59 
TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JE 
       95.74        43.43       103.10       115.53        86.76        27.65 
TCGA-D3-A2JF TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CB 
       62.07        66.48        66.08        59.57        58.06       166.52 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU 
       86.93        60.23        13.87         9.34       103.59        39.75 
TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A5GN 
       45.30       174.84       145.12        32.94        22.62       135.75 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GP 
      178.32        18.18       125.19        58.52       241.38       152.75 
TCGA-D9-A1JW TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 
        3.65        66.25        22.95        36.03       117.21        20.38 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-EB-A44Q 
      194.83       176.55        35.93        10.49       215.44        13.87 
TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A6L9 TCGA-EE-A17Y TCGA-EE-A17Z 
       10.36        68.25        54.02        24.89        27.22         8.65 
TCGA-EE-A181 TCGA-EE-A20B TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29R 
       33.73       133.81        78.97        63.78        72.07        14.47 
TCGA-EE-A29T TCGA-EE-A2A5 TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GL 
      369.93        39.29       340.14       161.03       208.04        79.66 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2M6 
       75.48       102.12       126.81        13.91        81.21       129.27 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MH TCGA-EE-A2MN TCGA-EE-A2MR TCGA-EE-A3AA 
       28.83        19.76        16.96        47.54       134.40       124.31 
TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3J4 
      122.73        28.77        54.51        41.59       172.18       127.20 
TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-ER-A197 TCGA-ER-A19C TCGA-ER-A19G 
       36.95        64.08        53.19        13.94        48.89       268.93 
TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19Q 
      152.35         6.44       131.51        61.05        44.05        50.89 
TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NF TCGA-ER-A3ET 
       37.25         8.88        43.82        23.34        16.37        80.32 
TCGA-ER-A3EV TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA 
       46.98       174.21       220.80        27.85        18.77        38.27 
TCGA-FR-A8YD TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z4 
       36.26       216.92        48.59       228.59       202.65        28.08 
TCGA-FS-A1Z7 TCGA-FS-A1ZD TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ 
        7.79        53.52        23.93       101.26        74.73       133.55 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A4F2 
       11.41       148.80        53.16        26.56        27.09        50.14 
TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TV 
       66.67        28.73       174.84        80.68         0.20        13.51 
TCGA-GF-A3OT TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A26D 
        9.90        84.72        10.13        64.44        32.48        39.58 
TCGA-GN-A4U3 TCGA-GN-A8LL TCGA-GN-A9SD TCGA-HR-A2OH TCGA-OD-A75X TCGA-QB-A6FS 
      121.91        21.37        59.41        65.88       297.90         7.23 
TCGA-QB-AA9O TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-AA1V 
       18.05         0.33         0.69       228.16        63.02        42.08 
TCGA-W3-AA21 TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZQ TCGA-WE-A8ZT 
      105.04        15.98        98.89        58.98        59.77        11.80 
TCGA-WE-A8ZX TCGA-WE-AAA3 TCGA-YG-AA3O TCGA-Z2-AA3S TCGA-Z2-AA3V 
       32.58        19.73        37.94        96.99        15.98 

$`8Q GAIN WILD-TYPE`
TCGA-3N-A9WB TCGA-BF-AAP0 TCGA-D3-A1Q3 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       17.03        14.93        16.67       112.57       133.25        28.08 
TCGA-D3-A1QA TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JD TCGA-D3-A2JG 
       90.90        65.49        23.77       168.00        11.87       113.52 
TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3C8 
       42.08        12.10       171.58       130.72        46.98        46.32 
TCGA-D3-A3CF TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL 
       24.53        55.73        56.35        63.81        26.89       125.79 
TCGA-D3-A5GO TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GK 
      137.92        30.84        79.59        23.61        26.43       170.20 
TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS 
       89.13       107.15       161.00        29.06       129.63       117.17 
TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JX TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 
      151.53        54.67         7.10        18.12        15.39        22.29 
TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-DA-A1HV TCGA-DA-A1I5 TCGA-DA-A1I7 
       18.44         9.90        25.18        48.89       107.34        61.18 
TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F8 
       53.92        65.92        23.44        68.09        28.60        15.68 
TCGA-EB-A5KH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EE-A17X TCGA-EE-A180 
       20.35        17.29        52.01         7.04        29.82        94.98 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A20F 
       14.70        26.89        68.15         4.96       151.27        91.56 
TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29H 
      168.26        13.55        63.35        85.08        13.97        64.64 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29S 
        2.60        56.84        18.61        56.42        66.74        61.28 
TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
       25.87       195.02        17.92        46.82       102.90        36.82 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
       86.14        59.28        67.43        48.72       107.38        54.74 
TCGA-EE-A2GR TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2MC TCGA-EE-A2MD 
       42.77        44.88        94.82        21.67        61.51        47.28 
TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK 
      103.27       268.73       103.20       204.66        96.23       158.63 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A2MT 
      216.66       167.90       248.65        43.23       162.48        71.21 
TCGA-EE-A2MU TCGA-EE-A3AC TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J8 TCGA-EE-A3JB 
       53.26        51.62        13.81       138.81        34.32       201.80 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 
       27.35        51.35       109.58       152.81        31.40        35.44 
TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19E 
       50.76         9.17        77.75        98.40        12.59        13.02 
TCGA-ER-A19F TCGA-ER-A19P TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NE TCGA-ER-A2NG 
       26.37       162.08       148.18        79.99        20.15        31.27 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A69P 
       32.05       247.04        33.21         6.77        92.98        15.72 
TCGA-FR-A8YC TCGA-FR-A8YE TCGA-FS-A1Z3 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC 
       34.82       104.42        20.91        27.72        48.85       357.37 
TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZW 
       40.27        15.45         9.70        32.75        47.38        49.48 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FW-A3R5 
       27.02        77.82        34.03        26.73        54.41        22.92 
TCGA-FW-A3TU TCGA-FW-A5DY TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 
       55.59        19.30         7.23         2.04        15.78       139.89 
TCGA-GN-A264 TCGA-GN-A268 TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A4U9 
      117.93        62.79        39.35        10.42        48.89        22.13 
TCGA-GN-A8LK TCGA-HR-A2OG TCGA-LH-A9QB TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1Q 
       50.10         0.23       368.78       121.08         4.01        69.07 
TCGA-W3-AA1R TCGA-W3-AA1W TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8ZO 
      111.09       219.16        24.03        49.05        61.15        67.63 
TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-YD-A89C TCGA-YD-A9TA 
       49.51        12.16        35.01        22.29         6.90        49.18 
TCGA-YG-AA3P TCGA-Z2-A8RT 
       14.43        27.58 

  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
             0.20              0.23 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
           369.93            368.78 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
           54.510            49.115 
[1] "0.2 - 369.9 (54.5)" "0.2 - 368.8 (49.1)"
[1] "hr=" "1.1"
D16V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  8Q GAIN MUTATED                   23             3
  8Q GAIN WILD-TYPE                 42             2
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  8Q GAIN MUTATED                                          41
  8Q GAIN WILD-TYPE                                        31
                   vv
clus                REGIONAL LYMPH NODE
  8Q GAIN MUTATED                    97
  8Q GAIN WILD-TYPE                 118
D16V4, multiclass
                                           clus
vv                                          8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  DISTANT METASTASIS                                     23                42
  PRIMARY TUMOR                                           3                 2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE              41                31
  REGIONAL LYMPH NODE                                    97               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                I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  8Q GAIN MUTATED             5       1      15        7       12       13
  8Q GAIN WILD-TYPE           7       6      13       11       15       11
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  8Q GAIN MUTATED           6         5         7        23         10
  8Q GAIN WILD-TYPE         8        14         5        14          5
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  8Q GAIN MUTATED           14         24        9
  8Q GAIN WILD-TYPE         18         36       11
D16V5, multiclass
             clus
vv            8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  I OR II NOS               5                 7
  STAGE 0                   1                 6
  STAGE I                  15                13
  STAGE IA                  7                11
  STAGE IB                 12                15
  STAGE II                 13                11
  STAGE IIA                 6                 8
  STAGE IIB                 5                14
  STAGE IIC                 7                 5
  STAGE III                23                14
  STAGE IIIA               10                 5
  STAGE IIIB               14                18
  STAGE IIIC               24                36
  STAGE IV                  9                11
[1] 14  2
[1] TRUE
[1] "dimension of contingency 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      37 36 32 29
  8Q GAIN WILD-TYPE    27 36 45 39
D16V6, multiclass
       clus
vv      8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  T0+T1              37                27
  T2                 36                36
  T3                 32                45
  T4                 29                39
[1] 4 2
[1] TRUE
[1] "dimension of 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   73 32 22 21
  8Q GAIN WILD-TYPE 96 31 16 28
D16V7, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  N0              73                96
  N1              32                31
  N2              22                16
  N3              21                28
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V8, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED   147   9
  8Q GAIN WILD-TYPE 166  12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED    147    9
  8Q GAIN WILD-TYPE  166   12
   clus
vv  8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  0             147               166
  1               9                12
[1] 2 2
[1] FALSE
D16V9, binary
                   cls
clus                 0  1
  8Q GAIN MUTATED   57 39
  8Q GAIN WILD-TYPE 75 49
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     57   39
  8Q GAIN WILD-TYPE   75   49
     clus
vv    8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  NO               57                75
  YES              39                49
[1] 2 2
[1] FALSE
D16V10, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED    26 139
  8Q GAIN WILD-TYPE  18 174
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     26  139
  8Q GAIN WILD-TYPE   18  174
     clus
vv    8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  NO               26                18
  YES             139               174
[1] 2 2
[1] FALSE
D16V11, continuous
D16V12, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED    61 104
  8Q GAIN WILD-TYPE  74 119
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     61  104
  8Q GAIN WILD-TYPE   74  119
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  FEMALE              61                74
  MALE               104               119
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  8Q GAIN MUTATED       4                         0   157
  8Q GAIN WILD-TYPE     1                         1   187
D16V13, multiclass
                           clus
vv                          8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  ASIAN                                   4                 1
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                 157               187
[1] 3 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     3 159
  8Q GAIN WILD-TYPE   4 185
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      3  159
  8Q GAIN WILD-TYPE    4  185
                        clus
vv                       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                 4
  NOT HISPANIC OR LATINO             159               185
[1] 2 2
[1] FALSE

Clustering(17) Variable = 9P GAIN MUTATION ANALYSIS
D17V1, survival
                   sevent
clus2                 0   1
  9P GAIN MUTATED     6   6
  9P GAIN WILD-TYPE 115 112
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               12               227 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                6               112 
$`9P GAIN MUTATED`
TCGA-D3-A1QA TCGA-D3-A2JA TCGA-D3-A5GN TCGA-D3-A8GM TCGA-EB-A5SH TCGA-EE-A184 
       76.41        15.75        45.70        70.62        50.07        67.50 
TCGA-ER-A19G TCGA-ER-A2NC TCGA-ER-A3ET TCGA-FS-A1Z0 TCGA-FS-A1ZJ TCGA-FS-A4F8 
      151.46        22.36        55.82       195.98        36.33       173.19 

$`9P GAIN WILD-TYPE`
TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
       60.46        12.99        14.83         8.42        15.72        31.89 
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QB TCGA-D3-A2J6 
      110.93        49.35       133.25        19.04        62.60        25.64 
TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JE 
       45.99        62.86       168.00        86.30         7.27         9.76 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP 
      107.61        36.30       171.58        64.83        66.08        43.53 
TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF 
       58.06        46.98       140.98        40.01        59.70        16.96 
TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51J 
       13.87         9.34        90.21        23.67       173.85       144.46 
TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GR TCGA-D3-A5GU 
       31.76        62.70        11.34        42.05       177.86       124.08 
TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GP 
       78.21        23.61       179.97       120.00        69.53       135.12 
TCGA-D3-A8GR TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6EC 
       36.53        10.78        15.02        16.90        18.44        57.90 
TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 
       22.85        48.66       106.85        31.96       150.61        82.85 
TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 
       32.42        64.83        58.85        25.12       214.59        14.96 
TCGA-EB-A44Q TCGA-EB-A5SG TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y 
        3.91        33.24        45.50         6.64        13.15        24.89 
TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A20C TCGA-EE-A20H TCGA-EE-A29B 
       62.37        20.38         0.00        75.55       155.90        75.22 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M 
       76.14        12.99         0.26        44.28        63.12        47.74 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A2 
       27.16        61.12       346.49       185.19       102.38         7.20 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ 
       77.98        26.14       239.11         0.20       189.40        68.65 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP 
       10.62        32.48        18.35        31.00       118.32         0.76 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 
        0.20        71.31        81.99       103.13        15.25         5.75 
TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK 
       23.77       209.79        94.19       171.85        63.25        67.50 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT 
      104.78       145.45       227.01        25.08       143.93        23.51 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
       53.26       124.31       122.73        51.62         4.41        54.51 
TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB 
        6.28        67.89       111.85        45.90         3.35       201.80 
TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 
      152.81        14.56        34.45         1.58        47.31         7.82 
TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19H TCGA-ER-A19L 
        4.54        53.29        39.81        11.47       150.12        99.06 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W 
       59.84        42.48       120.76        49.71        34.95       146.63 
TCGA-ER-A1A1 TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3EV 
       47.97         4.70        16.87        10.95       173.29        15.48 
TCGA-ER-A3PL TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FR-A8YC 
       32.05       174.21       209.23        26.20         5.65        10.06 
TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD 
      171.78        49.74         8.35        27.62       312.07        32.78 
TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS 
       35.90        12.92         7.82        78.61       130.95       136.27 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 
       35.28         4.47        23.21         5.29         3.06        30.90 
TCGA-FS-A4F4 TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
       66.67        13.28        80.68        55.59        11.54        19.30 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        9.90         6.05         1.91        53.29       117.93        84.72 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 
       17.06        42.48         7.59       120.53        34.49        46.92 
TCGA-GN-A8LK TCGA-GN-A9SD TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O 
       43.23        59.41        85.05       297.01         7.23        18.05 
TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1Q TCGA-W3-AA1R 
        0.33       174.12         1.97       120.07        44.05        79.99 
TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8ZM 
        8.09       185.13        92.84         1.15        59.64        62.99 
TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AA9Y 
       12.69        19.00        59.44        10.95        48.39         1.94 
TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-Z2-AA3S 
       26.60        16.64        15.65        28.21        91.23 

  9P GAIN MUTATED 9P GAIN WILD-TYPE 
            15.75              0.00 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
           195.98            346.49 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
            61.66             45.50 
[1] "15.8 - 196.0 (61.7)" "0.0 - 346.5 (45.5)" 
[1] "hr=" "1.3"
D17V2, survival
                   sevent
clus2                 0   1
  9P GAIN MUTATED     8   8
  9P GAIN WILD-TYPE 161 172
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               16               333 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                8               172 
$`9P GAIN MUTATED`
TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A2JA TCGA-D3-A5GN TCGA-D3-A5GS TCGA-D3-A8GM 
       31.59        90.90       115.53       135.75        18.18       107.15 
TCGA-EB-A5SH TCGA-EE-A184 TCGA-EE-A2M5 TCGA-ER-A19G TCGA-ER-A2NC TCGA-ER-A2NF 
       54.02        68.15        21.67       268.93        43.82        16.37 
TCGA-ER-A3ET TCGA-FS-A1Z0 TCGA-FS-A1ZJ TCGA-FS-A4F8 
       80.32       202.65        47.38       174.84 

$`9P GAIN WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q3 
       17.03        66.48        12.99        14.93        16.57        16.67 
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QB 
      112.04       112.57        71.80       133.25        28.08        95.74 
TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JC 
       43.43       103.10        65.49        23.77       168.00        86.76 
TCGA-D3-A2JD TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK 
       11.87        27.65        62.07       113.52        42.08        12.10 
TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 
      171.58        66.48        66.08        59.57       130.72        58.06 
TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF 
       46.98        46.32       166.52        86.93        60.23        24.53 
TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E 
       13.87         9.34       103.59        39.75        45.30       174.84 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R 
       55.73        56.35       145.12        32.94        22.62        63.81 
TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D3-A8GB 
       26.89       125.79       137.92       178.32       125.19        30.84 
TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GK 
       79.59        23.61        26.43        58.52       241.38       170.20 
TCGA-D3-A8GL TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS 
       89.13       161.00       152.75        29.06       129.63       117.17 
TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A1X3 TCGA-D9-A3Z1 
      151.53        54.67         3.65         7.10        18.12        15.39 
TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG 
       22.29        18.44         9.90        25.18        66.25        22.95 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 
       48.89        36.03       117.21        20.38       194.83       176.55 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB 
       35.93       107.34        61.18        53.92        65.92        23.44 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q 
       68.09        28.60        10.49       215.44        15.68        13.87 
TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV 
       10.36        20.35        68.25        17.29        52.01         7.04 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 
       24.89        29.82        27.22         8.65        94.98        33.73 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F 
       14.70        26.89         4.96       133.81       151.27        91.56 
TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D 
      168.26        13.55        63.35        85.08        78.97        13.97 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N 
       63.78        72.07        64.64         2.60        56.84        18.61 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V 
       56.42        66.74        14.47        61.28       369.93        25.87 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 
      195.02        17.92        46.82       102.90        36.82        39.29 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
       86.14        59.28        67.43       340.14       161.03       208.04 
TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN 
       48.72       107.38        54.74        79.66        75.48       102.12 
TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU 
      126.81        13.91        42.77        81.21        44.88        94.82 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME 
      129.27        28.83        19.76        61.51        47.28       103.27 
TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK 
      268.73       103.20        16.96       204.66        96.23       158.63 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR 
      216.66       167.90        47.54       248.65        43.23       134.40 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC 
      162.48        71.21        53.26       124.31       122.73        51.62 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 
       28.77        54.51        13.81        41.59       138.81       172.18 
TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB 
      127.20        36.95        64.08        34.32        53.19       201.80 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 
       27.35        51.35       109.58       152.81        31.40        35.44 
TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C 
       13.94        50.76         9.17        77.75        98.40        48.89 
TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L 
       12.59        13.02        26.37       152.35         6.44       131.51 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T 
       61.05        44.05       162.08        50.89        37.25         8.88 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A2NH 
      148.18        79.99        23.34        20.15        31.27        32.05 
TCGA-ER-A3ES TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A 
      247.04        46.98        33.21         6.77        92.98       174.21 
TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC 
       15.72       220.80        27.85        18.77        38.27        34.82 
TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z3 
       36.26       104.42       216.92        48.59       228.59        20.91 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD 
       28.08         7.79        27.72        48.85       357.37        53.52 
TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZK TCGA-FS-A1ZM 
       40.27        15.45         9.70        32.75        23.93       101.26 
TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU 
       74.73       133.55        11.41       148.80        53.16        26.56 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 
       49.48        27.09        27.02        77.82        50.14        66.67 
TCGA-FS-A4F5 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 
       28.73        34.03        26.73        54.41        80.68         0.20 
TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
       22.92        55.59        13.51        19.30         9.90         7.23 
TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 
        2.04        15.78       139.89       117.93        84.72        10.13 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A4U4 
       64.44        62.79        32.48        39.58       121.91        39.35 
TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A8LL TCGA-GN-A9SD 
       10.42        48.89        22.13        50.10        21.37        59.41 
TCGA-HR-A2OG TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O 
        0.23        65.88       368.78       297.90         7.23        18.05 
TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O 
        0.33         0.69       228.16        63.02       121.08         4.01 
TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8JZ 
       69.07       111.09        42.08       219.16       105.04        24.03 
TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO 
       49.05        61.15        15.98        98.89        58.98        67.63 
TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 
       59.77        11.80        32.58        49.51        12.16        35.01 
TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YD-A89C TCGA-YD-A9TA TCGA-YG-AA3O TCGA-YG-AA3P 
       19.73        22.29         6.90        49.18        37.94        14.43 
TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
       27.58        96.99        15.98 

  9P GAIN MUTATED 9P GAIN WILD-TYPE 
            16.37              0.20 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
           268.93            369.93 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
           74.235            50.140 
[1] "16.4 - 268.9 (74.2)" "0.2 - 369.9 (50.1)" 
[1] "hr=" "1.4"
D17V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  9P GAIN MUTATED                    3             1
  9P GAIN WILD-TYPE                 62             4
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  9P GAIN MUTATED                                           2
  9P GAIN WILD-TYPE                                        70
                   vv
clus                REGIONAL LYMPH NODE
  9P GAIN MUTATED                    10
  9P GAIN WILD-TYPE                 205
D17V4, multiclass
                                           clus
vv                                          9P GAIN MUTATED 9P GAIN WILD-TYPE
  DISTANT METASTASIS                                      3                62
  PRIMARY TUMOR                                           1                 4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               2                70
  REGIONAL LYMPH NODE                                    10               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"
                   vv
clus                I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  9P GAIN MUTATED             0       0       4        1        3        0
  9P GAIN WILD-TYPE          12       7      24       17       24       24
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  9P GAIN MUTATED           0         1         0         1          2
  9P GAIN WILD-TYPE        14        18        12        36         13
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  9P GAIN MUTATED            1          1        1
  9P GAIN WILD-TYPE         31         59       19
D17V5, multiclass
             clus
vv            9P GAIN MUTATED 9P GAIN WILD-TYPE
  I OR II NOS               0                12
  STAGE 0                   0                 7
  STAGE I                   4                24
  STAGE IA                  1                17
  STAGE IB                  3                24
  STAGE II                  0                24
  STAGE IIA                 0                14
  STAGE IIB                 1                18
  STAGE IIC                 0                12
  STAGE III                 1                36
  STAGE IIIA                2                13
  STAGE IIIB                1                31
  STAGE IIIC                1                59
  STAGE IV                  1                19
[1] 14  2
[1] TRUE
[1] "dimension of contingency 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       4  6  2  3
  9P GAIN WILD-TYPE    60 66 75 65
D17V6, multiclass
       clus
vv      9P GAIN MUTATED 9P GAIN WILD-TYPE
  T0+T1               4                60
  T2                  6                66
  T3                  2                75
  T4                  3                65
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  9P GAIN MUTATED    11   3   1   1
  9P GAIN WILD-TYPE 158  60  37  48
D17V7, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  N0              11               158
  N1               3                60
  N2               1                37
  N3               1                48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V8, binary
                   cls
clus                  0   1
  9P GAIN MUTATED    15   1
  9P GAIN WILD-TYPE 298  20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED     15    1
  9P GAIN WILD-TYPE  298   20
   clus
vv  9P GAIN MUTATED 9P GAIN WILD-TYPE
  0              15               298
  1               1                20
[1] 2 2
[1] FALSE
D17V9, binary
                   cls
clus                  0   1
  9P GAIN MUTATED     9   4
  9P GAIN WILD-TYPE 123  84
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      9    4
  9P GAIN WILD-TYPE  123   84
     clus
vv    9P GAIN MUTATED 9P GAIN WILD-TYPE
  NO                9               123
  YES               4                84
[1] 2 2
[1] FALSE
D17V10, binary
                   cls
clus                  0   1
  9P GAIN MUTATED     0  16
  9P GAIN WILD-TYPE  44 297
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      0   16
  9P GAIN WILD-TYPE   44  297
     clus
vv    9P GAIN MUTATED 9P GAIN WILD-TYPE
  NO                0                44
  YES              16               297
[1] 2 2
[1] FALSE
D17V11, continuous
D17V12, binary
                   cls
clus                  0   1
  9P GAIN MUTATED     6  10
  9P GAIN WILD-TYPE 129 213
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      6   10
  9P GAIN WILD-TYPE  129  213
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  FEMALE               6               129
  MALE                10               213
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  9P GAIN MUTATED       0                         0    16
  9P GAIN WILD-TYPE     5                         1   328
D17V13, multiclass
                           clus
vv                          9P GAIN MUTATED 9P GAIN WILD-TYPE
  ASIAN                                   0                 5
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  16               328
[1] 3 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     0  16
  9P GAIN WILD-TYPE   7 328
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      0   16
  9P GAIN WILD-TYPE    7  328
                        clus
vv                       9P GAIN MUTATED 9P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 7
  NOT HISPANIC OR LATINO              16               328
[1] 2 2
[1] FALSE

Clustering(18) Variable = 9Q GAIN MUTATION ANALYSIS
D18V1, survival
                   sevent
clus2                 0   1
  9Q GAIN MUTATED     4  10
  9Q GAIN WILD-TYPE 117 108
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               14               225 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               10               108 
$`9Q GAIN MUTATED`
TCGA-D3-A2JB TCGA-D3-A3ML TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A8GM TCGA-EE-A184 
      168.00        13.87        45.70       177.86        70.62        67.50 
TCGA-EE-A3J3 TCGA-ER-A19G TCGA-ER-A2NC TCGA-ER-A2ND TCGA-FR-A44A TCGA-FS-A1Z0 
       67.89       151.46        22.36         4.70       174.21       195.98 
TCGA-FS-A1ZJ TCGA-FS-A4F8 
       36.33       173.19 

$`9Q GAIN WILD-TYPE`
TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
       60.46        12.99        14.83         8.42        15.72        31.89 
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB 
      110.93        49.35       133.25        19.04        76.41        62.60 
TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JD 
       25.64        45.99        62.86        15.75        86.30         7.27 
TCGA-D3-A2JE TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
        9.76       107.61        36.30       171.58        64.83        66.08 
TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE 
       43.53        58.06        46.98       140.98        40.01        59.70 
TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51J 
       16.96         9.34        90.21        23.67       173.85       144.46 
TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GU TCGA-D3-A8GC 
       31.76        62.70        11.34        42.05       124.08        78.21 
TCGA-D3-A8GD TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GP TCGA-D3-A8GR 
       23.61       179.97       120.00        69.53       135.12        36.53 
TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6EC TCGA-D9-A6EG 
       10.78        15.02        16.90        18.44        57.90        22.85 
TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 
       48.66       106.85        31.96       150.61        82.85        32.42 
TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q 
       64.83        58.85        25.12       214.59        14.96         3.91 
TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y 
       33.24        50.07        45.50         6.64        13.15        24.89 
TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A20C TCGA-EE-A20H TCGA-EE-A29B 
       62.37        20.38         0.00        75.55       155.90        75.22 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M 
       76.14        12.99         0.26        44.28        63.12        47.74 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A2 
       27.16        61.12       346.49       185.19       102.38         7.20 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ 
       77.98        26.14       239.11         0.20       189.40        68.65 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP 
       10.62        32.48        18.35        31.00       118.32         0.76 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 
        0.20        71.31        81.99       103.13        15.25         5.75 
TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK 
       23.77       209.79        94.19       171.85        63.25        67.50 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT 
      104.78       145.45       227.01        25.08       143.93        23.51 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
       53.26       124.31       122.73        51.62         4.41        54.51 
TCGA-EE-A3AF TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JI 
        6.28       111.85        45.90         3.35       201.80       152.81 
TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A 
       14.56        34.45         1.58        47.31         7.82         4.54 
TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M 
       53.29        39.81        11.47       150.12        99.06        59.84 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 
       42.48       120.76        49.71        34.95       146.63        47.97 
TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL 
       16.87        10.95       173.29        55.82        15.48        32.05 
TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FS-A1YW TCGA-FS-A1YY 
      209.23        26.20         5.65        10.06       171.78        49.74 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF 
        8.35        27.62       312.07        32.78        35.90        12.92 
TCGA-FS-A1ZG TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU 
        7.82        78.61       130.95       136.27        35.28         4.47 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F9 
       23.21         5.29         3.06        30.90        66.67        13.28 
TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
       80.68        55.59        11.54        19.30         9.90         6.05 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 
        1.91        53.29       117.93        84.72        17.06        42.48 
TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-GN-A8LK TCGA-GN-A9SD 
        7.59       120.53        34.49        46.92        43.23        59.41 
TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 TCGA-W3-A824 
       85.05       297.01         7.23        18.05         0.33       174.12 
TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1V TCGA-W3-AA1W 
        1.97       120.07        44.05        79.99         8.09       185.13 
TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO 
       92.84         1.15        59.64        62.99        12.69        19.00 
TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 
       59.44        10.95        48.39         1.94        26.60        16.64 
TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-Z2-AA3S 
       15.65        28.21        91.23 

  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
              4.7               0.0 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
           195.98            346.49 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
           69.255            45.500 
[1] "4.7 - 196.0 (69.3)" "0.0 - 346.5 (45.5)"
[1] "hr=" "1.1"
D18V2, survival
                   sevent
clus2                 0   1
  9Q GAIN MUTATED     7  14
  9Q GAIN WILD-TYPE 162 166
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               21               328 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               14               166 
$`9Q GAIN MUTATED`
TCGA-D3-A1Q9 TCGA-D3-A2JB TCGA-D3-A3ML TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS 
       31.59       168.00        13.87       135.75       178.32        18.18 
TCGA-D3-A8GM TCGA-EE-A184 TCGA-EE-A2M5 TCGA-EE-A2MD TCGA-EE-A3J3 TCGA-ER-A19G 
      107.15        68.15        21.67        47.28       172.18       268.93 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NF TCGA-FR-A44A TCGA-FS-A1YX TCGA-FS-A1Z0 
       43.82        23.34        16.37       174.21        48.59       202.65 
TCGA-FS-A1ZJ TCGA-FS-A4F8 TCGA-YD-A9TA 
       47.38       174.84        49.18 

$`9Q GAIN WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q3 
       17.03        66.48        12.99        14.93        16.57        16.67 
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA 
      112.04       112.57        71.80       133.25        28.08        90.90 
TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA 
       95.74        43.43       103.10        65.49        23.77       115.53 
TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH 
       86.76        11.87        27.65        62.07       113.52        42.08 
TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ 
       12.10       171.58        66.48        66.08        59.57       130.72 
TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE 
       58.06        46.98        46.32       166.52        86.93        60.23 
TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E 
       24.53         9.34       103.59        39.75        45.30       174.84 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R 
       55.73        56.35       145.12        32.94        22.62        63.81 
TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GO TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GC 
       26.89       125.79       137.92       125.19        30.84        79.59 
TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL 
       23.61        26.43        58.52       241.38       170.20        89.13 
TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A148 
      161.00       152.75        29.06       129.63       117.17       151.53 
TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       54.67         3.65         7.10        18.12        15.39        22.29 
TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV 
       18.44         9.90        25.18        66.25        22.95        48.89 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 
       36.03       117.21        20.38       194.83       176.55        35.93 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
      107.34        61.18        53.92        65.92        23.44        68.09 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R 
       28.60        10.49       215.44        15.68        13.87        10.36 
TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV 
       20.35        68.25        54.02        17.29        52.01         7.04 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 
       24.89        29.82        27.22         8.65        94.98        33.73 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F 
       14.70        26.89         4.96       133.81       151.27        91.56 
TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D 
      168.26        13.55        63.35        85.08        78.97        13.97 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N 
       63.78        72.07        64.64         2.60        56.84        18.61 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V 
       56.42        66.74        14.47        61.28       369.93        25.87 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 
      195.02        17.92        46.82       102.90        36.82        39.29 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
       86.14        59.28        67.43       340.14       161.03       208.04 
TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN 
       48.72       107.38        54.74        79.66        75.48       102.12 
TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU 
      126.81        13.91        42.77        81.21        44.88        94.82 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2ME TCGA-EE-A2MF 
      129.27        28.83        19.76        61.51       103.27       268.73 
TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML 
      103.20        16.96       204.66        96.23       158.63       216.66 
TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS 
      167.90        47.54       248.65        43.23       134.40       162.48 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
       71.21        53.26       124.31       122.73        51.62        28.77 
TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J5 
       54.51        13.81        41.59       138.81       127.20        36.95 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE 
       64.08        34.32        53.19       201.80        27.35        51.35 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
      109.58       152.81        31.40        35.44        13.94        50.76 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E 
        9.17        77.75        98.40        48.89        12.59        13.02 
TCGA-ER-A19F TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
       26.37       152.35         6.44       131.51        61.05        44.05 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 
      162.08        50.89        37.25         8.88       148.18        79.99 
TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
       20.15        31.27        32.05       247.04        80.32        46.98 
TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 
       33.21         6.77        92.98        15.72       220.80        27.85 
TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW 
       18.77        38.27        34.82        36.26       104.42       216.92 
TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB 
      228.59        20.91        28.08         7.79        27.72        48.85 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH 
      357.37        53.52        40.27        15.45         9.70        32.75 
TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS 
       23.93       101.26        74.73       133.55        11.41       148.80 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 
       53.16        26.56        49.48        27.09        27.02        77.82 
TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC 
       50.14        66.67        28.73        34.03        26.73        54.41 
TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
       80.68         0.20        22.92        55.59        13.51        19.30 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 
        9.90         7.23         2.04        15.78       139.89       117.93 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
       84.72        10.13        64.44        62.79        32.48        39.58 
TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK 
      121.91        39.35        10.42        48.89        22.13        50.10 
TCGA-GN-A8LL TCGA-GN-A9SD TCGA-HR-A2OG TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X 
       21.37        59.41         0.23        65.88       368.78       297.90 
TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 
        7.23        18.05         0.33         0.69       228.16        63.02 
TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1V TCGA-W3-AA1W 
      121.08         4.01        69.07       111.09        42.08       219.16 
TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZM 
      105.04        24.03        49.05        61.15        15.98        98.89 
TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-A8ZY 
       58.98        67.63        59.77        11.80        32.58        49.51 
TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YD-A89C TCGA-YG-AA3O 
       12.16        35.01        19.73        22.29         6.90        37.94 
TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
       14.43        27.58        96.99        15.98 

  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
            13.87              0.20 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
           268.93            369.93 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
            49.18             51.12 
[1] "13.9 - 268.9 (49.2)" "0.2 - 369.9 (51.1)" 
[1] "hr=" "1"  
D18V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  9Q GAIN MUTATED                    5             1
  9Q GAIN WILD-TYPE                 60             4
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  9Q GAIN MUTATED                                           2
  9Q GAIN WILD-TYPE                                        70
                   vv
clus                REGIONAL LYMPH NODE
  9Q GAIN MUTATED                    13
  9Q GAIN WILD-TYPE                 202
D18V4, multiclass
                                           clus
vv                                          9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  DISTANT METASTASIS                                      5                60
  PRIMARY TUMOR                                           1                 4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               2                70
  REGIONAL LYMPH NODE                                    13               202
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  9Q GAIN MUTATED             0       1       5        1        3        2
  9Q GAIN WILD-TYPE          12       6      23       17       24       22
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  9Q GAIN MUTATED           0         1         0         1          1
  9Q GAIN WILD-TYPE        14        18        12        36         14
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  9Q GAIN MUTATED            1          2        1
  9Q GAIN WILD-TYPE         31         58       19
D18V5, multiclass
             clus
vv            9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  I OR II NOS               0                12
  STAGE 0                   1                 6
  STAGE I                   5                23
  STAGE IA                  1                17
  STAGE IB                  3                24
  STAGE II                  2                22
  STAGE IIA                 0                14
  STAGE IIB                 1                18
  STAGE IIC                 0                12
  STAGE III                 1                36
  STAGE IIIA                1                14
  STAGE IIIB                1                31
  STAGE IIIC                2                58
  STAGE IV                  1                19
[1] 14  2
[1] TRUE
[1] "dimension of contingency 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       6  6  4  2
  9Q GAIN WILD-TYPE    58 66 73 66
D18V6, multiclass
       clus
vv      9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  T0+T1               6                58
  T2                  6                66
  T3                  4                73
  T4                  2                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
  9Q GAIN MUTATED    14   2   2   2
  9Q GAIN WILD-TYPE 155  61  36  47
D18V7, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  N0              14               155
  N1               2                61
  N2               2                36
  N3               2                47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V8, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED    19   1
  9Q GAIN WILD-TYPE 294  20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     19    1
  9Q GAIN WILD-TYPE  294   20
   clus
vv  9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  0              19               294
  1               1                20
[1] 2 2
[1] FALSE
D18V9, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED    11   4
  9Q GAIN WILD-TYPE 121  84
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     11    4
  9Q GAIN WILD-TYPE  121   84
     clus
vv    9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  NO               11               121
  YES               4                84
[1] 2 2
[1] FALSE
D18V10, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED     0  21
  9Q GAIN WILD-TYPE  44 292
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      0   21
  9Q GAIN WILD-TYPE   44  292
     clus
vv    9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  NO                0                44
  YES              21               292
[1] 2 2
[1] FALSE
D18V11, continuous
D18V12, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED     9  12
  9Q GAIN WILD-TYPE 126 211
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      9   12
  9Q GAIN WILD-TYPE  126  211
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  FEMALE               9               126
  MALE                12               211
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  9Q GAIN MUTATED       0                         1    20
  9Q GAIN WILD-TYPE     5                         0   324
D18V13, multiclass
                           clus
vv                          9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  ASIAN                                   0                 5
  BLACK OR AFRICAN AMERICAN               1                 0
  WHITE                                  20               324
[1] 3 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     0  21
  9Q GAIN WILD-TYPE   7 323
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      0   21
  9Q GAIN WILD-TYPE    7  323
                        clus
vv                       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 7
  NOT HISPANIC OR LATINO              21               323
[1] 2 2
[1] FALSE

Clustering(19) Variable = 10P GAIN MUTATION ANALYSIS
D19V1, survival
                    sevent
clus2                  0   1
  10P GAIN MUTATED     3   6
  10P GAIN WILD-TYPE 118 112
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 9                230 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 6                112 
$`10P GAIN MUTATED`
TCGA-D3-A3C6 TCGA-D3-A3MR TCGA-D3-A8GM TCGA-D9-A6EC TCGA-DA-A1HY TCGA-EE-A29D 
       58.06        90.21        70.62        57.90       106.85        12.99 
TCGA-ER-A19C TCGA-ER-A19M TCGA-QB-AA9O 
       39.81        59.84        18.05 

$`10P GAIN WILD-TYPE`
TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
       60.46        12.99        14.83         8.42        15.72        31.89 
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB 
      110.93        49.35       133.25        19.04        76.41        62.60 
TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC 
       25.64        45.99        62.86        15.75       168.00        86.30 
TCGA-D3-A2JD TCGA-D3-A2JE TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN 
        7.27         9.76       107.61        36.30       171.58        64.83 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE 
       66.08        43.53        46.98       140.98        40.01        59.70 
TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51J 
       16.96        13.87         9.34        23.67       173.85       144.46 
TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR 
       31.76        62.70        11.34        42.05        45.70       177.86 
TCGA-D3-A5GU TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL 
      124.08        78.21        23.61       179.97       120.00        69.53 
TCGA-D3-A8GP TCGA-D3-A8GR TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 
      135.12        36.53        10.78        15.02        16.90        18.44 
TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 
       22.85        48.66        31.96       150.61        82.85        32.42 
TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q 
       64.83        58.85        25.12       214.59        14.96         3.91 
TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y 
       33.24        50.07        45.50         6.64        13.15        24.89 
TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A184 TCGA-EE-A20C TCGA-EE-A20H 
       62.37        20.38         0.00        67.50        75.55       155.90 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M 
       75.22        76.14         0.26        44.28        63.12        47.74 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A2 
       27.16        61.12       346.49       185.19       102.38         7.20 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ 
       77.98        26.14       239.11         0.20       189.40        68.65 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP 
       10.62        32.48        18.35        31.00       118.32         0.76 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 
        0.20        71.31        81.99       103.13        15.25         5.75 
TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK 
       23.77       209.79        94.19       171.85        63.25        67.50 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT 
      104.78       145.45       227.01        25.08       143.93        23.51 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
       53.26       124.31       122.73        51.62         4.41        54.51 
TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB 
        6.28        67.89       111.85        45.90         3.35       201.80 
TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 
      152.81        14.56        34.45         1.58        47.31         7.82 
TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L 
        4.54        53.29        11.47       151.46       150.12        99.06 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 
       42.48       120.76        49.71        34.95       146.63        47.97 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET 
       22.36         4.70        16.87        10.95       173.29        55.82 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7UA 
       15.48        32.05       174.21       209.23        26.20         5.65 
TCGA-FR-A8YC TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 
       10.06       171.78        49.74       195.98         8.35        27.62 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZJ 
      312.07        32.78        35.90        12.92         7.82        36.33 
TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW 
       78.61       130.95       136.27        35.28         4.47        23.21 
TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 
        5.29         3.06        30.90        66.67       173.19        13.28 
TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
       80.68        55.59        11.54        19.30         9.90         6.05 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 
        1.91        53.29       117.93        84.72        17.06        42.48 
TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-GN-A8LK TCGA-GN-A9SD 
        7.59       120.53        34.49        46.92        43.23        59.41 
TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A825 
       85.05       297.01         7.23         0.33       174.12         1.97 
TCGA-W3-A828 TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 
      120.07        44.05        79.99         8.09       185.13        92.84 
TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ 
        1.15        59.64        62.99        12.69        19.00        59.44 
TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 
       10.95        48.39         1.94        26.60        16.64        15.65 
TCGA-YG-AA3O TCGA-Z2-AA3S 
       28.21        91.23 

  10P GAIN MUTATED 10P GAIN WILD-TYPE 
             12.99               0.00 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
            106.85             346.49 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
             58.06              45.80 
[1] "13.0 - 106.8 (58.1)" "0.0 - 346.5 (45.8)" 
[1] "hr=" "1.6"
D19V2, survival
                    sevent
clus2                  0   1
  10P GAIN MUTATED     6   6
  10P GAIN WILD-TYPE 163 174
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                12                337 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 6                174 
$`10P GAIN MUTATED`
TCGA-D3-A3C6 TCGA-D3-A3MR TCGA-D3-A51N TCGA-D3-A8GM TCGA-D9-A6EC TCGA-DA-A1HY 
       58.06       103.59        22.62       107.15        66.25       117.21 
TCGA-EE-A29D TCGA-ER-A19C TCGA-ER-A19M TCGA-FW-A3I3 TCGA-GF-A6C9 TCGA-QB-AA9O 
       13.97        48.89        61.05         0.20        15.78        18.05 

$`10P GAIN WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q3 
       17.03        66.48        12.99        14.93        16.57        16.67 
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 
      112.04       112.57        71.80       133.25        28.08        31.59 
TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 
       90.90        95.74        43.43       103.10        65.49        23.77 
TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JE TCGA-D3-A2JF 
      115.53       168.00        86.76        11.87        27.65        62.07 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
      113.52        42.08        12.10       171.58        66.48        66.08 
TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC 
       59.57       130.72        46.98        46.32       166.52        86.93 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MU TCGA-D3-A3MV 
       60.23        24.53        13.87         9.34        39.75        45.30 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R 
      174.84        55.73        56.35       145.12        32.94        63.81 
TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       26.89       125.79       135.75       137.92       178.32        18.18 
TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GI 
      125.19        30.84        79.59        23.61        26.43        58.52 
TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GQ 
      241.38       170.20        89.13       161.00       152.75        29.06 
TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX 
      129.63       117.17       151.53        54.67         3.65         7.10 
TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EA 
       18.12        15.39        22.29        18.44         9.90        25.18 
TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 
       22.95        48.89        36.03        20.38       194.83       176.55 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB 
       35.93       107.34        61.18        53.92        65.92        23.44 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q 
       68.09        28.60        10.49       215.44        15.68        13.87 
TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN 
       10.36        20.35        68.25        54.02        17.29        52.01 
TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 
        7.04        24.89        29.82        27.22         8.65        94.98 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B 
       33.73        14.70        26.89        68.15         4.96       133.81 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
      151.27        91.56       168.26        13.55        63.35        85.08 
TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M 
       78.97        63.78        72.07        64.64         2.60        56.84 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T 
       18.61        56.42        66.74        14.47        61.28       369.93 
TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
       25.87       195.02        17.92        46.82       102.90        36.82 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE 
       39.29        86.14        59.28        67.43       340.14       161.03 
TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
      208.04        48.72       107.38        54.74        79.66        75.48 
TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT 
      102.12       126.81        13.91        42.77        81.21        44.88 
TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC 
       94.82        21.67       129.27        28.83        19.76        61.51 
TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
       47.28       103.27       268.73       103.20        16.96       204.66 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP 
       96.23       158.63       216.66       167.90        47.54       248.65 
TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA 
       43.23       134.40       162.48        71.21        53.26       124.31 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG 
      122.73        51.62        28.77        54.51        13.81        41.59 
TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 
      138.81       172.18       127.20        36.95        64.08        34.32 
TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI 
       53.19       201.80        27.35        51.35       109.58       152.81 
TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A 
       31.40        35.44        13.94        50.76         9.17        77.75 
TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H 
       98.40        12.59        13.02        26.37       268.93       152.35 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S 
        6.44       131.51        44.05       162.08        50.89        37.25 
TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
        8.88       148.18        79.99        43.82        23.34        20.15 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
       16.37        31.27        32.05       247.04        80.32        46.98 
TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 
       33.21         6.77        92.98       174.21        15.72       220.80 
TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE 
       27.85        18.77        38.27        34.82        36.26       104.42 
TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 
      216.92        48.59       228.59       202.65        20.91        28.08 
TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE 
        7.79        27.72        48.85       357.37        53.52        40.27 
TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM 
       15.45         9.70        32.75        47.38        23.93       101.26 
TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU 
       74.73       133.55        11.41       148.80        53.16        26.56 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 
       49.48        27.09        27.02        77.82        50.14        66.67 
TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD 
       28.73       174.84        34.03        26.73        54.41        80.68 
TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
       22.92        55.59        13.51        19.30         9.90         7.23 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 
        2.04       139.89       117.93        84.72        10.13        64.44 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 
       62.79        32.48        39.58       121.91        39.35        10.42 
TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A8LL TCGA-GN-A9SD TCGA-HR-A2OG 
       48.89        22.13        50.10        21.37        59.41         0.23 
TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 
       65.88       368.78       297.90         7.23         0.33         0.69 
TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1Q TCGA-W3-AA1R 
      228.16        63.02       121.08         4.01        69.07       111.09 
TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K5 
       42.08       219.16       105.04        24.03        49.05        61.15 
TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT 
       15.98        98.89        58.98        67.63        59.77        11.80 
TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 
       32.58        49.51        12.16        35.01        19.73        22.29 
TCGA-YD-A89C TCGA-YD-A9TA TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S 
        6.90        49.18        37.94        14.43        27.58        96.99 
TCGA-Z2-AA3V 
       15.98 

  10P GAIN MUTATED 10P GAIN WILD-TYPE 
              0.20               0.23 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
            117.21             369.93 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
            53.475             50.890 
[1] "0.2 - 117.2 (53.5)" "0.2 - 369.9 (50.9)"
[1] "hr=" "1.3"
D19V3, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  10P GAIN MUTATED                    2             1
  10P GAIN WILD-TYPE                 63             4
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  10P GAIN MUTATED                                           1
  10P GAIN WILD-TYPE                                        71
                    vv
clus                 REGIONAL LYMPH NODE
  10P GAIN MUTATED                     8
  10P GAIN WILD-TYPE                 207
D19V4, multiclass
                                           clus
vv                                          10P GAIN MUTATED 10P GAIN WILD-TYPE
  DISTANT METASTASIS                                       2                 63
  PRIMARY TUMOR                                            1                  4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                1                 71
  REGIONAL LYMPH NODE                                      8                207
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  10P GAIN MUTATED             0       0       1        0        2        0
  10P GAIN WILD-TYPE          12       7      27       18       25       24
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  10P GAIN MUTATED           0         1         0         1          1
  10P GAIN WILD-TYPE        14        18        12        36         14
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  10P GAIN MUTATED            1          3        2
  10P GAIN WILD-TYPE         31         57       18
D19V5, multiclass
             clus
vv            10P GAIN MUTATED 10P GAIN WILD-TYPE
  I OR II NOS                0                 12
  STAGE 0                    0                  7
  STAGE I                    1                 27
  STAGE IA                   0                 18
  STAGE IB                   2                 25
  STAGE II                   0                 24
  STAGE IIA                  0                 14
  STAGE IIB                  1                 18
  STAGE IIC                  0                 12
  STAGE III                  1                 36
  STAGE IIIA                 1                 14
  STAGE IIIB                 1                 31
  STAGE IIIC                 3                 57
  STAGE IV                   2                 18
[1] 14  2
[1] TRUE
[1] "dimension of contingency 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       2  4  3  1
  10P GAIN WILD-TYPE    62 68 74 67
D19V6, multiclass
       clus
vv      10P GAIN MUTATED 10P GAIN WILD-TYPE
  T0+T1                2                 62
  T2                   4                 68
  T3                   3                 74
  T4                   1                 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
  10P GAIN MUTATED     4   3   0   3
  10P GAIN WILD-TYPE 165  60  38  46
D19V7, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  N0                4                165
  N1                3                 60
  N2                0                 38
  N3                3                 46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V8, binary
                    cls
clus                   0   1
  10P GAIN MUTATED     9   2
  10P GAIN WILD-TYPE 304  19
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      9    2
  10P GAIN WILD-TYPE  304   19
   clus
vv  10P GAIN MUTATED 10P GAIN WILD-TYPE
  0                9                304
  1                2                 19
[1] 2 2
[1] FALSE
D19V9, binary
                    cls
clus                   0   1
  10P GAIN MUTATED     4   3
  10P GAIN WILD-TYPE 128  85
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      4    3
  10P GAIN WILD-TYPE  128   85
     clus
vv    10P GAIN MUTATED 10P GAIN WILD-TYPE
  NO                 4                128
  YES                3                 85
[1] 2 2
[1] FALSE
D19V10, binary
                    cls
clus                   0   1
  10P GAIN MUTATED     5   7
  10P GAIN WILD-TYPE  39 306
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      5    7
  10P GAIN WILD-TYPE   39  306
     clus
vv    10P GAIN MUTATED 10P GAIN WILD-TYPE
  NO                 5                 39
  YES                7                306
[1] 2 2
[1] FALSE
D19V11, continuous
D19V12, binary
                    cls
clus                   0   1
  10P GAIN MUTATED     3   9
  10P GAIN WILD-TYPE 132 214
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      3    9
  10P GAIN WILD-TYPE  132  214
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  FEMALE                3                132
  MALE                  9                214
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  10P GAIN MUTATED       0                         0    12
  10P GAIN WILD-TYPE     5                         1   332
D19V13, multiclass
                           clus
vv                          10P GAIN MUTATED 10P GAIN WILD-TYPE
  ASIAN                                    0                  5
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   12                332
[1] 3 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     0  12
  10P GAIN WILD-TYPE   7 332
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      0   12
  10P GAIN WILD-TYPE    7  332
                        clus
vv                       10P GAIN MUTATED 10P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  7
  NOT HISPANIC OR LATINO               12                332
[1] 2 2
[1] FALSE

Clustering(20) Variable = 10Q GAIN MUTATION ANALYSIS
D20V1, survival
                    sevent
clus2                  0   1
  10Q GAIN MUTATED     2   1
  10Q GAIN WILD-TYPE 119 117
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 3                236 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 1                117 
$`10Q GAIN MUTATED`
TCGA-DA-A1HY TCGA-ER-A3ET TCGA-QB-AA9O 
      106.85        55.82        18.05 

$`10Q GAIN WILD-TYPE`
TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
       60.46        12.99        14.83         8.42        15.72        31.89 
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB 
      110.93        49.35       133.25        19.04        76.41        62.60 
TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC 
       25.64        45.99        62.86        15.75       168.00        86.30 
TCGA-D3-A2JD TCGA-D3-A2JE TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN 
        7.27         9.76       107.61        36.30       171.58        64.83 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CC 
       66.08        43.53        58.06        46.98       140.98        40.01 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU 
       59.70        16.96        13.87         9.34        90.21        23.67 
TCGA-D3-A51E TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL 
      173.85       144.46        31.76        62.70        11.34        42.05 
TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GJ 
       45.70       177.86       124.08        78.21        23.61       179.97 
TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GP TCGA-D3-A8GR TCGA-D9-A1X3 
      120.00        69.53        70.62       135.12        36.53        10.78 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV 
       15.02        16.90        18.44        57.90        22.85        48.66 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC 
       31.96       150.61        82.85        32.42        64.83        58.85 
TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5SG TCGA-EB-A5SH 
       25.12       214.59        14.96         3.91        33.24        50.07 
TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A181 
       45.50         6.64        13.15        24.89        62.37        20.38 
TCGA-EE-A182 TCGA-EE-A184 TCGA-EE-A20C TCGA-EE-A20H TCGA-EE-A29B TCGA-EE-A29C 
        0.00        67.50        75.55       155.90        75.22        76.14 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P 
       12.99         0.26        44.28        63.12        47.74        27.16 
TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 
       61.12       346.49       185.19       102.38         7.20        77.98 
TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK 
       26.14       239.11         0.20       189.40        68.65        10.62 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR 
       32.48        18.35        31.00       118.32         0.76         0.20 
TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC 
       71.31        81.99       103.13        15.25         5.75        23.77 
TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML 
      209.79        94.19       171.85        63.25        67.50       104.78 
TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU 
      145.45       227.01        25.08       143.93        23.51        53.26 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
      124.31       122.73        51.62         4.41        54.51         6.28 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JI 
       67.89       111.85        45.90         3.35       201.80       152.81 
TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A 
       14.56        34.45         1.58        47.31         7.82         4.54 
TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L 
       53.29        39.81        11.47       151.46       150.12        99.06 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W 
       59.84        42.48       120.76        49.71        34.95       146.63 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A3ES 
       47.97        22.36         4.70        16.87        10.95       173.29 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7UA 
       15.48        32.05       174.21       209.23        26.20         5.65 
TCGA-FR-A8YC TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 
       10.06       171.78        49.74       195.98         8.35        27.62 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZJ 
      312.07        32.78        35.90        12.92         7.82        36.33 
TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW 
       78.61       130.95       136.27        35.28         4.47        23.21 
TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 
        5.29         3.06        30.90        66.67       173.19        13.28 
TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
       80.68        55.59        11.54        19.30         9.90         6.05 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 
        1.91        53.29       117.93        84.72        17.06        42.48 
TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-GN-A8LK TCGA-GN-A9SD 
        7.59       120.53        34.49        46.92        43.23        59.41 
TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A825 
       85.05       297.01         7.23         0.33       174.12         1.97 
TCGA-W3-A828 TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 
      120.07        44.05        79.99         8.09       185.13        92.84 
TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ 
        1.15        59.64        62.99        12.69        19.00        59.44 
TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 
       10.95        48.39         1.94        26.60        16.64        15.65 
TCGA-YG-AA3O TCGA-Z2-AA3S 
       28.21        91.23 

  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
             18.05               0.00 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
            106.85             346.49 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
            55.820             45.945 
[1] "18.1 - 106.8 (55.8)" "0.0 - 346.5 (45.9)" 
[1] "hr=" "1.4"
D20V2, survival
                    sevent
clus2                  0   1
  10Q GAIN MUTATED     2   1
  10Q GAIN WILD-TYPE 167 179
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 3                346 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 1                179 
$`10Q GAIN MUTATED`
TCGA-DA-A1HY TCGA-ER-A3ET TCGA-QB-AA9O 
      117.21        80.32        18.05 

$`10Q GAIN WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q3 
       17.03        66.48        12.99        14.93        16.57        16.67 
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 
      112.04       112.57        71.80       133.25        28.08        31.59 
TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 
       90.90        95.74        43.43       103.10        65.49        23.77 
TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JE TCGA-D3-A2JF 
      115.53       168.00        86.76        11.87        27.65        62.07 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
      113.52        42.08        12.10       171.58        66.48        66.08 
TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB 
       59.57       130.72        58.06        46.98        46.32       166.52 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR 
       86.93        60.23        24.53        13.87         9.34       103.59 
TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J 
       39.75        45.30       174.84        55.73        56.35       145.12 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN 
       32.94        22.62        63.81        26.89       125.79       135.75 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GC 
      137.92       178.32        18.18       125.19        30.84        79.59 
TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL 
       23.61        26.43        58.52       241.38       170.20        89.13 
TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS 
      107.15       161.00       152.75        29.06       129.63       117.17 
TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A1X3 TCGA-D9-A3Z1 
      151.53        54.67         3.65         7.10        18.12        15.39 
TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG 
       22.29        18.44         9.90        25.18        66.25        22.95 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 
       48.89        36.03        20.38       194.83       176.55        35.93 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
      107.34        61.18        53.92        65.92        23.44        68.09 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R 
       28.60        10.49       215.44        15.68        13.87        10.36 
TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV 
       20.35        68.25        54.02        17.29        52.01         7.04 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 
       24.89        29.82        27.22         8.65        94.98        33.73 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C 
       14.70        26.89        68.15         4.96       133.81       151.27 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C 
       91.56       168.26        13.55        63.35        85.08        78.97 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M 
       13.97        63.78        72.07        64.64         2.60        56.84 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T 
       18.61        56.42        66.74        14.47        61.28       369.93 
TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
       25.87       195.02        17.92        46.82       102.90        36.82 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE 
       39.29        86.14        59.28        67.43       340.14       161.03 
TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
      208.04        48.72       107.38        54.74        79.66        75.48 
TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT 
      102.12       126.81        13.91        42.77        81.21        44.88 
TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC 
       94.82        21.67       129.27        28.83        19.76        61.51 
TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
       47.28       103.27       268.73       103.20        16.96       204.66 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP 
       96.23       158.63       216.66       167.90        47.54       248.65 
TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA 
       43.23       134.40       162.48        71.21        53.26       124.31 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG 
      122.73        51.62        28.77        54.51        13.81        41.59 
TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 
      138.81       172.18       127.20        36.95        64.08        34.32 
TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI 
       53.19       201.80        27.35        51.35       109.58       152.81 
TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A 
       31.40        35.44        13.94        50.76         9.17        77.75 
TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G 
       98.40        48.89        12.59        13.02        26.37       268.93 
TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P 
      152.35         6.44       131.51        61.05        44.05       162.08 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
       50.89        37.25         8.88       148.18        79.99        43.82 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES 
       23.34        20.15        16.37        31.27        32.05       247.04 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       46.98        33.21         6.77        92.98       174.21        15.72 
TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD 
      220.80        27.85        18.77        38.27        34.82        36.26 
TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
      104.42       216.92        48.59       228.59       202.65        20.91 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD 
       28.08         7.79        27.72        48.85       357.37        53.52 
TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK 
       40.27        15.45         9.70        32.75        47.38        23.93 
TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT 
      101.26        74.73       133.55        11.41       148.80        53.16 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 
       26.56        49.48        27.09        27.02        77.82        50.14 
TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC 
       66.67        28.73       174.84        34.03        26.73        54.41 
TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
       80.68         0.20        22.92        55.59        13.51        19.30 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 
        9.90         7.23         2.04        15.78       139.89       117.93 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
       84.72        10.13        64.44        62.79        32.48        39.58 
TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK 
      121.91        39.35        10.42        48.89        22.13        50.10 
TCGA-GN-A8LL TCGA-GN-A9SD TCGA-HR-A2OG TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X 
       21.37        59.41         0.23        65.88       368.78       297.90 
TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 
        7.23         0.33         0.69       228.16        63.02       121.08 
TCGA-W3-AA1O TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 
        4.01        69.07       111.09        42.08       219.16       105.04 
TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN 
       24.03        49.05        61.15        15.98        98.89        58.98 
TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AA9Y 
       67.63        59.77        11.80        32.58        49.51        12.16 
TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YD-A89C TCGA-YD-A9TA TCGA-YG-AA3O 
       35.01        19.73        22.29         6.90        49.18        37.94 
TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
       14.43        27.58        96.99        15.98 

  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
             18.05               0.20 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
            117.21             369.93 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
            80.320             50.825 
[1] "18.1 - 117.2 (80.3)" "0.2 - 369.9 (50.8)" 
[1] "hr=" "1.6"
D20V3, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  10Q GAIN MUTATED                    0             0
  10Q GAIN WILD-TYPE                 65             5
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  10Q GAIN MUTATED                                           1
  10Q GAIN WILD-TYPE                                        71
                    vv
clus                 REGIONAL LYMPH NODE
  10Q GAIN MUTATED                     2
  10Q GAIN WILD-TYPE                 213
D20V4, multiclass
                                           clus
vv                                          10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  DISTANT METASTASIS                                       0                 65
  PRIMARY TUMOR                                            0                  5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                1                 71
  REGIONAL LYMPH NODE                                      2                213
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  10Q GAIN MUTATED             0       0       0        0        0        0
  10Q GAIN WILD-TYPE          12       7      28       18       27       24
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  10Q GAIN MUTATED           0         0         0         0          1
  10Q GAIN WILD-TYPE        14        19        12        37         14
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  10Q GAIN MUTATED            0          2        0
  10Q GAIN WILD-TYPE         32         58       20
D20V5, multiclass
             clus
vv            10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  I OR II NOS                0                 12
  STAGE 0                    0                  7
  STAGE I                    0                 28
  STAGE IA                   0                 18
  STAGE IB                   0                 27
  STAGE II                   0                 24
  STAGE IIA                  0                 14
  STAGE IIB                  0                 19
  STAGE IIC                  0                 12
  STAGE III                  0                 37
  STAGE IIIA                 1                 14
  STAGE IIIB                 0                 32
  STAGE IIIC                 2                 58
  STAGE IV                   0                 20
[1] 14  2
[1] TRUE
[1] "dimension of contingency 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       0  1  1  0
  10Q GAIN WILD-TYPE    64 71 76 68
D20V6, multiclass
[1] "Remove cluster labels:" "10Q GAIN MUTATED"      
clus
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 2                279 
        TCGA-3N-A9WB         TCGA-3N-A9WC         TCGA-3N-A9WD 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BF-AAP0         TCGA-D3-A1Q1         TCGA-D3-A1Q3 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q4         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q8         TCGA-D3-A1Q9         TCGA-D3-A1QA 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D3-A1QB         TCGA-D3-A2J6         TCGA-D3-A2J7 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D3-A2J8         TCGA-D3-A2J9         TCGA-D3-A2JA 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D3-A2JC         TCGA-D3-A2JD         TCGA-D3-A2JF 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D3-A2JG         TCGA-D3-A2JH         TCGA-D3-A2JK 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D3-A2JN         TCGA-D3-A2JP         TCGA-D3-A3BZ 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D3-A3C6         TCGA-D3-A3C7         TCGA-D3-A3CB 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D3-A3CC         TCGA-D3-A3CE         TCGA-D3-A3CF 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D3-A3ML         TCGA-D3-A3MR         TCGA-D3-A3MU 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D3-A3MV         TCGA-D3-A51E         TCGA-D3-A51F 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D3-A51H         TCGA-D3-A51J         TCGA-D3-A51N 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D3-A51R         TCGA-D3-A51T         TCGA-D3-A5GL 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D3-A5GN         TCGA-D3-A5GO         TCGA-D3-A5GR 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D3-A5GS         TCGA-D3-A5GU         TCGA-D3-A8GB 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D3-A8GD         TCGA-D3-A8GI         TCGA-D3-A8GJ 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D3-A8GK         TCGA-D3-A8GL         TCGA-D3-A8GM 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D3-A8GO         TCGA-D3-A8GP         TCGA-D3-A8GQ 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D3-A8GS         TCGA-D9-A1JW         TCGA-D9-A1X3 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D9-A3Z1         TCGA-D9-A3Z3         TCGA-D9-A4Z6 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D9-A6E9         TCGA-D9-A6EA         TCGA-D9-A6EC 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D9-A6EG         TCGA-DA-A1HV         TCGA-DA-A1HW 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I1         TCGA-DA-A1I2 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DA-A1I4         TCGA-DA-A1I5         TCGA-DA-A1I7 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IA         TCGA-DA-A1IB 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DA-A1IC         TCGA-DA-A3F2         TCGA-DA-A3F3 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EB-A5KH 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EB-A5SH         TCGA-EB-A5UN         TCGA-EB-A5VV 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EE-A17X         TCGA-EE-A17Y         TCGA-EE-A17Z 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EE-A180         TCGA-EE-A181         TCGA-EE-A182 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EE-A184         TCGA-EE-A185         TCGA-EE-A20B 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EE-A29B         TCGA-EE-A29C         TCGA-EE-A29D 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EE-A29E         TCGA-EE-A29G         TCGA-EE-A29H 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29M         TCGA-EE-A29P 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EE-A29Q         TCGA-EE-A29R         TCGA-EE-A29S 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EE-A29V         TCGA-EE-A29X         TCGA-EE-A2A0 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-EE-A2GB         TCGA-EE-A2GC 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EE-A2GD         TCGA-EE-A2GE         TCGA-EE-A2GH 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EE-A2GI         TCGA-EE-A2GJ         TCGA-EE-A2GK 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EE-A2GL         TCGA-EE-A2GM         TCGA-EE-A2GN 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EE-A2GO         TCGA-EE-A2GP         TCGA-EE-A2GR 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EE-A2GS         TCGA-EE-A2GT         TCGA-EE-A2GU 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EE-A2M5         TCGA-EE-A2M6         TCGA-EE-A2M7 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EE-A2M8         TCGA-EE-A2MC         TCGA-EE-A2MD 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EE-A2ME         TCGA-EE-A2MF         TCGA-EE-A2MG 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EE-A2MH         TCGA-EE-A2MI         TCGA-EE-A2MJ 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EE-A2MK         TCGA-EE-A2ML         TCGA-EE-A2MM 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EE-A2MN         TCGA-EE-A2MP         TCGA-EE-A2MQ 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EE-A2MR         TCGA-EE-A2MS         TCGA-EE-A2MT 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EE-A2MU         TCGA-EE-A3AA         TCGA-EE-A3AB 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EE-A3AC         TCGA-EE-A3AD         TCGA-EE-A3AE 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EE-A3AF         TCGA-EE-A3AG         TCGA-EE-A3AH 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EE-A3J3         TCGA-EE-A3J4         TCGA-EE-A3J5 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EE-A3J7         TCGA-EE-A3J8         TCGA-EE-A3JA 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EE-A3JB         TCGA-EE-A3JE         TCGA-EE-A3JH 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EE-A3JI         TCGA-ER-A193         TCGA-ER-A197 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-ER-A199         TCGA-ER-A19C         TCGA-ER-A19D 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-ER-A19E         TCGA-ER-A19M         TCGA-ER-A19O 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-ER-A19T         TCGA-ER-A2NC         TCGA-ER-A2ND 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-ER-A2NF         TCGA-ER-A2NG         TCGA-ER-A2NH 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-ER-A3EV         TCGA-ER-A3PL         TCGA-ER-A42K 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A3YO         TCGA-FR-A44A 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-FR-A729         TCGA-FR-A7U9         TCGA-FR-A7UA 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-FR-A8YC         TCGA-FR-A8YD         TCGA-FR-A8YE 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-FS-A1YW         TCGA-FS-A1YX         TCGA-FS-A1YY 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-FS-A1Z0         TCGA-FS-A1Z4         TCGA-FS-A1Z7 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZA         TCGA-FS-A1ZB         TCGA-FS-A1ZD 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZE         TCGA-FS-A1ZF         TCGA-FS-A1ZG 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZH         TCGA-FS-A1ZJ         TCGA-FS-A1ZK 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZM         TCGA-FS-A1ZP         TCGA-FS-A1ZR 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZS         TCGA-FS-A1ZT         TCGA-FS-A1ZU 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZW         TCGA-FS-A1ZY         TCGA-FS-A1ZZ 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-FS-A4F0         TCGA-FS-A4F2         TCGA-FS-A4F4 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-FS-A4F5         TCGA-FS-A4F8         TCGA-FS-A4F9 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-FS-A4FB         TCGA-FS-A4FC         TCGA-FS-A4FD 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-FW-A3I3         TCGA-FW-A3TV         TCGA-FW-A5DY 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-GF-A3OT         TCGA-GF-A4EO         TCGA-GF-A6C8 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-GN-A267         TCGA-GN-A268         TCGA-GN-A26A 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-GN-A26D         TCGA-GN-A4U3         TCGA-GN-A4U4 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-GN-A4U7         TCGA-GN-A4U9         TCGA-GN-A8LK 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-GN-A8LL         TCGA-GN-A9SD         TCGA-HR-A2OH 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-QB-A6FS         TCGA-W3-A824         TCGA-W3-A825 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-W3-A828         TCGA-W3-AA1R         TCGA-W3-AA1V 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-W3-AA1W         TCGA-W3-AA21         TCGA-WE-A8JZ 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-WE-A8K1         TCGA-WE-A8K5         TCGA-WE-A8ZN 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-WE-A8ZO         TCGA-WE-A8ZQ         TCGA-WE-A8ZT 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-WE-A8ZY         TCGA-WE-AA9Y         TCGA-WE-AAA0 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-WE-AAA3         TCGA-YD-A89C         TCGA-YG-AA3P 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-Z2-A8RT         TCGA-Z2-AA3S         TCGA-Z2-AA3V 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
                    vv
clus                  N0  N1  N2  N3
  10Q GAIN MUTATED     0   1   0   2
  10Q GAIN WILD-TYPE 169  62  38  47
D20V7, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  N0                0                169
  N1                1                 62
  N2                0                 38
  N3                2                 47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V8, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED     3   0
  10Q GAIN WILD-TYPE 310  21
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      3    0
  10Q GAIN WILD-TYPE  310   21
   clus
vv  10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  0                3                310
  1                0                 21
[1] 2 2
[1] FALSE
D20V9, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED     0   1
  10Q GAIN WILD-TYPE 132  87
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      0    1
  10Q GAIN WILD-TYPE  132   87
     clus
vv    10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  NO                 0                132
  YES                1                 87
[1] 2 2
[1] FALSE
D20V10, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED     1   2
  10Q GAIN WILD-TYPE  43 311
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      1    2
  10Q GAIN WILD-TYPE   43  311
     clus
vv    10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  NO                 1                 43
  YES                2                311
[1] 2 2
[1] FALSE
D20V11, continuous
[1] "Remove cluster labels:" "10Q GAIN MUTATED"      
clus
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 2                260 
        TCGA-3N-A9WB         TCGA-3N-A9WC         TCGA-3N-A9WD 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q3         TCGA-D3-A1Q4 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q6         TCGA-D3-A1Q7         TCGA-D3-A1Q9 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D3-A1QA         TCGA-D3-A2J6         TCGA-D3-A2J7 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D3-A2J8         TCGA-D3-A2J9         TCGA-D3-A2JA 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-A2JF         TCGA-D3-A2JG 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D3-A2JH         TCGA-D3-A2JK         TCGA-D3-A3BZ 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D3-A3C6         TCGA-D3-A3CB         TCGA-D3-A3CC 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D3-A3CF         TCGA-D3-A3ML         TCGA-D3-A3MU 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D3-A3MV         TCGA-D3-A51E         TCGA-D3-A51F 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D3-A51G         TCGA-D3-A51H         TCGA-D3-A51K 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D3-A51R         TCGA-D3-A51T         TCGA-D3-A5GL 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D3-A5GN         TCGA-D3-A5GO         TCGA-D3-A5GR 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D3-A5GS         TCGA-D3-A5GU         TCGA-D3-A8GB 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D3-A8GD         TCGA-D3-A8GI         TCGA-D3-A8GJ 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D3-A8GK         TCGA-D3-A8GL         TCGA-D3-A8GM 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D3-A8GO         TCGA-D3-A8GP         TCGA-D3-A8GQ 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D3-A8GR         TCGA-D3-A8GS         TCGA-D9-A1X3 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D9-A3Z1         TCGA-D9-A3Z3         TCGA-D9-A6E9 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D9-A6EA         TCGA-D9-A6EC         TCGA-D9-A6EG 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1I0         TCGA-DA-A1I4 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I8         TCGA-DA-A1IA 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DA-A1IB         TCGA-DA-A1IC         TCGA-DA-A3F2 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EB-A5SH 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EB-A5UL         TCGA-EB-A5UN         TCGA-EB-A5VV 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EE-A17X         TCGA-EE-A17Y         TCGA-EE-A17Z 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EE-A180         TCGA-EE-A181         TCGA-EE-A182 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EE-A184         TCGA-EE-A185         TCGA-EE-A20B 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EE-A29B         TCGA-EE-A29C         TCGA-EE-A29D 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EE-A29E         TCGA-EE-A29G         TCGA-EE-A29H 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29M         TCGA-EE-A29P 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EE-A29Q         TCGA-EE-A29R         TCGA-EE-A29S 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EE-A29V         TCGA-EE-A29W         TCGA-EE-A29X 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EE-A2A0         TCGA-EE-A2A1         TCGA-EE-A2A2 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EE-A2A5         TCGA-EE-A2A6         TCGA-EE-A2GB 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EE-A2GC         TCGA-EE-A2GD         TCGA-EE-A2GE 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EE-A2GH         TCGA-EE-A2GI         TCGA-EE-A2GJ 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EE-A2GK         TCGA-EE-A2GL         TCGA-EE-A2GM 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EE-A2GN         TCGA-EE-A2GO         TCGA-EE-A2GP 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EE-A2GR         TCGA-EE-A2GS         TCGA-EE-A2GT 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EE-A2GU         TCGA-EE-A2M5         TCGA-EE-A2M6 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EE-A2M7         TCGA-EE-A2M8         TCGA-EE-A2MC 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EE-A2MD         TCGA-EE-A2ME         TCGA-EE-A2MF 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EE-A2MG         TCGA-EE-A2MH         TCGA-EE-A2MI 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EE-A2MJ         TCGA-EE-A2MK         TCGA-EE-A2ML 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EE-A2MM         TCGA-EE-A2MN         TCGA-EE-A2MP 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EE-A2MQ         TCGA-EE-A2MR         TCGA-EE-A2MS 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EE-A2MT         TCGA-EE-A2MU         TCGA-EE-A3AE 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EE-A3AH         TCGA-EE-A3J3         TCGA-EE-A3J4 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EE-A3J5         TCGA-EE-A3J7         TCGA-EE-A3J8 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EE-A3JA         TCGA-EE-A3JB         TCGA-EE-A3JE 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EE-A3JH         TCGA-EE-A3JI         TCGA-ER-A197 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-ER-A198         TCGA-ER-A199         TCGA-ER-A19C 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19E         TCGA-ER-A19F 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-ER-A19G         TCGA-ER-A19H         TCGA-ER-A19M 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-ER-A19Q         TCGA-ER-A19T         TCGA-ER-A19W 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-ER-A2NC         TCGA-ER-A2ND         TCGA-ER-A2NF 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-ER-A2NG         TCGA-ER-A2NH         TCGA-ER-A3EV 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-ER-A42K         TCGA-FR-A3YN 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-FR-A44A         TCGA-FR-A729         TCGA-FR-A7U9 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-FR-A7UA         TCGA-FR-A8YC         TCGA-FR-A8YD 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-FR-A8YE         TCGA-FS-A1YW         TCGA-FS-A1YX 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-FS-A1YY         TCGA-FS-A1Z0         TCGA-FS-A1Z4 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-FS-A1Z7         TCGA-FS-A1ZA         TCGA-FS-A1ZB 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZD         TCGA-FS-A1ZE         TCGA-FS-A1ZF 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZG         TCGA-FS-A1ZH         TCGA-FS-A1ZJ 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZK         TCGA-FS-A1ZM         TCGA-FS-A1ZP 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A1ZS         TCGA-FS-A1ZT 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZU         TCGA-FS-A1ZW         TCGA-FS-A1ZY 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZZ         TCGA-FS-A4F0         TCGA-FS-A4F2 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-FS-A4F4         TCGA-FS-A4F5         TCGA-FS-A4F8 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-FS-A4F9         TCGA-FS-A4FB         TCGA-FS-A4FC 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-FS-A4FD         TCGA-FW-A3TV         TCGA-GF-A6C8 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A264         TCGA-GN-A267 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26A         TCGA-GN-A26D 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-GN-A4U3         TCGA-GN-A4U4         TCGA-GN-A4U7 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-GN-A4U9         TCGA-GN-A8LK         TCGA-GN-A8LL 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-GN-A9SD         TCGA-HR-A2OH         TCGA-W3-A824 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-W3-A825         TCGA-W3-A828         TCGA-W3-AA1V 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-W3-AA1W         TCGA-W3-AA21         TCGA-WE-A8JZ 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-WE-A8K1         TCGA-WE-A8K5         TCGA-WE-A8ZN 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-WE-A8ZO         TCGA-WE-A8ZQ         TCGA-WE-A8ZT 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-WE-A8ZY         TCGA-WE-AA9Y         TCGA-WE-AAA0 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-WE-AAA3         TCGA-YD-A89C         TCGA-YD-A9TA 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-YD-A9TB         TCGA-YG-AA3P         TCGA-Z2-A8RT 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-Z2-AA3S         TCGA-Z2-AA3V 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
D20V12, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED     1   2
  10Q GAIN WILD-TYPE 134 221
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      1    2
  10Q GAIN WILD-TYPE  134  221
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  FEMALE                1                134
  MALE                  2                221
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  10Q GAIN MUTATED       0                         0     3
  10Q GAIN WILD-TYPE     5                         1   341
D20V13, multiclass
                           clus
vv                          10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  ASIAN                                    0                  5
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                    3                341
[1] 3 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     0   3
  10Q GAIN WILD-TYPE   7 341
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      0    3
  10Q GAIN WILD-TYPE    7  341
                        clus
vv                       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  7
  NOT HISPANIC OR LATINO                3                341
[1] 2 2
[1] FALSE

Clustering(21) Variable = 11P GAIN MUTATION ANALYSIS
D21V1, survival
                    sevent
clus2                  0   1
  11P GAIN MUTATED    12   9
  11P GAIN WILD-TYPE 109 109
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                21                218 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 9                109 
$`11P GAIN MUTATED`
TCGA-D3-A2JC TCGA-D3-A2JE TCGA-D3-A2JP TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D9-A6EC 
       86.30         9.76        43.53       140.98        59.70        57.90 
TCGA-EE-A180 TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2GB TCGA-EE-A2GH TCGA-EE-A2GP 
       62.37       346.49       185.19        26.14       189.40         0.76 
TCGA-EE-A2MC TCGA-EE-A3JB TCGA-EE-A3JI TCGA-ER-A19N TCGA-FS-A1ZD TCGA-FS-A1ZS 
       23.77       201.80       152.81        42.48        32.78       136.27 
TCGA-GN-A268 TCGA-W3-A825 TCGA-WE-A8ZQ 
       42.48         1.97        59.44 

$`11P GAIN WILD-TYPE`
TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
       60.46        12.99        14.83         8.42        15.72        31.89 
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB 
      110.93        49.35       133.25        19.04        76.41        62.60 
TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JD 
       25.64        45.99        62.86        15.75       168.00         7.27 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A3C6 
      107.61        36.30       171.58        64.83        66.08        58.06 
TCGA-D3-A3C7 TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR 
       46.98        40.01        16.96        13.87         9.34        90.21 
TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T 
       23.67       173.85       144.46        31.76        62.70        11.34 
TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D3-A8GC TCGA-D3-A8GD 
       42.05        45.70       177.86       124.08        78.21        23.61 
TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GP TCGA-D3-A8GR 
      179.97       120.00        69.53        70.62       135.12        36.53 
TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6EG TCGA-DA-A1HV 
       10.78        15.02        16.90        18.44        22.85        48.66 
TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA 
      106.85        31.96       150.61        82.85        32.42        64.83 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5SG 
       58.85        25.12       214.59        14.96         3.91        33.24 
TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A181 
       50.07        45.50         6.64        13.15        24.89        20.38 
TCGA-EE-A182 TCGA-EE-A184 TCGA-EE-A20C TCGA-EE-A20H TCGA-EE-A29B TCGA-EE-A29C 
        0.00        67.50        75.55       155.90        75.22        76.14 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P 
       12.99         0.26        44.28        63.12        47.74        27.16 
TCGA-EE-A29Q TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GD TCGA-EE-A2GE 
       61.12       102.38         7.20        77.98       239.11         0.20 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO 
       68.65        10.62        32.48        18.35        31.00       118.32 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 
        0.20        71.31        81.99       103.13        15.25         5.75 
TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML 
      209.79        94.19       171.85        63.25        67.50       104.78 
TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU 
      145.45       227.01        25.08       143.93        23.51        53.26 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
      124.31       122.73        51.62         4.41        54.51         6.28 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-ER-A193 TCGA-ER-A195 
       67.89       111.85        45.90         3.35        14.56        34.45 
TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C 
        1.58        47.31         7.82         4.54        53.29        39.81 
TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19P 
       11.47       151.46       150.12        99.06        59.84       120.76 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
       49.71        34.95       146.63        47.97        22.36         4.70 
TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL 
       16.87        10.95       173.29        55.82        15.48        32.05 
TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FS-A1YW 
      174.21       209.23        26.20         5.65        10.06       171.78 
TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZE 
       49.74       195.98         8.35        27.62       312.07        35.90 
TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZT 
       12.92         7.82        36.33        78.61       130.95        35.28 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 
        4.47        23.21         5.29         3.06        30.90        66.67 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
      173.19        13.28        80.68        55.59        11.54        19.30 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        9.90         6.05         1.91        53.29       117.93        84.72 
TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-GN-A8LK 
       17.06         7.59       120.53        34.49        46.92        43.23 
TCGA-GN-A9SD TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 
       59.41        85.05       297.01         7.23        18.05         0.33 
TCGA-W3-A824 TCGA-W3-A828 TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1V TCGA-W3-AA1W 
      174.12       120.07        44.05        79.99         8.09       185.13 
TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO 
       92.84         1.15        59.64        62.99        12.69        19.00 
TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 
       10.95        48.39         1.94        26.60        16.64        15.65 
TCGA-YG-AA3O TCGA-Z2-AA3S 
       28.21        91.23 

  11P GAIN MUTATED 11P GAIN WILD-TYPE 
              0.76               0.00 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
            346.49             312.07 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
             59.44              45.80 
[1] "0.8 - 346.5 (59.4)" "0.0 - 312.1 (45.8)"
[1] "hr=" "1.7"
D21V2, survival
                    sevent
clus2                  0   1
  11P GAIN MUTATED    17  16
  11P GAIN WILD-TYPE 152 164
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                33                316 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                16                164 
$`11P GAIN MUTATED`
TCGA-D3-A2JC TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A2JP TCGA-D3-A3CB TCGA-D3-A3CE 
       86.76        27.65        62.07        59.57       166.52        60.23 
TCGA-D9-A6EC TCGA-DA-A3F3 TCGA-EE-A180 TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2GB 
       66.25        10.49        94.98       369.93       195.02        59.28 
TCGA-EE-A2GH TCGA-EE-A2GP TCGA-EE-A2M5 TCGA-EE-A2MC TCGA-EE-A3JB TCGA-EE-A3JI 
      208.04        13.91        21.67        61.51       201.80       152.81 
TCGA-ER-A19N TCGA-ER-A42K TCGA-FS-A1YX TCGA-FS-A1ZB TCGA-FS-A1ZD TCGA-FS-A1ZS 
       44.05         6.77        48.59        48.85        53.52       148.80 
TCGA-FS-A4F2 TCGA-GN-A266 TCGA-GN-A268 TCGA-GN-A26D TCGA-GN-A8LL TCGA-W3-A825 
       50.14        10.13        62.79        39.58        21.37        63.02 
TCGA-WE-A8K6 TCGA-WE-A8ZQ TCGA-WE-A8ZX 
       15.98        59.77        32.58 

$`11P GAIN WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q3 
       17.03        66.48        12.99        14.93        16.57        16.67 
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 
      112.04       112.57        71.80       133.25        28.08        31.59 
TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 
       90.90        95.74        43.43       103.10        65.49        23.77 
TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK 
      115.53       168.00        11.87       113.52        42.08        12.10 
TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 
      171.58        66.48        66.08       130.72        58.06        46.98 
TCGA-D3-A3C8 TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR 
       46.32        86.93        24.53        13.87         9.34       103.59 
TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J 
       39.75        45.30       174.84        55.73        56.35       145.12 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN 
       32.94        22.62        63.81        26.89       125.79       135.75 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GC 
      137.92       178.32        18.18       125.19        30.84        79.59 
TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL 
       23.61        26.43        58.52       241.38       170.20        89.13 
TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS 
      107.15       161.00       152.75        29.06       129.63       117.17 
TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A1X3 TCGA-D9-A3Z1 
      151.53        54.67         3.65         7.10        18.12        15.39 
TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EG TCGA-DA-A1HV 
       22.29        18.44         9.90        25.18        22.95        48.89 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 
       36.03       117.21        20.38       194.83       176.55        35.93 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
      107.34        61.18        53.92        65.92        23.44        68.09 
TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH 
       28.60       215.44        15.68        13.87        10.36        20.35 
TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 
       68.25        54.02        17.29        52.01         7.04        24.89 
TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
       29.82        27.22         8.65        33.73        14.70        26.89 
TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H 
       68.15         4.96       133.81       151.27        91.56       168.26 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
       13.55        63.35        85.08        78.97        13.97        63.78 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P 
       72.07        64.64         2.60        56.84        18.61        56.42 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A0 
       66.74        14.47        61.28        25.87        17.92        46.82 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GC TCGA-EE-A2GD 
      102.90        36.82        39.29        86.14        67.43       340.14 
TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
      161.03        48.72       107.38        54.74        79.66        75.48 
TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU 
      102.12       126.81        42.77        81.21        44.88        94.82 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF 
      129.27        28.83        19.76        47.28       103.27       268.73 
TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML 
      103.20        16.96       204.66        96.23       158.63       216.66 
TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS 
      167.90        47.54       248.65        43.23       134.40       162.48 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
       71.21        53.26       124.31       122.73        51.62        28.77 
TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 
       54.51        13.81        41.59       138.81       172.18       127.20 
TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE 
       36.95        64.08        34.32        53.19        27.35        51.35 
TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 
      109.58        31.40        35.44        13.94        50.76         9.17 
TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F 
       77.75        98.40        48.89        12.59        13.02        26.37 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19P 
      268.93       152.35         6.44       131.51        61.05       162.08 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
       50.89        37.25         8.88       148.18        79.99        43.82 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES 
       23.34        20.15        16.37        31.27        32.05       247.04 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       80.32        46.98        33.21        92.98       174.21        15.72 
TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD 
      220.80        27.85        18.77        38.27        34.82        36.26 
TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 
      104.42       216.92       228.59       202.65        20.91        28.08 
TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZC TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG 
        7.79        27.72       357.37        40.27        15.45         9.70 
TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ 
       32.75        47.38        23.93       101.26        74.73       133.55 
TCGA-FS-A1ZR TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ 
       11.41        53.16        26.56        49.48        27.09        27.02 
TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB 
       77.82        66.67        28.73       174.84        34.03        26.73 
TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV 
       54.41        80.68         0.20        22.92        55.59        13.51 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 
       19.30         9.90         7.23         2.04        15.78       139.89 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 
      117.93        84.72        64.44        32.48       121.91        39.35 
TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A9SD TCGA-HR-A2OG 
       10.42        48.89        22.13        50.10        59.41         0.23 
TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 
       65.88       368.78       297.90         7.23        18.05         0.33 
TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1Q TCGA-W3-AA1R 
        0.69       228.16       121.08         4.01        69.07       111.09 
TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K5 
       42.08       219.16       105.04        24.03        49.05        61.15 
TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AA9Y 
       98.89        58.98        67.63        11.80        49.51        12.16 
TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YD-A89C TCGA-YD-A9TA TCGA-YG-AA3O 
       35.01        19.73        22.29         6.90        49.18        37.94 
TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
       14.43        27.58        96.99        15.98 

  11P GAIN MUTATED 11P GAIN WILD-TYPE 
              6.77               0.20 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
            369.93             368.78 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
            59.570             49.805 
[1] "6.8 - 369.9 (59.6)" "0.2 - 368.8 (49.8)"
[1] "hr=" "1.2"
D21V3, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  11P GAIN MUTATED                    4             1
  11P GAIN WILD-TYPE                 61             4
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  11P GAIN MUTATED                                           5
  11P GAIN WILD-TYPE                                        67
                    vv
clus                 REGIONAL LYMPH NODE
  11P GAIN MUTATED                    25
  11P GAIN WILD-TYPE                 190
D21V4, multiclass
                                           clus
vv                                          11P GAIN MUTATED 11P GAIN WILD-TYPE
  DISTANT METASTASIS                                       4                 61
  PRIMARY TUMOR                                            1                  4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                5                 67
  REGIONAL LYMPH NODE                                     25                190
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  11P GAIN MUTATED             3       1       6        1        0        2
  11P GAIN WILD-TYPE           9       6      22       17       27       22
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  11P GAIN MUTATED           2         1         3         4          1
  11P GAIN WILD-TYPE        12        18         9        33         14
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  11P GAIN MUTATED            5          3        0
  11P GAIN WILD-TYPE         27         57       20
D21V5, multiclass
             clus
vv            11P GAIN MUTATED 11P GAIN WILD-TYPE
  I OR II NOS                3                  9
  STAGE 0                    1                  6
  STAGE I                    6                 22
  STAGE IA                   1                 17
  STAGE IB                   0                 27
  STAGE II                   2                 22
  STAGE IIA                  2                 12
  STAGE IIB                  1                 18
  STAGE IIC                  3                  9
  STAGE III                  4                 33
  STAGE IIIA                 1                 14
  STAGE IIIB                 5                 27
  STAGE IIIC                 3                 57
  STAGE IV                   0                 20
[1] 14  2
[1] TRUE
[1] "dimension of contingency 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       5  9  5  7
  11P GAIN WILD-TYPE    59 63 72 61
D21V6, multiclass
       clus
vv      11P GAIN MUTATED 11P GAIN WILD-TYPE
  T0+T1                5                 59
  T2                   9                 63
  T3                   5                 72
  T4                   7                 61
[1] 4 2
[1] TRUE
[1] "dimension of 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    19   7   2   3
  11P GAIN WILD-TYPE 150  56  36  46
D21V7, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  N0               19                150
  N1                7                 56
  N2                2                 36
  N3                3                 46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V8, binary
                    cls
clus                   0   1
  11P GAIN MUTATED    32   0
  11P GAIN WILD-TYPE 281  21
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED     32    0
  11P GAIN WILD-TYPE  281   21
   clus
vv  11P GAIN MUTATED 11P GAIN WILD-TYPE
  0               32                281
  1                0                 21
[1] 2 2
[1] FALSE
D21V9, binary
                    cls
clus                   0   1
  11P GAIN MUTATED    10   7
  11P GAIN WILD-TYPE 122  81
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED     10    7
  11P GAIN WILD-TYPE  122   81
     clus
vv    11P GAIN MUTATED 11P GAIN WILD-TYPE
  NO                10                122
  YES                7                 81
[1] 2 2
[1] FALSE
D21V10, binary
                    cls
clus                   0   1
  11P GAIN MUTATED     7  27
  11P GAIN WILD-TYPE  37 286
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      7   27
  11P GAIN WILD-TYPE   37  286
     clus
vv    11P GAIN MUTATED 11P GAIN WILD-TYPE
  NO                 7                 37
  YES               27                286
[1] 2 2
[1] FALSE
D21V11, continuous
D21V12, binary
                    cls
clus                   0   1
  11P GAIN MUTATED    13  22
  11P GAIN WILD-TYPE 122 201
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED     13   22
  11P GAIN WILD-TYPE  122  201
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  FEMALE               13                122
  MALE                 22                201
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  11P GAIN MUTATED       0                         0    34
  11P GAIN WILD-TYPE     5                         1   310
D21V13, multiclass
                           clus
vv                          11P GAIN MUTATED 11P GAIN WILD-TYPE
  ASIAN                                    0                  5
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   34                310
[1] 3 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     0  35
  11P GAIN WILD-TYPE   7 309
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      0   35
  11P GAIN WILD-TYPE    7  309
                        clus
vv                       11P GAIN MUTATED 11P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  7
  NOT HISPANIC OR LATINO               35                309
[1] 2 2
[1] FALSE

Clustering(22) Variable = 11Q GAIN MUTATION ANALYSIS
D22V1, survival
                    sevent
clus2                  0   1
  11Q GAIN MUTATED    12   6
  11Q GAIN WILD-TYPE 109 112
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                18                221 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 6                112 
$`11Q GAIN MUTATED`
TCGA-D3-A2JC TCGA-D3-A2JP TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D9-A6EC TCGA-EE-A29W 
       86.30        43.53       140.98        59.70        57.90       185.19 
TCGA-EE-A2GH TCGA-EE-A2GP TCGA-EE-A2MC TCGA-EE-A3JB TCGA-EE-A3JI TCGA-ER-A19N 
      189.40         0.76        23.77       201.80       152.81        42.48 
TCGA-FR-A729 TCGA-FS-A1ZD TCGA-FS-A1ZS TCGA-GF-A4EO TCGA-GN-A268 TCGA-WE-A8ZQ 
      209.23        32.78       136.27         6.05        42.48        59.44 

$`11Q GAIN WILD-TYPE`
TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
       60.46        12.99        14.83         8.42        15.72        31.89 
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB 
      110.93        49.35       133.25        19.04        76.41        62.60 
TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JD 
       25.64        45.99        62.86        15.75       168.00         7.27 
TCGA-D3-A2JE TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
        9.76       107.61        36.30       171.58        64.83        66.08 
TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO 
       58.06        46.98        40.01        16.96        13.87         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R 
       90.21        23.67       173.85       144.46        31.76        62.70 
TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D3-A8GC 
       11.34        42.05        45.70       177.86       124.08        78.21 
TCGA-D3-A8GD TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GP 
       23.61       179.97       120.00        69.53        70.62       135.12 
TCGA-D3-A8GR TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6EG 
       36.53        10.78        15.02        16.90        18.44        22.85 
TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 
       48.66       106.85        31.96       150.61        82.85        32.42 
TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q 
       64.83        58.85        25.12       214.59        14.96         3.91 
TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y 
       33.24        50.07        45.50         6.64        13.15        24.89 
TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A184 TCGA-EE-A20C TCGA-EE-A20H 
       62.37        20.38         0.00        67.50        75.55       155.90 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H 
       75.22        76.14        12.99         0.26        44.28        63.12 
TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A2A1 TCGA-EE-A2A2 
       47.74        27.16        61.12       346.49       102.38         7.20 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GJ TCGA-EE-A2GK 
       77.98        26.14       239.11         0.20        68.65        10.62 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GR TCGA-EE-A2GS 
       32.48        18.35        31.00       118.32         0.20        71.31 
TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MF TCGA-EE-A2MG 
       81.99       103.13        15.25         5.75       209.79        94.19 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP 
      171.85        63.25        67.50       104.78       145.45       227.01 
TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB 
       25.08       143.93        23.51        53.26       124.31       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 
       51.62         4.41        54.51         6.28        67.89       111.85 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
       45.90         3.35        14.56        34.45         1.58        47.31 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19G 
        7.82         4.54        53.29        39.81        11.47       151.46 
TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S 
      150.12        99.06        59.84       120.76        49.71        34.95 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NG 
      146.63        47.97        22.36         4.70        16.87        10.95 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A44A TCGA-FR-A7U8 
      173.29        55.82        15.48        32.05       174.21        26.20 
TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
        5.65        10.06       171.78        49.74       195.98         8.35 
TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZJ 
       27.62       312.07        35.90        12.92         7.82        36.33 
TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY 
       78.61       130.95        35.28         4.47        23.21         5.29 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FD 
        3.06        30.90        66.67       173.19        13.28        80.68 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GN-A262 
       55.59        11.54        19.30         9.90         1.91        53.29 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 
      117.93        84.72        17.06         7.59       120.53        34.49 
TCGA-GN-A4U8 TCGA-GN-A8LK TCGA-GN-A9SD TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS 
       46.92        43.23        59.41        85.05       297.01         7.23 
TCGA-QB-AA9O TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1Q 
       18.05         0.33       174.12         1.97       120.07        44.05 
TCGA-W3-AA1R TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8K5 
       79.99         8.09       185.13        92.84         1.15        59.64 
TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AA9Y 
       62.99        12.69        19.00        10.95        48.39         1.94 
TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-Z2-AA3S 
       26.60        16.64        15.65        28.21        91.23 

  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
              0.76               0.00 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
            209.23             346.49 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
             59.57              45.70 
[1] "0.8 - 209.2 (59.6)" "0.0 - 346.5 (45.7)"
[1] "hr=" "2.2"
D22V2, survival
                    sevent
clus2                  0   1
  11Q GAIN MUTATED    16  11
  11Q GAIN WILD-TYPE 153 169
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                27                322 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                11                169 
$`11Q GAIN MUTATED`
TCGA-D3-A2JC TCGA-D3-A2JF TCGA-D3-A2JP TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D9-A6EC 
       86.76        62.07        59.57       166.52        60.23        66.25 
TCGA-DA-A3F3 TCGA-EE-A29W TCGA-EE-A2GH TCGA-EE-A2GP TCGA-EE-A2M5 TCGA-EE-A2MC 
       10.49       195.02       208.04        13.91        21.67        61.51 
TCGA-EE-A3JB TCGA-EE-A3JI TCGA-ER-A19N TCGA-ER-A42K TCGA-FR-A729 TCGA-FS-A1YX 
      201.80       152.81        44.05         6.77       220.80        48.59 
TCGA-FS-A1ZB TCGA-FS-A1ZD TCGA-FS-A1ZS TCGA-FS-A4F2 TCGA-GF-A4EO TCGA-GN-A268 
       48.85        53.52       148.80        50.14         7.23        62.79 
TCGA-WE-A8K6 TCGA-WE-A8ZQ TCGA-WE-A8ZX 
       15.98        59.77        32.58 

$`11Q GAIN WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q3 
       17.03        66.48        12.99        14.93        16.57        16.67 
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 
      112.04       112.57        71.80       133.25        28.08        31.59 
TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 
       90.90        95.74        43.43       103.10        65.49        23.77 
TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JD TCGA-D3-A2JE TCGA-D3-A2JG TCGA-D3-A2JH 
      115.53       168.00        11.87        27.65       113.52        42.08 
TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A3BZ TCGA-D3-A3C6 
       12.10       171.58        66.48        66.08       130.72        58.06 
TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO 
       46.98        46.32        86.93        24.53        13.87         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
      103.59        39.75        45.30       174.84        55.73        56.35 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL 
      145.12        32.94        22.62        63.81        26.89       125.79 
TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GB 
      135.75       137.92       178.32        18.18       125.19        30.84 
TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GK 
       79.59        23.61        26.43        58.52       241.38       170.20 
TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR 
       89.13       107.15       161.00       152.75        29.06       129.63 
TCGA-D3-A8GS TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A1X3 
      117.17       151.53        54.67         3.65         7.10        18.12 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EG 
       15.39        22.29        18.44         9.90        25.18        22.95 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 
       48.89        36.03       117.21        20.38       194.83       176.55 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB 
       35.93       107.34        61.18        53.92        65.92        23.44 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R 
       68.09        28.60       215.44        15.68        13.87        10.36 
TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV 
       20.35        68.25        54.02        17.29        52.01         7.04 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 
       24.89        29.82        27.22         8.65        94.98        33.73 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C 
       14.70        26.89        68.15         4.96       133.81       151.27 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C 
       91.56       168.26        13.55        63.35        85.08        78.97 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M 
       13.97        63.78        72.07        64.64         2.60        56.84 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T 
       18.61        56.42        66.74        14.47        61.28       369.93 
TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 
       25.87        17.92        46.82       102.90        36.82        39.29 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GI 
       86.14        59.28        67.43       340.14       161.03        48.72 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO 
      107.38        54.74        79.66        75.48       102.12       126.81 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 
       42.77        81.21        44.88        94.82       129.27        28.83 
TCGA-EE-A2M8 TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH 
       19.76        47.28       103.27       268.73       103.20        16.96 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN 
      204.66        96.23       158.63       216.66       167.90        47.54 
TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU 
      248.65        43.23       134.40       162.48        71.21        53.26 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
      124.31       122.73        51.62        28.77        54.51        13.81 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 
       41.59       138.81       172.18       127.20        36.95        64.08 
TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 
       34.32        53.19        27.35        51.35       109.58        31.40 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B 
       35.44        13.94        50.76         9.17        77.75        98.40 
TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H 
       48.89        12.59        13.02        26.37       268.93       152.35 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S 
        6.44       131.51        61.05       162.08        50.89        37.25 
TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
        8.88       148.18        79.99        43.82        23.34        20.15 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
       16.37        31.27        32.05       247.04        80.32        46.98 
TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A7U9 
       33.21        92.98       174.21        15.72        27.85        18.77 
TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YY 
       38.27        34.82        36.26       104.42       216.92       228.59 
TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZC 
      202.65        20.91        28.08         7.79        27.72       357.37 
TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK 
       40.27        15.45         9.70        32.75        47.38        23.93 
TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZT TCGA-FS-A1ZU 
      101.26        74.73       133.55        11.41        53.16        26.56 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 
       49.48        27.09        27.02        77.82        66.67        28.73 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 
      174.84        34.03        26.73        54.41        80.68         0.20 
TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 
       22.92        55.59        13.51        19.30         9.90         2.04 
TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 
       15.78       139.89       117.93        84.72        10.13        64.44 
TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 
       32.48        39.58       121.91        39.35        10.42        48.89 
TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A8LL TCGA-GN-A9SD TCGA-HR-A2OG TCGA-HR-A2OH 
       22.13        50.10        21.37        59.41         0.23        65.88 
TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 TCGA-RP-A694 
      368.78       297.90         7.23        18.05         0.33         0.69 
TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1Q TCGA-W3-AA1R 
      228.16        63.02       121.08         4.01        69.07       111.09 
TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K5 
       42.08       219.16       105.04        24.03        49.05        61.15 
TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AA9Y 
       98.89        58.98        67.63        11.80        49.51        12.16 
TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YD-A89C TCGA-YD-A9TA TCGA-YG-AA3O 
       35.01        19.73        22.29         6.90        49.18        37.94 
TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
       14.43        27.58        96.99        15.98 

  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
              6.77               0.20 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
            220.80             369.93 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
            59.770             49.805 
[1] "6.8 - 220.8 (59.8)" "0.2 - 369.9 (49.8)"
[1] "hr=" "1.4"
D22V3, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  11Q GAIN MUTATED                    2             1
  11Q GAIN WILD-TYPE                 63             4
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  11Q GAIN MUTATED                                           4
  11Q GAIN WILD-TYPE                                        68
                    vv
clus                 REGIONAL LYMPH NODE
  11Q GAIN MUTATED                    22
  11Q GAIN WILD-TYPE                 193
D22V4, multiclass
                                           clus
vv                                          11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  DISTANT METASTASIS                                       2                 63
  PRIMARY TUMOR                                            1                  4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                4                 68
  REGIONAL LYMPH NODE                                     22                193
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  11Q GAIN MUTATED             3       1       7        1        0        1
  11Q GAIN WILD-TYPE           9       6      21       17       27       23
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  11Q GAIN MUTATED           2         1         1         3          1
  11Q GAIN WILD-TYPE        12        18        11        34         14
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  11Q GAIN MUTATED            4          3        0
  11Q GAIN WILD-TYPE         28         57       20
D22V5, multiclass
             clus
vv            11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  I OR II NOS                3                  9
  STAGE 0                    1                  6
  STAGE I                    7                 21
  STAGE IA                   1                 17
  STAGE IB                   0                 27
  STAGE II                   1                 23
  STAGE IIA                  2                 12
  STAGE IIB                  1                 18
  STAGE IIC                  1                 11
  STAGE III                  3                 34
  STAGE IIIA                 1                 14
  STAGE IIIB                 4                 28
  STAGE IIIC                 3                 57
  STAGE IV                   0                 20
[1] 14  2
[1] TRUE
[1] "dimension of contingency 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       7  8  4  4
  11Q GAIN WILD-TYPE    57 64 73 64
D22V6, multiclass
       clus
vv      11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  T0+T1                7                 57
  T2                   8                 64
  T3                   4                 73
  T4                   4                 64
[1] 4 2
[1] TRUE
[1] "dimension of 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    17   6   2   3
  11Q GAIN WILD-TYPE 152  57  36  46
D22V7, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  N0               17                152
  N1                6                 57
  N2                2                 36
  N3                3                 46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V8, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED    28   0
  11Q GAIN WILD-TYPE 285  21
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED     28    0
  11Q GAIN WILD-TYPE  285   21
   clus
vv  11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  0               28                285
  1                0                 21
[1] 2 2
[1] FALSE
D22V9, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED    10   4
  11Q GAIN WILD-TYPE 122  84
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED     10    4
  11Q GAIN WILD-TYPE  122   84
     clus
vv    11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  NO                10                122
  YES                4                 84
[1] 2 2
[1] FALSE
D22V10, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED     7  21
  11Q GAIN WILD-TYPE  37 292
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      7   21
  11Q GAIN WILD-TYPE   37  292
     clus
vv    11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  NO                 7                 37
  YES               21                292
[1] 2 2
[1] FALSE
D22V11, continuous
D22V12, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED    10  19
  11Q GAIN WILD-TYPE 125 204
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED     10   19
  11Q GAIN WILD-TYPE  125  204
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  FEMALE               10                125
  MALE                 19                204
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  11Q GAIN MUTATED       0                         0    28
  11Q GAIN WILD-TYPE     5                         1   316
D22V13, multiclass
                           clus
vv                          11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  ASIAN                                    0                  5
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   28                316
[1] 3 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     0  29
  11Q GAIN WILD-TYPE   7 315
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      0   29
  11Q GAIN WILD-TYPE    7  315
                        clus
vv                       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  7
  NOT HISPANIC OR LATINO               29                315
[1] 2 2
[1] FALSE

Clustering(23) Variable = 12P GAIN MUTATION ANALYSIS
D23V1, survival
                    sevent
clus2                  0   1
  12P GAIN MUTATED    18  29
  12P GAIN WILD-TYPE 103  89
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                47                192 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                29                 89 
$`12P GAIN MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q6 TCGA-D3-A2JN TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3CE 
        8.42        49.35        64.83        58.06        40.01        59.70 
TCGA-D3-A3CF TCGA-D3-A5GN TCGA-D3-A5GU TCGA-D3-A8GC TCGA-D3-A8GL TCGA-D9-A6EC 
       16.96        45.70       124.08        78.21        69.53        57.90 
TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A3F5 TCGA-EB-A44Q TCGA-EE-A17Y TCGA-EE-A180 
       32.42        64.83       214.59         3.91        24.89        62.37 
TCGA-EE-A20H TCGA-EE-A29D TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GH TCGA-EE-A2GU 
      155.90        12.99        77.98        26.14       189.40        81.99 
TCGA-EE-A2M6 TCGA-EE-A3AA TCGA-EE-A3AD TCGA-EE-A3JI TCGA-ER-A197 TCGA-ER-A19B 
      103.13       124.31         4.41       152.81         1.58        53.29 
TCGA-ER-A19C TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A3ET TCGA-ER-A3PL TCGA-FR-A729 
       39.81        99.06        59.84        55.82        32.05       209.23 
TCGA-FS-A1ZM TCGA-FS-A1ZU TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A8LK TCGA-W3-A825 
       78.61         4.47        17.06         7.59        43.23         1.97 
TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1W TCGA-W3-AA21 TCGA-YG-AA3O 
       44.05        79.99       185.13        92.84        28.21 

$`12P GAIN WILD-TYPE`
TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 
       60.46        12.99        14.83        15.72        31.89       110.93 
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
      133.25        19.04        76.41        62.60        25.64        45.99 
TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JE 
       62.86        15.75       168.00        86.30         7.27         9.76 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C7 
      107.61        36.30       171.58        66.08        43.53        46.98 
TCGA-D3-A3CB TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E 
      140.98        13.87         9.34        90.21        23.67       173.85 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GR 
      144.46        31.76        62.70        11.34        42.05       177.86 
TCGA-D3-A8GD TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GM TCGA-D3-A8GP TCGA-D3-A8GR 
       23.61       179.97       120.00        70.62       135.12        36.53 
TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6EG TCGA-DA-A1HV 
       10.78        15.02        16.90        18.44        22.85        48.66 
TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1IC TCGA-DA-A3F2 
      106.85        31.96       150.61        82.85        58.85        25.12 
TCGA-DA-A3F8 TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X 
       14.96        33.24        50.07        45.50         6.64        13.15 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A184 TCGA-EE-A20C TCGA-EE-A29B TCGA-EE-A29C 
       20.38         0.00        67.50        75.55        75.22        76.14 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29Q 
        0.26        44.28        63.12        47.74        27.16        61.12 
TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2GD TCGA-EE-A2GE 
      346.49       185.19       102.38         7.20       239.11         0.20 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO 
       68.65        10.62        32.48        18.35        31.00       118.32 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC 
        0.76         0.20        71.31        15.25         5.75        23.77 
TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML 
      209.79        94.19       171.85        63.25        67.50       104.78 
TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU 
      145.45       227.01        25.08       143.93        23.51        53.26 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 
      122.73        51.62        54.51         6.28        67.89       111.85 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A198 
       45.90         3.35       201.80        14.56        34.45        47.31 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19N 
        7.82         4.54        11.47       151.46       150.12        42.48 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
      120.76        49.71        34.95       146.63        47.97        22.36 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3EV TCGA-FR-A44A 
        4.70        16.87        10.95       173.29        15.48       174.21 
TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 
       26.20         5.65        10.06       171.78        49.74       195.98 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF 
        8.35        27.62       312.07        32.78        35.90        12.92 
TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZW 
        7.82        36.33       130.95       136.27        35.28        23.21 
TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 
        5.29         3.06        30.90        66.67       173.19        13.28 
TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
       80.68        55.59        11.54        19.30         9.90         6.05 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A268 TCGA-GN-A4U3 
        1.91        53.29       117.93        84.72        42.48       120.53 
TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-GN-A9SD TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS 
       34.49        46.92        59.41        85.05       297.01         7.23 
TCGA-QB-AA9O TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A828 TCGA-W3-AA1V TCGA-WE-A8K1 
       18.05         0.33       174.12       120.07         8.09         1.15 
TCGA-WE-A8K5 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT 
       59.64        62.99        12.69        19.00        59.44        10.95 
TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-Z2-AA3S 
       48.39         1.94        26.60        16.64        15.65        91.23 

  12P GAIN MUTATED 12P GAIN WILD-TYPE 
              1.58               0.00 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
            214.59             346.49 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
            57.900             43.905 
[1] "1.6 - 214.6 (57.9)" "0.0 - 346.5 (43.9)"
[1] "hr=" "1.3"
D23V2, survival
                    sevent
clus2                  0   1
  12P GAIN MUTATED    24  38
  12P GAIN WILD-TYPE 145 142
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                62                287 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                38                142 
$`12P GAIN MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q6 TCGA-D3-A1Q9 TCGA-D3-A2JN TCGA-D3-A3C6 TCGA-D3-A3CC 
       16.57        71.80        31.59        66.48        58.06        86.93 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MV TCGA-D3-A5GN TCGA-D3-A5GU TCGA-D3-A8GC 
       60.23        24.53        45.30       135.75       125.19        79.59 
TCGA-D3-A8GL TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-DA-A1HW TCGA-DA-A1I7 TCGA-DA-A1IA 
       89.13         9.90        66.25        36.03        61.18        65.92 
TCGA-DA-A3F5 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UL TCGA-EE-A17Y TCGA-EE-A180 
      215.44        13.87        20.35        17.29        27.22        94.98 
TCGA-EE-A20H TCGA-EE-A29D TCGA-EE-A29X TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
      168.26        13.97        17.92        39.29        86.14        59.28 
TCGA-EE-A2GH TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A3AA TCGA-EE-A3AD 
      208.04        94.82        21.67       129.27       124.31        28.77 
TCGA-EE-A3J5 TCGA-EE-A3JE TCGA-EE-A3JI TCGA-ER-A197 TCGA-ER-A19B TCGA-ER-A19C 
       36.95        51.35       152.81        13.94        98.40        48.89 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A3ET TCGA-ER-A3PL TCGA-FR-A729 
        6.44       131.51        61.05        80.32        33.21       220.80 
TCGA-FS-A1ZM TCGA-FS-A1ZU TCGA-FS-A4F2 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A8LK 
      101.26        26.56        50.14        64.44        32.48        50.10 
TCGA-W3-A825 TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8ZX 
       63.02        69.07       111.09       219.16       105.04        32.58 
TCGA-YG-AA3O TCGA-YG-AA3P 
       37.94        14.43 

$`12P GAIN WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
       17.03        66.48        12.99        14.93        16.67       112.04 
TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 
      112.57       133.25        28.08        90.90        95.74        43.43 
TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC 
      103.10        65.49        23.77       115.53       168.00        86.76 
TCGA-D3-A2JD TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK 
       11.87        27.65        62.07       113.52        42.08        12.10 
TCGA-D3-A2JL TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3C8 
      171.58        66.08        59.57       130.72        46.98        46.32 
TCGA-D3-A3CB TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E 
      166.52        13.87         9.34       103.59        39.75       174.84 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R 
       55.73        56.35       145.12        32.94        22.62        63.81 
TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A8GB 
       26.89       125.79       137.92       178.32        18.18        30.84 
TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GM 
       23.61        26.43        58.52       241.38       170.20       107.15 
TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A148 
      161.00       152.75        29.06       129.63       117.17       151.53 
TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       54.67         3.65         7.10        18.12        15.39        22.29 
TCGA-D9-A4Z6 TCGA-D9-A6EA TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I0 
       18.44        25.18        22.95        48.89       117.21        20.38 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A1IB 
      194.83       176.55        35.93       107.34        53.92        23.44 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EB-A44R TCGA-EB-A5SG 
       68.09        28.60        10.49        15.68        10.36        68.25 
TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Z 
       54.02        52.01         7.04        24.89        29.82         8.65 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B 
       33.73        14.70        26.89        68.15         4.96       133.81 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C 
      151.27        91.56        13.55        63.35        85.08        78.97 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N 
       63.78        72.07        64.64         2.60        56.84        18.61 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V 
       56.42        66.74        14.47        61.28       369.93        25.87 
TCGA-EE-A29W TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2GC TCGA-EE-A2GD 
      195.02        46.82       102.90        36.82        67.43       340.14 
TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
      161.03        48.72       107.38        54.74        79.66        75.48 
TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT 
      102.12       126.81        13.91        42.77        81.21        44.88 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF 
       28.83        19.76        61.51        47.28       103.27       268.73 
TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML 
      103.20        16.96       204.66        96.23       158.63       216.66 
TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS 
      167.90        47.54       248.65        43.23       134.40       162.48 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3AF 
       71.21        53.26       122.73        51.62        54.51        13.81 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 
       41.59       138.81       172.18       127.20        64.08        34.32 
TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 
       53.19       201.80        27.35       109.58        31.40        35.44 
TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F 
       50.76         9.17        77.75        12.59        13.02        26.37 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S 
      268.93       152.35        44.05       162.08        50.89        37.25 
TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
        8.88       148.18        79.99        43.82        23.34        20.15 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3EV TCGA-ER-A42K 
       16.37        31.27        32.05       247.04        46.98         6.77 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA 
       92.98       174.21        15.72        27.85        18.77        38.27 
TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY 
       34.82        36.26       104.42       216.92        48.59       228.59 
TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB 
      202.65        20.91        28.08         7.79        27.72        48.85 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH 
      357.37        53.52        40.27        15.45         9.70        32.75 
TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS 
       47.38        23.93        74.73       133.55        11.41       148.80 
TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 
       53.16        49.48        27.09        27.02        77.82        66.67 
TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD 
       28.73       174.84        34.03        26.73        54.41        80.68 
TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
        0.20        22.92        55.59        13.51        19.30         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        7.23         2.04        15.78       139.89       117.93        84.72 
TCGA-GN-A266 TCGA-GN-A268 TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 
       10.13        62.79        39.58       121.91        39.35        10.42 
TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LL TCGA-GN-A9SD TCGA-HR-A2OG TCGA-HR-A2OH 
       48.89        22.13        21.37        59.41         0.23        65.88 
TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 TCGA-RP-A694 
      368.78       297.90         7.23        18.05         0.33         0.69 
TCGA-W3-A824 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1V TCGA-WE-A8JZ TCGA-WE-A8K1 
      228.16       121.08         4.01        42.08        24.03        49.05 
TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ 
       61.15        15.98        98.89        58.98        67.63        59.77 
TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 
       11.80        49.51        12.16        35.01        19.73        22.29 
TCGA-YD-A89C TCGA-YD-A9TA TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
        6.90        49.18        27.58        96.99        15.98 

  12P GAIN MUTATED 12P GAIN WILD-TYPE 
              6.44               0.20 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
            220.80             369.93 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
             60.64              49.18 
[1] "6.4 - 220.8 (60.6)" "0.2 - 369.9 (49.2)"
[1] "hr=" "1.2"
D23V3, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  12P GAIN MUTATED                    9             2
  12P GAIN WILD-TYPE                 56             3
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  12P GAIN MUTATED                                          15
  12P GAIN WILD-TYPE                                        57
                    vv
clus                 REGIONAL LYMPH NODE
  12P GAIN MUTATED                    35
  12P GAIN WILD-TYPE                 180
D23V4, multiclass
                                           clus
vv                                          12P GAIN MUTATED 12P GAIN WILD-TYPE
  DISTANT METASTASIS                                       9                 56
  PRIMARY TUMOR                                            2                  3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               15                 57
  REGIONAL LYMPH NODE                                     35                180
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  12P GAIN MUTATED             0       0       9        2        6        3
  12P GAIN WILD-TYPE          12       7      19       16       21       21
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  12P GAIN MUTATED           0         1         3        11          5
  12P GAIN WILD-TYPE        14        18         9        26         10
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  12P GAIN MUTATED           11          6        2
  12P GAIN WILD-TYPE         21         54       18
D23V5, multiclass
             clus
vv            12P GAIN MUTATED 12P GAIN WILD-TYPE
  I OR II NOS                0                 12
  STAGE 0                    0                  7
  STAGE I                    9                 19
  STAGE IA                   2                 16
  STAGE IB                   6                 21
  STAGE II                   3                 21
  STAGE IIA                  0                 14
  STAGE IIB                  1                 18
  STAGE IIC                  3                  9
  STAGE III                 11                 26
  STAGE IIIA                 5                 10
  STAGE IIIB                11                 21
  STAGE IIIC                 6                 54
  STAGE IV                   2                 18
[1] 14  2
[1] TRUE
[1] "dimension of contingency 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      16 15 11 11
  12P GAIN WILD-TYPE    48 57 66 57
D23V6, multiclass
       clus
vv      12P GAIN MUTATED 12P GAIN WILD-TYPE
  T0+T1               16                 48
  T2                  15                 57
  T3                  11                 66
  T4                  11                 57
[1] 4 2
[1] TRUE
[1] "dimension of 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    25  22   5   6
  12P GAIN WILD-TYPE 144  41  33  43
D23V7, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  N0               25                144
  N1               22                 41
  N2                5                 33
  N3                6                 43
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V8, binary
                    cls
clus                   0   1
  12P GAIN MUTATED    57   2
  12P GAIN WILD-TYPE 256  19
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     57    2
  12P GAIN WILD-TYPE  256   19
   clus
vv  12P GAIN MUTATED 12P GAIN WILD-TYPE
  0               57                256
  1                2                 19
[1] 2 2
[1] FALSE
D23V9, binary
                    cls
clus                   0   1
  12P GAIN MUTATED    26  13
  12P GAIN WILD-TYPE 106  75
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     26   13
  12P GAIN WILD-TYPE  106   75
     clus
vv    12P GAIN MUTATED 12P GAIN WILD-TYPE
  NO                26                106
  YES               13                 75
[1] 2 2
[1] FALSE
D23V10, binary
                    cls
clus                   0   1
  12P GAIN MUTATED     9  53
  12P GAIN WILD-TYPE  35 260
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      9   53
  12P GAIN WILD-TYPE   35  260
     clus
vv    12P GAIN MUTATED 12P GAIN WILD-TYPE
  NO                 9                 35
  YES               53                260
[1] 2 2
[1] FALSE
D23V11, continuous
D23V12, binary
                    cls
clus                   0   1
  12P GAIN MUTATED    22  40
  12P GAIN WILD-TYPE 113 183
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     22   40
  12P GAIN WILD-TYPE  113  183
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  FEMALE               22                113
  MALE                 40                183
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  12P GAIN MUTATED       3                         0    57
  12P GAIN WILD-TYPE     2                         1   287
D23V13, multiclass
                           clus
vv                          12P GAIN MUTATED 12P GAIN WILD-TYPE
  ASIAN                                    3                  2
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   57                287
[1] 3 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     2  59
  12P GAIN WILD-TYPE   5 285
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      2   59
  12P GAIN WILD-TYPE    5  285
                        clus
vv                       12P GAIN MUTATED 12P GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  5
  NOT HISPANIC OR LATINO               59                285
[1] 2 2
[1] FALSE

Clustering(24) Variable = 12Q GAIN MUTATION ANALYSIS
D24V1, survival
                    sevent
clus2                  0   1
  12Q GAIN MUTATED    10  17
  12Q GAIN WILD-TYPE 111 101
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                27                212 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                17                101 
$`12Q GAIN MUTATED`
TCGA-D3-A1Q6 TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A3C6 TCGA-D3-A3CF TCGA-D3-A5GN 
       49.35        64.83        66.08        58.06        16.96        45.70 
TCGA-D3-A5GU TCGA-D3-A8GL TCGA-DA-A3F5 TCGA-EB-A44Q TCGA-EE-A17Y TCGA-EE-A180 
      124.08        69.53       214.59         3.91        24.89        62.37 
TCGA-EE-A29D TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GH TCGA-EE-A3JI TCGA-ER-A19B 
       12.99        77.98        26.14       189.40       152.81        53.29 
TCGA-ER-A19C TCGA-ER-A19L TCGA-FR-A729 TCGA-FS-A1ZM TCGA-GN-A267 TCGA-GN-A26A 
       39.81        99.06       209.23        78.61        17.06         7.59 
TCGA-GN-A8LK TCGA-W3-A825 TCGA-YG-AA3O 
       43.23         1.97        28.21 

$`12Q GAIN WILD-TYPE`
TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
       60.46        12.99        14.83         8.42        15.72        31.89 
TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 
      110.93       133.25        19.04        76.41        62.60        25.64 
TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
       45.99        62.86        15.75       168.00        86.30         7.27 
TCGA-D3-A2JE TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JP TCGA-D3-A3C7 
        9.76       107.61        36.30       171.58        43.53        46.98 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR 
      140.98        40.01        59.70        13.87         9.34        90.21 
TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T 
       23.67       173.85       144.46        31.76        62.70        11.34 
TCGA-D3-A5GL TCGA-D3-A5GR TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GJ TCGA-D3-A8GK 
       42.05       177.86        78.21        23.61       179.97       120.00 
TCGA-D3-A8GM TCGA-D3-A8GP TCGA-D3-A8GR TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       70.62       135.12        36.53        10.78        15.02        16.90 
TCGA-D9-A4Z6 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 
       18.44        57.90        22.85        48.66       106.85        31.96 
TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 
      150.61        82.85        32.42        64.83        58.85        25.12 
TCGA-DA-A3F8 TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X 
       14.96        33.24        50.07        45.50         6.64        13.15 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A184 TCGA-EE-A20C TCGA-EE-A20H TCGA-EE-A29B 
       20.38         0.00        67.50        75.55       155.90        75.22 
TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P 
       76.14         0.26        44.28        63.12        47.74        27.16 
TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2GD 
       61.12       346.49       185.19       102.38         7.20       239.11 
TCGA-EE-A2GE TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN 
        0.20        68.65        10.62        32.48        18.35        31.00 
TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 
      118.32         0.76         0.20        71.31        81.99       103.13 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI 
       15.25         5.75        23.77       209.79        94.19       171.85 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MR 
       63.25        67.50       104.78       145.45       227.01        25.08 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC 
      143.93        23.51        53.26       124.31       122.73        51.62 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 
        4.41        54.51         6.28        67.89       111.85        45.90 
TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
        3.35       201.80        14.56        34.45         1.58        47.31 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19M 
        7.82         4.54        11.47       151.46       150.12        59.84 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 
       42.48       120.76        49.71        34.95       146.63        47.97 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET 
       22.36         4.70        16.87        10.95       173.29        55.82 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A44A TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FR-A8YC 
       15.48        32.05       174.21        26.20         5.65        10.06 
TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZC 
      171.78        49.74       195.98         8.35        27.62       312.07 
TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZQ 
       32.78        35.90        12.92         7.82        36.33       130.95 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ 
      136.27        35.28         4.47        23.21         5.29         3.06 
TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TU 
       30.90        66.67       173.19        13.28        80.68        55.59 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 
       11.54        19.30         9.90         6.05         1.91        53.29 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A268 TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 
      117.93        84.72        42.48       120.53        34.49        46.92 
TCGA-GN-A9SD TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 
       59.41        85.05       297.01         7.23        18.05         0.33 
TCGA-W3-A824 TCGA-W3-A828 TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1V TCGA-W3-AA1W 
      174.12       120.07        44.05        79.99         8.09       185.13 
TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO 
       92.84         1.15        59.64        62.99        12.69        19.00 
TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 
       59.44        10.95        48.39         1.94        26.60        16.64 
TCGA-WE-AAA4 TCGA-Z2-AA3S 
       15.65        91.23 

  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
              1.97               0.00 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
            214.59             346.49 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
             53.29              45.70 
[1] "2.0 - 214.6 (53.3)" "0.0 - 346.5 (45.7)"
[1] "hr=" "1.2"
D24V2, survival
                    sevent
clus2                  0   1
  12Q GAIN MUTATED    14  22
  12Q GAIN WILD-TYPE 155 158
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                36                313 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                22                158 
$`12Q GAIN MUTATED`
TCGA-D3-A1Q6 TCGA-D3-A1Q9 TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A3C6 TCGA-D3-A3CF 
       71.80        31.59        66.48        66.08        58.06        24.53 
TCGA-D3-A5GN TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GL TCGA-DA-A1HW TCGA-DA-A3F5 
      135.75        18.18       125.19        89.13        36.03       215.44 
TCGA-EB-A44Q TCGA-EB-A5UL TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A29D TCGA-EE-A2A6 
       13.87        17.29        27.22        94.98        13.97        86.14 
TCGA-EE-A2GB TCGA-EE-A2GH TCGA-EE-A2M5 TCGA-EE-A3J5 TCGA-EE-A3JE TCGA-EE-A3JI 
       59.28       208.04        21.67        36.95        51.35       152.81 
TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19L TCGA-FR-A729 TCGA-FS-A1ZK TCGA-FS-A1ZM 
       98.40        48.89       131.51       220.80        23.93       101.26 
TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A8LK TCGA-W3-A825 TCGA-WE-A8ZX TCGA-YG-AA3O 
       64.44        32.48        50.10        63.02        32.58        37.94 

$`12Q GAIN WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q3 
       17.03        66.48        12.99        14.93        16.57        16.67 
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB 
      112.04       112.57       133.25        28.08        90.90        95.74 
TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB 
       43.43       103.10        65.49        23.77       115.53       168.00 
TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH 
       86.76        11.87        27.65        62.07       113.52        42.08 
TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3C8 
       12.10       171.58        59.57       130.72        46.98        46.32 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR 
      166.52        86.93        60.23        13.87         9.34       103.59 
TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J 
       39.75        45.30       174.84        55.73        56.35       145.12 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GO 
       32.94        22.62        63.81        26.89       125.79       137.92 
TCGA-D3-A5GR TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GI 
      178.32        30.84        79.59        23.61        26.43        58.52 
TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GQ 
      241.38       170.20       107.15       161.00       152.75        29.06 
TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX 
      129.63       117.17       151.53        54.67         3.65         7.10 
TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EA 
       18.12        15.39        22.29        18.44         9.90        25.18 
TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 
       66.25        22.95        48.89       117.21        20.38       194.83 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA 
      176.55        35.93       107.34        61.18        53.92        65.92 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EB-A44R 
       23.44        68.09        28.60        10.49        15.68        10.36 
TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 
       20.35        68.25        54.02        52.01         7.04        24.89 
TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 
       29.82         8.65        33.73        14.70        26.89        68.15 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I 
        4.96       133.81       151.27        91.56       168.26        13.55 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H 
       63.35        85.08        78.97        63.78        72.07        64.64 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
        2.60        56.84        18.61        56.42        66.74        14.47 
TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 
       61.28       369.93        25.87       195.02        17.92        46.82 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE 
      102.90        36.82        39.29        67.43       340.14       161.03 
TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN 
       48.72       107.38        54.74        79.66        75.48       102.12 
TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU 
      126.81        13.91        42.77        81.21        44.88        94.82 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME 
      129.27        28.83        19.76        61.51        47.28       103.27 
TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK 
      268.73       103.20        16.96       204.66        96.23       158.63 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR 
      216.66       167.90        47.54       248.65        43.23       134.40 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC 
      162.48        71.21        53.26       124.31       122.73        51.62 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 
       28.77        54.51        13.81        41.59       138.81       172.18 
TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JD 
      127.20        64.08        34.32        53.19       201.80        27.35 
TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 
      109.58        31.40        35.44        13.94        50.76         9.17 
TCGA-ER-A19A TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H 
       77.75        12.59        13.02        26.37       268.93       152.35 
TCGA-ER-A19J TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S 
        6.44        61.05        44.05       162.08        50.89        37.25 
TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
        8.88       148.18        79.99        43.82        23.34        20.15 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
       16.37        31.27        32.05       247.04        80.32        46.98 
TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A7U8 
       33.21         6.77        92.98       174.21        15.72        27.85 
TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW 
       18.77        38.27        34.82        36.26       104.42       216.92 
TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 
       48.59       228.59       202.65        20.91        28.08         7.79 
TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF 
       27.72        48.85       357.37        53.52        40.27        15.45 
TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR 
        9.70        32.75        47.38        74.73       133.55        11.41 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ 
      148.80        53.16        26.56        49.48        27.09        27.02 
TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 
       77.82        50.14        66.67        28.73       174.84        34.03 
TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU 
       26.73        54.41        80.68         0.20        22.92        55.59 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 
       13.51        19.30         9.90         7.23         2.04        15.78 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A268 TCGA-GN-A26D 
      139.89       117.93        84.72        10.13        62.79        39.58 
TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LL 
      121.91        39.35        10.42        48.89        22.13        21.37 
TCGA-GN-A9SD TCGA-HR-A2OG TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS 
       59.41         0.23        65.88       368.78       297.90         7.23 
TCGA-QB-AA9O TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A828 TCGA-W3-AA1O 
       18.05         0.33         0.69       228.16       121.08         4.01 
TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8JZ 
       69.07       111.09        42.08       219.16       105.04        24.03 
TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO 
       49.05        61.15        15.98        98.89        58.98        67.63 
TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 
       59.77        11.80        49.51        12.16        35.01        19.73 
TCGA-WE-AAA4 TCGA-YD-A89C TCGA-YD-A9TA TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S 
       22.29         6.90        49.18        14.43        27.58        96.99 
TCGA-Z2-AA3V 
       15.98 

  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
             13.87               0.20 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
            220.80             369.93 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
             58.67              50.14 
[1] "13.9 - 220.8 (58.7)" "0.2 - 369.9 (50.1)" 
[1] "hr=" "1.2"
D24V3, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  12Q GAIN MUTATED                    4             0
  12Q GAIN WILD-TYPE                 61             5
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  12Q GAIN MUTATED                                           9
  12Q GAIN WILD-TYPE                                        63
                    vv
clus                 REGIONAL LYMPH NODE
  12Q GAIN MUTATED                    23
  12Q GAIN WILD-TYPE                 192
D24V4, multiclass
                                           clus
vv                                          12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  DISTANT METASTASIS                                       4                 61
  PRIMARY TUMOR                                            0                  5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                9                 63
  REGIONAL LYMPH NODE                                     23                192
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  12Q GAIN MUTATED             0       0       6        1        3        2
  12Q GAIN WILD-TYPE          12       7      22       17       24       22
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  12Q GAIN MUTATED           0         0         0         6          2
  12Q GAIN WILD-TYPE        14        19        12        31         13
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  12Q GAIN MUTATED            7          5        1
  12Q GAIN WILD-TYPE         25         55       19
D24V5, multiclass
             clus
vv            12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  I OR II NOS                0                 12
  STAGE 0                    0                  7
  STAGE I                    6                 22
  STAGE IA                   1                 17
  STAGE IB                   3                 24
  STAGE II                   2                 22
  STAGE IIA                  0                 14
  STAGE IIB                  0                 19
  STAGE IIC                  0                 12
  STAGE III                  6                 31
  STAGE IIIA                 2                 13
  STAGE IIIB                 7                 25
  STAGE IIIC                 5                 55
  STAGE IV                   1                 19
[1] 14  2
[1] TRUE
[1] "dimension of contingency 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       9  8  5  7
  12Q GAIN WILD-TYPE    55 64 72 61
D24V6, multiclass
       clus
vv      12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  T0+T1                9                 55
  T2                   8                 64
  T3                   5                 72
  T4                   7                 61
[1] 4 2
[1] TRUE
[1] "dimension of 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    12  14   2   4
  12Q GAIN WILD-TYPE 157  49  36  45
D24V7, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  N0               12                157
  N1               14                 49
  N2                2                 36
  N3                4                 45
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V8, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED    32   1
  12Q GAIN WILD-TYPE 281  20
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     32    1
  12Q GAIN WILD-TYPE  281   20
   clus
vv  12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  0               32                281
  1                1                 20
[1] 2 2
[1] FALSE
D24V9, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED    15   8
  12Q GAIN WILD-TYPE 117  80
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     15    8
  12Q GAIN WILD-TYPE  117   80
     clus
vv    12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  NO                15                117
  YES                8                 80
[1] 2 2
[1] FALSE
D24V10, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED     2  34
  12Q GAIN WILD-TYPE  42 279
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      2   34
  12Q GAIN WILD-TYPE   42  279
     clus
vv    12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  NO                 2                 42
  YES               34                279
[1] 2 2
[1] FALSE
D24V11, continuous
D24V12, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED    10  26
  12Q GAIN WILD-TYPE 125 197
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     10   26
  12Q GAIN WILD-TYPE  125  197
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  FEMALE               10                125
  MALE                 26                197
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  12Q GAIN MUTATED       2                         0    33
  12Q GAIN WILD-TYPE     3                         1   311
D24V13, multiclass
                           clus
vv                          12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  ASIAN                                    2                  3
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   33                311
[1] 3 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     1  34
  12Q GAIN WILD-TYPE   6 310
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      1   34
  12Q GAIN WILD-TYPE    6  310
                        clus
vv                       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO               34                310
[1] 2 2
[1] FALSE

Clustering(25) Variable = 13Q GAIN MUTATION ANALYSIS
D25V1, survival
                    sevent
clus2                  0   1
  13Q GAIN MUTATED    21  43
  13Q GAIN WILD-TYPE 100  75
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                64                175 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                43                 75 
$`13Q GAIN MUTATED`
TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q6 TCGA-D3-A2JP TCGA-D3-A3C6 
       12.99         8.42        15.72        49.35        43.53        58.06 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A51T TCGA-D3-A5GU TCGA-D3-A8GL TCGA-D3-A8GM 
       40.01        59.70        11.34       124.08        69.53        70.62 
TCGA-DA-A1I7 TCGA-EB-A5SG TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A29B 
       32.42        33.24        24.89        62.37       155.90        75.22 
TCGA-EE-A29G TCGA-EE-A29P TCGA-EE-A2GB TCGA-EE-A2GH TCGA-EE-A2GM TCGA-EE-A2GN 
       44.28        27.16        26.14       189.40        18.35        31.00 
TCGA-EE-A2GP TCGA-EE-A2M7 TCGA-EE-A2MF TCGA-EE-A2MP TCGA-EE-A3AA TCGA-EE-A3AF 
        0.76        15.25       209.79       227.01       124.31         6.28 
TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-EE-A3JI TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19C 
       67.89        45.90       152.81         1.58         7.82        39.81 
TCGA-ER-A19D TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A2NC 
       11.47        99.06        59.84        42.48       120.76        22.36 
TCGA-ER-A3PL TCGA-FR-A729 TCGA-FR-A8YC TCGA-FS-A1YW TCGA-FS-A1Z0 TCGA-FS-A1Z3 
       32.05       209.23        10.06       171.78       195.98         8.35 
TCGA-FS-A1Z4 TCGA-FS-A1ZE TCGA-FS-A1ZJ TCGA-FS-A1ZQ TCGA-FS-A1ZT TCGA-FS-A1ZY 
       27.62        35.90        36.33       130.95        35.28         5.29 
TCGA-FS-A4FD TCGA-FW-A3TU TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-OD-A75X 
       80.68        55.59        84.72        17.06        42.48       297.01 
TCGA-QB-AA9O TCGA-W3-A824 TCGA-W3-A825 TCGA-WE-AAA3 
       18.05       174.12         1.97        16.64 

$`13Q GAIN WILD-TYPE`
TCGA-3N-A9WC TCGA-BF-AAP0 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       60.46        14.83        31.89       110.93       133.25        19.04 
TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA 
       76.41        62.60        25.64        45.99        62.86        15.75 
TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JE TCGA-D3-A2JG TCGA-D3-A2JH 
      168.00        86.30         7.27         9.76       107.61        36.30 
TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CF 
      171.58        64.83        66.08        46.98       140.98        16.96 
TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51J 
       13.87         9.34        90.21        23.67       173.85       144.46 
TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A8GC 
       31.76        62.70        42.05        45.70       177.86        78.21 
TCGA-D3-A8GD TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GP TCGA-D3-A8GR TCGA-D9-A1X3 
       23.61       179.97       120.00       135.12        36.53        10.78 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV 
       15.02        16.90        18.44        57.90        22.85        48.66 
TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1IA TCGA-DA-A1IC 
      106.85        31.96       150.61        82.85        64.83        58.85 
TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5SH TCGA-EB-A5UN 
       25.12       214.59        14.96         3.91        50.07        45.50 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A184 TCGA-EE-A20C 
        6.64        13.15        20.38         0.00        67.50        75.55 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29Q 
       76.14        12.99         0.26        63.12        47.74        61.12 
TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GD 
      346.49       185.19       102.38         7.20        77.98       239.11 
TCGA-EE-A2GE TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GO TCGA-EE-A2GR 
        0.20        68.65        10.62        32.48       118.32         0.20 
TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MG 
       71.31        81.99       103.13         5.75        23.77        94.19 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MR 
      171.85        63.25        67.50       104.78       145.45        25.08 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
      143.93        23.51        53.26       122.73        51.62         4.41 
TCGA-EE-A3AE TCGA-EE-A3J4 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-ER-A193 TCGA-ER-A195 
       54.51       111.85         3.35       201.80        14.56        34.45 
TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19Q 
       47.31         4.54        53.29       151.46       150.12        49.71 
TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NG 
       34.95       146.63        47.97         4.70        16.87        10.95 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-FR-A44A TCGA-FR-A7U8 TCGA-FR-A7UA 
      173.29        55.82        15.48       174.21        26.20         5.65 
TCGA-FS-A1YY TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZM 
       49.74       312.07        32.78        12.92         7.82        78.61 
TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 
      136.27         4.47        23.21         3.06        30.90        66.67 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
      173.19        13.28        11.54        19.30         9.90         6.05 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 
        1.91        53.29       117.93         7.59       120.53        34.49 
TCGA-GN-A4U8 TCGA-GN-A8LK TCGA-GN-A9SD TCGA-LH-A9QB TCGA-QB-A6FS TCGA-RP-A693 
       46.92        43.23        59.41        85.05         7.23         0.33 
TCGA-W3-A828 TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 
      120.07        44.05        79.99         8.09       185.13        92.84 
TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ 
        1.15        59.64        62.99        12.69        19.00        59.44 
TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-YG-AA3O 
       10.95        48.39         1.94        26.60        15.65        28.21 
TCGA-Z2-AA3S 
       91.23 

  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
              0.76               0.00 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
            297.01             346.49 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
            41.245             47.970 
[1] "0.8 - 297.0 (41.2)" "0.0 - 346.5 (48.0)"
[1] "hr=" "1.5"
D25V2, survival
                    sevent
clus2                  0   1
  13Q GAIN MUTATED    34  54
  13Q GAIN WILD-TYPE 135 126
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                88                261 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                54                126 
$`13Q GAIN MUTATED`
TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q6 TCGA-D3-A2JF TCGA-D3-A2JP 
       12.99        16.57        16.67        71.80        62.07        59.57 
TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A51T TCGA-D3-A5GO TCGA-D3-A5GU 
       58.06        86.93        60.23        26.89       137.92       125.19 
TCGA-D3-A8GI TCGA-D3-A8GL TCGA-D3-A8GM TCGA-DA-A1I7 TCGA-DA-A3F3 TCGA-EB-A44R 
       58.52        89.13       107.15        61.18        10.49        10.36 
TCGA-EB-A5SG TCGA-EB-A5UL TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A20B TCGA-EE-A20H 
       68.25        17.29        27.22        94.98       133.81       168.26 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29G TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A2A5 
       63.35        85.08        72.07        56.42        14.47        39.29 
TCGA-EE-A2GB TCGA-EE-A2GH TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2M7 
       59.28       208.04        75.48       102.12        13.91        28.83 
TCGA-EE-A2MF TCGA-EE-A2MP TCGA-EE-A3AA TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J7 
      268.73       248.65       124.31        13.81       172.18        64.08 
TCGA-EE-A3JA TCGA-EE-A3JI TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19C TCGA-ER-A19D 
       53.19       152.81        13.94         9.17        48.89        12.59 
TCGA-ER-A19E TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A2NC 
       13.02       131.51        61.05        44.05       162.08        43.82 
TCGA-ER-A3PL TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A8YC TCGA-FS-A1YW TCGA-FS-A1YX 
       33.21        15.72       220.80        34.82       216.92        48.59 
TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZE TCGA-FS-A1ZJ 
      202.65        20.91        28.08         7.79        40.27        47.38 
TCGA-FS-A1ZQ TCGA-FS-A1ZT TCGA-FS-A1ZY TCGA-FS-A4F2 TCGA-FS-A4FD TCGA-FW-A3TU 
      133.55        53.16        27.09        50.14        80.68        55.59 
TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A4U9 TCGA-HR-A2OG TCGA-OD-A75X 
       84.72        64.44        62.79        22.13         0.23       297.90 
TCGA-QB-AA9O TCGA-W3-A824 TCGA-W3-A825 TCGA-WE-A8JZ TCGA-WE-A8K6 TCGA-WE-A8ZX 
       18.05       228.16        63.02        24.03        15.98        32.58 
TCGA-WE-AAA3 TCGA-YD-A89C TCGA-YD-A9TA TCGA-Z2-A8RT 
       19.73         6.90        49.18        27.58 

$`13Q GAIN WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-BF-AAP0 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q7 
       17.03        66.48        14.93       112.04       112.57       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        31.59        90.90        95.74        43.43       103.10 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
       65.49        23.77       115.53       168.00        86.76        11.87 
TCGA-D3-A2JE TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       27.65       113.52        42.08        12.10       171.58        66.48 
TCGA-D3-A2JO TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CF 
       66.08       130.72        46.98        46.32       166.52        24.53 
TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E 
       13.87         9.34       103.59        39.75        45.30       174.84 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R 
       55.73        56.35       145.12        32.94        22.62        63.81 
TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A8GB TCGA-D3-A8GC 
      125.79       135.75       178.32        18.18        30.84        79.59 
TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GN TCGA-D3-A8GP 
       23.61        26.43       241.38       170.20       161.00       152.75 
TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW 
       29.06       129.63       117.17       151.53        54.67         3.65 
TCGA-D9-A1JX TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 
        7.10        18.12        15.39        22.29        18.44         9.90 
TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY 
       25.18        66.25        22.95        48.89        36.03       117.21 
TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I8 
       20.38       194.83       176.55        35.93       107.34        53.92 
TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 
       65.92        23.44        68.09        28.60       215.44        15.68 
TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 
       13.87        20.35        54.02        52.01         7.04        24.89 
TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 
       29.82         8.65        33.73        14.70        26.89        68.15 
TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29C TCGA-EE-A29D 
        4.96       151.27        91.56        13.55        78.97        13.97 
TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29Q 
       63.78        64.64         2.60        56.84        18.61        66.74 
TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 
       61.28       369.93        25.87       195.02        17.92        46.82 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE 
      102.90        36.82        86.14        67.43       340.14       161.03 
TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GO TCGA-EE-A2GR 
       48.72       107.38        54.74        79.66       126.81        42.77 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M8 
       81.21        44.88        94.82        21.67       129.27        19.76 
TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
       61.51        47.28       103.27       103.20        16.96       204.66 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MQ 
       96.23       158.63       216.66       167.90        47.54        43.23 
TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC 
      134.40       162.48        71.21        53.26       122.73        51.62 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J5 
       28.77        54.51        41.59       138.81       127.20        36.95 
TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 
       34.32       201.80        27.35        51.35       109.58        31.40 
TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19F TCGA-ER-A19G 
       35.44        50.76        77.75        98.40        26.37       268.93 
TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W 
      152.35         6.44        50.89        37.25         8.88       148.18 
TCGA-ER-A1A1 TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH 
       79.99        23.34        20.15        16.37        31.27        32.05 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A 
      247.04        80.32        46.98         6.77        92.98       174.21 
TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YY 
       27.85        18.77        38.27        36.26       104.42       228.59 
TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZG 
       27.72        48.85       357.37        53.52        15.45         9.70 
TCGA-FS-A1ZH TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZS 
       32.75        23.93       101.26        74.73        11.41       148.80 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 
       26.56        49.48        27.02        77.82        66.67        28.73 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FW-A3I3 TCGA-FW-A3R5 
      174.84        34.03        26.73        54.41         0.20        22.92 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 
       13.51        19.30         9.90         7.23         2.04        15.78 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A266 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U3 
      139.89       117.93        10.13        32.48        39.58       121.91 
TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A8LK TCGA-GN-A8LL TCGA-GN-A9SD 
       39.35        10.42        48.89        50.10        21.37        59.41 
TCGA-HR-A2OH TCGA-LH-A9QB TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A828 
       65.88       368.78         7.23         0.33         0.69       121.08 
TCGA-W3-AA1O TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 
        4.01        69.07       111.09        42.08       219.16       105.04 
TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ 
       49.05        61.15        98.89        58.98        67.63        59.77 
TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-YG-AA3O 
       11.80        49.51        12.16        35.01        22.29        37.94 
TCGA-YG-AA3P TCGA-Z2-AA3S TCGA-Z2-AA3V 
       14.43        96.99        15.98 

  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
              0.23               0.20 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
            297.90             369.93 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
            56.005             49.510 
[1] "0.2 - 297.9 (56.0)" "0.2 - 369.9 (49.5)"
[1] "hr=" "1.3"
D25V3, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  13Q GAIN MUTATED                   22             0
  13Q GAIN WILD-TYPE                 43             5
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  13Q GAIN MUTATED                                          19
  13Q GAIN WILD-TYPE                                        53
                    vv
clus                 REGIONAL LYMPH NODE
  13Q GAIN MUTATED                    51
  13Q GAIN WILD-TYPE                 164
D25V4, multiclass
                                           clus
vv                                          13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  DISTANT METASTASIS                                      22                 43
  PRIMARY TUMOR                                            0                  5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               19                 53
  REGIONAL LYMPH NODE                                     51                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                 I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  13Q GAIN MUTATED             3       1      12        4       10        4
  13Q GAIN WILD-TYPE           9       6      16       14       17       20
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  13Q GAIN MUTATED           1         6         6         6          4
  13Q GAIN WILD-TYPE        13        13         6        31         11
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  13Q GAIN MUTATED           11         12        3
  13Q GAIN WILD-TYPE         21         48       17
D25V5, multiclass
             clus
vv            13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  I OR II NOS                3                  9
  STAGE 0                    1                  6
  STAGE I                   12                 16
  STAGE IA                   4                 14
  STAGE IB                  10                 17
  STAGE II                   4                 20
  STAGE IIA                  1                 13
  STAGE IIB                  6                 13
  STAGE IIC                  6                  6
  STAGE III                  6                 31
  STAGE IIIA                 4                 11
  STAGE IIIB                11                 21
  STAGE IIIC                12                 48
  STAGE IV                   3                 17
[1] 14  2
[1] TRUE
[1] "dimension of contingency 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      15 26 12 19
  13Q GAIN WILD-TYPE    49 46 65 49
D25V6, multiclass
       clus
vv      13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  T0+T1               15                 49
  T2                  26                 46
  T3                  12                 65
  T4                  19                 49
[1] 4 2
[1] TRUE
[1] "dimension of 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    49  18   6   8
  13Q GAIN WILD-TYPE 120  45  32  41
D25V7, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  N0               49                120
  N1               18                 45
  N2                6                 32
  N3                8                 41
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V8, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED    81   3
  13Q GAIN WILD-TYPE 232  18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED     81    3
  13Q GAIN WILD-TYPE  232   18
   clus
vv  13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  0               81                232
  1                3                 18
[1] 2 2
[1] FALSE
D25V9, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED    29  25
  13Q GAIN WILD-TYPE 103  63
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED     29   25
  13Q GAIN WILD-TYPE  103   63
     clus
vv    13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  NO                29                103
  YES               25                 63
[1] 2 2
[1] FALSE
D25V10, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED    12  81
  13Q GAIN WILD-TYPE  32 232
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED     12   81
  13Q GAIN WILD-TYPE   32  232
     clus
vv    13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  NO                12                 32
  YES               81                232
[1] 2 2
[1] FALSE
D25V11, continuous
D25V12, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED    35  58
  13Q GAIN WILD-TYPE 100 165
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED     35   58
  13Q GAIN WILD-TYPE  100  165
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  FEMALE               35                100
  MALE                 58                165
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  13Q GAIN MUTATED       2                         0    89
  13Q GAIN WILD-TYPE     3                         1   255
D25V13, multiclass
                           clus
vv                          13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  ASIAN                                    2                  3
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   89                255
[1] 3 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     1  88
  13Q GAIN WILD-TYPE   6 256
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      1   88
  13Q GAIN WILD-TYPE    6  256
                        clus
vv                       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO               88                256
[1] 2 2
[1] FALSE

Clustering(26) Variable = 14Q GAIN MUTATION ANALYSIS
D26V1, survival
                    sevent
clus2                  0   1
  14Q GAIN MUTATED    15  15
  14Q GAIN WILD-TYPE 106 103
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                30                209 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                15                103 
$`14Q GAIN MUTATED`
TCGA-D3-A2JA TCGA-D3-A2JL TCGA-D3-A3C6 TCGA-D3-A8GK TCGA-D3-A8GM TCGA-DA-A1I2 
       15.75       171.58        58.06       120.00        70.62       150.61 
TCGA-DA-A1I7 TCGA-EB-A5SH TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A29D TCGA-EE-A29M 
       32.42        50.07        62.37       155.90        12.99        47.74 
TCGA-EE-A2GH TCGA-EE-A2GM TCGA-EE-A2GO TCGA-EE-A2MJ TCGA-EE-A2MU TCGA-EE-A3AE 
      189.40        18.35       118.32        63.25        53.26        54.51 
TCGA-ER-A19C TCGA-ER-A19L TCGA-ER-A19M TCGA-FR-A729 TCGA-FR-A8YC TCGA-FS-A1ZW 
       39.81        99.06        59.84       209.23        10.06        23.21 
TCGA-FS-A1ZY TCGA-GN-A265 TCGA-GN-A9SD TCGA-QB-AA9O TCGA-W3-A828 TCGA-WE-AAA3 
        5.29        84.72        59.41        18.05       120.07        16.64 

$`14Q GAIN WILD-TYPE`
TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
       60.46        12.99        14.83         8.42        15.72        31.89 
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB 
      110.93        49.35       133.25        19.04        76.41        62.60 
TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
       25.64        45.99        62.86       168.00        86.30         7.27 
TCGA-D3-A2JE TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP 
        9.76       107.61        36.30        64.83        66.08        43.53 
TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML 
       46.98       140.98        40.01        59.70        16.96        13.87 
TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51J TCGA-D3-A51K 
        9.34        90.21        23.67       173.85       144.46        31.76 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GU 
       62.70        11.34        42.05        45.70       177.86       124.08 
TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GJ TCGA-D3-A8GL TCGA-D3-A8GP TCGA-D3-A8GR 
       78.21        23.61       179.97        69.53       135.12        36.53 
TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6EC TCGA-D9-A6EG 
       10.78        15.02        16.90        18.44        57.90        22.85 
TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I5 TCGA-DA-A1IA TCGA-DA-A1IC 
       48.66       106.85        31.96        82.85        64.83        58.85 
TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5SG TCGA-EB-A5UN 
       25.12       214.59        14.96         3.91        33.24        45.50 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A184 
        6.64        13.15        24.89        20.38         0.00        67.50 
TCGA-EE-A20C TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H 
       75.55        75.22        76.14         0.26        44.28        63.12 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A2 
       27.16        61.12       346.49       185.19       102.38         7.20 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GJ TCGA-EE-A2GK 
       77.98        26.14       239.11         0.20        68.65        10.62 
TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU 
       32.48        31.00         0.76         0.20        71.31        81.99 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MG 
      103.13        15.25         5.75        23.77       209.79        94.19 
TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MR 
      171.85        67.50       104.78       145.45       227.01        25.08 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
      143.93        23.51       124.31       122.73        51.62         4.41 
TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB 
        6.28        67.89       111.85        45.90         3.35       201.80 
TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 
      152.81        14.56        34.45         1.58        47.31         7.82 
TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19N 
        4.54        53.29        11.47       151.46       150.12        42.48 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
      120.76        49.71        34.95       146.63        47.97        22.36 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
        4.70        16.87        10.95       173.29        55.82        15.48 
TCGA-ER-A3PL TCGA-FR-A44A TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FS-A1YW TCGA-FS-A1YY 
       32.05       174.21        26.20         5.65       171.78        49.74 
TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE 
      195.98         8.35        27.62       312.07        32.78        35.90 
TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS 
       12.92         7.82        36.33        78.61       130.95       136.27 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 
       35.28         4.47         3.06        30.90        66.67       173.19 
TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
       13.28        80.68        55.59        11.54        19.30         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 
        6.05         1.91        53.29       117.93        17.06        42.48 
TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-GN-A8LK TCGA-LH-A9QB 
        7.59       120.53        34.49        46.92        43.23        85.05 
TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-AA1Q 
      297.01         7.23         0.33       174.12         1.97        44.05 
TCGA-W3-AA1R TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8K5 
       79.99         8.09       185.13        92.84         1.15        59.64 
TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZY 
       62.99        12.69        19.00        59.44        10.95        48.39 
TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-Z2-AA3S 
        1.94        26.60        15.65        28.21        91.23 

  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
              5.29               0.00 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
            209.23             346.49 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
            58.735             44.050 
[1] "5.3 - 209.2 (58.7)" "0.0 - 346.5 (44.0)"
[1] "hr=" "1.1"
D26V2, survival
                    sevent
clus2                  0   1
  14Q GAIN MUTATED    19  21
  14Q GAIN WILD-TYPE 150 159
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                40                309 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                21                159 
$`14Q GAIN MUTATED`
TCGA-D3-A1Q9 TCGA-D3-A2JA TCGA-D3-A2JL TCGA-D3-A3C6 TCGA-D3-A8GK TCGA-D3-A8GM 
       31.59       115.53       171.58        58.06       170.20       107.15 
TCGA-D9-A6E9 TCGA-DA-A1I2 TCGA-DA-A1I7 TCGA-EB-A5SH TCGA-EE-A180 TCGA-EE-A20H 
        9.90       176.55        61.18        54.02        94.98       168.26 
TCGA-EE-A29D TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A2GH TCGA-EE-A2GM TCGA-EE-A2GO 
       13.97         2.60        56.84       208.04        75.48       126.81 
TCGA-EE-A2M5 TCGA-EE-A2MJ TCGA-EE-A2MU TCGA-EE-A3AE TCGA-EE-A3JH TCGA-ER-A19C 
       21.67        96.23        53.26        54.51       109.58        48.89 
TCGA-ER-A19L TCGA-ER-A19M TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A8YC TCGA-FR-A8YD 
      131.51        61.05        15.72       220.80        34.82        36.26 
TCGA-FS-A1ZP TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-GN-A265 TCGA-GN-A26D TCGA-GN-A9SD 
       74.73        49.48        27.09        84.72        39.58        59.41 
TCGA-QB-AA9O TCGA-W3-A828 TCGA-W3-AA1O TCGA-WE-AAA3 
       18.05       121.08         4.01        19.73 

$`14Q GAIN WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q3 
       17.03        66.48        12.99        14.93        16.57        16.67 
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA 
      112.04       112.57        71.80       133.25        28.08        90.90 
TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JB 
       95.74        43.43       103.10        65.49        23.77       168.00 
TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH 
       86.76        11.87        27.65        62.07       113.52        42.08 
TCGA-D3-A2JK TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C7 
       12.10        66.48        66.08        59.57       130.72        46.98 
TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML 
       46.32       166.52        86.93        60.23        24.53        13.87 
TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F 
        9.34       103.59        39.75        45.30       174.84        55.73 
TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T 
       56.35       145.12        32.94        22.62        63.81        26.89 
TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU 
      125.79       135.75       137.92       178.32        18.18       125.19 
TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GI TCGA-D3-A8GJ 
       30.84        79.59        23.61        26.43        58.52       241.38 
TCGA-D3-A8GL TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS 
       89.13       161.00       152.75        29.06       129.63       117.17 
TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A1X3 TCGA-D9-A3Z1 
      151.53        54.67         3.65         7.10        18.12        15.39 
TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV 
       22.29        18.44        25.18        66.25        22.95        48.89 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I4 TCGA-DA-A1I5 
       36.03       117.21        20.38       194.83        35.93       107.34 
TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
       53.92        65.92        23.44        68.09        28.60        10.49 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG 
      215.44        15.68        13.87        10.36        20.35        68.25 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y 
       17.29        52.01         7.04        24.89        29.82        27.22 
TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 
        8.65        33.73        14.70        26.89        68.15         4.96 
TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
      133.81       151.27        91.56        13.55        63.35        85.08 
TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29N TCGA-EE-A29P 
       78.97        63.78        72.07        64.64        18.61        56.42 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W 
       66.74        14.47        61.28       369.93        25.87       195.02 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
       17.92        46.82       102.90        36.82        39.29        86.14 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GJ 
       59.28        67.43       340.14       161.03        48.72       107.38 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
       54.74        79.66       102.12        13.91        42.77        81.21 
TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC 
       44.88        94.82       129.27        28.83        19.76        61.51 
TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
       47.28       103.27       268.73       103.20        16.96       204.66 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ 
      158.63       216.66       167.90        47.54       248.65        43.23 
TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC 
      134.40       162.48        71.21       124.31       122.73        51.62 
TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 
       28.77        13.81        41.59       138.81       172.18       127.20 
TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JD 
       36.95        64.08        34.32        53.19       201.80        27.35 
TCGA-EE-A3JE TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
       51.35       152.81        31.40        35.44        13.94        50.76 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F 
        9.17        77.75        98.40        12.59        13.02        26.37 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
      268.93       152.35         6.44        44.05       162.08        50.89 
TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
       37.25         8.88       148.18        79.99        43.82        23.34 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET 
       20.15        16.37        31.27        32.05       247.04        80.32 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A7U8 
       46.98        33.21         6.77        92.98       174.21        27.85 
TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY 
       18.77        38.27       104.42       216.92        48.59       228.59 
TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB 
      202.65        20.91        28.08         7.79        27.72        48.85 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH 
      357.37        53.52        40.27        15.45         9.70        32.75 
TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS 
       47.38        23.93       101.26       133.55        11.41       148.80 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 
       53.16        26.56        27.02        77.82        50.14        66.67 
TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD 
       28.73       174.84        34.03        26.73        54.41        80.68 
TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
        0.20        22.92        55.59        13.51        19.30         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A266 
        7.23         2.04        15.78       139.89       117.93        10.13 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 
       64.44        62.79        32.48       121.91        39.35        10.42 
TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A8LL TCGA-HR-A2OG TCGA-HR-A2OH 
       48.89        22.13        50.10        21.37         0.23        65.88 
TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 
      368.78       297.90         7.23         0.33         0.69       228.16 
TCGA-W3-A825 TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 
       63.02        69.07       111.09        42.08       219.16       105.04 
TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN 
       24.03        49.05        61.15        15.98        98.89        58.98 
TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AA9Y 
       67.63        59.77        11.80        32.58        49.51        12.16 
TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-YD-A89C TCGA-YD-A9TA TCGA-YG-AA3O TCGA-YG-AA3P 
       35.01        22.29         6.90        49.18        37.94        14.43 
TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
       27.58        96.99        15.98 

  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
               2.6                0.2 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
            220.80             369.93 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
            58.735             49.180 
[1] "2.6 - 220.8 (58.7)" "0.2 - 369.9 (49.2)"
[1] "hr=" "1.1"
D26V3, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  14Q GAIN MUTATED                    7             1
  14Q GAIN WILD-TYPE                 58             4
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  14Q GAIN MUTATED                                           6
  14Q GAIN WILD-TYPE                                        66
                    vv
clus                 REGIONAL LYMPH NODE
  14Q GAIN MUTATED                    27
  14Q GAIN WILD-TYPE                 188
D26V4, multiclass
                                           clus
vv                                          14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  DISTANT METASTASIS                                       7                 58
  PRIMARY TUMOR                                            1                  4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                6                 66
  REGIONAL LYMPH NODE                                     27                188
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  14Q GAIN MUTATED             1       1       5        3        4        3
  14Q GAIN WILD-TYPE          11       6      23       15       23       21
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  14Q GAIN MUTATED           1         3         3         4          2
  14Q GAIN WILD-TYPE        13        16         9        33         13
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  14Q GAIN MUTATED            3          6        0
  14Q GAIN WILD-TYPE         29         54       20
D26V5, multiclass
             clus
vv            14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  I OR II NOS                1                 11
  STAGE 0                    1                  6
  STAGE I                    5                 23
  STAGE IA                   3                 15
  STAGE IB                   4                 23
  STAGE II                   3                 21
  STAGE IIA                  1                 13
  STAGE IIB                  3                 16
  STAGE IIC                  3                  9
  STAGE III                  4                 33
  STAGE IIIA                 2                 13
  STAGE IIIB                 3                 29
  STAGE IIIC                 6                 54
  STAGE IV                   0                 20
[1] 14  2
[1] TRUE
[1] "dimension of contingency 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       5 10  9 10
  14Q GAIN WILD-TYPE    59 62 68 58
D26V6, multiclass
       clus
vv      14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  T0+T1                5                 59
  T2                  10                 62
  T3                   9                 68
  T4                  10                 58
[1] 4 2
[1] TRUE
[1] "dimension of 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    25   4   5   3
  14Q GAIN WILD-TYPE 144  59  33  46
D26V7, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  N0               25                144
  N1                4                 59
  N2                5                 33
  N3                3                 46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V8, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED    37   0
  14Q GAIN WILD-TYPE 276  21
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED     37    0
  14Q GAIN WILD-TYPE  276   21
   clus
vv  14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  0               37                276
  1                0                 21
[1] 2 2
[1] FALSE
D26V9, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED    15  13
  14Q GAIN WILD-TYPE 117  75
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED     15   13
  14Q GAIN WILD-TYPE  117   75
     clus
vv    14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  NO                15                117
  YES               13                 75
[1] 2 2
[1] FALSE
D26V10, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED     5  36
  14Q GAIN WILD-TYPE  39 277
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      5   36
  14Q GAIN WILD-TYPE   39  277
     clus
vv    14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  NO                 5                 39
  YES               36                277
[1] 2 2
[1] FALSE
D26V11, continuous
D26V12, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED    14  27
  14Q GAIN WILD-TYPE 121 196
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED     14   27
  14Q GAIN WILD-TYPE  121  196
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  FEMALE               14                121
  MALE                 27                196
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  14Q GAIN MUTATED       0                         0    41
  14Q GAIN WILD-TYPE     5                         1   303
D26V13, multiclass
                           clus
vv                          14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  ASIAN                                    0                  5
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   41                303
[1] 3 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     0  41
  14Q GAIN WILD-TYPE   7 303
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      0   41
  14Q GAIN WILD-TYPE    7  303
                        clus
vv                       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  7
  NOT HISPANIC OR LATINO               41                303
[1] 2 2
[1] FALSE

Clustering(27) Variable = 15Q GAIN MUTATION ANALYSIS
D27V1, survival
                    sevent
clus2                 0  1
  15Q GAIN MUTATED   24 28
  15Q GAIN WILD-TYPE 97 90
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                52                187 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                28                 90 
$`15Q GAIN MUTATED`
TCGA-D3-A1Q5 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JL TCGA-D3-A2JN 
      110.93        15.75        86.30         7.27       171.58        64.83 
TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A8GD TCGA-D3-A8GL TCGA-D3-A8GM TCGA-DA-A1I7 
      140.98        59.70        23.61        69.53        70.62        32.42 
TCGA-DA-A3F5 TCGA-EE-A17Y TCGA-EE-A20H TCGA-EE-A29D TCGA-EE-A29T TCGA-EE-A29W 
      214.59        24.89       155.90        12.99       346.49       185.19 
TCGA-EE-A2A1 TCGA-EE-A2GM TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2M6 TCGA-EE-A2M7 
      102.38        18.35       118.32         0.76       103.13        15.25 
TCGA-EE-A2MJ TCGA-EE-A2MP TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A3AA TCGA-EE-A3AE 
       63.25       227.01        25.08       143.93       124.31        54.51 
TCGA-EE-A3J3 TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A19C TCGA-ER-A19M TCGA-ER-A19P 
       67.89       152.81        14.56        39.81        59.84       120.76 
TCGA-ER-A19S TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A8YC TCGA-FS-A1Z3 TCGA-FS-A1ZD 
       34.95       174.21       209.23        10.06         8.35        32.78 
TCGA-FS-A1ZY TCGA-FS-A4FD TCGA-GF-A4EO TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A9SD 
        5.29        80.68         6.05       117.93        17.06        59.41 
TCGA-W3-A825 TCGA-W3-A828 TCGA-WE-A8ZM TCGA-WE-A8ZQ 
        1.97       120.07        62.99        59.44 

$`15Q GAIN WILD-TYPE`
TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
       60.46        12.99        14.83         8.42        15.72        31.89 
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 
       49.35       133.25        19.04        76.41        62.60        25.64 
TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JB TCGA-D3-A2JE TCGA-D3-A2JG TCGA-D3-A2JH 
       45.99        62.86       168.00         9.76       107.61        36.30 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CC TCGA-D3-A3CF 
       66.08        43.53        58.06        46.98        40.01        16.96 
TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51J 
       13.87         9.34        90.21        23.67       173.85       144.46 
TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR 
       31.76        62.70        11.34        42.05        45.70       177.86 
TCGA-D3-A5GU TCGA-D3-A8GC TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GP TCGA-D3-A8GR 
      124.08        78.21       179.97       120.00       135.12        36.53 
TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6EC TCGA-D9-A6EG 
       10.78        15.02        16.90        18.44        57.90        22.85 
TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1IA 
       48.66       106.85        31.96       150.61        82.85        64.83 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5SG TCGA-EB-A5SH 
       58.85        25.12        14.96         3.91        33.24        50.07 
TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 
       45.50         6.64        13.15        62.37        20.38         0.00 
TCGA-EE-A184 TCGA-EE-A20C TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G 
       67.50        75.55        75.22        76.14         0.26        44.28 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A2A2 TCGA-EE-A2A6 
       63.12        47.74        27.16        61.12         7.20        77.98 
TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK 
       26.14       239.11         0.20       189.40        68.65        10.62 
TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M8 
       32.48        31.00         0.20        71.31        81.99         5.75 
TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML 
       23.77       209.79        94.19       171.85        67.50       104.78 
TCGA-EE-A2MM TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
      145.45        23.51        53.26       122.73        51.62         4.41 
TCGA-EE-A3AF TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-ER-A195 
        6.28       111.85        45.90         3.35       201.80        34.45 
TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19D 
        1.58        47.31         7.82         4.54        53.29        11.47 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A19W 
      151.46       150.12        99.06        42.48        49.71       146.63 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A3ES 
       47.97        22.36         4.70        16.87        10.95       173.29 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FS-A1YW 
       55.82        15.48        32.05        26.20         5.65       171.78 
TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZE TCGA-FS-A1ZF 
       49.74       195.98        27.62       312.07        35.90        12.92 
TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT 
        7.82        36.33        78.61       130.95       136.27        35.28 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 
        4.47        23.21         3.06        30.90        66.67       173.19 
TCGA-FS-A4F9 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 
       13.28        55.59        11.54        19.30         9.90         1.91 
TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 
       53.29        84.72        42.48         7.59       120.53        34.49 
TCGA-GN-A4U8 TCGA-GN-A8LK TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O 
       46.92        43.23        85.05       297.01         7.23        18.05 
TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1V TCGA-W3-AA1W 
        0.33       174.12        44.05        79.99         8.09       185.13 
TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT 
       92.84         1.15        59.64        12.69        19.00        10.95 
TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O 
       48.39         1.94        26.60        16.64        15.65        28.21 
TCGA-Z2-AA3S 
       91.23 

  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
              0.76               0.00 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
            346.49             312.07 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
             63.12              43.53 
[1] "0.8 - 346.5 (63.1)" "0.0 - 312.1 (43.5)"
[1] "hr=" "1.2"
D27V2, survival
                    sevent
clus2                  0   1
  15Q GAIN MUTATED    39  41
  15Q GAIN WILD-TYPE 130 139
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                80                269 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                41                139 
$`15Q GAIN MUTATED`
TCGA-D3-A1Q5 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JD 
      112.57        31.59        23.77       115.53        86.76        11.87 
TCGA-D3-A2JF TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3MV 
       62.07       171.58        66.48       166.52        60.23        45.30 
TCGA-D3-A8GD TCGA-D3-A8GI TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GQ TCGA-D9-A149 
       23.61        58.52        89.13       107.15        29.06        54.67 
TCGA-D9-A6EA TCGA-DA-A1HW TCGA-DA-A1I7 TCGA-DA-A3F5 TCGA-EE-A17Y TCGA-EE-A183 
       25.18        36.03        61.18       215.44        27.22        26.89 
TCGA-EE-A20B TCGA-EE-A20H TCGA-EE-A29D TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A29X 
      133.81       168.26        13.97       369.93       195.02        17.92 
TCGA-EE-A2A1 TCGA-EE-A2GI TCGA-EE-A2GM TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2M6 
      102.90        48.72        75.48       126.81        13.91       129.27 
TCGA-EE-A2M7 TCGA-EE-A2MJ TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MR TCGA-EE-A2MS 
       28.83        96.23        47.54       248.65       134.40       162.48 
TCGA-EE-A3AA TCGA-EE-A3AE TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3J5 TCGA-EE-A3JH 
      124.31        54.51        41.59       172.18        36.95       109.58 
TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A19C TCGA-ER-A19M TCGA-ER-A19P TCGA-ER-A19S 
      152.81        31.40        48.89        61.05       162.08        37.25 
TCGA-ER-A19T TCGA-ER-A42K TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U9 
        8.88         6.77       174.21        15.72       220.80        18.77 
TCGA-FR-A8YC TCGA-FS-A1Z3 TCGA-FS-A1ZD TCGA-FS-A1ZY TCGA-FS-A4F2 TCGA-FS-A4FD 
       34.82        20.91        53.52        27.09        50.14        80.68 
TCGA-GF-A4EO TCGA-GF-A6C9 TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A9SD TCGA-HR-A2OG 
        7.23        15.78       117.93        64.44        59.41         0.23 
TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZQ 
       63.02       121.08         4.01        15.98        98.89        59.77 
TCGA-WE-A8ZX TCGA-YD-A9TA 
       32.58        49.18 

$`15Q GAIN WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q3 
       17.03        66.48        12.99        14.93        16.57        16.67 
TCGA-D3-A1Q4 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB 
      112.04        71.80       133.25        28.08        90.90        95.74 
TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JB TCGA-D3-A2JE TCGA-D3-A2JG 
       43.43       103.10        65.49       168.00        27.65       113.52 
TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 
       42.08        12.10        66.08        59.57       130.72        58.06 
TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO 
       46.98        46.32        86.93        24.53        13.87         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J 
      103.59        39.75       174.84        55.73        56.35       145.12 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN 
       32.94        22.62        63.81        26.89       125.79       135.75 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GC 
      137.92       178.32        18.18       125.19        30.84        79.59 
TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GR 
       26.43       241.38       170.20       161.00       152.75       129.63 
TCGA-D3-A8GS TCGA-D9-A148 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A1X3 TCGA-D9-A3Z1 
      117.17       151.53         3.65         7.10        18.12        15.39 
TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV 
       22.29        18.44         9.90        66.25        22.95        48.89 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
      117.21        20.38       194.83       176.55        35.93       107.34 
TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
       53.92        65.92        23.44        68.09        28.60        10.49 
TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH 
       15.68        13.87        10.36        20.35        68.25        54.02 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Z 
       17.29        52.01         7.04        24.89        29.82         8.65 
TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20C 
       94.98        33.73        14.70        68.15         4.96       151.27 
TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E 
       91.56        13.55        63.35        85.08        78.97        63.78 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P 
       72.07        64.64         2.60        56.84        18.61        56.42 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A2A0 TCGA-EE-A2A2 
       66.74        14.47        61.28        25.87        46.82        36.82 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE 
       39.29        86.14        59.28        67.43       340.14       161.03 
TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GR 
      208.04       107.38        54.74        79.66       102.12        42.77 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M8 TCGA-EE-A2MC 
       81.21        44.88        94.82        21.67        19.76        61.51 
TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
       47.28       103.27       268.73       103.20        16.96       204.66 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MQ TCGA-EE-A2MT TCGA-EE-A2MU 
      158.63       216.66       167.90        43.23        71.21        53.26 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J4 
      122.73        51.62        28.77        13.81       138.81       127.20 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE 
       64.08        34.32        53.19       201.80        27.35        51.35 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B 
       35.44        13.94        50.76         9.17        77.75        98.40 
TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J 
       12.59        13.02        26.37       268.93       152.35         6.44 
TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
      131.51        44.05        50.89       148.18        79.99        43.82 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES 
       23.34        20.15        16.37        31.27        32.05       247.04 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A7U8 TCGA-FR-A7UA 
       80.32        46.98        33.21        92.98        27.85        38.27 
TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
       36.26       104.42       216.92        48.59       228.59       202.65 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZE 
       28.08         7.79        27.72        48.85       357.37        40.27 
TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM 
       15.45         9.70        32.75        47.38        23.93       101.26 
TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU 
       74.73       133.55        11.41       148.80        53.16        26.56 
TCGA-FS-A1ZW TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 
       49.48        27.02        77.82        66.67        28.73       174.84 
TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU 
       34.03        26.73        54.41         0.20        22.92        55.59 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A265 
       13.51        19.30         9.90         2.04       139.89        84.72 
TCGA-GN-A266 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A4U4 
       10.13        62.79        32.48        39.58       121.91        39.35 
TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A8LL TCGA-HR-A2OH 
       10.42        48.89        22.13        50.10        21.37        65.88 
TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 TCGA-RP-A694 
      368.78       297.90         7.23        18.05         0.33         0.69 
TCGA-W3-A824 TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 
      228.16        69.07       111.09        42.08       219.16       105.04 
TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT 
       24.03        49.05        61.15        58.98        67.63        11.80 
TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YD-A89C 
       49.51        12.16        35.01        19.73        22.29         6.90 
TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
       37.94        14.43        27.58        96.99        15.98 

  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
              0.23               0.20 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
            369.93             368.78 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
            58.965             49.480 
[1] "0.2 - 369.9 (59.0)" "0.2 - 368.8 (49.5)"
[1] "hr=" "1.1"
D27V3, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  15Q GAIN MUTATED                   13             2
  15Q GAIN WILD-TYPE                 52             3
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  15Q GAIN MUTATED                                          15
  15Q GAIN WILD-TYPE                                        57
                    vv
clus                 REGIONAL LYMPH NODE
  15Q GAIN MUTATED                    54
  15Q GAIN WILD-TYPE                 161
D27V4, multiclass
                                           clus
vv                                          15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  DISTANT METASTASIS                                      13                 52
  PRIMARY TUMOR                                            2                  3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               15                 57
  REGIONAL LYMPH NODE                                     54                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                 I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  15Q GAIN MUTATED             6       2       8        5        5        8
  15Q GAIN WILD-TYPE           6       5      20       13       22       16
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  15Q GAIN MUTATED           2         4         2         8          2
  15Q GAIN WILD-TYPE        12        15        10        29         13
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  15Q GAIN MUTATED           11         11        3
  15Q GAIN WILD-TYPE         21         49       17
D27V5, multiclass
             clus
vv            15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  I OR II NOS                6                  6
  STAGE 0                    2                  5
  STAGE I                    8                 20
  STAGE IA                   5                 13
  STAGE IB                   5                 22
  STAGE II                   8                 16
  STAGE IIA                  2                 12
  STAGE IIB                  4                 15
  STAGE IIC                  2                 10
  STAGE III                  8                 29
  STAGE IIIA                 2                 13
  STAGE IIIB                11                 21
  STAGE IIIC                11                 49
  STAGE IV                   3                 17
[1] 14  2
[1] TRUE
[1] "dimension of contingency 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      16 19 16 13
  15Q GAIN WILD-TYPE    48 53 61 55
D27V6, multiclass
       clus
vv      15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  T0+T1               16                 48
  T2                  19                 53
  T3                  16                 61
  T4                  13                 55
[1] 4 2
[1] TRUE
[1] "dimension of 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    43  15   7  10
  15Q GAIN WILD-TYPE 126  48  31  39
D27V7, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  N0               43                126
  N1               15                 48
  N2                7                 31
  N3               10                 39
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V8, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED    75   3
  15Q GAIN WILD-TYPE 238  18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED     75    3
  15Q GAIN WILD-TYPE  238   18
   clus
vv  15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  0               75                238
  1                3                 18
[1] 2 2
[1] FALSE
D27V9, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED    29  16
  15Q GAIN WILD-TYPE 103  72
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED     29   16
  15Q GAIN WILD-TYPE  103   72
     clus
vv    15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  NO                29                103
  YES               16                 72
[1] 2 2
[1] FALSE
D27V10, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED    13  70
  15Q GAIN WILD-TYPE  31 243
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED     13   70
  15Q GAIN WILD-TYPE   31  243
     clus
vv    15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  NO                13                 31
  YES               70                243
[1] 2 2
[1] FALSE
D27V11, continuous
D27V12, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED    30  54
  15Q GAIN WILD-TYPE 105 169
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED     30   54
  15Q GAIN WILD-TYPE  105  169
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  FEMALE               30                105
  MALE                 54                169
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  15Q GAIN MUTATED       1                         0    81
  15Q GAIN WILD-TYPE     4                         1   263
D27V13, multiclass
                           clus
vv                          15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  ASIAN                                    1                  4
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   81                263
[1] 3 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  81
  15Q GAIN WILD-TYPE   6 263
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      1   81
  15Q GAIN WILD-TYPE    6  263
                        clus
vv                       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO               81                263
[1] 2 2
[1] FALSE

Clustering(28) Variable = 16P GAIN MUTATION ANALYSIS
D28V1, survival
                    sevent
clus2                  0   1
  16P GAIN MUTATED    17  21
  16P GAIN WILD-TYPE 104  97
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                38                201 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                21                 97 
$`16P GAIN MUTATED`
TCGA-D3-A1Q6 TCGA-D3-A2JE TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A5GR TCGA-D3-A8GJ 
       49.35         9.76        58.06        59.70       177.86       179.97 
TCGA-D3-A8GP TCGA-D3-A8GR TCGA-EE-A17Y TCGA-EE-A20H TCGA-EE-A29P TCGA-EE-A2A1 
      135.12        36.53        24.89       155.90        27.16       102.38 
TCGA-EE-A2GB TCGA-EE-A2GH TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2M6 TCGA-EE-A2M7 
       26.14       189.40        18.35        31.00       103.13        15.25 
TCGA-EE-A2MP TCGA-EE-A3AE TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-ER-A19B TCGA-ER-A19C 
      227.01        54.51        67.89        45.90        53.29        39.81 
TCGA-ER-A19D TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A3PL TCGA-FR-A729 
       11.47        59.84        42.48       120.76        32.05       209.23 
TCGA-FS-A1ZY TCGA-FS-A4F4 TCGA-FS-A4FD TCGA-GF-A4EO TCGA-GN-A9SD TCGA-QB-AA9O 
        5.29        66.67        80.68         6.05        59.41        18.05 
TCGA-W3-AA1V TCGA-WE-AAA3 
        8.09        16.64 

$`16P GAIN WILD-TYPE`
TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
       60.46        12.99        14.83         8.42        15.72        31.89 
TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 
      110.93       133.25        19.04        76.41        62.60        25.64 
TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
       45.99        62.86        15.75       168.00        86.30         7.27 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP 
      107.61        36.30       171.58        64.83        66.08        43.53 
TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO 
       46.98       140.98        40.01        16.96        13.87         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R 
       90.21        23.67       173.85       144.46        31.76        62.70 
TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GU TCGA-D3-A8GC TCGA-D3-A8GD 
       11.34        42.05        45.70       124.08        78.21        23.61 
TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 
      120.00        69.53        70.62        10.78        15.02        16.90 
TCGA-D9-A4Z6 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 
       18.44        57.90        22.85        48.66       106.85        31.96 
TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 
      150.61        82.85        32.42        64.83        58.85        25.12 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN 
      214.59        14.96         3.91        33.24        50.07        45.50 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A184 
        6.64        13.15        62.37        20.38         0.00        67.50 
TCGA-EE-A20C TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G 
       75.55        75.22        76.14        12.99         0.26        44.28 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A2 
       63.12        47.74        61.12       346.49       185.19         7.20 
TCGA-EE-A2A6 TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
       77.98       239.11         0.20        68.65        10.62        32.48 
TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M8 
      118.32         0.76         0.20        71.31        81.99         5.75 
TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK 
       23.77       209.79        94.19       171.85        63.25        67.50 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU 
      104.78       145.45        25.08       143.93        23.51        53.26 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3J4 
      124.31       122.73        51.62         4.41         6.28       111.85 
TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
        3.35       201.80       152.81        14.56        34.45         1.58 
TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L 
       47.31         7.82         4.54       151.46       150.12        99.06 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
       49.71        34.95       146.63        47.97        22.36         4.70 
TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-FR-A44A 
       16.87        10.95       173.29        55.82        15.48       174.21 
TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 
       26.20         5.65        10.06       171.78        49.74       195.98 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF 
        8.35        27.62       312.07        32.78        35.90        12.92 
TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT 
        7.82        36.33        78.61       130.95       136.27        35.28 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F8 TCGA-FS-A4F9 
        4.47        23.21         3.06        30.90       173.19        13.28 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GN-A262 
       55.59        11.54        19.30         9.90         1.91        53.29 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 
      117.93        84.72        17.06        42.48         7.59       120.53 
TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-GN-A8LK TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS 
       34.49        46.92        43.23        85.05       297.01         7.23 
TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1Q TCGA-W3-AA1R 
        0.33       174.12         1.97       120.07        44.05        79.99 
TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8ZM TCGA-WE-A8ZN 
      185.13        92.84         1.15        59.64        62.99        12.69 
TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 
       19.00        59.44        10.95        48.39         1.94        26.60 
TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-Z2-AA3S 
       15.65        28.21        91.23 

  16P GAIN MUTATED 16P GAIN WILD-TYPE 
              5.29               0.00 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
            227.01             346.49 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
             51.32              45.70 
[1] "5.3 - 227.0 (51.3)" "0.0 - 346.5 (45.7)"
[1] "hr=" "1.1"
D28V2, survival
                    sevent
clus2                  0   1
  16P GAIN MUTATED    24  28
  16P GAIN WILD-TYPE 145 152
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                52                297 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                28                152 
$`16P GAIN MUTATED`
TCGA-D3-A1Q6 TCGA-D3-A1Q9 TCGA-D3-A2JE TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A5GR 
       71.80        31.59        27.65        58.06        60.23       178.32 
TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GP TCGA-D3-A8GR TCGA-D3-A8GS TCGA-EE-A17Y 
       58.52       241.38       152.75       129.63       117.17        27.22 
TCGA-EE-A20B TCGA-EE-A20H TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A2A1 TCGA-EE-A2A5 
      133.81       168.26        56.42        14.47       102.90        39.29 
TCGA-EE-A2GB TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2M6 
       59.28       208.04        48.72        75.48       102.12       129.27 
TCGA-EE-A2M7 TCGA-EE-A2MP TCGA-EE-A3AE TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-ER-A19B 
       28.83       248.65        54.51       172.18        64.08        98.40 
TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A3PL 
       48.89        12.59        61.05        44.05       162.08        33.21 
TCGA-FR-A69P TCGA-FR-A729 TCGA-FS-A1YX TCGA-FS-A1ZP TCGA-FS-A1ZY TCGA-FS-A4F4 
       15.72       220.80        48.59        74.73        27.09        66.67 
TCGA-FS-A4F5 TCGA-FS-A4FD TCGA-GF-A4EO TCGA-GN-A9SD TCGA-HR-A2OG TCGA-QB-AA9O 
       28.73        80.68         7.23        59.41         0.23        18.05 
TCGA-W3-AA1V TCGA-WE-A8K6 TCGA-WE-AAA3 TCGA-Z2-AA3V 
       42.08        15.98        19.73        15.98 

$`16P GAIN WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q3 
       17.03        66.48        12.99        14.93        16.57        16.67 
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB 
      112.04       112.57       133.25        28.08        90.90        95.74 
TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB 
       43.43       103.10        65.49        23.77       115.53       168.00 
TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK 
       86.76        11.87        62.07       113.52        42.08        12.10 
TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C7 
      171.58        66.48        66.08        59.57       130.72        46.98 
TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO 
       46.32       166.52        86.93        24.53        13.87         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
      103.59        39.75        45.30       174.84        55.73        56.35 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL 
      145.12        32.94        22.62        63.81        26.89       125.79 
TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GC 
      135.75       137.92        18.18       125.19        30.84        79.59 
TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GN 
       23.61        26.43       170.20        89.13       107.15       161.00 
TCGA-D3-A8GQ TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A1X3 
       29.06       151.53        54.67         3.65         7.10        18.12 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC 
       15.39        22.29        18.44         9.90        25.18        66.25 
TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 
       22.95        48.89        36.03       117.21        20.38       194.83 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA 
      176.55        35.93       107.34        61.18        53.92        65.92 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 
       23.44        68.09        28.60        10.49       215.44        15.68 
TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL 
       13.87        10.36        20.35        68.25        54.02        17.29 
TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A180 
       52.01         7.04        24.89        29.82         8.65        94.98 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20C 
       33.73        14.70        26.89        68.15         4.96       151.27 
TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D 
       91.56        13.55        63.35        85.08        78.97        13.97 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N 
       63.78        72.07        64.64         2.60        56.84        18.61 
TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X 
       66.74        61.28       369.93        25.87       195.02        17.92 
TCGA-EE-A2A0 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE 
       46.82        36.82        86.14        67.43       340.14       161.03 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR 
      107.38        54.74        79.66       126.81        13.91        42.77 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M8 TCGA-EE-A2MC 
       81.21        44.88        94.82        21.67        19.76        61.51 
TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
       47.28       103.27       268.73       103.20        16.96       204.66 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MQ 
       96.23       158.63       216.66       167.90        47.54        43.23 
TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB 
      134.40       162.48        71.21        53.26       124.31       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J4 
       51.62        28.77        13.81        41.59       138.81       127.20 
TCGA-EE-A3J5 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE 
       36.95        34.32        53.19       201.80        27.35        51.35 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
      109.58       152.81        31.40        35.44        13.94        50.76 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H 
        9.17        77.75        13.02        26.37       268.93       152.35 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W 
        6.44       131.51        50.89        37.25         8.88       148.18 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
       79.99        43.82        23.34        20.15        16.37        31.27 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A42K TCGA-FR-A3YN 
       32.05       247.04        80.32        46.98         6.77        92.98 
TCGA-FR-A44A TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD 
      174.21        27.85        18.77        38.27        34.82        36.26 
TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 
      104.42       216.92       228.59       202.65        20.91        28.08 
TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE 
        7.79        27.72        48.85       357.37        53.52        40.27 
TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM 
       15.45         9.70        32.75        47.38        23.93       101.26 
TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW 
      133.55        11.41       148.80        53.16        26.56        49.48 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB 
       27.02        77.82        50.14       174.84        34.03        26.73 
TCGA-FS-A4FC TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
       54.41         0.20        22.92        55.59        13.51        19.30 
TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        9.90         2.04        15.78       139.89       117.93        84.72 
TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U3 
       10.13        64.44        62.79        32.48        39.58       121.91 
TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A8LL 
       39.35        10.42        48.89        22.13        50.10        21.37 
TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 
       65.88       368.78       297.90         7.23         0.33         0.69 
TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1Q TCGA-W3-AA1R 
      228.16        63.02       121.08         4.01        69.07       111.09 
TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8ZM 
      219.16       105.04        24.03        49.05        61.15        98.89 
TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-A8ZY 
       58.98        67.63        59.77        11.80        32.58        49.51 
TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-YD-A89C TCGA-YD-A9TA TCGA-YG-AA3O 
       12.16        35.01        22.29         6.90        49.18        37.94 
TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S 
       14.43        27.58        96.99 

  16P GAIN MUTATED 16P GAIN WILD-TYPE 
              0.23               0.20 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
            248.65             369.93 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
             58.90              49.51 
[1] "0.2 - 248.7 (58.9)" "0.2 - 369.9 (49.5)"
[1] "hr=" "1.1"
D28V3, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  16P GAIN MUTATED                    7             0
  16P GAIN WILD-TYPE                 58             5
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  16P GAIN MUTATED                                          15
  16P GAIN WILD-TYPE                                        57
                    vv
clus                 REGIONAL LYMPH NODE
  16P GAIN MUTATED                    33
  16P GAIN WILD-TYPE                 182
D28V4, multiclass
                                           clus
vv                                          16P GAIN MUTATED 16P GAIN WILD-TYPE
  DISTANT METASTASIS                                       7                 58
  PRIMARY TUMOR                                            0                  5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               15                 57
  REGIONAL LYMPH NODE                                     33                182
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  16P GAIN MUTATED             2       2       9        5        7        6
  16P GAIN WILD-TYPE          10       5      19       13       20       18
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  16P GAIN MUTATED           1         1         2         4          0
  16P GAIN WILD-TYPE        13        18        10        33         15
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  16P GAIN MUTATED            4          7        1
  16P GAIN WILD-TYPE         28         53       19
D28V5, multiclass
             clus
vv            16P GAIN MUTATED 16P GAIN WILD-TYPE
  I OR II NOS                2                 10
  STAGE 0                    2                  5
  STAGE I                    9                 19
  STAGE IA                   5                 13
  STAGE IB                   7                 20
  STAGE II                   6                 18
  STAGE IIA                  1                 13
  STAGE IIB                  1                 18
  STAGE IIC                  2                 10
  STAGE III                  4                 33
  STAGE IIIA                 0                 15
  STAGE IIIB                 4                 28
  STAGE IIIC                 7                 53
  STAGE IV                   1                 19
[1] 14  2
[1] TRUE
[1] "dimension of contingency 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 18 10  5
  16P GAIN WILD-TYPE    53 54 67 63
D28V6, multiclass
       clus
vv      16P GAIN MUTATED 16P GAIN WILD-TYPE
  T0+T1               11                 53
  T2                  18                 54
  T3                  10                 67
  T4                   5                 63
[1] 4 2
[1] TRUE
[1] "dimension of 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    36   7   3   5
  16P GAIN WILD-TYPE 133  56  35  44
D28V7, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  N0               36                133
  N1                7                 56
  N2                3                 35
  N3                5                 44
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V8, binary
                    cls
clus                   0   1
  16P GAIN MUTATED    51   1
  16P GAIN WILD-TYPE 262  20
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     51    1
  16P GAIN WILD-TYPE  262   20
   clus
vv  16P GAIN MUTATED 16P GAIN WILD-TYPE
  0               51                262
  1                1                 20
[1] 2 2
[1] FALSE
D28V9, binary
                    cls
clus                   0   1
  16P GAIN MUTATED    16  12
  16P GAIN WILD-TYPE 116  76
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     16   12
  16P GAIN WILD-TYPE  116   76
     clus
vv    16P GAIN MUTATED 16P GAIN WILD-TYPE
  NO                16                116
  YES               12                 76
[1] 2 2
[1] FALSE
D28V10, binary
                    cls
clus                   0   1
  16P GAIN MUTATED     5  50
  16P GAIN WILD-TYPE  39 263
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      5   50
  16P GAIN WILD-TYPE   39  263
     clus
vv    16P GAIN MUTATED 16P GAIN WILD-TYPE
  NO                 5                 39
  YES               50                263
[1] 2 2
[1] FALSE
D28V11, continuous
D28V12, binary
                    cls
clus                   0   1
  16P GAIN MUTATED    23  32
  16P GAIN WILD-TYPE 112 191
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     23   32
  16P GAIN WILD-TYPE  112  191
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  FEMALE               23                112
  MALE                 32                191
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16P GAIN MUTATED       1                         0    53
  16P GAIN WILD-TYPE     4                         1   291
D28V13, multiclass
                           clus
vv                          16P GAIN MUTATED 16P GAIN WILD-TYPE
  ASIAN                                    1                  4
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   53                291
[1] 3 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     1  51
  16P GAIN WILD-TYPE   6 293
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      1   51
  16P GAIN WILD-TYPE    6  293
                        clus
vv                       16P GAIN MUTATED 16P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO               51                293
[1] 2 2
[1] FALSE

Clustering(29) Variable = 16Q GAIN MUTATION ANALYSIS
D29V1, survival
                    sevent
clus2                  0   1
  16Q GAIN MUTATED    11  18
  16Q GAIN WILD-TYPE 110 100
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                29                210 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                18                100 
$`16Q GAIN MUTATED`
TCGA-D3-A1Q6 TCGA-D3-A2JE TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A5GR TCGA-D3-A8GP 
       49.35         9.76        58.06        59.70       177.86       135.12 
TCGA-D3-A8GR TCGA-EE-A17Y TCGA-EE-A20H TCGA-EE-A2A1 TCGA-EE-A2GB TCGA-EE-A2GM 
       36.53        24.89       155.90       102.38        26.14        18.35 
TCGA-EE-A2GN TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MP TCGA-EE-A3J3 TCGA-EE-A3J7 
       31.00       103.13        15.25       227.01        67.89        45.90 
TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19M TCGA-ER-A19P TCGA-ER-A3PL TCGA-FR-A729 
       39.81        11.47        59.84       120.76        32.05       209.23 
TCGA-FS-A1ZY TCGA-FS-A4F4 TCGA-GF-A4EO TCGA-GN-A9SD TCGA-W3-AA1V 
        5.29        66.67         6.05        59.41         8.09 

$`16Q GAIN WILD-TYPE`
TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
       60.46        12.99        14.83         8.42        15.72        31.89 
TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 
      110.93       133.25        19.04        76.41        62.60        25.64 
TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
       45.99        62.86        15.75       168.00        86.30         7.27 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP 
      107.61        36.30       171.58        64.83        66.08        43.53 
TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO 
       46.98       140.98        40.01        16.96        13.87         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R 
       90.21        23.67       173.85       144.46        31.76        62.70 
TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GU TCGA-D3-A8GC TCGA-D3-A8GD 
       11.34        42.05        45.70       124.08        78.21        23.61 
TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D9-A1X3 TCGA-D9-A3Z1 
      179.97       120.00        69.53        70.62        10.78        15.02 
TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY 
       16.90        18.44        57.90        22.85        48.66       106.85 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC 
       31.96       150.61        82.85        32.42        64.83        58.85 
TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5SG TCGA-EB-A5SH 
       25.12       214.59        14.96         3.91        33.24        50.07 
TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 
       45.50         6.64        13.15        62.37        20.38         0.00 
TCGA-EE-A184 TCGA-EE-A20C TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
       67.50        75.55        75.22        76.14        12.99         0.26 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T 
       44.28        63.12        47.74        27.16        61.12       346.49 
TCGA-EE-A29W TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
      185.19         7.20        77.98       239.11         0.20       189.40 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR 
       68.65        10.62        32.48       118.32         0.76         0.20 
TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MG 
       71.31        81.99         5.75        23.77       209.79        94.19 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MR 
      171.85        63.25        67.50       104.78       145.45        25.08 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC 
      143.93        23.51        53.26       124.31       122.73        51.62 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J4 TCGA-EE-A3J8 TCGA-EE-A3JB 
        4.41        54.51         6.28       111.85         3.35       201.80 
TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 
      152.81        14.56        34.45         1.58        47.31         7.82 
TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19N 
        4.54        53.29       151.46       150.12        99.06        42.48 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
       49.71        34.95       146.63        47.97        22.36         4.70 
TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-FR-A44A 
       16.87        10.95       173.29        55.82        15.48       174.21 
TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 
       26.20         5.65        10.06       171.78        49.74       195.98 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF 
        8.35        27.62       312.07        32.78        35.90        12.92 
TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT 
        7.82        36.33        78.61       130.95       136.27        35.28 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F8 TCGA-FS-A4F9 
        4.47        23.21         3.06        30.90       173.19        13.28 
TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 
       80.68        55.59        11.54        19.30         9.90         1.91 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
       53.29       117.93        84.72        17.06        42.48         7.59 
TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-GN-A8LK TCGA-LH-A9QB TCGA-OD-A75X 
      120.53        34.49        46.92        43.23        85.05       297.01 
TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 
        7.23        18.05         0.33       174.12         1.97       120.07 
TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8K5 
       44.05        79.99       185.13        92.84         1.15        59.64 
TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZY 
       62.99        12.69        19.00        59.44        10.95        48.39 
TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-Z2-AA3S 
        1.94        26.60        16.64        15.65        28.21        91.23 

  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
              5.29               0.00 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
            227.01             346.49 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
            49.350             45.845 
[1] "5.3 - 227.0 (49.4)" "0.0 - 346.5 (45.8)"
[1] "hr=" "1.3"
D29V2, survival
                    sevent
clus2                  0   1
  16Q GAIN MUTATED    17  22
  16Q GAIN WILD-TYPE 152 158
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                39                310 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                22                158 
$`16Q GAIN MUTATED`
TCGA-D3-A1Q6 TCGA-D3-A1Q9 TCGA-D3-A2JE TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A5GR 
       71.80        31.59        27.65        58.06        60.23       178.32 
TCGA-D3-A8GP TCGA-D3-A8GR TCGA-EE-A17Y TCGA-EE-A20B TCGA-EE-A20H TCGA-EE-A29R 
      152.75       129.63        27.22       133.81       168.26        14.47 
TCGA-EE-A2A1 TCGA-EE-A2GB TCGA-EE-A2GI TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2M6 
      102.90        59.28        48.72        75.48       102.12       129.27 
TCGA-EE-A2M7 TCGA-EE-A2MP TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-ER-A19C TCGA-ER-A19D 
       28.83       248.65       172.18        64.08        48.89        12.59 
TCGA-ER-A19E TCGA-ER-A19M TCGA-ER-A19P TCGA-ER-A3PL TCGA-FR-A69P TCGA-FR-A729 
       13.02        61.05       162.08        33.21        15.72       220.80 
TCGA-FS-A1YX TCGA-FS-A1ZY TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-GF-A4EO TCGA-GN-A9SD 
       48.59        27.09        66.67        28.73         7.23        59.41 
TCGA-HR-A2OG TCGA-W3-AA1V TCGA-WE-A8K6 
        0.23        42.08        15.98 

$`16Q GAIN WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q3 
       17.03        66.48        12.99        14.93        16.57        16.67 
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB 
      112.04       112.57       133.25        28.08        90.90        95.74 
TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB 
       43.43       103.10        65.49        23.77       115.53       168.00 
TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK 
       86.76        11.87        62.07       113.52        42.08        12.10 
TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C7 
      171.58        66.48        66.08        59.57       130.72        46.98 
TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO 
       46.32       166.52        86.93        24.53        13.87         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
      103.59        39.75        45.30       174.84        55.73        56.35 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL 
      145.12        32.94        22.62        63.81        26.89       125.79 
TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GC 
      135.75       137.92        18.18       125.19        30.84        79.59 
TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL 
       23.61        26.43        58.52       241.38       170.20        89.13 
TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GQ TCGA-D3-A8GS TCGA-D9-A148 TCGA-D9-A149 
      107.15       161.00        29.06       117.17       151.53        54.67 
TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 
        3.65         7.10        18.12        15.39        22.29        18.44 
TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW 
        9.90        25.18        66.25        22.95        48.89        36.03 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
      117.21        20.38       194.83       176.55        35.93       107.34 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
       61.18        53.92        65.92        23.44        68.09        28.60 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH 
       10.49       215.44        15.68        13.87        10.36        20.35 
TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 
       68.25        54.02        17.29        52.01         7.04        24.89 
TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
       29.82         8.65        94.98        33.73        14.70        26.89 
TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29A 
       68.15         4.96       151.27        91.56        13.55        63.35 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H 
       85.08        78.97        13.97        63.78        72.07        64.64 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29S 
        2.60        56.84        18.61        56.42        66.74        61.28 
TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A2 
      369.93        25.87       195.02        17.92        46.82        36.82 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
       39.29        86.14        67.43       340.14       161.03       208.04 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR 
      107.38        54.74        79.66       126.81        13.91        42.77 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M8 TCGA-EE-A2MC 
       81.21        44.88        94.82        21.67        19.76        61.51 
TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
       47.28       103.27       268.73       103.20        16.96       204.66 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MQ 
       96.23       158.63       216.66       167.90        47.54        43.23 
TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB 
      134.40       162.48        71.21        53.26       124.31       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH 
       51.62        28.77        54.51        13.81        41.59       138.81 
TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JD 
      127.20        36.95        34.32        53.19       201.80        27.35 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
       51.35       109.58       152.81        31.40        35.44        13.94 
TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19F TCGA-ER-A19G 
       50.76         9.17        77.75        98.40        26.37       268.93 
TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A19S 
      152.35         6.44       131.51        44.05        50.89        37.25 
TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
        8.88       148.18        79.99        43.82        23.34        20.15 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
       16.37        31.27        32.05       247.04        80.32        46.98 
TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA 
        6.77        92.98       174.21        27.85        18.77        38.27 
TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 
       34.82        36.26       104.42       216.92       228.59       202.65 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC 
       20.91        28.08         7.79        27.72        48.85       357.37 
TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ 
       53.52        40.27        15.45         9.70        32.75        47.38 
TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS 
       23.93       101.26        74.73       133.55        11.41       148.80 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 
       53.16        26.56        49.48        27.02        77.82        50.14 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 
      174.84        34.03        26.73        54.41        80.68         0.20 
TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 
       22.92        55.59        13.51        19.30         9.90         2.04 
TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 
       15.78       139.89       117.93        84.72        10.13        64.44 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 
       62.79        32.48        39.58       121.91        39.35        10.42 
TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A8LL TCGA-HR-A2OH TCGA-LH-A9QB 
       48.89        22.13        50.10        21.37        65.88       368.78 
TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 
      297.90         7.23        18.05         0.33         0.69       228.16 
TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1W 
       63.02       121.08         4.01        69.07       111.09       219.16 
TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8ZM TCGA-WE-A8ZN 
      105.04        24.03        49.05        61.15        98.89        58.98 
TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AA9Y 
       67.63        59.77        11.80        32.58        49.51        12.16 
TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YD-A89C TCGA-YD-A9TA TCGA-YG-AA3O 
       35.01        19.73        22.29         6.90        49.18        37.94 
TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
       14.43        27.58        96.99        15.98 

  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
              0.23               0.20 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
            248.65             369.93 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
             59.28              50.45 
[1] "0.2 - 248.7 (59.3)" "0.2 - 369.9 (50.5)"
[1] "hr=" "1"  
D29V3, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  16Q GAIN MUTATED                    5             0
  16Q GAIN WILD-TYPE                 60             5
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  16Q GAIN MUTATED                                          13
  16Q GAIN WILD-TYPE                                        59
                    vv
clus                 REGIONAL LYMPH NODE
  16Q GAIN MUTATED                    25
  16Q GAIN WILD-TYPE                 190
D29V4, multiclass
                                           clus
vv                                          16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  DISTANT METASTASIS                                       5                 60
  PRIMARY TUMOR                                            0                  5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               13                 59
  REGIONAL LYMPH NODE                                     25                190
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  16Q GAIN MUTATED             2       2       7        2        7        4
  16Q GAIN WILD-TYPE          10       5      21       16       20       20
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  16Q GAIN MUTATED           1         1         1         4          0
  16Q GAIN WILD-TYPE        13        18        11        33         15
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  16Q GAIN MUTATED            5          4        1
  16Q GAIN WILD-TYPE         27         56       19
D29V5, multiclass
             clus
vv            16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  I OR II NOS                2                 10
  STAGE 0                    2                  5
  STAGE I                    7                 21
  STAGE IA                   2                 16
  STAGE IB                   7                 20
  STAGE II                   4                 20
  STAGE IIA                  1                 13
  STAGE IIB                  1                 18
  STAGE IIC                  1                 11
  STAGE III                  4                 33
  STAGE IIIA                 0                 15
  STAGE IIIB                 5                 27
  STAGE IIIC                 4                 56
  STAGE IV                   1                 19
[1] 14  2
[1] TRUE
[1] "dimension of contingency 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       7 16  9  3
  16Q GAIN WILD-TYPE    57 56 68 65
D29V6, multiclass
       clus
vv      16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  T0+T1                7                 57
  T2                  16                 56
  T3                   9                 68
  T4                   3                 65
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  16Q GAIN MUTATED    27   8   2   3
  16Q GAIN WILD-TYPE 142  55  36  46
D29V7, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  N0               27                142
  N1                8                 55
  N2                2                 36
  N3                3                 46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V8, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED    40   1
  16Q GAIN WILD-TYPE 273  20
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     40    1
  16Q GAIN WILD-TYPE  273   20
   clus
vv  16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  0               40                273
  1                1                 20
[1] 2 2
[1] FALSE
D29V9, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED    13  10
  16Q GAIN WILD-TYPE 119  78
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     13   10
  16Q GAIN WILD-TYPE  119   78
     clus
vv    16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  NO                13                119
  YES               10                 78
[1] 2 2
[1] FALSE
D29V10, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED     3  40
  16Q GAIN WILD-TYPE  41 273
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      3   40
  16Q GAIN WILD-TYPE   41  273
     clus
vv    16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  NO                 3                 41
  YES               40                273
[1] 2 2
[1] FALSE
D29V11, continuous
D29V12, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED    20  23
  16Q GAIN WILD-TYPE 115 200
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     20   23
  16Q GAIN WILD-TYPE  115  200
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  FEMALE               20                115
  MALE                 23                200
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16Q GAIN MUTATED       1                         0    41
  16Q GAIN WILD-TYPE     4                         1   303
D29V13, multiclass
                           clus
vv                          16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  ASIAN                                    1                  4
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   41                303
[1] 3 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     1  39
  16Q GAIN WILD-TYPE   6 305
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      1   39
  16Q GAIN WILD-TYPE    6  305
                        clus
vv                       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO               39                305
[1] 2 2
[1] FALSE

Clustering(30) Variable = 17P GAIN MUTATION ANALYSIS
D30V1, survival
                    sevent
clus2                  0   1
  17P GAIN MUTATED    12  13
  17P GAIN WILD-TYPE 109 105
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                25                214 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                13                105 
$`17P GAIN MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A2JC TCGA-D3-A2JE TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A5GU 
        8.42        86.30         9.76        58.06        59.70       124.08 
TCGA-D3-A8GP TCGA-D9-A6EC TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-EE-A17Y TCGA-EE-A182 
      135.12        57.90        32.42        64.83        24.89         0.00 
TCGA-EE-A29D TCGA-EE-A29P TCGA-EE-A2A6 TCGA-EE-A2GH TCGA-EE-A2GM TCGA-EE-A2M7 
       12.99        27.16        77.98       189.40        18.35        15.25 
TCGA-ER-A2ND TCGA-ER-A3PL TCGA-FS-A1ZD TCGA-FS-A1ZM TCGA-FS-A1ZS TCGA-GN-A9SD 
        4.70        32.05        32.78        78.61       136.27        59.41 
TCGA-W3-A825 
        1.97 

$`17P GAIN WILD-TYPE`
TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 
       60.46        12.99        14.83        15.72        31.89       110.93 
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 
       49.35       133.25        19.04        76.41        62.60        25.64 
TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JD TCGA-D3-A2JG 
       45.99        62.86        15.75       168.00         7.27       107.61 
TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C7 
       36.30       171.58        64.83        66.08        43.53        46.98 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR 
      140.98        40.01        16.96        13.87         9.34        90.21 
TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T 
       23.67       173.85       144.46        31.76        62.70        11.34 
TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GJ 
       42.05        45.70       177.86        78.21        23.61       179.97 
TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GR TCGA-D9-A1X3 TCGA-D9-A3Z1 
      120.00        69.53        70.62        36.53        10.78        15.02 
TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 
       16.90        18.44        22.85        48.66       106.85        31.96 
TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 
      150.61        82.85        58.85        25.12       214.59        14.96 
TCGA-EB-A44Q TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X 
        3.91        33.24        50.07        45.50         6.64        13.15 
TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A184 TCGA-EE-A20C TCGA-EE-A20H TCGA-EE-A29B 
       62.37        20.38        67.50        75.55       155.90        75.22 
TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29Q 
       76.14         0.26        44.28        63.12        47.74        61.12 
TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2GB TCGA-EE-A2GD 
      346.49       185.19       102.38         7.20        26.14       239.11 
TCGA-EE-A2GE TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GO 
        0.20        68.65        10.62        32.48        31.00       118.32 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M8 
        0.76         0.20        71.31        81.99       103.13         5.75 
TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK 
       23.77       209.79        94.19       171.85        63.25        67.50 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT 
      104.78       145.45       227.01        25.08       143.93        23.51 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
       53.26       124.31       122.73        51.62         4.41        54.51 
TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB 
        6.28        67.89       111.85        45.90         3.35       201.80 
TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 
      152.81        14.56        34.45         1.58        47.31         7.82 
TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19H 
        4.54        53.29        39.81        11.47       151.46       150.12 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S 
       99.06        59.84        42.48       120.76        49.71        34.95 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A3ES 
      146.63        47.97        22.36        16.87        10.95       173.29 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7UA 
       55.82        15.48       174.21       209.23        26.20         5.65 
TCGA-FR-A8YC TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 
       10.06       171.78        49.74       195.98         8.35        27.62 
TCGA-FS-A1ZC TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZQ 
      312.07        35.90        12.92         7.82        36.33       130.95 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 
       35.28         4.47        23.21         5.29         3.06        30.90 
TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV 
       66.67       173.19        13.28        80.68        55.59        11.54 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 
       19.30         9.90         6.05         1.91        53.29       117.93 
TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 
       84.72        17.06        42.48         7.59       120.53        34.49 
TCGA-GN-A4U8 TCGA-GN-A8LK TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O 
       46.92        43.23        85.05       297.01         7.23        18.05 
TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A828 TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1V 
        0.33       174.12       120.07        44.05        79.99         8.09 
TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8ZM TCGA-WE-A8ZN 
      185.13        92.84         1.15        59.64        62.99        12.69 
TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 
       19.00        59.44        10.95        48.39         1.94        26.60 
TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-Z2-AA3S 
       16.64        15.65        28.21        91.23 

  17P GAIN MUTATED 17P GAIN WILD-TYPE 
               0.0                0.2 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
            189.40             346.49 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
            32.780             46.455 
[1] "0.0 - 189.4 (32.8)" "0.2 - 346.5 (46.5)"
[1] "hr=" "1.3"
D30V2, survival
                    sevent
clus2                  0   1
  17P GAIN MUTATED    17  19
  17P GAIN WILD-TYPE 152 161
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                36                313 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                19                161 
$`17P GAIN MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q9 TCGA-D3-A2JC TCGA-D3-A2JE TCGA-D3-A3BZ TCGA-D3-A3C6 
       16.57        31.59        86.76        27.65       130.72        58.06 
TCGA-D3-A3CE TCGA-D3-A3MV TCGA-D3-A5GU TCGA-D3-A8GP TCGA-D9-A6EC TCGA-DA-A1I7 
       60.23        45.30       125.19       152.75        66.25        61.18 
TCGA-DA-A1IA TCGA-EE-A17Y TCGA-EE-A182 TCGA-EE-A20F TCGA-EE-A29D TCGA-EE-A29N 
       65.92        27.22        14.70        91.56        13.97        18.61 
TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A2A6 TCGA-EE-A2GH TCGA-EE-A2GM TCGA-EE-A2M7 
       56.42        14.47        86.14       208.04        75.48        28.83 
TCGA-EE-A3AG TCGA-EE-A3JA TCGA-ER-A19T TCGA-ER-A2ND TCGA-ER-A3PL TCGA-FS-A1ZD 
       41.59        53.19         8.88        23.34        33.21        53.52 
TCGA-FS-A1ZM TCGA-FS-A1ZS TCGA-GN-A26D TCGA-GN-A9SD TCGA-W3-A825 TCGA-W3-AA1O 
      101.26       148.80        39.58        59.41        63.02         4.01 

$`17P GAIN WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
       17.03        66.48        12.99        14.93        16.67       112.04 
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB 
      112.57        71.80       133.25        28.08        90.90        95.74 
TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB 
       43.43       103.10        65.49        23.77       115.53       168.00 
TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL 
       11.87        62.07       113.52        42.08        12.10       171.58 
TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB 
       66.48        66.08        59.57        46.98        46.32       166.52 
TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU 
       86.93        24.53        13.87         9.34       103.59        39.75 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
      174.84        55.73        56.35       145.12        32.94        22.62 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR 
       63.81        26.89       125.79       135.75       137.92       178.32 
TCGA-D3-A5GS TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GI 
       18.18        30.84        79.59        23.61        26.43        58.52 
TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GQ 
      241.38       170.20        89.13       107.15       161.00        29.06 
TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX 
      129.63       117.17       151.53        54.67         3.65         7.10 
TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EA 
       18.12        15.39        22.29        18.44         9.90        25.18 
TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 
       22.95        48.89        36.03       117.21        20.38       194.83 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A1IB TCGA-DA-A1IC 
      176.55        35.93       107.34        53.92        23.44        68.09 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R 
       28.60        10.49       215.44        15.68        13.87        10.36 
TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV 
       20.35        68.25        54.02        17.29        52.01         7.04 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A183 
       24.89        29.82         8.65        94.98        33.73        26.89 
TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20H TCGA-EE-A20I 
       68.15         4.96       133.81       151.27       168.26        13.55 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H 
       63.35        85.08        78.97        63.78        72.07        64.64 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V 
        2.60        56.84        66.74        61.28       369.93        25.87 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 
      195.02        17.92        46.82       102.90        36.82        39.29 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GJ 
       59.28        67.43       340.14       161.03        48.72       107.38 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR 
       54.74        79.66       102.12       126.81        13.91        42.77 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M8 
       81.21        44.88        94.82        21.67       129.27        19.76 
TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH 
       61.51        47.28       103.27       268.73       103.20        16.96 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN 
      204.66        96.23       158.63       216.66       167.90        47.54 
TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU 
      248.65        43.23       134.40       162.48        71.21        53.26 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
      124.31       122.73        51.62        28.77        54.51        13.81 
TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 
      138.81       172.18       127.20        36.95        64.08        34.32 
TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 
      201.80        27.35        51.35       109.58       152.81        31.40 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B 
       35.44        13.94        50.76         9.17        77.75        98.40 
TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H 
       48.89        12.59        13.02        26.37       268.93       152.35 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
        6.44       131.51        61.05        44.05       162.08        50.89 
TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NF 
       37.25       148.18        79.99        43.82        20.15        16.37 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A42K 
       31.27        32.05       247.04        80.32        46.98         6.77 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 
       92.98       174.21        15.72       220.80        27.85        18.77 
TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YX 
       38.27        34.82        36.26       104.42       216.92        48.59 
TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA 
      228.59       202.65        20.91        28.08         7.79        27.72 
TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH 
       48.85       357.37        40.27        15.45         9.70        32.75 
TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZT 
       47.38        23.93        74.73       133.55        11.41        53.16 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 
       26.56        49.48        27.09        27.02        77.82        50.14 
TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC 
       66.67        28.73       174.84        34.03        26.73        54.41 
TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
       80.68         0.20        22.92        55.59        13.51        19.30 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 
        9.90         7.23         2.04        15.78       139.89       117.93 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 
       84.72        10.13        64.44        62.79        32.48       121.91 
TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A8LL 
       39.35        10.42        48.89        22.13        50.10        21.37 
TCGA-HR-A2OG TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O 
        0.23        65.88       368.78       297.90         7.23        18.05 
TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A828 TCGA-W3-AA1Q TCGA-W3-AA1R 
        0.33         0.69       228.16       121.08        69.07       111.09 
TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K5 
       42.08       219.16       105.04        24.03        49.05        61.15 
TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT 
       15.98        98.89        58.98        67.63        59.77        11.80 
TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 
       32.58        49.51        12.16        35.01        19.73        22.29 
TCGA-YD-A89C TCGA-YD-A9TA TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S 
        6.90        49.18        37.94        14.43        27.58        96.99 
TCGA-Z2-AA3V 
       15.98 

  17P GAIN MUTATED 17P GAIN WILD-TYPE 
              4.01               0.20 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
            208.04             369.93 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
             54.97              50.14 
[1] "4.0 - 208.0 (55.0)" "0.2 - 369.9 (50.1)"
[1] "hr=" "1.2"
D30V3, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  17P GAIN MUTATED                    5             2
  17P GAIN WILD-TYPE                 60             3
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  17P GAIN MUTATED                                           7
  17P GAIN WILD-TYPE                                        65
                    vv
clus                 REGIONAL LYMPH NODE
  17P GAIN MUTATED                    23
  17P GAIN WILD-TYPE                 192
D30V4, multiclass
                                           clus
vv                                          17P GAIN MUTATED 17P GAIN WILD-TYPE
  DISTANT METASTASIS                                       5                 60
  PRIMARY TUMOR                                            2                  3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                7                 65
  REGIONAL LYMPH NODE                                     23                192
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  17P GAIN MUTATED             2       0       3        2        3        2
  17P GAIN WILD-TYPE          10       7      25       16       24       22
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  17P GAIN MUTATED           1         1         3         6          1
  17P GAIN WILD-TYPE        13        18         9        31         14
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  17P GAIN MUTATED            5          6        2
  17P GAIN WILD-TYPE         27         54       18
D30V5, multiclass
             clus
vv            17P GAIN MUTATED 17P GAIN WILD-TYPE
  I OR II NOS                2                 10
  STAGE 0                    0                  7
  STAGE I                    3                 25
  STAGE IA                   2                 16
  STAGE IB                   3                 24
  STAGE II                   2                 22
  STAGE IIA                  1                 13
  STAGE IIB                  1                 18
  STAGE IIC                  3                  9
  STAGE III                  6                 31
  STAGE IIIA                 1                 14
  STAGE IIIB                 5                 27
  STAGE IIIC                 6                 54
  STAGE IV                   2                 18
[1] 14  2
[1] TRUE
[1] "dimension of contingency 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      10  9  7  7
  17P GAIN WILD-TYPE    54 63 70 61
D30V6, multiclass
       clus
vv      17P GAIN MUTATED 17P GAIN WILD-TYPE
  T0+T1               10                 54
  T2                   9                 63
  T3                   7                 70
  T4                   7                 61
[1] 4 2
[1] TRUE
[1] "dimension of 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    17   7   8   4
  17P GAIN WILD-TYPE 152  56  30  45
D30V7, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  N0               17                152
  N1                7                 56
  N2                8                 30
  N3                4                 45
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V8, binary
                    cls
clus                   0   1
  17P GAIN MUTATED    34   2
  17P GAIN WILD-TYPE 279  19
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED     34    2
  17P GAIN WILD-TYPE  279   19
   clus
vv  17P GAIN MUTATED 17P GAIN WILD-TYPE
  0               34                279
  1                2                 19
[1] 2 2
[1] FALSE
D30V9, binary
                    cls
clus                   0   1
  17P GAIN MUTATED    11  11
  17P GAIN WILD-TYPE 121  77
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED     11   11
  17P GAIN WILD-TYPE  121   77
     clus
vv    17P GAIN MUTATED 17P GAIN WILD-TYPE
  NO                11                121
  YES               11                 77
[1] 2 2
[1] FALSE
D30V10, binary
                    cls
clus                   0   1
  17P GAIN MUTATED     5  32
  17P GAIN WILD-TYPE  39 281
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      5   32
  17P GAIN WILD-TYPE   39  281
     clus
vv    17P GAIN MUTATED 17P GAIN WILD-TYPE
  NO                 5                 39
  YES               32                281
[1] 2 2
[1] FALSE
D30V11, continuous
D30V12, binary
                    cls
clus                   0   1
  17P GAIN MUTATED    16  21
  17P GAIN WILD-TYPE 119 202
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED     16   21
  17P GAIN WILD-TYPE  119  202
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  FEMALE               16                119
  MALE                 21                202
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  17P GAIN MUTATED       1                         0    36
  17P GAIN WILD-TYPE     4                         1   308
D30V13, multiclass
                           clus
vv                          17P GAIN MUTATED 17P GAIN WILD-TYPE
  ASIAN                                    1                  4
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   36                308
[1] 3 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     1  35
  17P GAIN WILD-TYPE   6 309
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      1   35
  17P GAIN WILD-TYPE    6  309
                        clus
vv                       17P GAIN MUTATED 17P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO               35                309
[1] 2 2
[1] FALSE

Clustering(31) Variable = 17Q GAIN MUTATION ANALYSIS
D31V1, survival
                    sevent
clus2                  0   1
  17Q GAIN MUTATED    20  21
  17Q GAIN WILD-TYPE 101  97
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                41                198 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                21                 97 
$`17Q GAIN MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1QA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JE 
        8.42        15.72        76.41       168.00        86.30         9.76 
TCGA-D3-A2JL TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A8GM TCGA-D3-A8GP TCGA-DA-A1HV 
      171.58        58.06        59.70        70.62       135.12        48.66 
TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A182 
       32.42        64.83        58.85        24.89        20.38         0.00 
TCGA-EE-A184 TCGA-EE-A29D TCGA-EE-A29P TCGA-EE-A2A6 TCGA-EE-A2GH TCGA-EE-A2GM 
       67.50        12.99        27.16        77.98       189.40        18.35 
TCGA-EE-A2M7 TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A3AC TCGA-ER-A2NC TCGA-ER-A3PL 
       15.25        25.08       143.93        51.62        22.36        32.05 
TCGA-FS-A1ZD TCGA-FS-A1ZM TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-GN-A265 TCGA-GN-A268 
       32.78        78.61       136.27         4.47        84.72        42.48 
TCGA-GN-A9SD TCGA-QB-A6FS TCGA-W3-A825 TCGA-WE-A8K1 TCGA-WE-AAA3 
       59.41         7.23         1.97         1.15        16.64 

$`17Q GAIN WILD-TYPE`
TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 
       60.46        12.99        14.83        31.89       110.93        49.35 
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 
      133.25        19.04        62.60        25.64        45.99        62.86 
TCGA-D3-A2JA TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JN TCGA-D3-A2JO 
       15.75         7.27       107.61        36.30        64.83        66.08 
TCGA-D3-A2JP TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3ML 
       43.53        46.98       140.98        40.01        16.96        13.87 
TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51J TCGA-D3-A51K 
        9.34        90.21        23.67       173.85       144.46        31.76 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GU 
       62.70        11.34        42.05        45.70       177.86       124.08 
TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GR 
       78.21        23.61       179.97       120.00        69.53        36.53 
TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6EC TCGA-D9-A6EG 
       10.78        15.02        16.90        18.44        57.90        22.85 
TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A3F2 TCGA-DA-A3F5 
      106.85        31.96       150.61        82.85        25.12       214.59 
TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A6L9 
       14.96         3.91        33.24        50.07        45.50         6.64 
TCGA-EE-A17X TCGA-EE-A180 TCGA-EE-A20C TCGA-EE-A20H TCGA-EE-A29B TCGA-EE-A29C 
       13.15        62.37        75.55       155.90        75.22        76.14 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29Q TCGA-EE-A29T 
        0.26        44.28        63.12        47.74        61.12       346.49 
TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE 
      185.19       102.38         7.20        26.14       239.11         0.20 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP 
       68.65        10.62        32.48        31.00       118.32         0.76 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M8 TCGA-EE-A2MC 
        0.20        71.31        81.99       103.13         5.75        23.77 
TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML 
      209.79        94.19       171.85        63.25        67.50       104.78 
TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB 
      145.45       227.01        23.51        53.26       124.31       122.73 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 
        4.41        54.51         6.28        67.89       111.85        45.90 
TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
        3.35       201.80       152.81        14.56        34.45         1.58 
TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D 
       47.31         7.82         4.54        53.29        39.81        11.47 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P 
      151.46       150.12        99.06        59.84        42.48       120.76 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2ND TCGA-ER-A2NE 
       49.71        34.95       146.63        47.97         4.70        16.87 
TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-FR-A44A TCGA-FR-A729 
       10.95       173.29        55.82        15.48       174.21       209.23 
TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 
       26.20         5.65        10.06       171.78        49.74       195.98 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG 
        8.35        27.62       312.07        35.90        12.92         7.82 
TCGA-FS-A1ZJ TCGA-FS-A1ZQ TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ 
       36.33       130.95        35.28        23.21         5.29         3.06 
TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TU 
       30.90        66.67       173.19        13.28        80.68        55.59 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 
       11.54        19.30         9.90         6.05         1.91        53.29 
TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 
      117.93        17.06         7.59       120.53        34.49        46.92 
TCGA-GN-A8LK TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-AA9O TCGA-RP-A693 TCGA-W3-A824 
       43.23        85.05       297.01        18.05         0.33       174.12 
TCGA-W3-A828 TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 
      120.07        44.05        79.99         8.09       185.13        92.84 
TCGA-WE-A8K5 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT 
       59.64        62.99        12.69        19.00        59.44        10.95 
TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-Z2-AA3S 
       48.39         1.94        26.60        15.65        28.21        91.23 

  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
               0.0                0.2 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
            189.40             346.49 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
            42.480             46.455 
[1] "0.0 - 189.4 (42.5)" "0.2 - 346.5 (46.5)"
[1] "hr=" "1.3"
D31V2, survival
                    sevent
clus2                  0   1
  17Q GAIN MUTATED    33  31
  17Q GAIN WILD-TYPE 136 149
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                64                285 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                31                149 
$`17Q GAIN MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A2JB TCGA-D3-A2JC 
       16.57        16.67        31.59        90.90       168.00        86.76 
TCGA-D3-A2JE TCGA-D3-A2JL TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3MV 
       27.65       171.58       130.72        58.06        60.23        45.30 
TCGA-D3-A5GS TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D9-A1JW TCGA-D9-A6E9 
       18.18       107.15       161.00       152.75         3.65         9.90 
TCGA-DA-A1HV TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-EE-A17Y TCGA-EE-A181 
       48.89        61.18        65.92        68.09        27.22        33.73 
TCGA-EE-A182 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20F TCGA-EE-A29D TCGA-EE-A29L 
       14.70        68.15         4.96        91.56        13.97         2.60 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A2A6 TCGA-EE-A2GC TCGA-EE-A2GH 
       18.61        56.42        14.47        86.14        67.43       208.04 
TCGA-EE-A2GM TCGA-EE-A2M7 TCGA-EE-A2MD TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A3AC 
       75.48        28.83        47.28       134.40       162.48        51.62 
TCGA-EE-A3J5 TCGA-EE-A3JA TCGA-ER-A19T TCGA-ER-A2NC TCGA-ER-A3PL TCGA-FR-A3YN 
       36.95        53.19         8.88        43.82        33.21        92.98 
TCGA-FS-A1YX TCGA-FS-A1ZD TCGA-FS-A1ZM TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-GN-A265 
       48.59        53.52       101.26       148.80        26.56        84.72 
TCGA-GN-A268 TCGA-GN-A26D TCGA-GN-A9SD TCGA-QB-A6FS TCGA-RP-A694 TCGA-W3-A825 
       62.79        39.58        59.41         7.23         0.69        63.02 
TCGA-W3-AA1O TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-AAA3 
        4.01        24.03        49.05        19.73 

$`17Q GAIN WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q4 TCGA-D3-A1Q5 
       17.03        66.48        12.99        14.93       112.04       112.57 
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       71.80       133.25        28.08        95.74        43.43       103.10 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG 
       65.49        23.77       115.53        11.87        62.07       113.52 
TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C7 
       42.08        12.10        66.48        66.08        59.57        46.98 
TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO 
       46.32       166.52        86.93        24.53        13.87         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J 
      103.59        39.75       174.84        55.73        56.35       145.12 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN 
       32.94        22.62        63.81        26.89       125.79       135.75 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GD 
      137.92       178.32       125.19        30.84        79.59        23.61 
TCGA-D3-A8GE TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GQ 
       26.43        58.52       241.38       170.20        89.13        29.06 
TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JX TCGA-D9-A1X3 
      129.63       117.17       151.53        54.67         7.10        18.12 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG 
       15.39        22.29        18.44        25.18        66.25        22.95 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 
       36.03       117.21        20.38       194.83       176.55        35.93 
TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 
      107.34        53.92        23.44        28.60        10.49       215.44 
TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH 
       15.68        13.87        10.36        20.35        68.25        54.02 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Z 
       17.29        52.01         7.04        24.89        29.82         8.65 
TCGA-EE-A180 TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20H TCGA-EE-A20I 
       94.98        26.89       133.81       151.27       168.26        13.55 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H 
       63.35        85.08        78.97        63.78        72.07        64.64 
TCGA-EE-A29M TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W 
       56.84        66.74        61.28       369.93        25.87       195.02 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2GB 
       17.92        46.82       102.90        36.82        39.29        59.28 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
      340.14       161.03        48.72       107.38        54.74        79.66 
TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT 
      102.12       126.81        13.91        42.77        81.21        44.88 
TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2ME 
       94.82        21.67       129.27        19.76        61.51       103.27 
TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK 
      268.73       103.20        16.96       204.66        96.23       158.63 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MT 
      216.66       167.90        47.54       248.65        43.23        71.21 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
       53.26       124.31       122.73        28.77        54.51        13.81 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 
       41.59       138.81       172.18       127.20        64.08        34.32 
TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 
      201.80        27.35        51.35       109.58       152.81        31.40 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B 
       35.44        13.94        50.76         9.17        77.75        98.40 
TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H 
       48.89        12.59        13.02        26.37       268.93       152.35 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
        6.44       131.51        61.05        44.05       162.08        50.89 
TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF 
       37.25       148.18        79.99        23.34        20.15        16.37 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A42K 
       31.27        32.05       247.04        80.32        46.98         6.77 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA 
      174.21        15.72       220.80        27.85        18.77        38.27 
TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 
       34.82        36.26       104.42       216.92       228.59       202.65 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC 
       20.91        28.08         7.79        27.72        48.85       357.37 
TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK 
       40.27        15.45         9.70        32.75        47.38        23.93 
TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A1ZY 
       74.73       133.55        11.41        53.16        49.48        27.09 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 
       27.02        77.82        50.14        66.67        28.73       174.84 
TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 
       34.03        26.73        54.41        80.68         0.20        22.92 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 
       55.59        13.51        19.30         9.90         7.23         2.04 
TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A26A 
       15.78       139.89       117.93        10.13        64.44        32.48 
TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK 
      121.91        39.35        10.42        48.89        22.13        50.10 
TCGA-GN-A8LL TCGA-HR-A2OG TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-AA9O 
       21.37         0.23        65.88       368.78       297.90        18.05 
TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A828 TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1V 
        0.33       228.16       121.08        69.07       111.09        42.08 
TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN 
      219.16       105.04        61.15        15.98        98.89        58.98 
TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AA9Y 
       67.63        59.77        11.80        32.58        49.51        12.16 
TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-YD-A89C TCGA-YD-A9TA TCGA-YG-AA3O TCGA-YG-AA3P 
       35.01        22.29         6.90        49.18        37.94        14.43 
TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
       27.58        96.99        15.98 

  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
              0.69               0.20 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
            208.04             369.93 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
            50.335             50.890 
[1] "0.7 - 208.0 (50.3)" "0.2 - 369.9 (50.9)"
[1] "hr=" "1.1"
D31V3, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  17Q GAIN MUTATED                    9             2
  17Q GAIN WILD-TYPE                 56             3
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  17Q GAIN MUTATED                                          10
  17Q GAIN WILD-TYPE                                        62
                    vv
clus                 REGIONAL LYMPH NODE
  17Q GAIN MUTATED                    44
  17Q GAIN WILD-TYPE                 171
D31V4, multiclass
                                           clus
vv                                          17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  DISTANT METASTASIS                                       9                 56
  PRIMARY TUMOR                                            2                  3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               10                 62
  REGIONAL LYMPH NODE                                     44                171
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  17Q GAIN MUTATED             4       1       5        2        6        5
  17Q GAIN WILD-TYPE           8       6      23       16       21       19
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  17Q GAIN MUTATED           1         4         5         7          1
  17Q GAIN WILD-TYPE        13        15         7        30         14
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  17Q GAIN MUTATED            8         10        4
  17Q GAIN WILD-TYPE         24         50       16
D31V5, multiclass
             clus
vv            17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  I OR II NOS                4                  8
  STAGE 0                    1                  6
  STAGE I                    5                 23
  STAGE IA                   2                 16
  STAGE IB                   6                 21
  STAGE II                   5                 19
  STAGE IIA                  1                 13
  STAGE IIB                  4                 15
  STAGE IIC                  5                  7
  STAGE III                  7                 30
  STAGE IIIA                 1                 14
  STAGE IIIB                 8                 24
  STAGE IIIC                10                 50
  STAGE IV                   4                 16
[1] 14  2
[1] TRUE
[1] "dimension of contingency 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      12 15 14 15
  17Q GAIN WILD-TYPE    52 57 63 53
D31V6, multiclass
       clus
vv      17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  T0+T1               12                 52
  T2                  15                 57
  T3                  14                 63
  T4                  15                 53
[1] 4 2
[1] TRUE
[1] "dimension of 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    33  10  12   7
  17Q GAIN WILD-TYPE 136  53  26  42
D31V7, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  N0               33                136
  N1               10                 53
  N2               12                 26
  N3                7                 42
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V8, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED    59   4
  17Q GAIN WILD-TYPE 254  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     59    4
  17Q GAIN WILD-TYPE  254   17
   clus
vv  17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  0               59                254
  1                4                 17
[1] 2 2
[1] FALSE
D31V9, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED    21  21
  17Q GAIN WILD-TYPE 111  67
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     21   21
  17Q GAIN WILD-TYPE  111   67
     clus
vv    17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  NO                21                111
  YES               21                 67
[1] 2 2
[1] FALSE
D31V10, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED    10  55
  17Q GAIN WILD-TYPE  34 258
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     10   55
  17Q GAIN WILD-TYPE   34  258
     clus
vv    17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  NO                10                 34
  YES               55                258
[1] 2 2
[1] FALSE
D31V11, continuous
D31V12, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED    26  39
  17Q GAIN WILD-TYPE 109 184
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     26   39
  17Q GAIN WILD-TYPE  109  184
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  FEMALE               26                109
  MALE                 39                184
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  17Q GAIN MUTATED       1                         1    62
  17Q GAIN WILD-TYPE     4                         0   282
D31V13, multiclass
                           clus
vv                          17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  ASIAN                                    1                  4
  BLACK OR AFRICAN AMERICAN                1                  0
  WHITE                                   62                282
[1] 3 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     1  62
  17Q GAIN WILD-TYPE   6 282
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      1   62
  17Q GAIN WILD-TYPE    6  282
                        clus
vv                       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO               62                282
[1] 2 2
[1] FALSE

Clustering(32) Variable = 18P GAIN MUTATION ANALYSIS
D32V1, survival
                    sevent
clus2                  0   1
  18P GAIN MUTATED    19  15
  18P GAIN WILD-TYPE 102 103
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                34                205 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                15                103 
$`18P GAIN MUTATED`
TCGA-D3-A1Q5 TCGA-D3-A1QA TCGA-D3-A2JE TCGA-D3-A2JN TCGA-D3-A3CC TCGA-D3-A3CE 
      110.93        76.41         9.76        64.83        40.01        59.70 
TCGA-D3-A51E TCGA-D3-A51K TCGA-D3-A8GP TCGA-D9-A6EC TCGA-DA-A1I1 TCGA-EB-A6L9 
      173.85        31.76       135.12        57.90        31.96         6.64 
TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A29E TCGA-EE-A29P TCGA-EE-A2GB TCGA-EE-A2GH 
       62.37        20.38         0.26        27.16        26.14       189.40 
TCGA-EE-A2GM TCGA-EE-A2MP TCGA-ER-A197 TCGA-ER-A19W TCGA-ER-A3EV TCGA-ER-A3PL 
       18.35       227.01         1.58       146.63        15.48        32.05 
TCGA-FR-A729 TCGA-FS-A1Z0 TCGA-FS-A1ZC TCGA-FS-A1ZJ TCGA-FS-A1ZT TCGA-FS-A1ZU 
      209.23       195.98       312.07        36.33        35.28         4.47 
TCGA-GF-A4EO TCGA-GN-A267 TCGA-GN-A26A TCGA-WE-AAA3 
        6.05        17.06         7.59        16.64 

$`18P GAIN WILD-TYPE`
TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
       60.46        12.99        14.83         8.42        15.72        31.89 
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       49.35       133.25        19.04        62.60        25.64        45.99 
TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG 
       62.86        15.75       168.00        86.30         7.27       107.61 
TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3C7 
       36.30       171.58        66.08        43.53        58.06        46.98 
TCGA-D3-A3CB TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU 
      140.98        16.96        13.87         9.34        90.21        23.67 
TCGA-D3-A51J TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR 
      144.46        62.70        11.34        42.05        45.70       177.86 
TCGA-D3-A5GU TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL 
      124.08        78.21        23.61       179.97       120.00        69.53 
TCGA-D3-A8GM TCGA-D3-A8GR TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 
       70.62        36.53        10.78        15.02        16.90        18.44 
TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 
       22.85        48.66       106.85       150.61        82.85        32.42 
TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q 
       64.83        58.85        25.12       214.59        14.96         3.91 
TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A182 
       33.24        50.07        45.50        13.15        24.89         0.00 
TCGA-EE-A184 TCGA-EE-A20C TCGA-EE-A20H TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D 
       67.50        75.55       155.90        75.22        76.14        12.99 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W 
       44.28        63.12        47.74        61.12       346.49       185.19 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GJ 
      102.38         7.20        77.98       239.11         0.20        68.65 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR 
       10.62        32.48        31.00       118.32         0.76         0.20 
TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC 
       71.31        81.99       103.13        15.25         5.75        23.77 
TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML 
      209.79        94.19       171.85        63.25        67.50       104.78 
TCGA-EE-A2MM TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA 
      145.45        25.08       143.93        23.51        53.26       124.31 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J3 
      122.73        51.62         4.41        54.51         6.28        67.89 
TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JI TCGA-ER-A193 
      111.85        45.90         3.35       201.80       152.81        14.56 
TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C 
       34.45        47.31         7.82         4.54        53.29        39.81 
TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
       11.47       151.46       150.12        99.06        59.84        42.48 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
      120.76        49.71        34.95        47.97        22.36         4.70 
TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-FR-A44A TCGA-FR-A7U8 
       16.87        10.95       173.29        55.82       174.21        26.20 
TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1Z4 
        5.65        10.06       171.78        49.74         8.35        27.62 
TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZM TCGA-FS-A1ZQ 
       32.78        35.90        12.92         7.82        78.61       130.95 
TCGA-FS-A1ZS TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 
      136.27        23.21         5.29         3.06        30.90        66.67 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
      173.19        13.28        80.68        55.59        11.54        19.30 
TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A268 
        9.90         1.91        53.29       117.93        84.72        42.48 
TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-GN-A8LK TCGA-GN-A9SD TCGA-LH-A9QB 
      120.53        34.49        46.92        43.23        59.41        85.05 
TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A825 
      297.01         7.23        18.05         0.33       174.12         1.97 
TCGA-W3-A828 TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 
      120.07        44.05        79.99         8.09       185.13        92.84 
TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ 
        1.15        59.64        62.99        12.69        19.00        59.44 
TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-YG-AA3O 
       10.95        48.39         1.94        26.60        15.65        28.21 
TCGA-Z2-AA3S 
       91.23 

  18P GAIN MUTATED 18P GAIN WILD-TYPE 
              0.26               0.00 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
            312.07             346.49 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
            33.665             47.310 
[1] "0.3 - 312.1 (33.7)" "0.0 - 346.5 (47.3)"
[1] "hr=" "1.3"
D32V2, survival
                    sevent
clus2                  0   1
  18P GAIN MUTATED    27  25
  18P GAIN WILD-TYPE 142 155
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                52                297 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                25                155 
$`18P GAIN MUTATED`
TCGA-D3-A1Q5 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A2J9 TCGA-D3-A2JE TCGA-D3-A2JN 
      112.57        31.59        90.90        23.77        27.65        66.48 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A51E TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A8GP 
       86.93        60.23       174.84        32.94        22.62       152.75 
TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-EB-A5UL 
       25.18        66.25        36.03        20.38       194.83        17.29 
TCGA-EB-A6L9 TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A29E TCGA-EE-A29L TCGA-EE-A29P 
       24.89        94.98        33.73        63.78         2.60        56.42 
TCGA-EE-A2GB TCGA-EE-A2GH TCGA-EE-A2GM TCGA-EE-A2M5 TCGA-EE-A2MP TCGA-EE-A3J5 
       59.28       208.04        75.48        21.67       248.65        36.95 
TCGA-ER-A197 TCGA-ER-A19W TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A729 
       13.94       148.18        46.98        33.21        92.98       220.80 
TCGA-FS-A1YX TCGA-FS-A1Z0 TCGA-FS-A1ZC TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZT 
       48.59       202.65       357.37        47.38        23.93        53.16 
TCGA-FS-A1ZU TCGA-FS-A4F2 TCGA-GF-A4EO TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A26D 
       26.56        50.14         7.23        64.44        32.48        39.58 
TCGA-HR-A2OG TCGA-WE-A8K6 TCGA-WE-AAA3 TCGA-YD-A9TA 
        0.23        15.98        19.73        49.18 

$`18P GAIN WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q3 
       17.03        66.48        12.99        14.93        16.57        16.67 
TCGA-D3-A1Q4 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QB TCGA-D3-A2J6 
      112.04        71.80       133.25        28.08        95.74        43.43 
TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
      103.10        65.49       115.53       168.00        86.76        11.87 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JO 
       62.07       113.52        42.08        12.10       171.58        66.08 
TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB 
       59.57       130.72        58.06        46.98        46.32       166.52 
TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV 
       24.53        13.87         9.34       103.59        39.75        45.30 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL 
       55.73        56.35       145.12        63.81        26.89       125.79 
TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GB 
      135.75       137.92       178.32        18.18       125.19        30.84 
TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GK 
       79.59        23.61        26.43        58.52       241.38       170.20 
TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS 
       89.13       107.15       161.00        29.06       129.63       117.17 
TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A1X3 TCGA-D9-A3Z1 
      151.53        54.67         3.65         7.10        18.12        15.39 
TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY 
       22.29        18.44         9.90        22.95        48.89       117.21 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA 
      176.55        35.93       107.34        61.18        53.92        65.92 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 
       23.44        68.09        28.60        10.49       215.44        15.68 
TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN 
       13.87        10.36        20.35        68.25        54.02        52.01 
TCGA-EB-A5VV TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A182 TCGA-EE-A183 
        7.04        29.82        27.22         8.65        14.70        26.89 
TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H 
       68.15         4.96       133.81       151.27        91.56       168.26 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29G 
       13.55        63.35        85.08        78.97        13.97        72.07 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
       64.64        56.84        18.61        66.74        14.47        61.28 
TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 
      369.93        25.87       195.02        17.92        46.82       102.90 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE 
       36.82        39.29        86.14        67.43       340.14       161.03 
TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GO 
       48.72       107.38        54.74        79.66       102.12       126.81 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M6 
       13.91        42.77        81.21        44.88        94.82       129.27 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF 
       28.83        19.76        61.51        47.28       103.27       268.73 
TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML 
      103.20        16.96       204.66        96.23       158.63       216.66 
TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT 
      167.90        47.54        43.23       134.40       162.48        71.21 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
       53.26       124.31       122.73        51.62        28.77        54.51 
TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 
       13.81        41.59       138.81       172.18       127.20        64.08 
TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH 
       34.32        53.19       201.80        27.35        51.35       109.58 
TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A 
      152.81        31.40        35.44        50.76         9.17        77.75 
TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G 
       98.40        48.89        12.59        13.02        26.37       268.93 
TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P 
      152.35         6.44       131.51        61.05        44.05       162.08 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
       50.89        37.25         8.88        79.99        43.82        23.34 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET 
       20.15        16.37        31.27        32.05       247.04        80.32 
TCGA-ER-A42K TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA 
        6.77       174.21        15.72        27.85        18.77        38.27 
TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z3 
       34.82        36.26       104.42       216.92       228.59        20.91 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZD TCGA-FS-A1ZE 
       28.08         7.79        27.72        48.85        53.52        40.27 
TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ 
       15.45         9.70        32.75       101.26        74.73       133.55 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 
       11.41       148.80        49.48        27.09        27.02        77.82 
TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC 
       66.67        28.73       174.84        34.03        26.73        54.41 
TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
       80.68         0.20        22.92        55.59        13.51        19.30 
TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        9.90         2.04        15.78       139.89       117.93        84.72 
TCGA-GN-A266 TCGA-GN-A268 TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 
       10.13        62.79       121.91        39.35        10.42        48.89 
TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A8LL TCGA-GN-A9SD TCGA-HR-A2OH TCGA-LH-A9QB 
       22.13        50.10        21.37        59.41        65.88       368.78 
TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 
      297.90         7.23        18.05         0.33         0.69       228.16 
TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1V 
       63.02       121.08         4.01        69.07       111.09        42.08 
TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8ZM 
      219.16       105.04        24.03        49.05        61.15        98.89 
TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-A8ZY 
       58.98        67.63        59.77        11.80        32.58        49.51 
TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-YD-A89C TCGA-YG-AA3O TCGA-YG-AA3P 
       12.16        35.01        22.29         6.90        37.94        14.43 
TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
       27.58        96.99        15.98 

  18P GAIN MUTATED 18P GAIN WILD-TYPE 
              0.23               0.20 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
            357.37             369.93 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
            47.985             52.010 
[1] "0.2 - 357.4 (48.0)" "0.2 - 369.9 (52.0)"
[1] "hr=" "1.1"
D32V3, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  18P GAIN MUTATED                   10             2
  18P GAIN WILD-TYPE                 55             3
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  18P GAIN MUTATED                                          11
  18P GAIN WILD-TYPE                                        61
                    vv
clus                 REGIONAL LYMPH NODE
  18P GAIN MUTATED                    29
  18P GAIN WILD-TYPE                 186
D32V4, multiclass
                                           clus
vv                                          18P GAIN MUTATED 18P GAIN WILD-TYPE
  DISTANT METASTASIS                                      10                 55
  PRIMARY TUMOR                                            2                  3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               11                 61
  REGIONAL LYMPH NODE                                     29                186
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  18P GAIN MUTATED             4       0       6        1        2        2
  18P GAIN WILD-TYPE           8       7      22       17       25       22
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  18P GAIN MUTATED           0         0         6         8          3
  18P GAIN WILD-TYPE        14        19         6        29         12
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  18P GAIN MUTATED            7          8        3
  18P GAIN WILD-TYPE         25         52       17
D32V5, multiclass
             clus
vv            18P GAIN MUTATED 18P GAIN WILD-TYPE
  I OR II NOS                4                  8
  STAGE 0                    0                  7
  STAGE I                    6                 22
  STAGE IA                   1                 17
  STAGE IB                   2                 25
  STAGE II                   2                 22
  STAGE IIA                  0                 14
  STAGE IIB                  0                 19
  STAGE IIC                  6                  6
  STAGE III                  8                 29
  STAGE IIIA                 3                 12
  STAGE IIIB                 7                 25
  STAGE IIIC                 8                 52
  STAGE IV                   3                 17
[1] 14  2
[1] TRUE
[1] "dimension of contingency 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       8 11  5 18
  18P GAIN WILD-TYPE    56 61 72 50
D32V6, multiclass
       clus
vv      18P GAIN MUTATED 18P GAIN WILD-TYPE
  T0+T1                8                 56
  T2                  11                 61
  T3                   5                 72
  T4                  18                 50
[1] 4 2
[1] TRUE
[1] "dimension of 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    24  13   4   9
  18P GAIN WILD-TYPE 145  50  34  40
D32V7, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  N0               24                145
  N1               13                 50
  N2                4                 34
  N3                9                 40
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V8, binary
                    cls
clus                   0   1
  18P GAIN MUTATED    46   3
  18P GAIN WILD-TYPE 267  18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED     46    3
  18P GAIN WILD-TYPE  267   18
   clus
vv  18P GAIN MUTATED 18P GAIN WILD-TYPE
  0               46                267
  1                3                 18
[1] 2 2
[1] FALSE
D32V9, binary
                    cls
clus                   0   1
  18P GAIN MUTATED    16  15
  18P GAIN WILD-TYPE 116  73
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED     16   15
  18P GAIN WILD-TYPE  116   73
     clus
vv    18P GAIN MUTATED 18P GAIN WILD-TYPE
  NO                16                116
  YES               15                 73
[1] 2 2
[1] FALSE
D32V10, binary
                    cls
clus                   0   1
  18P GAIN MUTATED     5  48
  18P GAIN WILD-TYPE  39 265
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      5   48
  18P GAIN WILD-TYPE   39  265
     clus
vv    18P GAIN MUTATED 18P GAIN WILD-TYPE
  NO                 5                 39
  YES               48                265
[1] 2 2
[1] FALSE
D32V11, continuous
D32V12, binary
                    cls
clus                   0   1
  18P GAIN MUTATED    24  29
  18P GAIN WILD-TYPE 111 194
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED     24   29
  18P GAIN WILD-TYPE  111  194
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  FEMALE               24                111
  MALE                 29                194
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18P GAIN MUTATED       1                         0    51
  18P GAIN WILD-TYPE     4                         1   293
D32V13, multiclass
                           clus
vv                          18P GAIN MUTATED 18P GAIN WILD-TYPE
  ASIAN                                    1                  4
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   51                293
[1] 3 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     1  51
  18P GAIN WILD-TYPE   6 293
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      1   51
  18P GAIN WILD-TYPE    6  293
                        clus
vv                       18P GAIN MUTATED 18P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO               51                293
[1] 2 2
[1] FALSE

Clustering(33) Variable = 18Q GAIN MUTATION ANALYSIS
D33V1, survival
                    sevent
clus2                  0   1
  18Q GAIN MUTATED    17  10
  18Q GAIN WILD-TYPE 104 108
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                27                212 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                10                108 
$`18Q GAIN MUTATED`
TCGA-D3-A1Q5 TCGA-D3-A1QA TCGA-D3-A2JE TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3CC 
      110.93        76.41         9.76        64.83        43.53        40.01 
TCGA-D3-A51E TCGA-D3-A51K TCGA-D3-A8GP TCGA-DA-A1I1 TCGA-EE-A180 TCGA-EE-A29P 
      173.85        31.76       135.12        31.96        62.37        27.16 
TCGA-EE-A2GB TCGA-EE-A2GH TCGA-EE-A2GM TCGA-EE-A2MP TCGA-ER-A197 TCGA-ER-A3PL 
       26.14       189.40        18.35       227.01         1.58        32.05 
TCGA-FR-A729 TCGA-FS-A1Z0 TCGA-FS-A1ZC TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-GF-A4EO 
      209.23       195.98       312.07        35.28         4.47         6.05 
TCGA-GN-A267 TCGA-GN-A26A TCGA-WE-AAA3 
       17.06         7.59        16.64 

$`18Q GAIN WILD-TYPE`
TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
       60.46        12.99        14.83         8.42        15.72        31.89 
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       49.35       133.25        19.04        62.60        25.64        45.99 
TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG 
       62.86        15.75       168.00        86.30         7.27       107.61 
TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JO TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CB 
       36.30       171.58        66.08        58.06        46.98       140.98 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU 
       59.70        16.96        13.87         9.34        90.21        23.67 
TCGA-D3-A51J TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR 
      144.46        62.70        11.34        42.05        45.70       177.86 
TCGA-D3-A5GU TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL 
      124.08        78.21        23.61       179.97       120.00        69.53 
TCGA-D3-A8GM TCGA-D3-A8GR TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 
       70.62        36.53        10.78        15.02        16.90        18.44 
TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I2 TCGA-DA-A1I5 
       57.90        22.85        48.66       106.85       150.61        82.85 
TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 
       32.42        64.83        58.85        25.12       214.59        14.96 
TCGA-EB-A44Q TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X 
        3.91        33.24        50.07        45.50         6.64        13.15 
TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A184 TCGA-EE-A20C TCGA-EE-A20H 
       24.89        20.38         0.00        67.50        75.55       155.90 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H 
       75.22        76.14        12.99         0.26        44.28        63.12 
TCGA-EE-A29M TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A2 
       47.74        61.12       346.49       185.19       102.38         7.20 
TCGA-EE-A2A6 TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
       77.98       239.11         0.20        68.65        10.62        32.48 
TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU 
       31.00       118.32         0.76         0.20        71.31        81.99 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MG 
      103.13        15.25         5.75        23.77       209.79        94.19 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MR 
      171.85        63.25        67.50       104.78       145.45        25.08 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC 
      143.93        23.51        53.26       124.31       122.73        51.62 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 
        4.41        54.51         6.28        67.89       111.85        45.90 
TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A198 
        3.35       201.80       152.81        14.56        34.45        47.31 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19G 
        7.82         4.54        53.29        39.81        11.47       151.46 
TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
      150.12        99.06        59.84        42.48       120.76        49.71 
TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
       34.95       146.63        47.97        22.36         4.70        16.87 
TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-FR-A44A TCGA-FR-A7U8 
       10.95       173.29        55.82        15.48       174.21        26.20 
TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1Z4 
        5.65        10.06       171.78        49.74         8.35        27.62 
TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM 
       32.78        35.90        12.92         7.82        36.33        78.61 
TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 
      130.95       136.27        23.21         5.29         3.06        30.90 
TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV 
       66.67       173.19        13.28        80.68        55.59        11.54 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
       19.30         9.90         1.91        53.29       117.93        84.72 
TCGA-GN-A268 TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-GN-A8LK TCGA-GN-A9SD 
       42.48       120.53        34.49        46.92        43.23        59.41 
TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 TCGA-W3-A824 
       85.05       297.01         7.23        18.05         0.33       174.12 
TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1V TCGA-W3-AA1W 
        1.97       120.07        44.05        79.99         8.09       185.13 
TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO 
       92.84         1.15        59.64        62.99        12.69        19.00 
TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 
       59.44        10.95        48.39         1.94        26.60        15.65 
TCGA-YG-AA3O TCGA-Z2-AA3S 
       28.21        91.23 

  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
              1.58               0.00 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
            312.07             346.49 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
            35.280             47.145 
[1] "1.6 - 312.1 (35.3)" "0.0 - 346.5 (47.1)"
[1] "hr=" "1.8"
D33V2, survival
                    sevent
clus2                  0   1
  18Q GAIN MUTATED    25  17
  18Q GAIN WILD-TYPE 144 163
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                42                307 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                17                163 
$`18Q GAIN MUTATED`
TCGA-D3-A1Q5 TCGA-D3-A1QA TCGA-D3-A2J9 TCGA-D3-A2JE TCGA-D3-A2JN TCGA-D3-A2JP 
      112.57        90.90        23.77        27.65        66.48        59.57 
TCGA-D3-A3CC TCGA-D3-A51E TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A8GP TCGA-D9-A6EA 
       86.93       174.84        32.94        22.62       152.75        25.18 
TCGA-DA-A1HW TCGA-DA-A1I1 TCGA-EB-A5UL TCGA-EE-A180 TCGA-EE-A29L TCGA-EE-A29P 
       36.03       194.83        17.29        94.98         2.60        56.42 
TCGA-EE-A2GB TCGA-EE-A2GH TCGA-EE-A2GM TCGA-EE-A2M5 TCGA-EE-A2MP TCGA-EE-A3J5 
       59.28       208.04        75.48        21.67       248.65        36.95 
TCGA-ER-A197 TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A729 TCGA-FS-A1YX TCGA-FS-A1Z0 
       13.94        33.21        92.98       220.80        48.59       202.65 
TCGA-FS-A1ZC TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A4F2 TCGA-GF-A4EO TCGA-GN-A267 
      357.37        53.16        26.56        50.14         7.23        64.44 
TCGA-GN-A26A TCGA-GN-A26D TCGA-HR-A2OG TCGA-WE-A8JZ TCGA-WE-A8K6 TCGA-WE-AAA3 
       32.48        39.58         0.23        24.03        15.98        19.73 

$`18Q GAIN WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q3 
       17.03        66.48        12.99        14.93        16.57        16.67 
TCGA-D3-A1Q4 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QB 
      112.04        71.80       133.25        28.08        31.59        95.74 
TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC 
       43.43       103.10        65.49       115.53       168.00        86.76 
TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL 
       11.87        62.07       113.52        42.08        12.10       171.58 
TCGA-D3-A2JO TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB 
       66.08       130.72        58.06        46.98        46.32       166.52 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU 
       60.23        24.53        13.87         9.34       103.59        39.75 
TCGA-D3-A3MV TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51R TCGA-D3-A51T 
       45.30        55.73        56.35       145.12        63.81        26.89 
TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU 
      125.79       135.75       137.92       178.32        18.18       125.19 
TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GI TCGA-D3-A8GJ 
       30.84        79.59        23.61        26.43        58.52       241.38 
TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GQ TCGA-D3-A8GR 
      170.20        89.13       107.15       161.00        29.06       129.63 
TCGA-D3-A8GS TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A1X3 
      117.17       151.53        54.67         3.65         7.10        18.12 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-D9-A6EG 
       15.39        22.29        18.44         9.90        66.25        22.95 
TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
       48.89       117.21        20.38       176.55        35.93       107.34 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
       61.18        53.92        65.92        23.44        68.09        28.60 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH 
       10.49       215.44        15.68        13.87        10.36        20.35 
TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X 
       68.25        54.02        52.01         7.04        24.89        29.82 
TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 
       27.22         8.65        33.73        14.70        26.89        68.15 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I 
        4.96       133.81       151.27        91.56       168.26        13.55 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G 
       63.35        85.08        78.97        13.97        63.78        72.07 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
       64.64        56.84        18.61        66.74        14.47        61.28 
TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 
      369.93        25.87       195.02        17.92        46.82       102.90 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE 
       36.82        39.29        86.14        67.43       340.14       161.03 
TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GO 
       48.72       107.38        54.74        79.66       102.12       126.81 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M6 
       13.91        42.77        81.21        44.88        94.82       129.27 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF 
       28.83        19.76        61.51        47.28       103.27       268.73 
TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML 
      103.20        16.96       204.66        96.23       158.63       216.66 
TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT 
      167.90        47.54        43.23       134.40       162.48        71.21 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
       53.26       124.31       122.73        51.62        28.77        54.51 
TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 
       13.81        41.59       138.81       172.18       127.20        64.08 
TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH 
       34.32        53.19       201.80        27.35        51.35       109.58 
TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A 
      152.81        31.40        35.44        50.76         9.17        77.75 
TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G 
       98.40        48.89        12.59        13.02        26.37       268.93 
TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P 
      152.35         6.44       131.51        61.05        44.05       162.08 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
       50.89        37.25         8.88       148.18        79.99        43.82 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES 
       23.34        20.15        16.37        31.27        32.05       247.04 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A42K TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A7U8 
       80.32        46.98         6.77       174.21        15.72        27.85 
TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW 
       18.77        38.27        34.82        36.26       104.42       216.92 
TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB 
      228.59        20.91        28.08         7.79        27.72        48.85 
TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ 
       53.52        40.27        15.45         9.70        32.75        47.38 
TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS 
       23.93       101.26        74.73       133.55        11.41       148.80 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 
       49.48        27.09        27.02        77.82        66.67        28.73 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 
      174.84        34.03        26.73        54.41        80.68         0.20 
TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 
       22.92        55.59        13.51        19.30         9.90         2.04 
TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A268 
       15.78       139.89       117.93        84.72        10.13        62.79 
TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK 
      121.91        39.35        10.42        48.89        22.13        50.10 
TCGA-GN-A8LL TCGA-GN-A9SD TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS 
       21.37        59.41        65.88       368.78       297.90         7.23 
TCGA-QB-AA9O TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 
       18.05         0.33         0.69       228.16        63.02       121.08 
TCGA-W3-AA1O TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 
        4.01        69.07       111.09        42.08       219.16       105.04 
TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ 
       49.05        61.15        98.89        58.98        67.63        59.77 
TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 
       11.80        32.58        49.51        12.16        35.01        22.29 
TCGA-YD-A89C TCGA-YD-A9TA TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S 
        6.90        49.18        37.94        14.43        27.58        96.99 
TCGA-Z2-AA3V 
       15.98 

  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
              0.23               0.20 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
            357.37             369.93 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
            49.365             51.350 
[1] "0.2 - 357.4 (49.4)" "0.2 - 369.9 (51.4)"
[1] "hr=" "1.4"
D33V3, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  18Q GAIN MUTATED                    7             1
  18Q GAIN WILD-TYPE                 58             4
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  18Q GAIN MUTATED                                          10
  18Q GAIN WILD-TYPE                                        62
                    vv
clus                 REGIONAL LYMPH NODE
  18Q GAIN MUTATED                    25
  18Q GAIN WILD-TYPE                 190
D33V4, multiclass
                                           clus
vv                                          18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  DISTANT METASTASIS                                       7                 58
  PRIMARY TUMOR                                            1                  4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               10                 62
  REGIONAL LYMPH NODE                                     25                190
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  18Q GAIN MUTATED             4       1       5        1        2        0
  18Q GAIN WILD-TYPE           8       6      23       17       25       24
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  18Q GAIN MUTATED           0         0         6         6          2
  18Q GAIN WILD-TYPE        14        19         6        31         13
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  18Q GAIN MUTATED            6          8        2
  18Q GAIN WILD-TYPE         26         52       18
D33V5, multiclass
             clus
vv            18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  I OR II NOS                4                  8
  STAGE 0                    1                  6
  STAGE I                    5                 23
  STAGE IA                   1                 17
  STAGE IB                   2                 25
  STAGE II                   0                 24
  STAGE IIA                  0                 14
  STAGE IIB                  0                 19
  STAGE IIC                  6                  6
  STAGE III                  6                 31
  STAGE IIIA                 2                 13
  STAGE IIIB                 6                 26
  STAGE IIIC                 8                 52
  STAGE IV                   2                 18
[1] 14  2
[1] TRUE
[1] "dimension of contingency 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       8 10  2 15
  18Q GAIN WILD-TYPE    56 62 75 53
D33V6, multiclass
       clus
vv      18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  T0+T1                8                 56
  T2                  10                 62
  T3                   2                 75
  T4                  15                 53
[1] 4 2
[1] TRUE
[1] "dimension of 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    21  11   3   8
  18Q GAIN WILD-TYPE 148  52  35  41
D33V7, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  N0               21                148
  N1               11                 52
  N2                3                 35
  N3                8                 41
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V8, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED    40   2
  18Q GAIN WILD-TYPE 273  19
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED     40    2
  18Q GAIN WILD-TYPE  273   19
   clus
vv  18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  0               40                273
  1                2                 19
[1] 2 2
[1] FALSE
D33V9, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED    12  13
  18Q GAIN WILD-TYPE 120  75
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED     12   13
  18Q GAIN WILD-TYPE  120   75
     clus
vv    18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  NO                12                120
  YES               13                 75
[1] 2 2
[1] FALSE
D33V10, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED     5  39
  18Q GAIN WILD-TYPE  39 274
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      5   39
  18Q GAIN WILD-TYPE   39  274
     clus
vv    18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  NO                 5                 39
  YES               39                274
[1] 2 2
[1] FALSE
D33V11, continuous
D33V12, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED    20  24
  18Q GAIN WILD-TYPE 115 199
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED     20   24
  18Q GAIN WILD-TYPE  115  199
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  FEMALE               20                115
  MALE                 24                199
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18Q GAIN MUTATED       0                         0    42
  18Q GAIN WILD-TYPE     5                         1   302
D33V13, multiclass
                           clus
vv                          18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  ASIAN                                    0                  5
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   42                302
[1] 3 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     1  41
  18Q GAIN WILD-TYPE   6 303
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      1   41
  18Q GAIN WILD-TYPE    6  303
                        clus
vv                       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO               41                303
[1] 2 2
[1] FALSE

Clustering(34) Variable = 19P GAIN MUTATION ANALYSIS
D34V1, survival
                    sevent
clus2                  0   1
  19P GAIN MUTATED    21  21
  19P GAIN WILD-TYPE 100  97
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                42                197 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                21                 97 
$`19P GAIN MUTATED`
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1QB TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JE 
      110.93        49.35        62.60        15.75        86.30         9.76 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A5GU TCGA-D9-A6EC TCGA-EB-A5SH TCGA-EE-A17Y 
       66.08        43.53       124.08        57.90        50.07        24.89 
TCGA-EE-A180 TCGA-EE-A29E TCGA-EE-A29P TCGA-EE-A2GH TCGA-EE-A2GO TCGA-EE-A2GS 
       62.37         0.26        27.16       189.40       118.32        71.31 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MM TCGA-EE-A3JI TCGA-ER-A199 TCGA-ER-A2ND 
      103.13        15.25       145.45       152.81         7.82         4.70 
TCGA-ER-A2NG TCGA-ER-A3PL TCGA-FR-A729 TCGA-FS-A1Z3 TCGA-FS-A1ZC TCGA-FS-A1ZD 
       10.95        32.05       209.23         8.35       312.07        32.78 
TCGA-FS-A1ZM TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-GN-A267 TCGA-QB-AA9O 
       78.61       136.27         4.47         5.29        17.06        18.05 
TCGA-W3-AA21 TCGA-WE-A8ZQ TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA3 TCGA-YG-AA3O 
       92.84        59.44        48.39         1.94        16.64        28.21 

$`19P GAIN WILD-TYPE`
TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
       60.46        12.99        14.83         8.42        15.72        31.89 
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 
      133.25        19.04        76.41        25.64        45.99        62.86 
TCGA-D3-A2JB TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN 
      168.00         7.27       107.61        36.30       171.58        64.83 
TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF 
       58.06        46.98       140.98        40.01        59.70        16.96 
TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51J 
       13.87         9.34        90.21        23.67       173.85       144.46 
TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR 
       31.76        62.70        11.34        42.05        45.70       177.86 
TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM 
       78.21        23.61       179.97       120.00        69.53        70.62 
TCGA-D3-A8GP TCGA-D3-A8GR TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 
      135.12        36.53        10.78        15.02        16.90        18.44 
TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 
       22.85        48.66       106.85        31.96       150.61        82.85 
TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 
       32.42        64.83        58.85        25.12       214.59        14.96 
TCGA-EB-A44Q TCGA-EB-A5SG TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A181 
        3.91        33.24        45.50         6.64        13.15        20.38 
TCGA-EE-A182 TCGA-EE-A184 TCGA-EE-A20C TCGA-EE-A20H TCGA-EE-A29B TCGA-EE-A29C 
        0.00        67.50        75.55       155.90        75.22        76.14 
TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29Q TCGA-EE-A29T 
       12.99        44.28        63.12        47.74        61.12       346.49 
TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD 
      185.19       102.38         7.20        77.98        26.14       239.11 
TCGA-EE-A2GE TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN 
        0.20        68.65        10.62        32.48        18.35        31.00 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GU TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MF 
        0.76         0.20        81.99         5.75        23.77       209.79 
TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MP 
       94.19       171.85        63.25        67.50       104.78       227.01 
TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB 
       25.08       143.93        23.51        53.26       124.31       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 
       51.62         4.41        54.51         6.28        67.89       111.85 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
       45.90         3.35       201.80        14.56        34.45         1.58 
TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19G 
       47.31         4.54        53.29        39.81        11.47       151.46 
TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
      150.12        99.06        59.84        42.48       120.76        49.71 
TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A3ES 
       34.95       146.63        47.97        22.36        16.87       173.29 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-FR-A44A TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FR-A8YC 
       55.82        15.48       174.21        26.20         5.65        10.06 
TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1ZE TCGA-FS-A1ZF 
      171.78        49.74       195.98        27.62        35.90        12.92 
TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZQ TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A1ZZ 
        7.82        36.33       130.95        35.28        23.21         3.06 
TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TU 
       30.90        66.67       173.19        13.28        80.68        55.59 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 
       11.54        19.30         9.90         6.05         1.91        53.29 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 
      117.93        84.72        42.48         7.59       120.53        34.49 
TCGA-GN-A4U8 TCGA-GN-A8LK TCGA-GN-A9SD TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS 
       46.92        43.23        59.41        85.05       297.01         7.23 
TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1Q TCGA-W3-AA1R 
        0.33       174.12         1.97       120.07        44.05        79.99 
TCGA-W3-AA1V TCGA-W3-AA1W TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8ZM TCGA-WE-A8ZN 
        8.09       185.13         1.15        59.64        62.99        12.69 
TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-Z2-AA3S 
       19.00        10.95        26.60        15.65        91.23 

  19P GAIN MUTATED 19P GAIN WILD-TYPE 
              0.26               0.00 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
            312.07             346.49 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
             48.87              45.90 
[1] "0.3 - 312.1 (48.9)" "0.0 - 346.5 (45.9)"
[1] "hr=" "1"  
D34V2, survival
                    sevent
clus2                  0   1
  19P GAIN MUTATED    27  28
  19P GAIN WILD-TYPE 142 152
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                55                294 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                28                152 
$`19P GAIN MUTATED`
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1QB TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JE 
      112.57        71.80        95.74       115.53        86.76        27.65 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A5GU TCGA-D3-A8GI TCGA-D9-A6E9 TCGA-D9-A6EC 
       66.08        59.57       125.19        58.52         9.90        66.25 
TCGA-EB-A5SH TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A29E TCGA-EE-A29L TCGA-EE-A29P 
       54.02        27.22        94.98        63.78         2.60        56.42 
TCGA-EE-A29R TCGA-EE-A2GH TCGA-EE-A2GO TCGA-EE-A2GS TCGA-EE-A2M6 TCGA-EE-A2M7 
       14.47       208.04       126.81        81.21       129.27        28.83 
TCGA-EE-A2MM TCGA-EE-A3JI TCGA-ER-A199 TCGA-ER-A19E TCGA-ER-A2ND TCGA-ER-A2NG 
      167.90       152.81         9.17        13.02        23.34        31.27 
TCGA-ER-A3PL TCGA-FR-A729 TCGA-FS-A1YX TCGA-FS-A1Z3 TCGA-FS-A1ZC TCGA-FS-A1ZD 
       33.21       220.80        48.59        20.91       357.37        53.52 
TCGA-FS-A1ZM TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A4F2 TCGA-FS-A4F5 
      101.26       148.80        26.56        27.09        50.14        28.73 
TCGA-FW-A3I3 TCGA-GF-A6C9 TCGA-GN-A266 TCGA-GN-A267 TCGA-HR-A2OG TCGA-QB-AA9O 
        0.20        15.78        10.13        64.44         0.23        18.05 
TCGA-W3-AA21 TCGA-WE-A8ZQ TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA3 
      105.04        59.77        32.58        49.51        12.16        19.73 
TCGA-YG-AA3O 
       37.94 

$`19P GAIN WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q3 
       17.03        66.48        12.99        14.93        16.57        16.67 
TCGA-D3-A1Q4 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A2J6 
      112.04       133.25        28.08        31.59        90.90        43.43 
TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JD TCGA-D3-A2JF 
      103.10        65.49        23.77       168.00        11.87        62.07 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A3BZ 
      113.52        42.08        12.10       171.58        66.48       130.72 
TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE 
       58.06        46.98        46.32       166.52        86.93        60.23 
TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV 
       24.53        13.87         9.34       103.59        39.75        45.30 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
      174.84        55.73        56.35       145.12        32.94        22.62 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR 
       63.81        26.89       125.79       135.75       137.92       178.32 
TCGA-D3-A5GS TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GJ 
       18.18        30.84        79.59        23.61        26.43       241.38 
TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GQ 
      170.20        89.13       107.15       161.00       152.75        29.06 
TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX 
      129.63       117.17       151.53        54.67         3.65         7.10 
TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6EA TCGA-D9-A6EG 
       18.12        15.39        22.29        18.44        25.18        22.95 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 
       48.89        36.03       117.21        20.38       194.83       176.55 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB 
       35.93       107.34        61.18        53.92        65.92        23.44 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q 
       68.09        28.60        10.49       215.44        15.68        13.87 
TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV 
       10.36        20.35        68.25        17.29        52.01         7.04 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
       24.89        29.82         8.65        33.73        14.70        26.89 
TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H 
       68.15         4.96       133.81       151.27        91.56       168.26 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29G 
       13.55        63.35        85.08        78.97        13.97        72.07 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29T 
       64.64        56.84        18.61        66.74        61.28       369.93 
TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
       25.87       195.02        17.92        46.82       102.90        36.82 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE 
       39.29        86.14        59.28        67.43       340.14       161.03 
TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN 
       48.72       107.38        54.74        79.66        75.48       102.12 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M8 
       13.91        42.77        44.88        94.82        21.67        19.76 
TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH 
       61.51        47.28       103.27       268.73       103.20        16.96 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MN TCGA-EE-A2MP 
      204.66        96.23       158.63       216.66        47.54       248.65 
TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA 
       43.23       134.40       162.48        71.21        53.26       124.31 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG 
      122.73        51.62        28.77        54.51        13.81        41.59 
TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 
      138.81       172.18       127.20        36.95        64.08        34.32 
TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 
       53.19       201.80        27.35        51.35       109.58        31.40 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C 
       35.44        13.94        50.76        77.75        98.40        48.89 
TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L 
       12.59        26.37       268.93       152.35         6.44       131.51 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T 
       61.05        44.05       162.08        50.89        37.25         8.88 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NH 
      148.18        79.99        43.82        20.15        16.37        32.05 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A 
      247.04        80.32        46.98         6.77        92.98       174.21 
TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD 
       15.72        27.85        18.77        38.27        34.82        36.26 
TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1Z7 
      104.42       216.92       228.59       202.65        28.08         7.79 
TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH 
       27.72        48.85        40.27        15.45         9.70        32.75 
TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZT 
       47.38        23.93        74.73       133.55        11.41        53.16 
TCGA-FS-A1ZW TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 
       49.48        27.02        77.82        66.67       174.84        34.03 
TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV 
       26.73        54.41        80.68        22.92        55.59        13.51 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 
       19.30         9.90         7.23         2.04       139.89       117.93 
TCGA-GN-A265 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A4U4 
       84.72        62.79        32.48        39.58       121.91        39.35 
TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A8LL TCGA-GN-A9SD 
       10.42        48.89        22.13        50.10        21.37        59.41 
TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 
       65.88       368.78       297.90         7.23         0.33         0.69 
TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1Q TCGA-W3-AA1R 
      228.16        63.02       121.08         4.01        69.07       111.09 
TCGA-W3-AA1V TCGA-W3-AA1W TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8K6 
       42.08       219.16        24.03        49.05        61.15        15.98 
TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-AAA0 TCGA-WE-AAA4 
       98.89        58.98        67.63        11.80        35.01        22.29 
TCGA-YD-A89C TCGA-YD-A9TA TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
        6.90        49.18        14.43        27.58        96.99        15.98 

  19P GAIN MUTATED 19P GAIN WILD-TYPE 
              0.20               0.33 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
            357.37             369.93 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
            53.520             50.825 
[1] "0.2 - 357.4 (53.5)" "0.3 - 369.9 (50.8)"
[1] "hr=" "1"  
D34V3, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  19P GAIN MUTATED                    9             2
  19P GAIN WILD-TYPE                 56             3
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  19P GAIN MUTATED                                          13
  19P GAIN WILD-TYPE                                        59
                    vv
clus                 REGIONAL LYMPH NODE
  19P GAIN MUTATED                    31
  19P GAIN WILD-TYPE                 184
D34V4, multiclass
                                           clus
vv                                          19P GAIN MUTATED 19P GAIN WILD-TYPE
  DISTANT METASTASIS                                       9                 56
  PRIMARY TUMOR                                            2                  3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               13                 59
  REGIONAL LYMPH NODE                                     31                184
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  19P GAIN MUTATED             2       0       8        1        4        2
  19P GAIN WILD-TYPE          10       7      20       17       23       22
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  19P GAIN MUTATED           3         1         3         6          4
  19P GAIN WILD-TYPE        11        18         9        31         11
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  19P GAIN MUTATED            4         11        3
  19P GAIN WILD-TYPE         28         49       17
D34V5, multiclass
             clus
vv            19P GAIN MUTATED 19P GAIN WILD-TYPE
  I OR II NOS                2                 10
  STAGE 0                    0                  7
  STAGE I                    8                 20
  STAGE IA                   1                 17
  STAGE IB                   4                 23
  STAGE II                   2                 22
  STAGE IIA                  3                 11
  STAGE IIB                  1                 18
  STAGE IIC                  3                  9
  STAGE III                  6                 31
  STAGE IIIA                 4                 11
  STAGE IIIB                 4                 28
  STAGE IIIC                11                 49
  STAGE IV                   3                 17
[1] 14  2
[1] TRUE
[1] "dimension of contingency 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       8 13 12 11
  19P GAIN WILD-TYPE    56 59 65 57
D34V6, multiclass
       clus
vv      19P GAIN MUTATED 19P GAIN WILD-TYPE
  T0+T1                8                 56
  T2                  13                 59
  T3                  12                 65
  T4                  11                 57
[1] 4 2
[1] TRUE
[1] "dimension of 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    28   9   4   9
  19P GAIN WILD-TYPE 141  54  34  40
D34V7, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  N0               28                141
  N1                9                 54
  N2                4                 34
  N3                9                 40
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V8, binary
                    cls
clus                   0   1
  19P GAIN MUTATED    48   3
  19P GAIN WILD-TYPE 265  18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     48    3
  19P GAIN WILD-TYPE  265   18
   clus
vv  19P GAIN MUTATED 19P GAIN WILD-TYPE
  0               48                265
  1                3                 18
[1] 2 2
[1] FALSE
D34V9, binary
                    cls
clus                   0   1
  19P GAIN MUTATED    21  14
  19P GAIN WILD-TYPE 111  74
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     21   14
  19P GAIN WILD-TYPE  111   74
     clus
vv    19P GAIN MUTATED 19P GAIN WILD-TYPE
  NO                21                111
  YES               14                 74
[1] 2 2
[1] FALSE
D34V10, binary
                    cls
clus                   0   1
  19P GAIN MUTATED     9  46
  19P GAIN WILD-TYPE  35 267
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      9   46
  19P GAIN WILD-TYPE   35  267
     clus
vv    19P GAIN MUTATED 19P GAIN WILD-TYPE
  NO                 9                 35
  YES               46                267
[1] 2 2
[1] FALSE
D34V11, continuous
D34V12, binary
                    cls
clus                   0   1
  19P GAIN MUTATED    24  31
  19P GAIN WILD-TYPE 111 192
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     24   31
  19P GAIN WILD-TYPE  111  192
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  FEMALE               24                111
  MALE                 31                192
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  19P GAIN MUTATED       1                         0    51
  19P GAIN WILD-TYPE     4                         1   293
D34V13, multiclass
                           clus
vv                          19P GAIN MUTATED 19P GAIN WILD-TYPE
  ASIAN                                    1                  4
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   51                293
[1] 3 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     1  52
  19P GAIN WILD-TYPE   6 292
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      1   52
  19P GAIN WILD-TYPE    6  292
                        clus
vv                       19P GAIN MUTATED 19P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO               52                292
[1] 2 2
[1] FALSE

Clustering(35) Variable = 19Q GAIN MUTATION ANALYSIS
D35V1, survival
                    sevent
clus2                  0   1
  19Q GAIN MUTATED    19  23
  19Q GAIN WILD-TYPE 102  95
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                42                197 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                23                 95 
$`19Q GAIN MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JE 
        8.42       110.93        49.35        15.75        86.30         9.76 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3CE TCGA-D9-A6EC TCGA-EB-A5SH TCGA-EE-A17Y 
       66.08        43.53        59.70        57.90        50.07        24.89 
TCGA-EE-A180 TCGA-EE-A29E TCGA-EE-A29P TCGA-EE-A29T TCGA-EE-A2GD TCGA-EE-A2GH 
       62.37         0.26        27.16       346.49       239.11       189.40 
TCGA-EE-A2GS TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A3JI TCGA-ER-A197 TCGA-ER-A199 
       71.31       103.13        15.25       152.81         1.58         7.82 
TCGA-ER-A2NG TCGA-ER-A3ET TCGA-ER-A3PL TCGA-FS-A1Z3 TCGA-FS-A1ZC TCGA-FS-A1ZD 
       10.95        55.82        32.05         8.35       312.07        32.78 
TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-GN-A267 
       78.61       130.95       136.27         4.47         5.29        17.06 
TCGA-QB-AA9O TCGA-WE-A8ZQ TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA3 TCGA-YG-AA3O 
       18.05        59.44        48.39         1.94        16.64        28.21 

$`19Q GAIN WILD-TYPE`
TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q7 
       60.46        12.99        14.83        15.72        31.89       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 
       19.04        76.41        62.60        25.64        45.99        62.86 
TCGA-D3-A2JB TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN 
      168.00         7.27       107.61        36.30       171.58        64.83 
TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3ML 
       58.06        46.98       140.98        40.01        16.96        13.87 
TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51J TCGA-D3-A51K 
        9.34        90.21        23.67       173.85       144.46        31.76 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GU 
       62.70        11.34        42.05        45.70       177.86       124.08 
TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM 
       78.21        23.61       179.97       120.00        69.53        70.62 
TCGA-D3-A8GP TCGA-D3-A8GR TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 
      135.12        36.53        10.78        15.02        16.90        18.44 
TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 
       22.85        48.66       106.85        31.96       150.61        82.85 
TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 
       32.42        64.83        58.85        25.12       214.59        14.96 
TCGA-EB-A44Q TCGA-EB-A5SG TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A181 
        3.91        33.24        45.50         6.64        13.15        20.38 
TCGA-EE-A182 TCGA-EE-A184 TCGA-EE-A20C TCGA-EE-A20H TCGA-EE-A29B TCGA-EE-A29C 
        0.00        67.50        75.55       155.90        75.22        76.14 
TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29Q TCGA-EE-A29W 
       12.99        44.28        63.12        47.74        61.12       185.19 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GJ 
      102.38         7.20        77.98        26.14         0.20        68.65 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP 
       10.62        32.48        18.35        31.00       118.32         0.76 
TCGA-EE-A2GR TCGA-EE-A2GU TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MG 
        0.20        81.99         5.75        23.77       209.79        94.19 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP 
      171.85        63.25        67.50       104.78       145.45       227.01 
TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB 
       25.08       143.93        23.51        53.26       124.31       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 
       51.62         4.41        54.51         6.28        67.89       111.85 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A198 
       45.90         3.35       201.80        14.56        34.45        47.31 
TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19H 
        4.54        53.29        39.81        11.47       151.46       150.12 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S 
       99.06        59.84        42.48       120.76        49.71        34.95 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A3ES 
      146.63        47.97        22.36         4.70        16.87       173.29 
TCGA-ER-A3EV TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FR-A8YC 
       15.48       174.21       209.23        26.20         5.65        10.06 
TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1ZE TCGA-FS-A1ZF 
      171.78        49.74       195.98        27.62        35.90        12.92 
TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A1ZZ TCGA-FS-A4F0 
        7.82        36.33        35.28        23.21         3.06        30.90 
TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV 
       66.67       173.19        13.28        80.68        55.59        11.54 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 
       19.30         9.90         6.05         1.91        53.29       117.93 
TCGA-GN-A265 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 
       84.72        42.48         7.59       120.53        34.49        46.92 
TCGA-GN-A8LK TCGA-GN-A9SD TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A693 
       43.23        59.41        85.05       297.01         7.23         0.33 
TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1V 
      174.12         1.97       120.07        44.05        79.99         8.09 
TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8ZM TCGA-WE-A8ZN 
      185.13        92.84         1.15        59.64        62.99        12.69 
TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-Z2-AA3S 
       19.00        10.95        26.60        15.65        91.23 

  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
              0.26               0.00 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
            346.49             297.01 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
             45.96              45.99 
[1] "0.3 - 346.5 (46.0)" "0.0 - 297.0 (46.0)"
[1] "hr=" "1.1"
D35V2, survival
                    sevent
clus2                  0   1
  19Q GAIN MUTATED    26  29
  19Q GAIN WILD-TYPE 143 151
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                55                294 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                29                151 
$`19Q GAIN MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JE 
       16.57       112.57        71.80       115.53        86.76        27.65 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3CE TCGA-D3-A8GI TCGA-D9-A6E9 TCGA-D9-A6EC 
       66.08        59.57        60.23        58.52         9.90        66.25 
TCGA-EB-A5SH TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A29E TCGA-EE-A29L TCGA-EE-A29P 
       54.02        27.22        94.98        63.78         2.60        56.42 
TCGA-EE-A29R TCGA-EE-A29T TCGA-EE-A2GD TCGA-EE-A2GH TCGA-EE-A2GS TCGA-EE-A2M6 
       14.47       369.93       340.14       208.04        81.21       129.27 
TCGA-EE-A2M7 TCGA-EE-A3JI TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19E TCGA-ER-A2NG 
       28.83       152.81        13.94         9.17        13.02        31.27 
TCGA-ER-A3ET TCGA-ER-A3PL TCGA-FS-A1YX TCGA-FS-A1Z3 TCGA-FS-A1ZC TCGA-FS-A1ZD 
       80.32        33.21        48.59        20.91       357.37        53.52 
TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A4F5 
      101.26       133.55       148.80        26.56        27.09        28.73 
TCGA-FW-A3I3 TCGA-GF-A6C9 TCGA-GN-A266 TCGA-GN-A267 TCGA-HR-A2OG TCGA-QB-AA9O 
        0.20        15.78        10.13        64.44         0.23        18.05 
TCGA-WE-A8JZ TCGA-WE-A8ZQ TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA3 
       24.03        59.77        32.58        49.51        12.16        19.73 
TCGA-YG-AA3O 
       37.94 

$`19Q GAIN WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
       17.03        66.48        12.99        14.93        16.67       112.04 
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 
      133.25        28.08        31.59        90.90        95.74        43.43 
TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JD TCGA-D3-A2JF 
      103.10        65.49        23.77       168.00        11.87        62.07 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A3BZ 
      113.52        42.08        12.10       171.58        66.48       130.72 
TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CF 
       58.06        46.98        46.32       166.52        86.93        24.53 
TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E 
       13.87         9.34       103.59        39.75        45.30       174.84 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R 
       55.73        56.35       145.12        32.94        22.62        63.81 
TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       26.89       125.79       135.75       137.92       178.32        18.18 
TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GJ 
      125.19        30.84        79.59        23.61        26.43       241.38 
TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GQ 
      170.20        89.13       107.15       161.00       152.75        29.06 
TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX 
      129.63       117.17       151.53        54.67         3.65         7.10 
TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6EA TCGA-D9-A6EG 
       18.12        15.39        22.29        18.44        25.18        22.95 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 
       48.89        36.03       117.21        20.38       194.83       176.55 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB 
       35.93       107.34        61.18        53.92        65.92        23.44 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q 
       68.09        28.60        10.49       215.44        15.68        13.87 
TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV 
       10.36        20.35        68.25        17.29        52.01         7.04 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
       24.89        29.82         8.65        33.73        14.70        26.89 
TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H 
       68.15         4.96       133.81       151.27        91.56       168.26 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29G 
       13.55        63.35        85.08        78.97        13.97        72.07 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29V 
       64.64        56.84        18.61        66.74        61.28        25.87 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 
      195.02        17.92        46.82       102.90        36.82        39.29 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GJ 
       86.14        59.28        67.43       161.03        48.72       107.38 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP 
       54.74        79.66        75.48       102.12       126.81        13.91 
TCGA-EE-A2GR TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M8 TCGA-EE-A2MC 
       42.77        44.88        94.82        21.67        19.76        61.51 
TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
       47.28       103.27       268.73       103.20        16.96       204.66 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP 
       96.23       158.63       216.66       167.90        47.54       248.65 
TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA 
       43.23       134.40       162.48        71.21        53.26       124.31 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG 
      122.73        51.62        28.77        54.51        13.81        41.59 
TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 
      138.81       172.18       127.20        36.95        64.08        34.32 
TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 
       53.19       201.80        27.35        51.35       109.58        31.40 
TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D 
       35.44        50.76        77.75        98.40        48.89        12.59 
TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
       26.37       268.93       152.35         6.44       131.51        61.05 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W 
       44.05       162.08        50.89        37.25         8.88       148.18 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NH 
       79.99        43.82        23.34        20.15        16.37        32.05 
TCGA-ER-A3ES TCGA-ER-A3EV TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
      247.04        46.98         6.77        92.98       174.21        15.72 
TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD 
      220.80        27.85        18.77        38.27        34.82        36.26 
TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1Z7 
      104.42       216.92       228.59       202.65        28.08         7.79 
TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH 
       27.72        48.85        40.27        15.45         9.70        32.75 
TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZT TCGA-FS-A1ZW 
       47.38        23.93        74.73        11.41        53.16        49.48 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 
       27.02        77.82        50.14        66.67       174.84        34.03 
TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV 
       26.73        54.41        80.68        22.92        55.59        13.51 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 
       19.30         9.90         7.23         2.04       139.89       117.93 
TCGA-GN-A265 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A4U4 
       84.72        62.79        32.48        39.58       121.91        39.35 
TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A8LL TCGA-GN-A9SD 
       10.42        48.89        22.13        50.10        21.37        59.41 
TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 
       65.88       368.78       297.90         7.23         0.33         0.69 
TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1Q TCGA-W3-AA1R 
      228.16        63.02       121.08         4.01        69.07       111.09 
TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8K6 
       42.08       219.16       105.04        49.05        61.15        15.98 
TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-AAA0 TCGA-WE-AAA4 
       98.89        58.98        67.63        11.80        35.01        22.29 
TCGA-YD-A89C TCGA-YD-A9TA TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
        6.90        49.18        14.43        27.58        96.99        15.98 

  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
              0.20               0.33 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
            369.93             368.78 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
             49.51              51.12 
[1] "0.2 - 369.9 (49.5)" "0.3 - 368.8 (51.1)"
[1] "hr=" "1"  
D35V3, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  19Q GAIN MUTATED                    9             2
  19Q GAIN WILD-TYPE                 56             3
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  19Q GAIN MUTATED                                          13
  19Q GAIN WILD-TYPE                                        59
                    vv
clus                 REGIONAL LYMPH NODE
  19Q GAIN MUTATED                    30
  19Q GAIN WILD-TYPE                 185
D35V4, multiclass
                                           clus
vv                                          19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  DISTANT METASTASIS                                       9                 56
  PRIMARY TUMOR                                            2                  3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               13                 59
  REGIONAL LYMPH NODE                                     30                185
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  19Q GAIN MUTATED             3       0       5        1        3        1
  19Q GAIN WILD-TYPE           9       7      23       17       24       23
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  19Q GAIN MUTATED           3         2         2         6          5
  19Q GAIN WILD-TYPE        11        17        10        31         10
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  19Q GAIN MUTATED            6         11        3
  19Q GAIN WILD-TYPE         26         49       17
D35V5, multiclass
             clus
vv            19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  I OR II NOS                3                  9
  STAGE 0                    0                  7
  STAGE I                    5                 23
  STAGE IA                   1                 17
  STAGE IB                   3                 24
  STAGE II                   1                 23
  STAGE IIA                  3                 11
  STAGE IIB                  2                 17
  STAGE IIC                  2                 10
  STAGE III                  6                 31
  STAGE IIIA                 5                 10
  STAGE IIIB                 6                 26
  STAGE IIIC                11                 49
  STAGE IV                   3                 17
[1] 14  2
[1] TRUE
[1] "dimension of contingency 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       6 11 12 13
  19Q GAIN WILD-TYPE    58 61 65 55
D35V6, multiclass
       clus
vv      19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  T0+T1                6                 58
  T2                  11                 61
  T3                  12                 65
  T4                  13                 55
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  19Q GAIN MUTATED    24  13   3   9
  19Q GAIN WILD-TYPE 145  50  35  40
D35V7, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  N0               24                145
  N1               13                 50
  N2                3                 35
  N3                9                 40
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V8, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED    48   3
  19Q GAIN WILD-TYPE 265  18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     48    3
  19Q GAIN WILD-TYPE  265   18
   clus
vv  19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  0               48                265
  1                3                 18
[1] 2 2
[1] FALSE
D35V9, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED    17  16
  19Q GAIN WILD-TYPE 115  72
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     17   16
  19Q GAIN WILD-TYPE  115   72
     clus
vv    19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  NO                17                115
  YES               16                 72
[1] 2 2
[1] FALSE
D35V10, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED     9  46
  19Q GAIN WILD-TYPE  35 267
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      9   46
  19Q GAIN WILD-TYPE   35  267
     clus
vv    19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  NO                 9                 35
  YES               46                267
[1] 2 2
[1] FALSE
D35V11, continuous
D35V12, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED    24  31
  19Q GAIN WILD-TYPE 111 192
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     24   31
  19Q GAIN WILD-TYPE  111  192
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  FEMALE               24                111
  MALE                 31                192
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  19Q GAIN MUTATED       1                         0    50
  19Q GAIN WILD-TYPE     4                         1   294
D35V13, multiclass
                           clus
vv                          19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  ASIAN                                    1                  4
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   50                294
[1] 3 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     1  51
  19Q GAIN WILD-TYPE   6 293
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      1   51
  19Q GAIN WILD-TYPE    6  293
                        clus
vv                       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO               51                293
[1] 2 2
[1] FALSE

Clustering(36) Variable = 20P GAIN MUTATION ANALYSIS
D36V1, survival
                    sevent
clus2                 0  1
  20P GAIN MUTATED   45 52
  20P GAIN WILD-TYPE 76 66
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                97                142 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                52                 66 
$`20P GAIN MUTATED`
TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A2JA TCGA-D3-A2JD 
       12.99        14.83         8.42       110.93        15.75         7.27 
TCGA-D3-A2JE TCGA-D3-A2JH TCGA-D3-A2JN TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CE 
        9.76        36.30        64.83        58.06       140.98        59.70 
TCGA-D3-A3MR TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A5GR 
       90.21       144.46        31.76        62.70        45.70       177.86 
TCGA-D3-A5GU TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GM TCGA-D3-A8GP TCGA-D9-A3Z3 
      124.08        78.21        23.61        70.62       135.12        16.90 
TCGA-D9-A6EC TCGA-DA-A1I2 TCGA-DA-A1I7 TCGA-DA-A3F5 TCGA-EB-A6L9 TCGA-EE-A17Y 
       57.90       150.61        32.42       214.59         6.64        24.89 
TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A20H TCGA-EE-A29D TCGA-EE-A29T TCGA-EE-A29W 
       62.37        20.38       155.90        12.99       346.49       185.19 
TCGA-EE-A2A1 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GM 
      102.38        77.98        26.14         0.20       189.40        18.35 
TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 
       31.00       118.32         0.76        81.99       103.13        15.25 
TCGA-EE-A2M8 TCGA-EE-A2MP TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC 
        5.75       227.01        53.26       124.31       122.73        51.62 
TCGA-EE-A3AE TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-EE-A3JB TCGA-EE-A3JI TCGA-ER-A199 
       54.51        67.89        45.90       201.80       152.81         7.82 
TCGA-ER-A19B TCGA-ER-A19G TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19P TCGA-ER-A19Q 
       53.29       151.46        99.06        59.84       120.76        49.71 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A3EV TCGA-FR-A44A TCGA-FR-A729 TCGA-FS-A1Z0 
       22.36         4.70        15.48       174.21       209.23       195.98 
TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM 
       27.62       312.07        32.78         7.82        36.33        78.61 
TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A4F8 TCGA-FS-A4FD 
      130.95       136.27         4.47         5.29       173.19        80.68 
TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A8LK TCGA-GN-A9SD 
      117.93        17.06        42.48         7.59        43.23        59.41 
TCGA-OD-A75X TCGA-QB-A6FS TCGA-W3-A825 TCGA-W3-AA21 TCGA-WE-A8ZQ TCGA-WE-A8ZY 
      297.01         7.23         1.97        92.84        59.44        48.39 
TCGA-WE-AAA3 
       16.64 

$`20P GAIN WILD-TYPE`
TCGA-3N-A9WC TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       60.46        15.72        31.89        49.35       133.25        19.04 
TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JB 
       76.41        62.60        25.64        45.99        62.86       168.00 
TCGA-D3-A2JC TCGA-D3-A2JG TCGA-D3-A2JL TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C7 
       86.30       107.61       171.58        66.08        43.53        46.98 
TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MU TCGA-D3-A51E 
       40.01        16.96        13.87         9.34        23.67       173.85 
TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GR 
       11.34        42.05       179.97       120.00        69.53        36.53 
TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A4Z6 TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY 
       10.78        15.02        18.44        22.85        48.66       106.85 
TCGA-DA-A1I1 TCGA-DA-A1I5 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F8 
       31.96        82.85        64.83        58.85        25.12        14.96 
TCGA-EB-A44Q TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A182 
        3.91        33.24        50.07        45.50        13.15         0.00 
TCGA-EE-A184 TCGA-EE-A20C TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G 
       67.50        75.55        75.22        76.14         0.26        44.28 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A2A2 TCGA-EE-A2GD 
       63.12        47.74        27.16        61.12         7.20       239.11 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2MC 
       68.65        10.62        32.48         0.20        71.31        23.77 
TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML 
      209.79        94.19       171.85        63.25        67.50       104.78 
TCGA-EE-A2MM TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AD TCGA-EE-A3AF 
      145.45        25.08       143.93        23.51         4.41         6.28 
TCGA-EE-A3J4 TCGA-EE-A3J8 TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
      111.85         3.35        14.56        34.45         1.58        47.31 
TCGA-ER-A19A TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19H TCGA-ER-A19N TCGA-ER-A19S 
        4.54        39.81        11.47       150.12        42.48        34.95 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET 
      146.63        47.97        16.87        10.95       173.29        55.82 
TCGA-ER-A3PL TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FS-A1YW TCGA-FS-A1YY 
       32.05        26.20         5.65        10.06       171.78        49.74 
TCGA-FS-A1Z3 TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A1ZZ 
        8.35        35.90        12.92        35.28        23.21         3.06 
TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F9 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
       30.90        66.67        13.28        55.59        11.54        19.30 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A4U3 
        9.90         6.05         1.91        53.29        84.72       120.53 
TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-LH-A9QB TCGA-QB-AA9O TCGA-RP-A693 TCGA-W3-A824 
       34.49        46.92        85.05        18.05         0.33       174.12 
TCGA-W3-A828 TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1V TCGA-W3-AA1W TCGA-WE-A8K1 
      120.07        44.05        79.99         8.09       185.13         1.15 
TCGA-WE-A8K5 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-AA9Y 
       59.64        62.99        12.69        19.00        10.95         1.94 
TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-Z2-AA3S 
       26.60        15.65        28.21        91.23 

  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               0.2                0.0 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
            346.49             239.11 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
             58.06              39.91 
[1] "0.2 - 346.5 (58.1)" "0.0 - 239.1 (39.9)"
[1] "hr=" "1.3"
D36V2, survival
                    sevent
clus2                  0   1
  20P GAIN MUTATED    64  75
  20P GAIN WILD-TYPE 105 105
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               139                210 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                75                105 
$`20P GAIN MUTATED`
TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q9 TCGA-D3-A2JA 
       12.99        14.93        16.57       112.57        31.59       115.53 
TCGA-D3-A2JD TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A2JH TCGA-D3-A2JN TCGA-D3-A3C6 
       11.87        27.65        62.07        42.08        66.48        58.06 
TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3MR TCGA-D3-A3MV TCGA-D3-A51J TCGA-D3-A51K 
      166.52        60.23       103.59        45.30       145.12        32.94 
TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D3-A8GC TCGA-D3-A8GD 
       63.81       135.75       178.32       125.19        79.59        23.61 
TCGA-D3-A8GI TCGA-D3-A8GM TCGA-D3-A8GP TCGA-D9-A1JX TCGA-D9-A3Z3 TCGA-D9-A6E9 
       58.52       107.15       152.75         7.10        22.29         9.90 
TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I7 
       25.18        66.25        36.03        20.38       176.55        61.18 
TCGA-DA-A3F5 TCGA-EB-A5UL TCGA-EB-A6L9 TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A181 
      215.44        17.29        24.89        27.22        94.98        33.73 
TCGA-EE-A20B TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29D TCGA-EE-A29R TCGA-EE-A29T 
      133.81       168.26        63.35        13.97        14.47       369.93 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
      195.02        17.92       102.90        39.29        86.14        59.28 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO 
      161.03       208.04        48.72        75.48       102.12       126.81 
TCGA-EE-A2GP TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 
       13.91        94.82        21.67       129.27        28.83        19.76 
TCGA-EE-A2MH TCGA-EE-A2MP TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC 
       16.96       248.65        53.26       124.31       122.73        51.62 
TCGA-EE-A3AE TCGA-EE-A3J3 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-EE-A3JB 
       54.51       172.18        36.95        64.08        53.19       201.80 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19G TCGA-ER-A19J 
      109.58       152.81         9.17        98.40       268.93         6.44 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19T TCGA-ER-A2NC 
      131.51        61.05       162.08        50.89         8.88        43.82 
TCGA-ER-A2ND TCGA-ER-A3EV TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       23.34        46.98         6.77        92.98       174.21        15.72 
TCGA-FR-A729 TCGA-FR-A8YD TCGA-FS-A1YX TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1Z7 
      220.80        36.26        48.59       202.65        28.08         7.79 
TCGA-FS-A1ZA TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZK 
       27.72       357.37        53.52         9.70        47.38        23.93 
TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A4F2 
      101.26       133.55       148.80        26.56        27.09        50.14 
TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-GF-A6C9 TCGA-GN-A264 
       28.73       174.84        80.68         0.20        15.78       117.93 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U9 TCGA-GN-A8LK 
       64.44        62.79        32.48        39.58        22.13        50.10 
TCGA-GN-A9SD TCGA-HR-A2OH TCGA-OD-A75X TCGA-QB-A6FS TCGA-W3-A825 TCGA-W3-AA21 
       59.41        65.88       297.90         7.23        63.02       105.04 
TCGA-WE-A8JZ TCGA-WE-A8K6 TCGA-WE-A8ZQ TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AAA3 
       24.03        15.98        59.77        32.58        49.51        19.73 
TCGA-YD-A9TA 
       49.18 

$`20P GAIN WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       17.03        66.48        16.67       112.04        71.80       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 
       28.08        90.90        95.74        43.43       103.10        65.49 
TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JG TCGA-D3-A2JK TCGA-D3-A2JL 
       23.77       168.00        86.76       113.52        12.10       171.58 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CC 
       66.08        59.57       130.72        46.98        46.32        86.93 
TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F 
       24.53        13.87         9.34        39.75       174.84        55.73 
TCGA-D3-A51H TCGA-D3-A51N TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GO TCGA-D3-A5GS 
       56.35        22.62        26.89       125.79       137.92        18.18 
TCGA-D3-A8GB TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GN 
       30.84        26.43       241.38       170.20        89.13       161.00 
TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW 
       29.06       129.63       117.17       151.53        54.67         3.65 
TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A4Z6 TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY 
       18.12        15.39        18.44        22.95        48.89       117.21 
TCGA-DA-A1I1 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB 
      194.83        35.93       107.34        53.92        65.92        23.44 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R 
       68.09        28.60        10.49        15.68        13.87        10.36 
TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EE-A17X 
       20.35        68.25        54.02        52.01         7.04        29.82 
TCGA-EE-A17Z TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20C 
        8.65        14.70        26.89        68.15         4.96       151.27 
TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G 
       91.56        13.55        85.08        78.97        63.78        72.07 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
       64.64         2.60        56.84        18.61        56.42        66.74 
TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A2A0 TCGA-EE-A2A2 TCGA-EE-A2GC TCGA-EE-A2GD 
       61.28        25.87        46.82        36.82        67.43       340.14 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT 
      107.38        54.74        79.66        42.77        81.21        44.88 
TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI 
       61.51        47.28       103.27       268.73       103.20       204.66 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MQ 
       96.23       158.63       216.66       167.90        47.54        43.23 
TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG 
      134.40       162.48        71.21        28.77        13.81        41.59 
TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J8 TCGA-EE-A3JD TCGA-EE-A3JE TCGA-ER-A193 
      138.81       127.20        34.32        27.35        51.35        31.40 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19C TCGA-ER-A19D 
       35.44        13.94        50.76        77.75        48.89        12.59 
TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19H TCGA-ER-A19N TCGA-ER-A19S TCGA-ER-A19W 
       13.02        26.37       152.35        44.05        37.25       148.18 
TCGA-ER-A1A1 TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES 
       79.99        20.15        16.37        31.27        32.05       247.04 
TCGA-ER-A3ET TCGA-ER-A3PL TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC 
       80.32        33.21        27.85        18.77        38.27        34.82 
TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1ZB TCGA-FS-A1ZE 
      104.42       216.92       228.59        20.91        48.85        40.27 
TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZT TCGA-FS-A1ZW 
       15.45        32.75        74.73        11.41        53.16        49.48 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC 
       27.02        77.82        66.67        34.03        26.73        54.41 
TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
       22.92        55.59        13.51        19.30         9.90         7.23 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A4U3 TCGA-GN-A4U4 
        2.04       139.89        84.72        10.13       121.91        39.35 
TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A8LL TCGA-HR-A2OG TCGA-LH-A9QB TCGA-QB-AA9O 
       10.42        48.89        21.37         0.23       368.78        18.05 
TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1Q 
        0.33         0.69       228.16       121.08         4.01        69.07 
TCGA-W3-AA1R TCGA-W3-AA1V TCGA-W3-AA1W TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8ZM 
      111.09        42.08       219.16        49.05        61.15        98.89 
TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 
       58.98        67.63        11.80        12.16        35.01        22.29 
TCGA-YD-A89C TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
        6.90        37.94        14.43        27.58        96.99        15.98 

  20P GAIN MUTATED 20P GAIN WILD-TYPE 
              0.20               0.23 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
            369.93             368.78 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
             54.51              48.89 
[1] "0.2 - 369.9 (54.5)" "0.2 - 368.8 (48.9)"
[1] "hr=" "1.1"
D36V3, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  20P GAIN MUTATED                   25             4
  20P GAIN WILD-TYPE                 40             1
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  20P GAIN MUTATED                                          27
  20P GAIN WILD-TYPE                                        45
                    vv
clus                 REGIONAL LYMPH NODE
  20P GAIN MUTATED                    89
  20P GAIN WILD-TYPE                 126
D36V4, multiclass
                                           clus
vv                                          20P GAIN MUTATED 20P GAIN WILD-TYPE
  DISTANT METASTASIS                                      25                 40
  PRIMARY TUMOR                                            4                  1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               27                 45
  REGIONAL LYMPH NODE                                     89                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                 I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  20P GAIN MUTATED             8       2      16        9       14        7
  20P GAIN WILD-TYPE           4       5      12        9       13       17
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  20P GAIN MUTATED           5         3         5        17          7
  20P GAIN WILD-TYPE         9        16         7        20          8
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  20P GAIN MUTATED           15         21        5
  20P GAIN WILD-TYPE         17         39       15
D36V5, multiclass
             clus
vv            20P GAIN MUTATED 20P GAIN WILD-TYPE
  I OR II NOS                8                  4
  STAGE 0                    2                  5
  STAGE I                   16                 12
  STAGE IA                   9                  9
  STAGE IB                  14                 13
  STAGE II                   7                 17
  STAGE IIA                  5                  9
  STAGE IIB                  3                 16
  STAGE IIC                  5                  7
  STAGE III                 17                 20
  STAGE IIIA                 7                  8
  STAGE IIIB                15                 17
  STAGE IIIC                21                 39
  STAGE IV                   5                 15
[1] 14  2
[1] TRUE
[1] "dimension of contingency 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      31 35 22 29
  20P GAIN WILD-TYPE    33 37 55 39
D36V6, multiclass
       clus
vv      20P GAIN MUTATED 20P GAIN WILD-TYPE
  T0+T1               31                 33
  T2                  35                 37
  T3                  22                 55
  T4                  29                 39
[1] 4 2
[1] TRUE
[1] "dimension of 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   74 28 14 17
  20P GAIN WILD-TYPE 95 35 24 32
D36V7, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  N0               74                 95
  N1               28                 35
  N2               14                 24
  N3               17                 32
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V8, binary
                    cls
clus                   0   1
  20P GAIN MUTATED   132   5
  20P GAIN WILD-TYPE 181  16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED    132    5
  20P GAIN WILD-TYPE  181   16
   clus
vv  20P GAIN MUTATED 20P GAIN WILD-TYPE
  0              132                181
  1                5                 16
[1] 2 2
[1] FALSE
D36V9, binary
                    cls
clus                  0  1
  20P GAIN MUTATED   58 31
  20P GAIN WILD-TYPE 74 57
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     58   31
  20P GAIN WILD-TYPE   74   57
     clus
vv    20P GAIN MUTATED 20P GAIN WILD-TYPE
  NO                58                 74
  YES               31                 57
[1] 2 2
[1] FALSE
D36V10, binary
                    cls
clus                   0   1
  20P GAIN MUTATED    15 129
  20P GAIN WILD-TYPE  29 184
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     15  129
  20P GAIN WILD-TYPE   29  184
     clus
vv    20P GAIN MUTATED 20P GAIN WILD-TYPE
  NO                15                 29
  YES              129                184
[1] 2 2
[1] FALSE
D36V11, continuous
D36V12, binary
                    cls
clus                   0   1
  20P GAIN MUTATED    56  89
  20P GAIN WILD-TYPE  79 134
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     56   89
  20P GAIN WILD-TYPE   79  134
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  FEMALE               56                 79
  MALE                 89                134
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  20P GAIN MUTATED       2                         0   140
  20P GAIN WILD-TYPE     3                         1   204
D36V13, multiclass
                           clus
vv                          20P GAIN MUTATED 20P GAIN WILD-TYPE
  ASIAN                                    2                  3
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                  140                204
[1] 3 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     2 139
  20P GAIN WILD-TYPE   5 205
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      2  139
  20P GAIN WILD-TYPE    5  205
                        clus
vv                       20P GAIN MUTATED 20P GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  5
  NOT HISPANIC OR LATINO              139                205
[1] 2 2
[1] FALSE

Clustering(37) Variable = 20Q GAIN MUTATION ANALYSIS
D37V1, survival
                    sevent
clus2                 0  1
  20Q GAIN MUTATED   60 61
  20Q GAIN WILD-TYPE 61 57
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               121                118 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                61                 57 
$`20Q GAIN MUTATED`
TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A2JA TCGA-D3-A2JC 
       12.99        14.83         8.42       110.93        15.75        86.30 
TCGA-D3-A2JD TCGA-D3-A2JE TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JP 
        7.27         9.76        36.30       171.58        64.83        43.53 
TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51J 
       58.06       140.98        59.70        90.21        23.67       144.46 
TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D3-A8GC 
       31.76        62.70        45.70       177.86       124.08        78.21 
TCGA-D3-A8GD TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GP TCGA-D9-A3Z3 TCGA-D9-A6EC 
       23.61        69.53        70.62       135.12        16.90        57.90 
TCGA-DA-A1HV TCGA-DA-A1I2 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A3F5 TCGA-EB-A5SH 
       48.66       150.61        32.42        64.83       214.59        50.07 
TCGA-EB-A6L9 TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A184 TCGA-EE-A20H TCGA-EE-A29D 
        6.64        24.89        62.37        67.50       155.90        12.99 
TCGA-EE-A29E TCGA-EE-A29P TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A6 
        0.26        27.16       346.49       185.19       102.38        77.98 
TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO 
       26.14         0.20       189.40        18.35        31.00       118.32 
TCGA-EE-A2GP TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MG 
        0.76        81.99       103.13        15.25         5.75        94.19 
TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC 
      227.01       143.93        53.26       124.31       122.73        51.62 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-EE-A3JB TCGA-EE-A3JI 
        4.41        54.51        67.89        45.90       201.80       152.81 
TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19G TCGA-ER-A19L TCGA-ER-A19M 
        1.58         7.82        53.29       151.46        99.06        59.84 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19W TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NG 
      120.76        49.71       146.63        22.36         4.70        10.95 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A44A TCGA-FR-A729 TCGA-FS-A1Z0 TCGA-FS-A1Z4 
       15.48        32.05       174.21       209.23       195.98        27.62 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ 
      312.07        32.78         7.82        36.33        78.61       130.95 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A4F8 TCGA-FS-A4FD 
      136.27        35.28         4.47         5.29       173.19        80.68 
TCGA-GF-A4EO TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
        6.05       117.93        84.72        17.06        42.48         7.59 
TCGA-GN-A8LK TCGA-GN-A9SD TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O TCGA-W3-A825 
       43.23        59.41       297.01         7.23        18.05         1.97 
TCGA-W3-AA1R TCGA-W3-AA21 TCGA-WE-A8ZM TCGA-WE-A8ZQ TCGA-WE-A8ZY TCGA-WE-AAA3 
       79.99        92.84        62.99        59.44        48.39        16.64 
TCGA-YG-AA3O 
       28.21 

$`20Q GAIN WILD-TYPE`
TCGA-3N-A9WC TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       60.46        15.72        31.89        49.35       133.25        19.04 
TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JB 
       76.41        62.60        25.64        45.99        62.86       168.00 
TCGA-D3-A2JG TCGA-D3-A2JO TCGA-D3-A3C7 TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3ML 
      107.61        66.08        46.98        40.01        16.96        13.87 
TCGA-D3-A3MO TCGA-D3-A51E TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A8GJ TCGA-D3-A8GK 
        9.34       173.85        11.34        42.05       179.97       120.00 
TCGA-D3-A8GR TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A4Z6 TCGA-D9-A6EG TCGA-DA-A1HY 
       36.53        10.78        15.02        18.44        22.85       106.85 
TCGA-DA-A1I1 TCGA-DA-A1I5 TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F8 TCGA-EB-A44Q 
       31.96        82.85        58.85        25.12        14.96         3.91 
TCGA-EB-A5SG TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A20C 
       33.24        45.50        13.15        20.38         0.00        75.55 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29Q 
       75.22        76.14        44.28        63.12        47.74        61.12 
TCGA-EE-A2A2 TCGA-EE-A2GD TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GR 
        7.20       239.11        68.65        10.62        32.48         0.20 
TCGA-EE-A2GS TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK 
       71.31        23.77       209.79       171.85        63.25        67.50 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A3AF TCGA-EE-A3J4 
      104.78       145.45        25.08        23.51         6.28       111.85 
TCGA-EE-A3J8 TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19C 
        3.35        14.56        34.45        47.31         4.54        39.81 
TCGA-ER-A19D TCGA-ER-A19H TCGA-ER-A19N TCGA-ER-A19S TCGA-ER-A1A1 TCGA-ER-A2NE 
       11.47       150.12        42.48        34.95        47.97        16.87 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FS-A1YW 
      173.29        55.82        26.20         5.65        10.06       171.78 
TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZW TCGA-FS-A1ZZ 
       49.74         8.35        35.90        12.92        23.21         3.06 
TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F9 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
       30.90        66.67        13.28        55.59        11.54        19.30 
TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 
        9.90         1.91        53.29       120.53        34.49        46.92 
TCGA-LH-A9QB TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A828 TCGA-W3-AA1Q TCGA-W3-AA1V 
       85.05         0.33       174.12       120.07        44.05         8.09 
TCGA-W3-AA1W TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT 
      185.13         1.15        59.64        12.69        19.00        10.95 
TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-Z2-AA3S 
        1.94        26.60        15.65        91.23 

  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               0.2                0.0 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
            346.49             239.11 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
            57.900             36.215 
[1] "0.2 - 346.5 (57.9)" "0.0 - 239.1 (36.2)"
[1] "hr=" "1.3"
D37V2, survival
                    sevent
clus2                 0  1
  20Q GAIN MUTATED   81 90
  20Q GAIN WILD-TYPE 88 90
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               171                178 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                90                 90 
$`20Q GAIN MUTATED`
TCGA-3N-A9WB TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q9 
       17.03        12.99        14.93        16.57       112.57        31.59 
TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A2JH 
      115.53        86.76        11.87        27.65        62.07        42.08 
TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CE 
      171.58        66.48        59.57        58.06       166.52        60.23 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R 
      103.59        39.75        45.30       145.12        32.94        63.81 
TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D3-A8GC TCGA-D3-A8GD 
      135.75       137.92       178.32       125.19        79.59        23.61 
TCGA-D3-A8GI TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D9-A148 
       58.52        89.13       107.15       152.75        29.06       151.53 
TCGA-D9-A1JX TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HV 
        7.10        22.29         9.90        25.18        66.25        48.89 
TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A3F5 
       36.03        20.38       176.55        61.18        65.92       215.44 
TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A6L9 TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A183 
       54.02        17.29        24.89        27.22        94.98        26.89 
TCGA-EE-A184 TCGA-EE-A20B TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29D TCGA-EE-A29E 
       68.15       133.81       168.26        63.35        13.97        63.78 
TCGA-EE-A29L TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A29X 
        2.60        56.42        14.47       369.93       195.02        17.92 
TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH 
      102.90        39.29        86.14        59.28       161.03       208.04 
TCGA-EE-A2GI TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GU 
       48.72        75.48       102.12       126.81        13.91        94.82 
TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MG TCGA-EE-A2MH 
       21.67       129.27        28.83        19.76       103.20        16.96 
TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC 
      248.65       162.48        53.26       124.31       122.73        51.62 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3J5 TCGA-EE-A3J7 
       28.77        54.51        41.59       172.18        36.95        64.08 
TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A197 TCGA-ER-A199 
       53.19       201.80       109.58       152.81        13.94         9.17 
TCGA-ER-A19B TCGA-ER-A19G TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19P 
       98.40       268.93         6.44       131.51        61.05       162.08 
TCGA-ER-A19Q TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NG 
       50.89         8.88       148.18        43.82        23.34        31.27 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       46.98        33.21         6.77        92.98       174.21        15.72 
TCGA-FR-A729 TCGA-FR-A8YD TCGA-FS-A1YX TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1Z7 
      220.80        36.26        48.59       202.65        28.08         7.79 
TCGA-FS-A1ZA TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZK 
       27.72       357.37        53.52         9.70        47.38        23.93 
TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZY 
      101.26       133.55       148.80        53.16        26.56        27.09 
TCGA-FS-A4F2 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-GF-A4EO 
       50.14        28.73       174.84        80.68         0.20         7.23 
TCGA-GF-A6C9 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
       15.78       117.93        84.72        64.44        62.79        32.48 
TCGA-GN-A26D TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A8LL TCGA-GN-A9SD TCGA-HR-A2OH 
       39.58        22.13        50.10        21.37        59.41        65.88 
TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O TCGA-W3-A825 TCGA-W3-AA1R TCGA-W3-AA21 
      297.90         7.23        18.05        63.02       111.09       105.04 
TCGA-WE-A8JZ TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZQ TCGA-WE-A8ZX TCGA-WE-A8ZY 
       24.03        15.98        98.89        59.77        32.58        49.51 
TCGA-WE-AAA3 TCGA-YD-A9TA TCGA-YG-AA3O 
       19.73        49.18        37.94 

$`20Q GAIN WILD-TYPE`
TCGA-3N-A9WC TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       66.48        16.67       112.04        71.80       133.25        28.08 
TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 
       90.90        95.74        43.43       103.10        65.49        23.77 
TCGA-D3-A2JB TCGA-D3-A2JG TCGA-D3-A2JK TCGA-D3-A2JO TCGA-D3-A3BZ TCGA-D3-A3C7 
      168.00       113.52        12.10        66.08       130.72        46.98 
TCGA-D3-A3C8 TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A51E 
       46.32        86.93        24.53        13.87         9.34       174.84 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51N TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GS 
       55.73        56.35        22.62        26.89       125.79        18.18 
TCGA-D3-A8GB TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GN TCGA-D3-A8GR 
       30.84        26.43       241.38       170.20       161.00       129.63 
TCGA-D3-A8GS TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A4Z6 
      117.17        54.67         3.65        18.12        15.39        18.44 
TCGA-D9-A6EG TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I8 
       22.95       117.21       194.83        35.93       107.34        53.92 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EB-A44Q 
       23.44        68.09        28.60        10.49        15.68        13.87 
TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EE-A17X 
       10.36        20.35        68.25        52.01         7.04        29.82 
TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A20F 
        8.65        33.73        14.70         4.96       151.27        91.56 
TCGA-EE-A20I TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M 
       13.55        85.08        78.97        72.07        64.64        56.84 
TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A2A0 TCGA-EE-A2A2 
       18.61        66.74        61.28        25.87        46.82        36.82 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GR 
       67.43       340.14       107.38        54.74        79.66        42.77 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF 
       81.21        44.88        61.51        47.28       103.27       268.73 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN 
      204.66        96.23       158.63       216.66       167.90        47.54 
TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J4 
       43.23       134.40        71.21        13.81       138.81       127.20 
TCGA-EE-A3J8 TCGA-EE-A3JD TCGA-EE-A3JE TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A198 
       34.32        27.35        51.35        31.40        35.44        50.76 
TCGA-ER-A19A TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19H 
       77.75        48.89        12.59        13.02        26.37       152.35 
TCGA-ER-A19N TCGA-ER-A19S TCGA-ER-A1A1 TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NH 
       44.05        37.25        79.99        20.15        16.37        32.05 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC 
      247.04        80.32        27.85        18.77        38.27        34.82 
TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1ZB TCGA-FS-A1ZE 
      104.42       216.92       228.59        20.91        48.85        40.27 
TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZW TCGA-FS-A1ZZ 
       15.45        32.75        74.73        11.41        49.48        27.02 
TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FW-A3R5 
       77.82        66.67        34.03        26.73        54.41        22.92 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GN-A262 
       55.59        13.51        19.30         9.90         2.04       139.89 
TCGA-GN-A266 TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-HR-A2OG 
       10.13       121.91        39.35        10.42        48.89         0.23 
TCGA-LH-A9QB TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A828 TCGA-W3-AA1O 
      368.78         0.33         0.69       228.16       121.08         4.01 
TCGA-W3-AA1Q TCGA-W3-AA1V TCGA-W3-AA1W TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8ZN 
       69.07        42.08       219.16        49.05        61.15        58.98 
TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-YD-A89C 
       67.63        11.80        12.16        35.01        22.29         6.90 
TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
       14.43        27.58        96.99        15.98 

  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
              0.20               0.23 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
            369.93             368.78 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
             54.51              47.41 
[1] "0.2 - 369.9 (54.5)" "0.2 - 368.8 (47.4)"
[1] "hr=" "1.1"
D37V3, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  20Q GAIN MUTATED                   31             4
  20Q GAIN WILD-TYPE                 34             1
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  20Q GAIN MUTATED                                          32
  20Q GAIN WILD-TYPE                                        40
                    vv
clus                 REGIONAL LYMPH NODE
  20Q GAIN MUTATED                   109
  20Q GAIN WILD-TYPE                 106
D37V4, multiclass
                                           clus
vv                                          20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  DISTANT METASTASIS                                      31                 34
  PRIMARY TUMOR                                            4                  1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               32                 40
  REGIONAL LYMPH NODE                                    109                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                 I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  20Q GAIN MUTATED             9       3      17       10       15       10
  20Q GAIN WILD-TYPE           3       4      11        8       12       14
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  20Q GAIN MUTATED           5         3         7        22          8
  20Q GAIN WILD-TYPE         9        16         5        15          7
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  20Q GAIN MUTATED           21         26        6
  20Q GAIN WILD-TYPE         11         34       14
D37V5, multiclass
             clus
vv            20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  I OR II NOS                9                  3
  STAGE 0                    3                  4
  STAGE I                   17                 11
  STAGE IA                  10                  8
  STAGE IB                  15                 12
  STAGE II                  10                 14
  STAGE IIA                  5                  9
  STAGE IIB                  3                 16
  STAGE IIC                  7                  5
  STAGE III                 22                 15
  STAGE IIIA                 8                  7
  STAGE IIIB                21                 11
  STAGE IIIC                26                 34
  STAGE IV                   6                 14
[1] 14  2
[1] TRUE
[1] "dimension of contingency 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      38 40 28 35
  20Q GAIN WILD-TYPE    26 32 49 33
D37V6, multiclass
       clus
vv      20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  T0+T1               38                 26
  T2                  40                 32
  T3                  28                 49
  T4                  35                 33
[1] 4 2
[1] TRUE
[1] "dimension of 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   84 35 18 23
  20Q GAIN WILD-TYPE 85 28 20 26
D37V7, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  N0               84                 85
  N1               35                 28
  N2               18                 20
  N3               23                 26
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V8, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED   159   7
  20Q GAIN WILD-TYPE 154  14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED    159    7
  20Q GAIN WILD-TYPE  154   14
   clus
vv  20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  0              159                154
  1                7                 14
[1] 2 2
[1] FALSE
D37V9, binary
                    cls
clus                  0  1
  20Q GAIN MUTATED   67 38
  20Q GAIN WILD-TYPE 65 50
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     67   38
  20Q GAIN WILD-TYPE   65   50
     clus
vv    20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  NO                67                 65
  YES               38                 50
[1] 2 2
[1] FALSE
D37V10, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED    23 153
  20Q GAIN WILD-TYPE  21 160
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     23  153
  20Q GAIN WILD-TYPE   21  160
     clus
vv    20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  NO                23                 21
  YES              153                160
[1] 2 2
[1] FALSE
D37V11, continuous
D37V12, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED    66 111
  20Q GAIN WILD-TYPE  69 112
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     66  111
  20Q GAIN WILD-TYPE   69  112
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  FEMALE               66                 69
  MALE                111                112
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  20Q GAIN MUTATED       2                         0   171
  20Q GAIN WILD-TYPE     3                         1   173
D37V13, multiclass
                           clus
vv                          20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  ASIAN                                    2                  3
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                  171                173
[1] 3 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     3 170
  20Q GAIN WILD-TYPE   4 174
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      3  170
  20Q GAIN WILD-TYPE    4  174
                        clus
vv                       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                  4
  NOT HISPANIC OR LATINO              170                174
[1] 2 2
[1] FALSE

Clustering(38) Variable = 21Q GAIN MUTATION ANALYSIS
D38V1, survival
                    sevent
clus2                 0  1
  21Q GAIN MUTATED   25 19
  21Q GAIN WILD-TYPE 96 99
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                44                195 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                19                 99 
$`21Q GAIN MUTATED`
TCGA-D3-A1Q3 TCGA-D3-A2J7 TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CC 
       15.72        45.99        43.53        58.06       140.98        40.01 
TCGA-D3-A3MR TCGA-D3-A5GN TCGA-D3-A5GU TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GM 
       90.21        45.70       124.08        78.21        23.61        70.62 
TCGA-D9-A6EC TCGA-EB-A6L9 TCGA-EE-A184 TCGA-EE-A20H TCGA-EE-A29D TCGA-EE-A2A1 
       57.90         6.64        67.50       155.90        12.99       102.38 
TCGA-EE-A2GH TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2MP TCGA-EE-A3AA TCGA-EE-A3J3 
      189.40        18.35        31.00       227.01       124.31        67.89 
TCGA-EE-A3J7 TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19L TCGA-ER-A19P TCGA-ER-A2NG 
       45.90        53.29        11.47        99.06       120.76        10.95 
TCGA-ER-A3PL TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FS-A1Z4 TCGA-FS-A1ZD 
       32.05       174.21       209.23        26.20        27.62        32.78 
TCGA-FS-A1ZJ TCGA-FS-A1ZS TCGA-GF-A4EO TCGA-GN-A8LK TCGA-W3-A825 TCGA-W3-AA1W 
       36.33       136.27         6.05        43.23         1.97       185.13 
TCGA-WE-A8ZM TCGA-WE-AAA3 
       62.99        16.64 

$`21Q GAIN WILD-TYPE`
TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 
       60.46        12.99        14.83         8.42        31.89       110.93 
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 
       49.35       133.25        19.04        76.41        62.60        25.64 
TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JE 
       62.86        15.75       168.00        86.30         7.27         9.76 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A3C7 
      107.61        36.30       171.58        64.83        66.08        46.98 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MU TCGA-D3-A51E 
       59.70        16.96        13.87         9.34        23.67       173.85 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GR 
      144.46        31.76        62.70        11.34        42.05       177.86 
TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GP TCGA-D3-A8GR TCGA-D9-A1X3 
      179.97       120.00        69.53       135.12        36.53        10.78 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY 
       15.02        16.90        18.44        22.85        48.66       106.85 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC 
       31.96       150.61        82.85        32.42        64.83        58.85 
TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5SG TCGA-EB-A5SH 
       25.12       214.59        14.96         3.91        33.24        50.07 
TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 
       45.50        13.15        24.89        62.37        20.38         0.00 
TCGA-EE-A20C TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H 
       75.55        75.22        76.14         0.26        44.28        63.12 
TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A2 
       47.74        27.16        61.12       346.49       185.19         7.20 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GJ TCGA-EE-A2GK 
       77.98        26.14       239.11         0.20        68.65        10.62 
TCGA-EE-A2GL TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU 
       32.48       118.32         0.76         0.20        71.31        81.99 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MG 
      103.13        15.25         5.75        23.77       209.79        94.19 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MR 
      171.85        63.25        67.50       104.78       145.45        25.08 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
      143.93        23.51        53.26       122.73        51.62         4.41 
TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J4 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JI 
       54.51         6.28       111.85         3.35       201.80       152.81 
TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A 
       14.56        34.45         1.58        47.31         7.82         4.54 
TCGA-ER-A19C TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19Q 
       39.81       151.46       150.12        59.84        42.48        49.71 
TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
       34.95       146.63        47.97        22.36         4.70        16.87 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FS-A1YW 
      173.29        55.82        15.48         5.65        10.06       171.78 
TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1ZC TCGA-FS-A1ZE TCGA-FS-A1ZF 
       49.74       195.98         8.35       312.07        35.90        12.92 
TCGA-FS-A1ZG TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW 
        7.82        78.61       130.95        35.28         4.47        23.21 
TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 
        5.29         3.06        30.90        66.67       173.19        13.28 
TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 
       80.68        55.59        11.54        19.30         9.90         1.91 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
       53.29       117.93        84.72        17.06        42.48         7.59 
TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-GN-A9SD TCGA-LH-A9QB TCGA-OD-A75X 
      120.53        34.49        46.92        59.41        85.05       297.01 
TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A828 TCGA-W3-AA1Q 
        7.23        18.05         0.33       174.12       120.07        44.05 
TCGA-W3-AA1R TCGA-W3-AA1V TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8ZN 
       79.99         8.09        92.84         1.15        59.64        12.69 
TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 
       19.00        59.44        10.95        48.39         1.94        26.60 
TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-Z2-AA3S 
       15.65        28.21        91.23 

  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
              1.97               0.00 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
            227.01             346.49 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
             49.64              45.50 
[1] "2.0 - 227.0 (49.6)" "0.0 - 346.5 (45.5)"
[1] "hr=" "1.3"
D38V2, survival
                    sevent
clus2                  0   1
  21Q GAIN MUTATED    36  27
  21Q GAIN WILD-TYPE 133 153
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                63                286 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                27                153 
$`21Q GAIN MUTATED`
TCGA-D3-A1Q3 TCGA-D3-A1Q9 TCGA-D3-A2J7 TCGA-D3-A2JF TCGA-D3-A2JP TCGA-D3-A3C6 
       16.67        31.59       103.10        62.07        59.57        58.06 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3MR TCGA-D3-A3MV TCGA-D3-A5GN TCGA-D3-A5GU 
      166.52        86.93       103.59        45.30       135.75       125.19 
TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GI TCGA-D3-A8GM TCGA-D9-A6EC TCGA-EB-A6L9 
       79.59        23.61        58.52       107.15        66.25        24.89 
TCGA-EE-A184 TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29D TCGA-EE-A29L TCGA-EE-A29R 
       68.15       168.26        63.35        13.97         2.60        14.47 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-EE-A2GH TCGA-EE-A2GM TCGA-EE-A2GN 
       46.82       102.90        39.29       208.04        75.48       102.12 
TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A3AA TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-ER-A19B 
      248.65        43.23       124.31       172.18        64.08        98.40 
TCGA-ER-A19D TCGA-ER-A19L TCGA-ER-A19P TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3PL 
       12.59       131.51       162.08        16.37        31.27        33.21 
TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FS-A1Z4 
        6.77        92.98       174.21       220.80        27.85        28.08 
TCGA-FS-A1ZD TCGA-FS-A1ZJ TCGA-FS-A1ZS TCGA-FS-A4F2 TCGA-FW-A3I3 TCGA-GF-A4EO 
       53.52        47.38       148.80        50.14         0.20         7.23 
TCGA-GN-A26D TCGA-GN-A8LK TCGA-W3-A825 TCGA-W3-AA1W TCGA-WE-A8JZ TCGA-WE-A8K6 
       39.58        50.10        63.02       219.16        24.03        15.98 
TCGA-WE-A8ZM TCGA-WE-A8ZX TCGA-WE-AAA3 
       98.89        32.58        19.73 

$`21Q GAIN WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q4 
       17.03        66.48        12.99        14.93        16.57       112.04 
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB 
      112.57        71.80       133.25        28.08        90.90        95.74 
TCGA-D3-A2J6 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC 
       43.43        65.49        23.77       115.53       168.00        86.76 
TCGA-D3-A2JD TCGA-D3-A2JE TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL 
       11.87        27.65       113.52        42.08        12.10       171.58 
TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CE 
       66.48        66.08       130.72        46.98        46.32        60.23 
TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F 
       24.53        13.87         9.34        39.75       174.84        55.73 
TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T 
       56.35       145.12        32.94        22.62        63.81        26.89 
TCGA-D3-A5GL TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A8GB TCGA-D3-A8GE 
      125.79       137.92       178.32        18.18        30.84        26.43 
TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GQ 
      241.38       170.20        89.13       161.00       152.75        29.06 
TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX 
      129.63       117.17       151.53        54.67         3.65         7.10 
TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EA 
       18.12        15.39        22.29        18.44         9.90        25.18 
TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 
       22.95        48.89        36.03       117.21        20.38       194.83 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA 
      176.55        35.93       107.34        61.18        53.92        65.92 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 
       23.44        68.09        28.60        10.49       215.44        15.68 
TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL 
       13.87        10.36        20.35        68.25        54.02        17.29 
TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 
       52.01         7.04        29.82        27.22         8.65        94.98 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C 
       33.73        14.70        26.89         4.96       133.81       151.27 
TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G 
       91.56        13.55        85.08        78.97        63.78        72.07 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29S 
       64.64        56.84        18.61        56.42        66.74        61.28 
TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A2 TCGA-EE-A2A6 
      369.93        25.87       195.02        17.92        36.82        86.14 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GJ 
       59.28        67.43       340.14       161.03        48.72       107.38 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
       54.74        79.66       126.81        13.91        42.77        81.21 
TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 
       44.88        94.82        21.67       129.27        28.83        19.76 
TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH 
       61.51        47.28       103.27       268.73       103.20        16.96 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN 
      204.66        96.23       158.63       216.66       167.90        47.54 
TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC 
      134.40       162.48        71.21        53.26       122.73        51.62 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J4 
       28.77        54.51        13.81        41.59       138.81       127.20 
TCGA-EE-A3J5 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE 
       36.95        34.32        53.19       201.80        27.35        51.35 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
      109.58       152.81        31.40        35.44        13.94        50.76 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19C TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G 
        9.17        77.75        48.89        13.02        26.37       268.93 
TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A19S 
      152.35         6.44        61.05        44.05        50.89        37.25 
TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
        8.88       148.18        79.99        43.82        23.34        20.15 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-FR-A69P TCGA-FR-A7U9 
       32.05       247.04        80.32        46.98        15.72        18.77 
TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YX 
       38.27        34.82        36.26       104.42       216.92        48.59 
TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB 
      228.59       202.65        20.91         7.79        27.72        48.85 
TCGA-FS-A1ZC TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZK 
      357.37        40.27        15.45         9.70        32.75        23.93 
TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZT TCGA-FS-A1ZU 
      101.26        74.73       133.55        11.41        53.16        26.56 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 
       49.48        27.09        27.02        77.82        66.67        28.73 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3R5 
      174.84        34.03        26.73        54.41        80.68        22.92 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GF-A6C9 
       55.59        13.51        19.30         9.90         2.04        15.78 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
      139.89       117.93        84.72        10.13        64.44        62.79 
TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A4U9 
       32.48       121.91        39.35        10.42        48.89        22.13 
TCGA-GN-A8LL TCGA-GN-A9SD TCGA-HR-A2OG TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X 
       21.37        59.41         0.23        65.88       368.78       297.90 
TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A828 
        7.23        18.05         0.33         0.69       228.16       121.08 
TCGA-W3-AA1O TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1V TCGA-W3-AA21 TCGA-WE-A8K1 
        4.01        69.07       111.09        42.08       105.04        49.05 
TCGA-WE-A8K5 TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZY 
       61.15        58.98        67.63        59.77        11.80        49.51 
TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-YD-A89C TCGA-YD-A9TA TCGA-YG-AA3O 
       12.16        35.01        22.29         6.90        49.18        37.94 
TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
       14.43        27.58        96.99        15.98 

  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
              0.20               0.23 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
            248.65             369.93 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
             59.57              49.33 
[1] "0.2 - 248.7 (59.6)" "0.2 - 369.9 (49.3)"
[1] "hr=" "1.3"
D38V3, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  21Q GAIN MUTATED                   11             2
  21Q GAIN WILD-TYPE                 54             3
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  21Q GAIN MUTATED                                          13
  21Q GAIN WILD-TYPE                                        59
                    vv
clus                 REGIONAL LYMPH NODE
  21Q GAIN MUTATED                    41
  21Q GAIN WILD-TYPE                 174
D38V4, multiclass
                                           clus
vv                                          21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  DISTANT METASTASIS                                      11                 54
  PRIMARY TUMOR                                            2                  3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               13                 59
  REGIONAL LYMPH NODE                                     41                174
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  21Q GAIN MUTATED             4       0       9        2        9        3
  21Q GAIN WILD-TYPE           8       7      19       16       18       21
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  21Q GAIN MUTATED           3         1         5         2          3
  21Q GAIN WILD-TYPE        11        18         7        35         12
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  21Q GAIN MUTATED            6         14        2
  21Q GAIN WILD-TYPE         26         46       18
D38V5, multiclass
             clus
vv            21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  I OR II NOS                4                  8
  STAGE 0                    0                  7
  STAGE I                    9                 19
  STAGE IA                   2                 16
  STAGE IB                   9                 18
  STAGE II                   3                 21
  STAGE IIA                  3                 11
  STAGE IIB                  1                 18
  STAGE IIC                  5                  7
  STAGE III                  2                 35
  STAGE IIIA                 3                 12
  STAGE IIIB                 6                 26
  STAGE IIIC                14                 46
  STAGE IV                   2                 18
[1] 14  2
[1] TRUE
[1] "dimension of contingency 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      11 19 13 13
  21Q GAIN WILD-TYPE    53 53 64 55
D38V6, multiclass
       clus
vv      21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  T0+T1               11                 53
  T2                  19                 53
  T3                  13                 64
  T4                  13                 55
[1] 4 2
[1] TRUE
[1] "dimension of 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    39  10   5  10
  21Q GAIN WILD-TYPE 130  53  33  39
D38V7, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  N0               39                130
  N1               10                 53
  N2                5                 33
  N3               10                 39
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V8, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED    61   2
  21Q GAIN WILD-TYPE 252  19
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED     61    2
  21Q GAIN WILD-TYPE  252   19
   clus
vv  21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  0               61                252
  1                2                 19
[1] 2 2
[1] FALSE
D38V9, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED    20  23
  21Q GAIN WILD-TYPE 112  65
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED     20   23
  21Q GAIN WILD-TYPE  112   65
     clus
vv    21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  NO                20                112
  YES               23                 65
[1] 2 2
[1] FALSE
D38V10, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED     8  58
  21Q GAIN WILD-TYPE  36 255
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      8   58
  21Q GAIN WILD-TYPE   36  255
     clus
vv    21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  NO                 8                 36
  YES               58                255
[1] 2 2
[1] FALSE
D38V11, continuous
D38V12, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED    26  41
  21Q GAIN WILD-TYPE 109 182
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED     26   41
  21Q GAIN WILD-TYPE  109  182
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  FEMALE               26                109
  MALE                 41                182
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  21Q GAIN MUTATED       1                         0    65
  21Q GAIN WILD-TYPE     4                         1   279
D38V13, multiclass
                           clus
vv                          21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  ASIAN                                    1                  4
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   65                279
[1] 3 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     1  64
  21Q GAIN WILD-TYPE   6 280
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      1   64
  21Q GAIN WILD-TYPE    6  280
                        clus
vv                       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO               64                280
[1] 2 2
[1] FALSE

Clustering(39) Variable = 22Q GAIN MUTATION ANALYSIS
D39V1, survival
                    sevent
clus2                 0  1
  22Q GAIN MUTATED   44 38
  22Q GAIN WILD-TYPE 77 80
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                82                157 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                38                 80 
$`22Q GAIN MUTATED`
TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A2J7 TCGA-D3-A2JA TCGA-D3-A2JE TCGA-D3-A2JO 
       12.99         8.42        45.99        15.75         9.76        66.08 
TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3MO TCGA-D3-A3MU 
       43.53        58.06        40.01        59.70         9.34        23.67 
TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A8GC TCGA-D3-A8GM TCGA-D9-A3Z1 TCGA-D9-A6EC 
       45.70       177.86        78.21        70.62        15.02        57.90 
TCGA-DA-A1HV TCGA-DA-A1I1 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A3F5 TCGA-EB-A5SG 
       48.66        31.96        32.42        64.83       214.59        33.24 
TCGA-EB-A5SH TCGA-EB-A6L9 TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A29M 
       50.07         6.64        24.89        62.37       155.90        47.74 
TCGA-EE-A29Q TCGA-EE-A29W TCGA-EE-A2GB TCGA-EE-A2GH TCGA-EE-A2GM TCGA-EE-A2GN 
       61.12       185.19        26.14       189.40        18.35        31.00 
TCGA-EE-A2GO TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MJ TCGA-EE-A2MR TCGA-EE-A2MS 
      118.32       103.13        15.25        63.25        25.08       143.93 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3J7 
       53.26       124.31       122.73         4.41        54.51        45.90 
TCGA-EE-A3JB TCGA-ER-A19C TCGA-ER-A19G TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19W 
      201.80        39.81       151.46        99.06        59.84       146.63 
TCGA-ER-A2NG TCGA-ER-A3ET TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7UA TCGA-FS-A1YY 
       10.95        55.82       174.21       209.23         5.65        49.74 
TCGA-FS-A1ZD TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU 
       32.78        78.61       130.95       136.27        35.28         4.47 
TCGA-FS-A1ZW TCGA-FS-A4FD TCGA-FW-A3TU TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 
       23.21        80.68        55.59       117.93        84.72        17.06 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A8LK TCGA-QB-A6FS TCGA-W3-AA1R TCGA-WE-A8K5 
       42.48         7.59        43.23         7.23        79.99        59.64 
TCGA-WE-A8ZM TCGA-WE-A8ZY TCGA-WE-AAA3 TCGA-YG-AA3O 
       62.99        48.39        16.64        28.21 

$`22Q GAIN WILD-TYPE`
TCGA-3N-A9WC TCGA-BF-AAP0 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 
       60.46        14.83        15.72        31.89       110.93        49.35 
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J8 
      133.25        19.04        76.41        62.60        25.64        62.86 
TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL 
      168.00        86.30         7.27       107.61        36.30       171.58 
TCGA-D3-A2JN TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MR 
       64.83        46.98       140.98        16.96        13.87        90.21 
TCGA-D3-A51E TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL 
      173.85       144.46        31.76        62.70        11.34        42.05 
TCGA-D3-A5GU TCGA-D3-A8GD TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GP 
      124.08        23.61       179.97       120.00        69.53       135.12 
TCGA-D3-A8GR TCGA-D9-A1X3 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6EG TCGA-DA-A1HY 
       36.53        10.78        16.90        18.44        22.85       106.85 
TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F8 TCGA-EB-A44Q 
      150.61        82.85        58.85        25.12        14.96         3.91 
TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A184 TCGA-EE-A20C 
       45.50        13.15        20.38         0.00        67.50        75.55 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H 
       75.22        76.14        12.99         0.26        44.28        63.12 
TCGA-EE-A29P TCGA-EE-A29T TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GD 
       27.16       346.49       102.38         7.20        77.98       239.11 
TCGA-EE-A2GE TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GP TCGA-EE-A2GR 
        0.20        68.65        10.62        32.48         0.76         0.20 
TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MG 
       71.31        81.99         5.75        23.77       209.79        94.19 
TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MT 
      171.85        67.50       104.78       145.45       227.01        23.51 
TCGA-EE-A3AC TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J8 TCGA-EE-A3JI 
       51.62         6.28        67.89       111.85         3.35       152.81 
TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A 
       14.56        34.45         1.58        47.31         7.82         4.54 
TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19H TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
       53.29        11.47       150.12        42.48       120.76        49.71 
TCGA-ER-A19S TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A3ES 
       34.95        47.97        22.36         4.70        16.87       173.29 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A7U8 TCGA-FR-A8YC TCGA-FS-A1YW TCGA-FS-A1Z0 
       15.48        32.05        26.20        10.06       171.78       195.98 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG 
        8.35        27.62       312.07        35.90        12.92         7.82 
TCGA-FS-A1ZJ TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 
       36.33         5.29         3.06        30.90        66.67       173.19 
TCGA-FS-A4F9 TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 
       13.28        11.54        19.30         9.90         6.05         1.91 
TCGA-GN-A262 TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-GN-A9SD TCGA-LH-A9QB 
       53.29       120.53        34.49        46.92        59.41        85.05 
TCGA-OD-A75X TCGA-QB-AA9O TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 
      297.01        18.05         0.33       174.12         1.97       120.07 
TCGA-W3-AA1Q TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8ZN 
       44.05         8.09       185.13        92.84         1.15        12.69 
TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 
       19.00        59.44        10.95         1.94        26.60        15.65 
TCGA-Z2-AA3S 
       91.23 

  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
              4.41               0.00 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
            214.59             346.49 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
            49.905             42.050 
[1] "4.4 - 214.6 (49.9)" "0.0 - 346.5 (42.0)"
[1] "hr=" "1.1"
D39V2, survival
                    sevent
clus2                  0   1
  22Q GAIN MUTATED    60  60
  22Q GAIN WILD-TYPE 109 120
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
               120                229 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                60                120 
$`22Q GAIN MUTATED`
TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q9 TCGA-D3-A2J7 TCGA-D3-A2JA TCGA-D3-A2JE 
       12.99        16.57        31.59       103.10       115.53        27.65 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3MO 
       66.08        59.57        58.06        86.93        60.23         9.34 
TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A8GC 
       39.75        45.30       135.75       178.32        18.18        79.59 
TCGA-D3-A8GI TCGA-D3-A8GM TCGA-D3-A8GQ TCGA-D9-A148 TCGA-D9-A3Z1 TCGA-D9-A6E9 
       58.52       107.15        29.06       151.53        15.39         9.90 
TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I1 
       25.18        66.25        48.89        36.03        20.38       194.83 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A3F5 TCGA-EB-A5KH 
       61.18        53.92        65.92        23.44       215.44        20.35 
TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A6L9 TCGA-EE-A17Y TCGA-EE-A180 
       68.25        54.02        17.29        24.89        27.22        94.98 
TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29R 
      168.26         2.60        56.84        18.61        66.74        14.47 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A5 TCGA-EE-A2GB TCGA-EE-A2GH TCGA-EE-A2GI 
      195.02        17.92        39.29        59.28       208.04        48.72 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MJ 
       75.48       102.12       126.81       129.27        28.83        96.23 
TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB 
       43.23       134.40       162.48        53.26       124.31       122.73 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AG TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3JB 
       28.77        54.51        41.59        36.95        64.08       201.80 
TCGA-EE-A3JD TCGA-ER-A19C TCGA-ER-A19G TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19W 
       27.35        48.89       268.93       131.51        61.05       148.18 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ET TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       16.37        31.27        80.32        92.98       174.21        15.72 
TCGA-FR-A729 TCGA-FR-A7UA TCGA-FS-A1YY TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZD 
      220.80        38.27       228.59         7.79        27.72        53.52 
TCGA-FS-A1ZH TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU 
       32.75       101.26       133.55       148.80        53.16        26.56 
TCGA-FS-A1ZW TCGA-FS-A4F2 TCGA-FS-A4F5 TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU 
       49.48        50.14        28.73        80.68         0.20        55.59 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
      117.93        84.72        64.44        62.79        32.48        39.58 
TCGA-GN-A4U7 TCGA-GN-A8LK TCGA-HR-A2OH TCGA-QB-A6FS TCGA-W3-AA1R TCGA-WE-A8JZ 
       10.42        50.10        65.88         7.23       111.09        24.03 
TCGA-WE-A8K5 TCGA-WE-A8ZM TCGA-WE-A8ZY TCGA-WE-AAA3 TCGA-YD-A89C TCGA-YG-AA3O 
       61.15        98.89        49.51        19.73         6.90        37.94 

$`22Q GAIN WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-BF-AAP0 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 
       17.03        66.48        14.93        16.67       112.04       112.57 
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 
       71.80       133.25        28.08        90.90        95.74        43.43 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF 
       65.49        23.77       168.00        86.76        11.87        62.07 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A3BZ 
      113.52        42.08        12.10       171.58        66.48       130.72 
TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MR 
       46.98        46.32       166.52        24.53        13.87       103.59 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
      174.84        55.73        56.35       145.12        32.94        22.62 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GO TCGA-D3-A5GU TCGA-D3-A8GB 
       63.81        26.89       125.79       137.92       125.19        30.84 
TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GN 
       23.61        26.43       241.38       170.20        89.13       161.00 
TCGA-D3-A8GP TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX 
      152.75       129.63       117.17        54.67         3.65         7.10 
TCGA-D9-A1X3 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6EG TCGA-DA-A1HY TCGA-DA-A1I2 
       18.12        22.29        18.44        22.95       117.21       176.55 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 
       35.93       107.34        68.09        28.60        10.49        15.68 
TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EE-A17X TCGA-EE-A17Z 
       13.87        10.36        52.01         7.04        29.82         8.65 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B 
       33.73        14.70        26.89        68.15         4.96       133.81 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C 
      151.27        91.56        13.55        63.35        85.08        78.97 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29P TCGA-EE-A29S 
       13.97        63.78        72.07        64.64        56.42        61.28 
TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 
      369.93        25.87        46.82       102.90        36.82        86.14 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
       67.43       340.14       161.03       107.38        54.74        79.66 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 
       13.91        42.77        81.21        44.88        94.82        21.67 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG 
       19.76        61.51        47.28       103.27       268.73       103.20 
TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN 
       16.96       204.66       158.63       216.66       167.90        47.54 
TCGA-EE-A2MP TCGA-EE-A2MT TCGA-EE-A3AC TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J3 
      248.65        71.21        51.62        13.81       138.81       172.18 
TCGA-EE-A3J4 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI 
      127.20        34.32        53.19        51.35       109.58       152.81 
TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A 
       31.40        35.44        13.94        50.76         9.17        77.75 
TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19H TCGA-ER-A19J 
       98.40        12.59        13.02        26.37       152.35         6.44 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A1A1 
       44.05       162.08        50.89        37.25         8.88        79.99 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3EV 
       43.82        23.34        20.15        32.05       247.04        46.98 
TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A8YC TCGA-FR-A8YD 
       33.21         6.77        27.85        18.77        34.82        36.26 
TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 
      104.42       216.92        48.59       202.65        20.91        28.08 
TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZJ 
       48.85       357.37        40.27        15.45         9.70        47.38 
TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 
       23.93        74.73        11.41        27.09        27.02        77.82 
TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FW-A3R5 
       66.67       174.84        34.03        26.73        54.41        22.92 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 
       13.51        19.30         9.90         7.23         2.04        15.78 
TCGA-GN-A262 TCGA-GN-A266 TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-GN-A4U9 
      139.89        10.13       121.91        39.35        48.89        22.13 
TCGA-GN-A8LL TCGA-GN-A9SD TCGA-HR-A2OG TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-AA9O 
       21.37        59.41         0.23       368.78       297.90        18.05 
TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O 
        0.33         0.69       228.16        63.02       121.08         4.01 
TCGA-W3-AA1Q TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8K6 
       69.07        42.08       219.16       105.04        49.05        15.98 
TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-AA9Y 
       58.98        67.63        59.77        11.80        32.58        12.16 
TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-YD-A9TA TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S 
       35.01        22.29        49.18        14.43        27.58        96.99 
TCGA-Z2-AA3V 
       15.98 

  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
              0.20               0.23 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
            268.93             369.93 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
            54.265             48.850 
[1] "0.2 - 268.9 (54.3)" "0.2 - 369.9 (48.9)"
[1] "hr=" "1"  
D39V3, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  22Q GAIN MUTATED                   17             4
  22Q GAIN WILD-TYPE                 48             1
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  22Q GAIN MUTATED                                          30
  22Q GAIN WILD-TYPE                                        42
                    vv
clus                 REGIONAL LYMPH NODE
  22Q GAIN MUTATED                    73
  22Q GAIN WILD-TYPE                 142
D39V4, multiclass
                                           clus
vv                                          22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  DISTANT METASTASIS                                      17                 48
  PRIMARY TUMOR                                            4                  1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               30                 42
  REGIONAL LYMPH NODE                                     73                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                 I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  22Q GAIN MUTATED             3       2       9        5        9        6
  22Q GAIN WILD-TYPE           9       5      19       13       18       18
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  22Q GAIN MUTATED           4         3         5        17          9
  22Q GAIN WILD-TYPE        10        16         7        20          6
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  22Q GAIN MUTATED           13         23        6
  22Q GAIN WILD-TYPE         19         37       14
D39V5, multiclass
             clus
vv            22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  I OR II NOS                3                  9
  STAGE 0                    2                  5
  STAGE I                    9                 19
  STAGE IA                   5                 13
  STAGE IB                   9                 18
  STAGE II                   6                 18
  STAGE IIA                  4                 10
  STAGE IIB                  3                 16
  STAGE IIC                  5                  7
  STAGE III                 17                 20
  STAGE IIIA                 9                  6
  STAGE IIIB                13                 19
  STAGE IIIC                23                 37
  STAGE IV                   6                 14
[1] 14  2
[1] TRUE
[1] "dimension of contingency 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      25 30 23 22
  22Q GAIN WILD-TYPE    39 42 54 46
D39V6, multiclass
       clus
vv      22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  T0+T1               25                 39
  T2                  30                 42
  T3                  23                 54
  T4                  22                 46
[1] 4 2
[1] TRUE
[1] "dimension of 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    47  26  17  21
  22Q GAIN WILD-TYPE 122  37  21  28
D39V7, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  N0               47                122
  N1               26                 37
  N2               17                 21
  N3               21                 28
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V8, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED   106   7
  22Q GAIN WILD-TYPE 207  14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED    106    7
  22Q GAIN WILD-TYPE  207   14
   clus
vv  22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  0              106                207
  1                7                 14
[1] 2 2
[1] FALSE
D39V9, binary
                    cls
clus                  0  1
  22Q GAIN MUTATED   48 32
  22Q GAIN WILD-TYPE 84 56
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED     48   32
  22Q GAIN WILD-TYPE   84   56
     clus
vv    22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  NO                48                 84
  YES               32                 56
[1] 2 2
[1] FALSE
D39V10, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED    15 109
  22Q GAIN WILD-TYPE  29 204
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED     15  109
  22Q GAIN WILD-TYPE   29  204
     clus
vv    22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  NO                15                 29
  YES              109                204
[1] 2 2
[1] FALSE
D39V11, continuous
D39V12, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED    51  73
  22Q GAIN WILD-TYPE  84 150
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED     51   73
  22Q GAIN WILD-TYPE   84  150
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  FEMALE               51                 84
  MALE                 73                150
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  22Q GAIN MUTATED       3                         0   118
  22Q GAIN WILD-TYPE     2                         1   226
D39V13, multiclass
                           clus
vv                          22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  ASIAN                                    3                  2
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                  118                226
[1] 3 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     1 120
  22Q GAIN WILD-TYPE   6 224
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      1  120
  22Q GAIN WILD-TYPE    6  224
                        clus
vv                       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO              120                224
[1] 2 2
[1] FALSE

Clustering(40) Variable = XP GAIN MUTATION ANALYSIS
D40V1, survival
                   sevent
clus2                 0   1
  XP GAIN MUTATED     8  12
  XP GAIN WILD-TYPE 113 106
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               20               219 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               12               106 
$`XP GAIN MUTATED`
TCGA-D3-A1Q3 TCGA-D3-A2JA TCGA-D3-A2JE TCGA-D3-A3CE TCGA-D3-A3MU TCGA-EE-A184 
       15.72        15.75         9.76        59.70        23.67        67.50 
TCGA-EE-A2GN TCGA-EE-A2MU TCGA-EE-A3J7 TCGA-ER-A19M TCGA-ER-A2NC TCGA-FR-A729 
       31.00        53.26        45.90        59.84        22.36       209.23 
TCGA-FR-A8YC TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A4FD TCGA-GN-A264 TCGA-GN-A265 
       10.06         4.47         5.29        80.68       117.93        84.72 
TCGA-GN-A4U3 TCGA-W3-AA1W 
      120.53       185.13 

$`XP GAIN WILD-TYPE`
TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 
       60.46        12.99        14.83         8.42        31.89       110.93 
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 
       49.35       133.25        19.04        76.41        62.60        25.64 
TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG 
       45.99        62.86       168.00        86.30         7.27       107.61 
TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 
       36.30       171.58        64.83        66.08        43.53        58.06 
TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO 
       46.98       140.98        40.01        16.96        13.87         9.34 
TCGA-D3-A3MR TCGA-D3-A51E TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T 
       90.21       173.85       144.46        31.76        62.70        11.34 
TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D3-A8GC TCGA-D3-A8GD 
       42.05        45.70       177.86       124.08        78.21        23.61 
TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GP TCGA-D3-A8GR 
      179.97       120.00        69.53        70.62       135.12        36.53 
TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6EC TCGA-D9-A6EG 
       10.78        15.02        16.90        18.44        57.90        22.85 
TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 
       48.66       106.85        31.96       150.61        82.85        32.42 
TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q 
       64.83        58.85        25.12       214.59        14.96         3.91 
TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y 
       33.24        50.07        45.50         6.64        13.15        24.89 
TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A20C TCGA-EE-A20H TCGA-EE-A29B 
       62.37        20.38         0.00        75.55       155.90        75.22 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M 
       76.14        12.99         0.26        44.28        63.12        47.74 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A2 
       27.16        61.12       346.49       185.19       102.38         7.20 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ 
       77.98        26.14       239.11         0.20       189.40        68.65 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR 
       10.62        32.48        18.35       118.32         0.76         0.20 
TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC 
       71.31        81.99       103.13        15.25         5.75        23.77 
TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML 
      209.79        94.19       171.85        63.25        67.50       104.78 
TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AA 
      145.45       227.01        25.08       143.93        23.51       124.31 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J3 
      122.73        51.62         4.41        54.51         6.28        67.89 
TCGA-EE-A3J4 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 
      111.85         3.35       201.80       152.81        14.56        34.45 
TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C 
        1.58        47.31         7.82         4.54        53.29        39.81 
TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A19P 
       11.47       151.46       150.12        99.06        42.48       120.76 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2ND TCGA-ER-A2NE 
       49.71        34.95       146.63        47.97         4.70        16.87 
TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A44A 
       10.95       173.29        55.82        15.48        32.05       174.21 
TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
       26.20         5.65       171.78        49.74       195.98         8.35 
TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG 
       27.62       312.07        32.78        35.90        12.92         7.82 
TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZW 
       36.33        78.61       130.95       136.27        35.28        23.21 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FW-A3TU 
        3.06        30.90        66.67       173.19        13.28        55.59 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 
       11.54        19.30         9.90         6.05         1.91        53.29 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-GN-A8LK 
       17.06        42.48         7.59        34.49        46.92        43.23 
TCGA-GN-A9SD TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 
       59.41        85.05       297.01         7.23        18.05         0.33 
TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1V 
      174.12         1.97       120.07        44.05        79.99         8.09 
TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO 
       92.84         1.15        59.64        62.99        12.69        19.00 
TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 
       59.44        10.95        48.39         1.94        26.60        16.64 
TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-Z2-AA3S 
       15.65        28.21        91.23 

  XP GAIN MUTATED XP GAIN WILD-TYPE 
             4.47              0.00 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
           209.23            346.49 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
            49.58             45.99 
[1] "4.5 - 209.2 (49.6)" "0.0 - 346.5 (46.0)"
[1] "hr=" "1.3"
D40V2, survival
                   sevent
clus2                 0   1
  XP GAIN MUTATED    14  23
  XP GAIN WILD-TYPE 155 157
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               37               312 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               23               157 
$`XP GAIN MUTATED`
TCGA-3N-A9WB TCGA-D3-A1Q3 TCGA-D3-A2JA TCGA-D3-A2JE TCGA-D3-A3CE TCGA-D3-A3MU 
       17.03        16.67       115.53        27.65        60.23        39.75 
TCGA-D3-A3MV TCGA-D3-A8GQ TCGA-DA-A3F3 TCGA-EB-A5KH TCGA-EE-A184 TCGA-EE-A29A 
       45.30        29.06        10.49        20.35        68.15        63.35 
TCGA-EE-A29R TCGA-EE-A2GN TCGA-EE-A2MU TCGA-EE-A3AG TCGA-EE-A3J7 TCGA-ER-A19M 
       14.47       102.12        53.26        41.59        64.08        61.05 
TCGA-ER-A2NC TCGA-FR-A3YN TCGA-FR-A729 TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FS-A1ZA 
       43.82        92.98       220.80        34.82        36.26        27.72 
TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A4FD TCGA-GN-A264 
       23.93        74.73        26.56        27.09        80.68       117.93 
TCGA-GN-A265 TCGA-GN-A26D TCGA-GN-A4U3 TCGA-W3-AA1O TCGA-W3-AA1W TCGA-WE-A8K6 
       84.72        39.58       121.91         4.01       219.16        15.98 
TCGA-YD-A89C 
        6.90 

$`XP GAIN WILD-TYPE`
TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 
       66.48        12.99        14.93        16.57       112.04       112.57 
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB 
       71.80       133.25        28.08        31.59        90.90        95.74 
TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JC 
       43.43       103.10        65.49        23.77       168.00        86.76 
TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL 
       11.87        62.07       113.52        42.08        12.10       171.58 
TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 
       66.48        66.08        59.57       130.72        58.06        46.98 
TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO 
       46.32       166.52        86.93        24.53        13.87         9.34 
TCGA-D3-A3MR TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K 
      103.59       174.84        55.73        56.35       145.12        32.94 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO 
       22.62        63.81        26.89       125.79       135.75       137.92 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GD 
      178.32        18.18       125.19        30.84        79.59        23.61 
TCGA-D3-A8GE TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM 
       26.43        58.52       241.38       170.20        89.13       107.15 
TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A148 TCGA-D9-A149 
      161.00       152.75       129.63       117.17       151.53        54.67 
TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 
        3.65         7.10        18.12        15.39        22.29        18.44 
TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW 
        9.90        25.18        66.25        22.95        48.89        36.03 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
      117.21        20.38       194.83       176.55        35.93       107.34 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
       61.18        53.92        65.92        23.44        68.09        28.60 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH 
      215.44        15.68        13.87        10.36        68.25        54.02 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y 
       17.29        52.01         7.04        24.89        29.82        27.22 
TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 
        8.65        94.98        33.73        14.70        26.89         4.96 
TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29B 
      133.81       151.27        91.56       168.26        13.55        85.08 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L 
       78.97        13.97        63.78        72.07        64.64         2.60 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29T 
       56.84        18.61        56.42        66.74        61.28       369.93 
TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
       25.87       195.02        17.92        46.82       102.90        36.82 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE 
       39.29        86.14        59.28        67.43       340.14       161.03 
TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
      208.04        48.72       107.38        54.74        79.66        75.48 
TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU 
      126.81        13.91        42.77        81.21        44.88        94.82 
TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD 
       21.67       129.27        28.83        19.76        61.51        47.28 
TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ 
      103.27       268.73       103.20        16.96       204.66        96.23 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ 
      158.63       216.66       167.90        47.54       248.65        43.23 
TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC 
      134.40       162.48        71.21       124.31       122.73        51.62 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 
       28.77        54.51        13.81       138.81       172.18       127.20 
TCGA-EE-A3J5 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE 
       36.95        34.32        53.19       201.80        27.35        51.35 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
      109.58       152.81        31.40        35.44        13.94        50.76 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E 
        9.17        77.75        98.40        48.89        12.59        13.02 
TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19N 
       26.37       268.93       152.35         6.44       131.51        44.05 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 
      162.08        50.89        37.25         8.88       148.18        79.99 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES 
       23.34        20.15        16.37        31.27        32.05       247.04 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A44A TCGA-FR-A69P 
       80.32        46.98        33.21         6.77       174.21        15.72 
TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YX 
       27.85        18.77        38.27       104.42       216.92        48.59 
TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZB 
      228.59       202.65        20.91        28.08         7.79        48.85 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH 
      357.37        53.52        40.27        15.45         9.70        32.75 
TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT 
       47.38       101.26       133.55        11.41       148.80        53.16 
TCGA-FS-A1ZW TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 
       49.48        27.02        77.82        50.14        66.67        28.73 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FW-A3I3 TCGA-FW-A3R5 
      174.84        34.03        26.73        54.41         0.20        22.92 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 
       55.59        13.51        19.30         9.90         7.23         2.04 
TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
       15.78       139.89        10.13        64.44        62.79        32.48 
TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A8LL 
       39.35        10.42        48.89        22.13        50.10        21.37 
TCGA-GN-A9SD TCGA-HR-A2OG TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS 
       59.41         0.23        65.88       368.78       297.90         7.23 
TCGA-QB-AA9O TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 
       18.05         0.33         0.69       228.16        63.02       121.08 
TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1V TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K1 
       69.07       111.09        42.08       105.04        24.03        49.05 
TCGA-WE-A8K5 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT 
       61.15        98.89        58.98        67.63        59.77        11.80 
TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 
       32.58        49.51        12.16        35.01        19.73        22.29 
TCGA-YD-A9TA TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
       49.18        37.94        14.43        27.58        96.99        15.98 

  XP GAIN MUTATED XP GAIN WILD-TYPE 
             4.01              0.20 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
           220.80            369.93 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
           41.590            51.815 
[1] "4.0 - 220.8 (41.6)" "0.2 - 369.9 (51.8)"
[1] "hr=" "1.5"
D40V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  XP GAIN MUTATED                   14             0
  XP GAIN WILD-TYPE                 51             5
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  XP GAIN MUTATED                                           7
  XP GAIN WILD-TYPE                                        65
                   vv
clus                REGIONAL LYMPH NODE
  XP GAIN MUTATED                    18
  XP GAIN WILD-TYPE                 197
D40V4, multiclass
                                           clus
vv                                          XP GAIN MUTATED XP GAIN WILD-TYPE
  DISTANT METASTASIS                                     14                51
  PRIMARY TUMOR                                           0                 5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               7                65
  REGIONAL LYMPH NODE                                    18               197
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  XP GAIN MUTATED             1       1       2        3        4        4
  XP GAIN WILD-TYPE          11       6      26       15       23       20
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  XP GAIN MUTATED           1         2         4         5          3
  XP GAIN WILD-TYPE        13        17         8        32         12
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  XP GAIN MUTATED            4          3        0
  XP GAIN WILD-TYPE         28         57       20
D40V5, multiclass
             clus
vv            XP GAIN MUTATED XP GAIN WILD-TYPE
  I OR II NOS               1                11
  STAGE 0                   1                 6
  STAGE I                   2                26
  STAGE IA                  3                15
  STAGE IB                  4                23
  STAGE II                  4                20
  STAGE IIA                 1                13
  STAGE IIB                 2                17
  STAGE IIC                 4                 8
  STAGE III                 5                32
  STAGE IIIA                3                12
  STAGE IIIB                4                28
  STAGE IIIC                3                57
  STAGE IV                  0                20
[1] 14  2
[1] TRUE
[1] "dimension of contingency 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       8  9  9  6
  XP GAIN WILD-TYPE    56 63 68 62
D40V6, multiclass
       clus
vv      XP GAIN MUTATED XP GAIN WILD-TYPE
  T0+T1               8                56
  T2                  9                63
  T3                  9                68
  T4                  6                62
[1] 4 2
[1] TRUE
[1] "dimension of 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    20   7   6   2
  XP GAIN WILD-TYPE 149  56  32  47
D40V7, multiclass
    clus
vv   XP GAIN MUTATED XP GAIN WILD-TYPE
  N0              20               149
  N1               7                56
  N2               6                32
  N3               2                47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V8, binary
                   cls
clus                  0   1
  XP GAIN MUTATED    36   0
  XP GAIN WILD-TYPE 277  21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED     36    0
  XP GAIN WILD-TYPE  277   21
   clus
vv  XP GAIN MUTATED XP GAIN WILD-TYPE
  0              36               277
  1               0                21
[1] 2 2
[1] FALSE
D40V9, binary
                   cls
clus                  0   1
  XP GAIN MUTATED    14  11
  XP GAIN WILD-TYPE 118  77
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED     14   11
  XP GAIN WILD-TYPE  118   77
     clus
vv    XP GAIN MUTATED XP GAIN WILD-TYPE
  NO               14               118
  YES              11                77
[1] 2 2
[1] FALSE
D40V10, binary
                   cls
clus                  0   1
  XP GAIN MUTATED     5  34
  XP GAIN WILD-TYPE  39 279
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED      5   34
  XP GAIN WILD-TYPE   39  279
     clus
vv    XP GAIN MUTATED XP GAIN WILD-TYPE
  NO                5                39
  YES              34               279
[1] 2 2
[1] FALSE
D40V11, continuous
D40V12, binary
                   cls
clus                  0   1
  XP GAIN MUTATED    11  28
  XP GAIN WILD-TYPE 124 195
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED     11   28
  XP GAIN WILD-TYPE  124  195
        clus
vv       XP GAIN MUTATED XP GAIN WILD-TYPE
  FEMALE              11               124
  MALE                28               195
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  XP GAIN MUTATED       1                         0    38
  XP GAIN WILD-TYPE     4                         1   306
D40V13, multiclass
                           clus
vv                          XP GAIN MUTATED XP GAIN WILD-TYPE
  ASIAN                                   1                 4
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  38               306
[1] 3 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     0  38
  XP GAIN WILD-TYPE   7 306
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED      0   38
  XP GAIN WILD-TYPE    7  306
                        clus
vv                       XP GAIN MUTATED XP GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 7
  NOT HISPANIC OR LATINO              38               306
[1] 2 2
[1] FALSE

Clustering(41) Variable = XQ GAIN MUTATION ANALYSIS
D41V1, survival
                   sevent
clus2                 0   1
  XQ GAIN MUTATED     7  16
  XQ GAIN WILD-TYPE 114 102
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               23               216 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               16               102 
$`XQ GAIN MUTATED`
TCGA-D3-A1Q3 TCGA-D3-A2JA TCGA-D3-A2JE TCGA-D3-A2JG TCGA-D3-A3CE TCGA-D3-A3MU 
       15.72        15.75         9.76       107.61        59.70        23.67 
TCGA-EE-A184 TCGA-EE-A2GN TCGA-EE-A2MU TCGA-EE-A3J7 TCGA-ER-A19M TCGA-ER-A2NC 
       67.50        31.00        53.26        45.90        59.84        22.36 
TCGA-ER-A2ND TCGA-FR-A729 TCGA-FR-A8YC TCGA-FS-A1ZG TCGA-FS-A1ZU TCGA-FS-A1ZY 
        4.70       209.23        10.06         7.82         4.47         5.29 
TCGA-FS-A4FD TCGA-FW-A3TV TCGA-GN-A264 TCGA-GN-A268 TCGA-WE-A8ZT 
       80.68        11.54       117.93        42.48        10.95 

$`XQ GAIN WILD-TYPE`
TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 
       60.46        12.99        14.83         8.42        31.89       110.93 
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 
       49.35       133.25        19.04        76.41        62.60        25.64 
TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JH 
       45.99        62.86       168.00        86.30         7.27        36.30 
TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3C7 
      171.58        64.83        66.08        43.53        58.06        46.98 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR 
      140.98        40.01        16.96        13.87         9.34        90.21 
TCGA-D3-A51E TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL 
      173.85       144.46        31.76        62.70        11.34        42.05 
TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GJ 
       45.70       177.86       124.08        78.21        23.61       179.97 
TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GP TCGA-D3-A8GR TCGA-D9-A1X3 
      120.00        69.53        70.62       135.12        36.53        10.78 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV 
       15.02        16.90        18.44        57.90        22.85        48.66 
TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA 
      106.85        31.96       150.61        82.85        32.42        64.83 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5SG 
       58.85        25.12       214.59        14.96         3.91        33.24 
TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A180 
       50.07        45.50         6.64        13.15        24.89        62.37 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A20C TCGA-EE-A20H TCGA-EE-A29B TCGA-EE-A29C 
       20.38         0.00        75.55       155.90        75.22        76.14 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P 
       12.99         0.26        44.28        63.12        47.74        27.16 
TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 
       61.12       346.49       185.19       102.38         7.20        77.98 
TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK 
       26.14       239.11         0.20       189.40        68.65        10.62 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
       32.48        18.35       118.32         0.76         0.20        71.31 
TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MF 
       81.99       103.13        15.25         5.75        23.77       209.79 
TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM 
       94.19       171.85        63.25        67.50       104.78       145.45 
TCGA-EE-A2MP TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AB 
      227.01        25.08       143.93        23.51       124.31       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 
       51.62         4.41        54.51         6.28        67.89       111.85 
TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
        3.35       201.80       152.81        14.56        34.45         1.58 
TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D 
       47.31         7.82         4.54        53.29        39.81        11.47 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
      151.46       150.12        99.06        42.48       120.76        49.71 
TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A3ES 
       34.95       146.63        47.97        16.87        10.95       173.29 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A44A TCGA-FR-A7U8 TCGA-FR-A7UA 
       55.82        15.48        32.05       174.21        26.20         5.65 
TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZC 
      171.78        49.74       195.98         8.35        27.62       312.07 
TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ 
       32.78        35.90        12.92        36.33        78.61       130.95 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 
      136.27        35.28        23.21         3.06        30.90        66.67 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FW-A3TU TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
      173.19        13.28        55.59        19.30         9.90         6.05 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A4U3 
        1.91        53.29        84.72        17.06         7.59       120.53 
TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-GN-A8LK TCGA-GN-A9SD TCGA-LH-A9QB TCGA-OD-A75X 
       34.49        46.92        43.23        59.41        85.05       297.01 
TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 
        7.23        18.05         0.33       174.12         1.97       120.07 
TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 
       44.05        79.99         8.09       185.13        92.84         1.15 
TCGA-WE-A8K5 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZY 
       59.64        62.99        12.69        19.00        59.44        48.39 
TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-Z2-AA3S 
        1.94        26.60        16.64        15.65        28.21        91.23 

  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
             4.47              0.00 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
           209.23            346.49 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
           23.670            47.525 
[1] "4.5 - 209.2 (23.7)" "0.0 - 346.5 (47.5)"
[1] "hr=" "2.2"
D41V2, survival
                   sevent
clus2                 0   1
  XQ GAIN MUTATED    14  26
  XQ GAIN WILD-TYPE 155 154
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               40               309 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               26               154 
$`XQ GAIN MUTATED`
TCGA-3N-A9WB TCGA-D3-A1Q3 TCGA-D3-A2JA TCGA-D3-A2JE TCGA-D3-A2JG TCGA-D3-A3CE 
       17.03        16.67       115.53        27.65       113.52        60.23 
TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A8GQ TCGA-DA-A3F3 TCGA-EB-A5KH TCGA-EE-A184 
       39.75        45.30        29.06        10.49        20.35        68.15 
TCGA-EE-A29A TCGA-EE-A29R TCGA-EE-A2GN TCGA-EE-A2MU TCGA-EE-A3AG TCGA-EE-A3J7 
       63.35        14.47       102.12        53.26        41.59        64.08 
TCGA-ER-A19M TCGA-ER-A2NC TCGA-ER-A2ND TCGA-FR-A3YN TCGA-FR-A729 TCGA-FR-A8YC 
       61.05        43.82        23.34        92.98       220.80        34.82 
TCGA-FR-A8YD TCGA-FS-A1ZG TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZU TCGA-FS-A1ZY 
       36.26         9.70        23.93        74.73        26.56        27.09 
TCGA-FS-A4FD TCGA-FW-A3TV TCGA-GF-A6C9 TCGA-GN-A264 TCGA-GN-A268 TCGA-GN-A26D 
       80.68        13.51        15.78       117.93        62.79        39.58 
TCGA-W3-AA1O TCGA-WE-A8K6 TCGA-WE-A8ZT TCGA-YD-A89C 
        4.01        15.98        11.80         6.90 

$`XQ GAIN WILD-TYPE`
TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 
       66.48        12.99        14.93        16.57       112.04       112.57 
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB 
       71.80       133.25        28.08        31.59        90.90        95.74 
TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JC 
       43.43       103.10        65.49        23.77       168.00        86.76 
TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       11.87        62.07        42.08        12.10       171.58        66.48 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 
       66.08        59.57       130.72        58.06        46.98        46.32 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR 
      166.52        86.93        24.53        13.87         9.34       103.59 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
      174.84        55.73        56.35       145.12        32.94        22.62 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR 
       63.81        26.89       125.79       135.75       137.92       178.32 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GE 
       18.18       125.19        30.84        79.59        23.61        26.43 
TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GN 
       58.52       241.38       170.20        89.13       107.15       161.00 
TCGA-D3-A8GP TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW 
      152.75       129.63       117.17       151.53        54.67         3.65 
TCGA-D9-A1JX TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 
        7.10        18.12        15.39        22.29        18.44         9.90 
TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY 
       25.18        66.25        22.95        48.89        36.03       117.21 
TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 
       20.38       194.83       176.55        35.93       107.34        61.18 
TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 
       53.92        65.92        23.44        68.09        28.60       215.44 
TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL 
       15.68        13.87        10.36        68.25        54.02        17.29 
TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
       52.01         7.04        24.89        29.82        27.22         8.65 
TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B 
       94.98        33.73        14.70        26.89         4.96       133.81 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29B TCGA-EE-A29C 
      151.27        91.56       168.26        13.55        85.08        78.97 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M 
       13.97        63.78        72.07        64.64         2.60        56.84 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V 
       18.61        56.42        66.74        61.28       369.93        25.87 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 
      195.02        17.92        46.82       102.90        36.82        39.29 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
       86.14        59.28        67.43       340.14       161.03       208.04 
TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GO 
       48.72       107.38        54.74        79.66        75.48       126.81 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 
       13.91        42.77        81.21        44.88        94.82        21.67 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME 
      129.27        28.83        19.76        61.51        47.28       103.27 
TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK 
      268.73       103.20        16.96       204.66        96.23       158.63 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR 
      216.66       167.90        47.54       248.65        43.23       134.40 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
      162.48        71.21       124.31       122.73        51.62        28.77 
TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 
       54.51        13.81       138.81       172.18       127.20        36.95 
TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH 
       34.32        53.19       201.80        27.35        51.35       109.58 
TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 
      152.81        31.40        35.44        13.94        50.76         9.17 
TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F 
       77.75        98.40        48.89        12.59        13.02        26.37 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A19P 
      268.93       152.35         6.44       131.51        44.05       162.08 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NE 
       50.89        37.25         8.88       148.18        79.99        20.15 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
       16.37        31.27        32.05       247.04        80.32        46.98 
TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A7U9 
       33.21         6.77       174.21        15.72        27.85        18.77 
TCGA-FR-A7UA TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
       38.27       104.42       216.92        48.59       228.59       202.65 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC 
       20.91        28.08         7.79        27.72        48.85       357.37 
TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZM 
       53.52        40.27        15.45        32.75        47.38       101.26 
TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A1ZZ 
      133.55        11.41       148.80        53.16        49.48        27.02 
TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 
       77.82        50.14        66.67        28.73       174.84        34.03 
TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A5DY 
       26.73        54.41         0.20        22.92        55.59        19.30 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A266 
        9.90         7.23         2.04       139.89        84.72        10.13 
TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 
       64.44        32.48       121.91        39.35        10.42        48.89 
TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A8LL TCGA-GN-A9SD TCGA-HR-A2OG TCGA-HR-A2OH 
       22.13        50.10        21.37        59.41         0.23        65.88 
TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 TCGA-RP-A694 
      368.78       297.90         7.23        18.05         0.33         0.69 
TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1V 
      228.16        63.02       121.08        69.07       111.09        42.08 
TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8ZM 
      219.16       105.04        24.03        49.05        61.15        98.89 
TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AA9Y 
       58.98        67.63        59.77        32.58        49.51        12.16 
TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YD-A9TA TCGA-YG-AA3O TCGA-YG-AA3P 
       35.01        19.73        22.29        49.18        37.94        14.43 
TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
       27.58        96.99        15.98 

  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
             4.01              0.20 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
           220.80            369.93 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
            37.92             53.19 
[1] "4.0 - 220.8 (37.9)" "0.2 - 369.9 (53.2)"
[1] "hr=" "2"  
D41V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  XQ GAIN MUTATED                   13             0
  XQ GAIN WILD-TYPE                 52             5
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  XQ GAIN MUTATED                                           7
  XQ GAIN WILD-TYPE                                        65
                   vv
clus                REGIONAL LYMPH NODE
  XQ GAIN MUTATED                    21
  XQ GAIN WILD-TYPE                 194
D41V4, multiclass
                                           clus
vv                                          XQ GAIN MUTATED XQ GAIN WILD-TYPE
  DISTANT METASTASIS                                     13                52
  PRIMARY TUMOR                                           0                 5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               7                65
  REGIONAL LYMPH NODE                                    21               194
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  XQ GAIN MUTATED             0       1       2        3        4        3
  XQ GAIN WILD-TYPE          12       6      26       15       23       21
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  XQ GAIN MUTATED           1         3         4         5          4
  XQ GAIN WILD-TYPE        13        16         8        32         11
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  XQ GAIN MUTATED            4          5        1
  XQ GAIN WILD-TYPE         28         55       19
D41V5, multiclass
             clus
vv            XQ GAIN MUTATED XQ GAIN WILD-TYPE
  I OR II NOS               0                12
  STAGE 0                   1                 6
  STAGE I                   2                26
  STAGE IA                  3                15
  STAGE IB                  4                23
  STAGE II                  3                21
  STAGE IIA                 1                13
  STAGE IIB                 3                16
  STAGE IIC                 4                 8
  STAGE III                 5                32
  STAGE IIIA                4                11
  STAGE IIIB                4                28
  STAGE IIIC                5                55
  STAGE IV                  1                19
[1] 14  2
[1] TRUE
[1] "dimension of contingency 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      10  9  9  7
  XQ GAIN WILD-TYPE    54 63 68 61
D41V6, multiclass
       clus
vv      XQ GAIN MUTATED XQ GAIN WILD-TYPE
  T0+T1              10                54
  T2                  9                63
  T3                  9                68
  T4                  7                61
[1] 4 2
[1] TRUE
[1] "dimension of 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    19   8   7   3
  XQ GAIN WILD-TYPE 150  55  31  46
D41V7, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  N0              19               150
  N1               8                55
  N2               7                31
  N3               3                46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V8, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED    37   1
  XQ GAIN WILD-TYPE 276  20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     37    1
  XQ GAIN WILD-TYPE  276   20
   clus
vv  XQ GAIN MUTATED XQ GAIN WILD-TYPE
  0              37               276
  1               1                20
[1] 2 2
[1] FALSE
D41V9, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED    15  12
  XQ GAIN WILD-TYPE 117  76
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     15   12
  XQ GAIN WILD-TYPE  117   76
     clus
vv    XQ GAIN MUTATED XQ GAIN WILD-TYPE
  NO               15               117
  YES              12                76
[1] 2 2
[1] FALSE
D41V10, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED     5  36
  XQ GAIN WILD-TYPE  39 277
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      5   36
  XQ GAIN WILD-TYPE   39  277
     clus
vv    XQ GAIN MUTATED XQ GAIN WILD-TYPE
  NO                5                39
  YES              36               277
[1] 2 2
[1] FALSE
D41V11, continuous
D41V12, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED    15  26
  XQ GAIN WILD-TYPE 120 197
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     15   26
  XQ GAIN WILD-TYPE  120  197
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  FEMALE              15               120
  MALE                26               197
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  XQ GAIN MUTATED       1                         0    40
  XQ GAIN WILD-TYPE     4                         1   304
D41V13, multiclass
                           clus
vv                          XQ GAIN MUTATED XQ GAIN WILD-TYPE
  ASIAN                                   1                 4
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  40               304
[1] 3 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     0  40
  XQ GAIN WILD-TYPE   7 304
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      0   40
  XQ GAIN WILD-TYPE    7  304
                        clus
vv                       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 7
  NOT HISPANIC OR LATINO              40               304
[1] 2 2
[1] FALSE

Clustering(42) Variable = 1P LOSS MUTATION ANALYSIS
D42V1, survival
                   sevent
clus2                 0   1
  1P LOSS MUTATED    22  16
  1P LOSS WILD-TYPE  99 102
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               38               201 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               16               102 
$`1P LOSS MUTATED`
TCGA-D3-A1Q4 TCGA-D3-A3CC TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D9-A1X3 TCGA-D9-A4Z6 
       31.89        40.01        45.70       177.86        10.78        18.44 
TCGA-DA-A1I2 TCGA-DA-A1I7 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A20H TCGA-EE-A2GE 
      150.61        32.42       214.59        14.96       155.90         0.20 
TCGA-EE-A2GH TCGA-EE-A2GO TCGA-EE-A2GR TCGA-EE-A2MK TCGA-EE-A2MP TCGA-EE-A2MS 
      189.40       118.32         0.20        67.50       227.01       143.93 
TCGA-EE-A3AD TCGA-EE-A3J3 TCGA-ER-A193 TCGA-ER-A197 TCGA-ER-A19C TCGA-ER-A19D 
        4.41        67.89        14.56         1.58        39.81        11.47 
TCGA-ER-A19L TCGA-ER-A2ND TCGA-ER-A2NG TCGA-ER-A3EV TCGA-FS-A1ZT TCGA-FS-A1ZW 
       99.06         4.70        10.95        15.48        35.28        23.21 
TCGA-FS-A4F8 TCGA-FW-A3TV TCGA-QB-AA9O TCGA-WE-A8K5 TCGA-WE-A8ZM TCGA-WE-A8ZQ 
      173.19        11.54        18.05        59.64        62.99        59.44 
TCGA-WE-AA9Y TCGA-WE-AAA3 
        1.94        16.64 

$`1P LOSS WILD-TYPE`
TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q5 
       60.46        12.99        14.83         8.42        15.72       110.93 
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 
       49.35       133.25        19.04        76.41        62.60        25.64 
TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
       45.99        62.86        15.75       168.00        86.30         7.27 
TCGA-D3-A2JE TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
        9.76       107.61        36.30       171.58        64.83        66.08 
TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3CF 
       43.53        58.06        46.98       140.98        59.70        16.96 
TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51J 
       13.87         9.34        90.21        23.67       173.85       144.46 
TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GU TCGA-D3-A8GC 
       31.76        62.70        11.34        42.05       124.08        78.21 
TCGA-D3-A8GD TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GP 
       23.61       179.97       120.00        69.53        70.62       135.12 
TCGA-D3-A8GR TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV 
       36.53        15.02        16.90        57.90        22.85        48.66 
TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I5 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 
      106.85        31.96        82.85        64.83        58.85        25.12 
TCGA-EB-A44Q TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X 
        3.91        33.24        50.07        45.50         6.64        13.15 
TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A184 TCGA-EE-A20C 
       24.89        62.37        20.38         0.00        67.50        75.55 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H 
       75.22        76.14        12.99         0.26        44.28        63.12 
TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 
       47.74        27.16        61.12       346.49       185.19       102.38 
TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GJ TCGA-EE-A2GK 
        7.20        77.98        26.14       239.11        68.65        10.62 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2GU 
       32.48        18.35        31.00         0.76        71.31        81.99 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MG 
      103.13        15.25         5.75        23.77       209.79        94.19 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MR TCGA-EE-A2MT 
      171.85        63.25       104.78       145.45        25.08        23.51 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3AF 
       53.26       124.31       122.73        51.62        54.51         6.28 
TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JI TCGA-ER-A195 
      111.85        45.90         3.35       201.80       152.81        34.45 
TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19G TCGA-ER-A19H 
       47.31         7.82         4.54        53.29       151.46       150.12 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W 
       59.84        42.48       120.76        49.71        34.95       146.63 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3PL 
       47.97        22.36        16.87       173.29        55.82        32.05 
TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FS-A1YW 
      174.21       209.23        26.20         5.65        10.06       171.78 
TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD 
       49.74       195.98         8.35        27.62       312.07        32.78 
TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ 
       35.90        12.92         7.82        36.33        78.61       130.95 
TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 
      136.27         4.47         5.29         3.06        30.90        66.67 
TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
       13.28        80.68        55.59        19.30         9.90         6.05 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 
        1.91        53.29       117.93        84.72        17.06        42.48 
TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-GN-A8LK TCGA-GN-A9SD 
        7.59       120.53        34.49        46.92        43.23        59.41 
TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A825 
       85.05       297.01         7.23         0.33       174.12         1.97 
TCGA-W3-A828 TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 
      120.07        44.05        79.99         8.09       185.13        92.84 
TCGA-WE-A8K1 TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AAA0 
        1.15        12.69        19.00        10.95        48.39        26.60 
TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-Z2-AA3S 
       15.65        28.21        91.23 

  1P LOSS MUTATED 1P LOSS WILD-TYPE 
              0.2               0.0 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
           227.01            346.49 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
            33.85             47.74 
[1] "0.2 - 227.0 (33.9)" "0.0 - 346.5 (47.7)"
[1] "hr=" "1.2"
D42V2, survival
                   sevent
clus2                 0   1
  1P LOSS MUTATED    31  20
  1P LOSS WILD-TYPE 138 160
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               51               298 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               20               160 
$`1P LOSS MUTATED`
TCGA-D3-A1Q4 TCGA-D3-A1Q9 TCGA-D3-A3CC TCGA-D3-A3MV TCGA-D3-A5GN TCGA-D3-A5GR 
      112.04        31.59        86.93        45.30       135.75       178.32 
TCGA-D3-A5GS TCGA-D9-A1X3 TCGA-D9-A4Z6 TCGA-DA-A1I2 TCGA-DA-A1I7 TCGA-DA-A1I8 
       18.18        18.12        18.44       176.55        61.18        53.92 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44R TCGA-EE-A20H TCGA-EE-A29R TCGA-EE-A2GE 
      215.44        15.68        10.36       168.26        14.47       161.03 
TCGA-EE-A2GH TCGA-EE-A2GO TCGA-EE-A2GR TCGA-EE-A2MK TCGA-EE-A2MP TCGA-EE-A2MS 
      208.04       126.81        42.77       158.63       248.65       162.48 
TCGA-EE-A3AD TCGA-EE-A3J3 TCGA-ER-A193 TCGA-ER-A197 TCGA-ER-A19C TCGA-ER-A19D 
       28.77       172.18        31.40        13.94        48.89        12.59 
TCGA-ER-A19L TCGA-ER-A2ND TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3EV TCGA-FR-A69P 
      131.51        23.34        31.27        32.05        46.98        15.72 
TCGA-FR-A7U9 TCGA-FS-A1Z7 TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A4F8 TCGA-FW-A3TV 
       18.77         7.79        53.16        49.48       174.84        13.51 
TCGA-GN-A26D TCGA-QB-AA9O TCGA-WE-A8K5 TCGA-WE-A8ZM TCGA-WE-A8ZQ TCGA-WE-AA9Y 
       39.58        18.05        61.15        98.89        59.77        12.16 
TCGA-WE-AAA3 TCGA-YD-A89C TCGA-YG-AA3P 
       19.73         6.90        14.43 

$`1P LOSS WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q3 
       17.03        66.48        12.99        14.93        16.57        16.67 
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB 
      112.57        71.80       133.25        28.08        90.90        95.74 
TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB 
       43.43       103.10        65.49        23.77       115.53       168.00 
TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH 
       86.76        11.87        27.65        62.07       113.52        42.08 
TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ 
       12.10       171.58        66.48        66.08        59.57       130.72 
TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3CF 
       58.06        46.98        46.32       166.52        60.23        24.53 
TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F 
       13.87         9.34       103.59        39.75       174.84        55.73 
TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T 
       56.35       145.12        32.94        22.62        63.81        26.89 
TCGA-D3-A5GL TCGA-D3-A5GO TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GD 
      125.79       137.92       125.19        30.84        79.59        23.61 
TCGA-D3-A8GE TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM 
       26.43        58.52       241.38       170.20        89.13       107.15 
TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A148 
      161.00       152.75        29.06       129.63       117.17       151.53 
TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 
       54.67         3.65         7.10        15.39        22.29         9.90 
TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY 
       25.18        66.25        22.95        48.89        36.03       117.21 
TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1IA TCGA-DA-A1IB 
       20.38       194.83        35.93       107.34        65.92        23.44 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5SG 
       68.09        28.60        10.49        13.87        20.35        68.25 
TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X 
       54.02        17.29        52.01         7.04        24.89        29.82 
TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
       27.22         8.65        94.98        33.73        14.70        26.89 
TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I 
       68.15         4.96       133.81       151.27        91.56        13.55 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G 
       63.35        85.08        78.97        13.97        63.78        72.07 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
       64.64         2.60        56.84        18.61        56.42        66.74 
TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 
       61.28       369.93        25.87       195.02        17.92        46.82 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC 
      102.90        36.82        39.29        86.14        59.28        67.43 
TCGA-EE-A2GD TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
      340.14        48.72       107.38        54.74        79.66        75.48 
TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 
      102.12        13.91        81.21        44.88        94.82        21.67 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME 
      129.27        28.83        19.76        61.51        47.28       103.27 
TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2ML 
      268.73       103.20        16.96       204.66        96.23       216.66 
TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A2MU 
      167.90        47.54        43.23       134.40        71.21        53.26 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG 
      124.31       122.73        51.62        54.51        13.81        41.59 
TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA 
      138.81       127.20        36.95        64.08        34.32        53.19 
TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 
      201.80        27.35        51.35       109.58       152.81        35.44 
TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19E TCGA-ER-A19F 
       50.76         9.17        77.75        98.40        13.02        26.37 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P 
      268.93       152.35         6.44        61.05        44.05       162.08 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
       50.89        37.25         8.88       148.18        79.99        43.82 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3PL TCGA-ER-A42K 
       20.15        16.37       247.04        80.32        33.21         6.77 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FR-A8YC 
       92.98       174.21       220.80        27.85        38.27        34.82 
TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
       36.26       104.42       216.92        48.59       228.59       202.65 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD 
       20.91        28.08        27.72        48.85       357.37        53.52 
TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK 
       40.27        15.45         9.70        32.75        47.38        23.93 
TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZU 
      101.26        74.73       133.55        11.41       148.80        26.56 
TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 
       27.09        27.02        77.82        50.14        66.67        28.73 
TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 
       34.03        26.73        54.41        80.68         0.20        22.92 
TCGA-FW-A3TU TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 
       55.59        19.30         9.90         7.23         2.04        15.78 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
      139.89       117.93        84.72        10.13        64.44        62.79 
TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A4U9 
       32.48       121.91        39.35        10.42        48.89        22.13 
TCGA-GN-A8LK TCGA-GN-A8LL TCGA-GN-A9SD TCGA-HR-A2OG TCGA-HR-A2OH TCGA-LH-A9QB 
       50.10        21.37        59.41         0.23        65.88       368.78 
TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 
      297.90         7.23         0.33         0.69       228.16        63.02 
TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1V TCGA-W3-AA1W 
      121.08         4.01        69.07       111.09        42.08       219.16 
TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K6 TCGA-WE-A8ZN TCGA-WE-A8ZO 
      105.04        24.03        49.05        15.98        58.98        67.63 
TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-YD-A9TA 
       11.80        32.58        49.51        35.01        22.29        49.18 
TCGA-YG-AA3O TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
       37.94        27.58        96.99        15.98 

  1P LOSS MUTATED 1P LOSS WILD-TYPE 
              6.9               0.2 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
           248.65            369.93 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
             45.3              52.6 
[1] "6.9 - 248.7 (45.3)" "0.2 - 369.9 (52.6)"
[1] "hr=" "1.4"
D42V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  1P LOSS MUTATED                    7             0
  1P LOSS WILD-TYPE                 58             5
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  1P LOSS MUTATED                                          11
  1P LOSS WILD-TYPE                                        61
                   vv
clus                REGIONAL LYMPH NODE
  1P LOSS MUTATED                    33
  1P LOSS WILD-TYPE                 182
D42V4, multiclass
                                           clus
vv                                          1P LOSS MUTATED 1P LOSS WILD-TYPE
  DISTANT METASTASIS                                      7                58
  PRIMARY TUMOR                                           0                 5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE              11                61
  REGIONAL LYMPH NODE                                    33               182
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  1P LOSS MUTATED             0       0       7        1        2        3
  1P LOSS WILD-TYPE          12       7      21       17       25       21
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  1P LOSS MUTATED           1         2         2         6          0
  1P LOSS WILD-TYPE        13        17        10        31         15
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  1P LOSS MUTATED            8         15        2
  1P LOSS WILD-TYPE         24         45       18
D42V5, multiclass
             clus
vv            1P LOSS MUTATED 1P LOSS WILD-TYPE
  I OR II NOS               0                12
  STAGE 0                   0                 7
  STAGE I                   7                21
  STAGE IA                  1                17
  STAGE IB                  2                25
  STAGE II                  3                21
  STAGE IIA                 1                13
  STAGE IIB                 2                17
  STAGE IIC                 2                10
  STAGE III                 6                31
  STAGE IIIA                0                15
  STAGE IIIB                8                24
  STAGE IIIC               15                45
  STAGE IV                  2                18
[1] 14  2
[1] TRUE
[1] "dimension of contingency 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      10 14  8 14
  1P LOSS WILD-TYPE    54 58 69 54
D42V6, multiclass
       clus
vv      1P LOSS MUTATED 1P LOSS WILD-TYPE
  T0+T1              10                54
  T2                 14                58
  T3                  8                69
  T4                 14                54
[1] 4 2
[1] TRUE
[1] "dimension of 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    18  11   9  10
  1P LOSS WILD-TYPE 151  52  29  39
D42V7, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  N0              18               151
  N1              11                52
  N2               9                29
  N3              10                39
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V8, binary
                   cls
clus                  0   1
  1P LOSS MUTATED    45   2
  1P LOSS WILD-TYPE 268  19
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     45    2
  1P LOSS WILD-TYPE  268   19
   clus
vv  1P LOSS MUTATED 1P LOSS WILD-TYPE
  0              45               268
  1               2                19
[1] 2 2
[1] FALSE
D42V9, binary
                   cls
clus                  0   1
  1P LOSS MUTATED    17  15
  1P LOSS WILD-TYPE 115  73
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     17   15
  1P LOSS WILD-TYPE  115   73
     clus
vv    1P LOSS MUTATED 1P LOSS WILD-TYPE
  NO               17               115
  YES              15                73
[1] 2 2
[1] FALSE
D42V10, binary
                   cls
clus                  0   1
  1P LOSS MUTATED     4  48
  1P LOSS WILD-TYPE  40 265
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      4   48
  1P LOSS WILD-TYPE   40  265
     clus
vv    1P LOSS MUTATED 1P LOSS WILD-TYPE
  NO                4                40
  YES              48               265
[1] 2 2
[1] FALSE
D42V11, continuous
D42V12, binary
                   cls
clus                  0   1
  1P LOSS MUTATED    22  30
  1P LOSS WILD-TYPE 113 193
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     22   30
  1P LOSS WILD-TYPE  113  193
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  FEMALE              22               113
  MALE                30               193
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  1P LOSS MUTATED       1                         0    49
  1P LOSS WILD-TYPE     4                         1   295
D42V13, multiclass
                           clus
vv                          1P LOSS MUTATED 1P LOSS WILD-TYPE
  ASIAN                                   1                 4
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  49               295
[1] 3 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     1  51
  1P LOSS WILD-TYPE   6 293
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      1   51
  1P LOSS WILD-TYPE    6  293
                        clus
vv                       1P LOSS MUTATED 1P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 6
  NOT HISPANIC OR LATINO              51               293
[1] 2 2
[1] FALSE

Clustering(43) Variable = 1Q LOSS MUTATION ANALYSIS
D43V1, survival
                   sevent
clus2                 0   1
  1Q LOSS MUTATED    10  10
  1Q LOSS WILD-TYPE 111 108
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               20               219 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               10               108 
$`1Q LOSS MUTATED`
TCGA-D3-A3CC TCGA-D3-A5GR TCGA-D9-A1X3 TCGA-D9-A4Z6 TCGA-DA-A1I2 TCGA-DA-A1I7 
       40.01       177.86        10.78        18.44       150.61        32.42 
TCGA-DA-A3F8 TCGA-EE-A20H TCGA-EE-A2M6 TCGA-EE-A2MP TCGA-EE-A3J3 TCGA-ER-A193 
       14.96       155.90       103.13       227.01        67.89        14.56 
TCGA-ER-A19C TCGA-ER-A2NG TCGA-ER-A3EV TCGA-FS-A4F8 TCGA-QB-AA9O TCGA-W3-AA1V 
       39.81        10.95        15.48       173.19        18.05         8.09 
TCGA-WE-A8ZQ TCGA-WE-AAA3 
       59.44        16.64 

$`1Q LOSS WILD-TYPE`
TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
       60.46        12.99        14.83         8.42        15.72        31.89 
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB 
      110.93        49.35       133.25        19.04        76.41        62.60 
TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC 
       25.64        45.99        62.86        15.75       168.00        86.30 
TCGA-D3-A2JD TCGA-D3-A2JE TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN 
        7.27         9.76       107.61        36.30       171.58        64.83 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CE 
       66.08        43.53        58.06        46.98       140.98        59.70 
TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E 
       16.96        13.87         9.34        90.21        23.67       173.85 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN 
      144.46        31.76        62.70        11.34        42.05        45.70 
TCGA-D3-A5GU TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL 
      124.08        78.21        23.61       179.97       120.00        69.53 
TCGA-D3-A8GM TCGA-D3-A8GP TCGA-D3-A8GR TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6EC 
       70.62       135.12        36.53        15.02        16.90        57.90 
TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I5 TCGA-DA-A1IA 
       22.85        48.66       106.85        31.96        82.85        64.83 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-EB-A44Q TCGA-EB-A5SG TCGA-EB-A5SH 
       58.85        25.12       214.59         3.91        33.24        50.07 
TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A181 
       45.50         6.64        13.15        24.89        62.37        20.38 
TCGA-EE-A182 TCGA-EE-A184 TCGA-EE-A20C TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D 
        0.00        67.50        75.55        75.22        76.14        12.99 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29Q 
        0.26        44.28        63.12        47.74        27.16        61.12 
TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB 
      346.49       185.19       102.38         7.20        77.98        26.14 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
      239.11         0.20       189.40        68.65        10.62        32.48 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
       18.35        31.00       118.32         0.76         0.20        71.31 
TCGA-EE-A2GU TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MG 
       81.99        15.25         5.75        23.77       209.79        94.19 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MR 
      171.85        63.25        67.50       104.78       145.45        25.08 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC 
      143.93        23.51        53.26       124.31       122.73        51.62 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 
        4.41        54.51         6.28       111.85        45.90         3.35 
TCGA-EE-A3JB TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 
      201.80       152.81        34.45         1.58        47.31         7.82 
TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L 
        4.54        53.29        11.47       151.46       150.12        99.06 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W 
       59.84        42.48       120.76        49.71        34.95       146.63 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A3ES TCGA-ER-A3ET 
       47.97        22.36         4.70        16.87       173.29        55.82 
TCGA-ER-A3PL TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FR-A8YC 
       32.05       174.21       209.23        26.20         5.65        10.06 
TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZC 
      171.78        49.74       195.98         8.35        27.62       312.07 
TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM 
       32.78        35.90        12.92         7.82        36.33        78.61 
TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY 
      130.95       136.27        35.28         4.47        23.21         5.29 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TU 
        3.06        30.90        66.67        13.28        80.68        55.59 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 
       11.54        19.30         9.90         6.05         1.91        53.29 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 
      117.93        84.72        17.06        42.48         7.59       120.53 
TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-GN-A8LK TCGA-GN-A9SD TCGA-LH-A9QB TCGA-OD-A75X 
       34.49        46.92        43.23        59.41        85.05       297.01 
TCGA-QB-A6FS TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1Q 
        7.23         0.33       174.12         1.97       120.07        44.05 
TCGA-W3-AA1R TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8ZM 
       79.99       185.13        92.84         1.15        59.64        62.99 
TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 
       12.69        19.00        10.95        48.39         1.94        26.60 
TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-Z2-AA3S 
       15.65        28.21        91.23 

  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
             8.09              0.00 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
           227.01            346.49 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
           36.115            46.980 
[1] "8.1 - 227.0 (36.1)" "0.0 - 346.5 (47.0)"
[1] "hr=" "1"  
D43V2, survival
                   sevent
clus2                 0   1
  1Q LOSS MUTATED    14  13
  1Q LOSS WILD-TYPE 155 167
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               27               322 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               13               167 
$`1Q LOSS MUTATED`
TCGA-D3-A1Q9 TCGA-D3-A3CC TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D9-A1X3 TCGA-D9-A4Z6 
       31.59        86.93       178.32        18.18        18.12        18.44 
TCGA-DA-A1I2 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A3F8 TCGA-EE-A20H TCGA-EE-A29X 
      176.55        61.18        53.92        15.68       168.26        17.92 
TCGA-EE-A2M6 TCGA-EE-A2MP TCGA-EE-A3J3 TCGA-ER-A193 TCGA-ER-A19C TCGA-ER-A2NG 
      129.27       248.65       172.18        31.40        48.89        31.27 
TCGA-ER-A3EV TCGA-FR-A69P TCGA-FR-A7U9 TCGA-FS-A4F8 TCGA-QB-AA9O TCGA-W3-AA1V 
       46.98        15.72        18.77       174.84        18.05        42.08 
TCGA-WE-A8ZQ TCGA-WE-AAA3 TCGA-YD-A89C 
       59.77        19.73         6.90 

$`1Q LOSS WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q3 
       17.03        66.48        12.99        14.93        16.57        16.67 
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA 
      112.04       112.57        71.80       133.25        28.08        90.90 
TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA 
       95.74        43.43       103.10        65.49        23.77       115.53 
TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A2JG 
      168.00        86.76        11.87        27.65        62.07       113.52 
TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP 
       42.08        12.10       171.58        66.48        66.08        59.57 
TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CE 
      130.72        58.06        46.98        46.32       166.52        60.23 
TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV 
       24.53        13.87         9.34       103.59        39.75        45.30 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
      174.84        55.73        56.35       145.12        32.94        22.62 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GU 
       63.81        26.89       125.79       135.75       137.92       125.19 
TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GI TCGA-D3-A8GJ 
       30.84        79.59        23.61        26.43        58.52       241.38 
TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GQ 
      170.20        89.13       107.15       161.00       152.75        29.06 
TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX 
      129.63       117.17       151.53        54.67         3.65         7.10 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG 
       15.39        22.29         9.90        25.18        66.25        22.95 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I4 
       48.89        36.03       117.21        20.38       194.83        35.93 
TCGA-DA-A1I5 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
      107.34        65.92        23.44        68.09        28.60        10.49 
TCGA-DA-A3F5 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH 
      215.44        13.87        10.36        20.35        68.25        54.02 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y 
       17.29        52.01         7.04        24.89        29.82        27.22 
TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 
        8.65        94.98        33.73        14.70        26.89        68.15 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29A 
        4.96       133.81       151.27        91.56        13.55        63.35 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H 
       85.08        78.97        13.97        63.78        72.07        64.64 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
        2.60        56.84        18.61        56.42        66.74        14.47 
TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A2A0 TCGA-EE-A2A1 
       61.28       369.93        25.87       195.02        46.82       102.90 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD 
       36.82        39.29        86.14        59.28        67.43       340.14 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
      161.03       208.04        48.72       107.38        54.74        79.66 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
       75.48       102.12       126.81        13.91        42.77        81.21 
TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC 
       44.88        94.82        21.67        28.83        19.76        61.51 
TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
       47.28       103.27       268.73       103.20        16.96       204.66 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MQ 
       96.23       158.63       216.66       167.90        47.54        43.23 
TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB 
      134.40       162.48        71.21        53.26       124.31       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH 
       51.62        28.77        54.51        13.81        41.59       138.81 
TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB 
      127.20        36.95        64.08        34.32        53.19       201.80 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 
       27.35        51.35       109.58       152.81        35.44        13.94 
TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19E 
       50.76         9.17        77.75        98.40        12.59        13.02 
TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
       26.37       268.93       152.35         6.44       131.51        61.05 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W 
       44.05       162.08        50.89        37.25         8.88       148.18 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NH 
       79.99        43.82        23.34        20.15        16.37        32.05 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A 
      247.04        80.32        33.21         6.77        92.98       174.21 
TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE 
      220.80        27.85        38.27        34.82        36.26       104.42 
TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 
      216.92        48.59       228.59       202.65        20.91        28.08 
TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE 
        7.79        27.72        48.85       357.37        53.52        40.27 
TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM 
       15.45         9.70        32.75        47.38        23.93       101.26 
TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU 
       74.73       133.55        11.41       148.80        53.16        26.56 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 
       49.48        27.09        27.02        77.82        50.14        66.67 
TCGA-FS-A4F5 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 
       28.73        34.03        26.73        54.41        80.68         0.20 
TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
       22.92        55.59        13.51        19.30         9.90         7.23 
TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 
        2.04        15.78       139.89       117.93        84.72        10.13 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A4U4 
       64.44        62.79        32.48        39.58       121.91        39.35 
TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A8LL TCGA-GN-A9SD 
       10.42        48.89        22.13        50.10        21.37        59.41 
TCGA-HR-A2OG TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A693 
        0.23        65.88       368.78       297.90         7.23         0.33 
TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1Q 
        0.69       228.16        63.02       121.08         4.01        69.07 
TCGA-W3-AA1R TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K5 
      111.09       219.16       105.04        24.03        49.05        61.15 
TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-A8ZX 
       15.98        98.89        58.98        67.63        11.80        32.58 
TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-YD-A9TA TCGA-YG-AA3O 
       49.51        12.16        35.01        22.29        49.18        37.94 
TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
       14.43        27.58        96.99        15.98 

  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
              6.9               0.2 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
           248.65            369.93 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
           42.080            51.815 
[1] "6.9 - 248.7 (42.1)" "0.2 - 369.9 (51.8)"
[1] "hr=" "1.1"
D43V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  1Q LOSS MUTATED                    3             0
  1Q LOSS WILD-TYPE                 62             5
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  1Q LOSS MUTATED                                           5
  1Q LOSS WILD-TYPE                                        67
                   vv
clus                REGIONAL LYMPH NODE
  1Q LOSS MUTATED                    19
  1Q LOSS WILD-TYPE                 196
D43V4, multiclass
                                           clus
vv                                          1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  DISTANT METASTASIS                                      3                62
  PRIMARY TUMOR                                           0                 5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               5                67
  REGIONAL LYMPH NODE                                    19               196
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  1Q LOSS MUTATED             0       0       5        1        2        1
  1Q LOSS WILD-TYPE          12       7      23       17       25       23
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  1Q LOSS MUTATED           1         1         1         2          0
  1Q LOSS WILD-TYPE        13        18        11        35         15
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  1Q LOSS MUTATED            3          8        1
  1Q LOSS WILD-TYPE         29         52       19
D43V5, multiclass
             clus
vv            1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  I OR II NOS               0                12
  STAGE 0                   0                 7
  STAGE I                   5                23
  STAGE IA                  1                17
  STAGE IB                  2                25
  STAGE II                  1                23
  STAGE IIA                 1                13
  STAGE IIB                 1                18
  STAGE IIC                 1                11
  STAGE III                 2                35
  STAGE IIIA                0                15
  STAGE IIIB                3                29
  STAGE IIIC                8                52
  STAGE IV                  1                19
[1] 14  2
[1] TRUE
[1] "dimension of contingency 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       6  6  6  7
  1Q LOSS WILD-TYPE    58 66 71 61
D43V6, multiclass
       clus
vv      1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  T0+T1               6                58
  T2                  6                66
  T3                  6                71
  T4                  7                61
[1] 4 2
[1] TRUE
[1] "dimension of 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    11   3   6   5
  1Q LOSS WILD-TYPE 158  60  32  44
D43V7, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  N0              11               158
  N1               3                60
  N2               6                32
  N3               5                44
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V8, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED    24   1
  1Q LOSS WILD-TYPE 289  20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED     24    1
  1Q LOSS WILD-TYPE  289   20
   clus
vv  1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  0              24               289
  1               1                20
[1] 2 2
[1] FALSE
D43V9, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED     9   8
  1Q LOSS WILD-TYPE 123  80
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      9    8
  1Q LOSS WILD-TYPE  123   80
     clus
vv    1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  NO                9               123
  YES               8                80
[1] 2 2
[1] FALSE
D43V10, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED     3  24
  1Q LOSS WILD-TYPE  41 289
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      3   24
  1Q LOSS WILD-TYPE   41  289
     clus
vv    1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  NO                3                41
  YES              24               289
[1] 2 2
[1] FALSE
D43V11, continuous
D43V12, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED    10  17
  1Q LOSS WILD-TYPE 125 206
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED     10   17
  1Q LOSS WILD-TYPE  125  206
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  FEMALE              10               125
  MALE                17               206
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  1Q LOSS MUTATED       0                         0    26
  1Q LOSS WILD-TYPE     5                         1   318
D43V13, multiclass
                           clus
vv                          1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  ASIAN                                   0                 5
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  26               318
[1] 3 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     0  27
  1Q LOSS WILD-TYPE   7 317
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      0   27
  1Q LOSS WILD-TYPE    7  317
                        clus
vv                       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 7
  NOT HISPANIC OR LATINO              27               317
[1] 2 2
[1] FALSE

Clustering(44) Variable = 2P LOSS MUTATION ANALYSIS
D44V1, survival
                   sevent
clus2                 0   1
  2P LOSS MUTATED    12  20
  2P LOSS WILD-TYPE 109  98
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               32               207 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               20                98 
$`2P LOSS MUTATED`
TCGA-D3-A2JC TCGA-D3-A2JG TCGA-D3-A3C6 TCGA-D3-A3CF TCGA-D3-A3MR TCGA-D3-A3MU 
       86.30       107.61        58.06        16.96        90.21        23.67 
TCGA-D3-A51T TCGA-D3-A8GM TCGA-D9-A1X3 TCGA-D9-A3Z3 TCGA-DA-A1I2 TCGA-EE-A180 
       11.34        70.62        10.78        16.90       150.61        62.37 
TCGA-EE-A29P TCGA-EE-A2GH TCGA-EE-A2GR TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2MS 
       27.16       189.40         0.20        63.25        67.50       143.93 
TCGA-EE-A3AD TCGA-EE-A3J3 TCGA-ER-A19C TCGA-ER-A19P TCGA-ER-A3PL TCGA-FR-A8YC 
        4.41        67.89        39.81       120.76        32.05        10.06 
TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-GN-A264 TCGA-GN-A267 TCGA-OD-A75X 
      171.78        49.74       195.98       117.93        17.06       297.01 
TCGA-W3-AA21 TCGA-WE-AA9Y 
       92.84         1.94 

$`2P LOSS WILD-TYPE`
TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
       60.46        12.99        14.83         8.42        15.72        31.89 
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB 
      110.93        49.35       133.25        19.04        76.41        62.60 
TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JD 
       25.64        45.99        62.86        15.75       168.00         7.27 
TCGA-D3-A2JE TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP 
        9.76        36.30       171.58        64.83        66.08        43.53 
TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3ML TCGA-D3-A3MO 
       46.98       140.98        40.01        59.70        13.87         9.34 
TCGA-D3-A51E TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A5GL TCGA-D3-A5GN 
      173.85       144.46        31.76        62.70        42.05        45.70 
TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GJ TCGA-D3-A8GK 
      177.86       124.08        78.21        23.61       179.97       120.00 
TCGA-D3-A8GL TCGA-D3-A8GP TCGA-D3-A8GR TCGA-D9-A3Z1 TCGA-D9-A4Z6 TCGA-D9-A6EC 
       69.53       135.12        36.53        15.02        18.44        57.90 
TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I5 TCGA-DA-A1I7 
       22.85        48.66       106.85        31.96        82.85        32.42 
TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q 
       64.83        58.85        25.12       214.59        14.96         3.91 
TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y 
       33.24        50.07        45.50         6.64        13.15        24.89 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A184 TCGA-EE-A20C TCGA-EE-A20H TCGA-EE-A29B 
       20.38         0.00        67.50        75.55       155.90        75.22 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M 
       76.14        12.99         0.26        44.28        63.12        47.74 
TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 
       61.12       346.49       185.19       102.38         7.20        77.98 
TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
       26.14       239.11         0.20        68.65        10.62        32.48 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2GU 
       18.35        31.00       118.32         0.76        71.31        81.99 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MG 
      103.13        15.25         5.75        23.77       209.79        94.19 
TCGA-EE-A2MI TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MR TCGA-EE-A2MT 
      171.85       104.78       145.45       227.01        25.08        23.51 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3AF 
       53.26       124.31       122.73        51.62        54.51         6.28 
TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JI TCGA-ER-A193 
      111.85        45.90         3.35       201.80       152.81        14.56 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B 
       34.45         1.58        47.31         7.82         4.54        53.29 
TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
       11.47       151.46       150.12        99.06        59.84        42.48 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
       49.71        34.95       146.63        47.97        22.36         4.70 
TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-FR-A44A 
       16.87        10.95       173.29        55.82        15.48       174.21 
TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZC 
      209.23        26.20         5.65         8.35        27.62       312.07 
TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM 
       32.78        35.90        12.92         7.82        36.33        78.61 
TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY 
      130.95       136.27        35.28         4.47        23.21         5.29 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FD 
        3.06        30.90        66.67       173.19        13.28        80.68 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 
       55.59        11.54        19.30         9.90         6.05         1.91 
TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 
       53.29        84.72        42.48         7.59       120.53        34.49 
TCGA-GN-A4U8 TCGA-GN-A8LK TCGA-GN-A9SD TCGA-LH-A9QB TCGA-QB-A6FS TCGA-QB-AA9O 
       46.92        43.23        59.41        85.05         7.23        18.05 
TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1Q TCGA-W3-AA1R 
        0.33       174.12         1.97       120.07        44.05        79.99 
TCGA-W3-AA1V TCGA-W3-AA1W TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8ZM TCGA-WE-A8ZN 
        8.09       185.13         1.15        59.64        62.99        12.69 
TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AAA0 TCGA-WE-AAA3 
       19.00        59.44        10.95        48.39        26.60        16.64 
TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-Z2-AA3S 
       15.65        28.21        91.23 

  2P LOSS MUTATED 2P LOSS WILD-TYPE 
              0.2               0.0 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
           297.01            346.49 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
            62.81             45.50 
[1] "0.2 - 297.0 (62.8)" "0.0 - 346.5 (45.5)"
[1] "hr=" "1.1"
D44V2, survival
                   sevent
clus2                 0   1
  2P LOSS MUTATED    22  24
  2P LOSS WILD-TYPE 147 156
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               46               303 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               24               156 
$`2P LOSS MUTATED`
TCGA-D3-A2JC TCGA-D3-A2JG TCGA-D3-A3C6 TCGA-D3-A3CF TCGA-D3-A3MR TCGA-D3-A3MU 
       86.76       113.52        58.06        24.53       103.59        39.75 
TCGA-D3-A51T TCGA-D3-A5GO TCGA-D3-A8GM TCGA-D3-A8GS TCGA-D9-A149 TCGA-D9-A1X3 
       26.89       137.92       107.15       117.17        54.67        18.12 
TCGA-D9-A3Z3 TCGA-D9-A6EA TCGA-DA-A1I2 TCGA-EE-A180 TCGA-EE-A20B TCGA-EE-A20F 
       22.29        25.18       176.55        94.98       133.81        91.56 
TCGA-EE-A20I TCGA-EE-A29P TCGA-EE-A2GC TCGA-EE-A2GH TCGA-EE-A2GR TCGA-EE-A2MJ 
       13.55        56.42        67.43       208.04        42.77        96.23 
TCGA-EE-A2MK TCGA-EE-A2MS TCGA-EE-A3AD TCGA-EE-A3J3 TCGA-EE-A3JA TCGA-EE-A3JE 
      158.63       162.48        28.77       172.18        53.19        51.35 
TCGA-ER-A19C TCGA-ER-A19P TCGA-ER-A3PL TCGA-FR-A8YC TCGA-FS-A1YW TCGA-FS-A1YY 
       48.89       162.08        33.21        34.82       216.92       228.59 
TCGA-FS-A1Z0 TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A26D TCGA-HR-A2OG TCGA-HR-A2OH 
      202.65       117.93        64.44        39.58         0.23        65.88 
TCGA-OD-A75X TCGA-W3-AA21 TCGA-WE-AA9Y TCGA-YG-AA3P 
      297.90       105.04        12.16        14.43 

$`2P LOSS WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q3 
       17.03        66.48        12.99        14.93        16.57        16.67 
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 
      112.04       112.57        71.80       133.25        28.08        31.59 
TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 
       90.90        95.74        43.43       103.10        65.49        23.77 
TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JD TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A2JH 
      115.53       168.00        11.87        27.65        62.07        42.08 
TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ 
       12.10       171.58        66.48        66.08        59.57       130.72 
TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3ML 
       46.98        46.32       166.52        86.93        60.23        13.87 
TCGA-D3-A3MO TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J 
        9.34        45.30       174.84        55.73        56.35       145.12 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR 
       32.94        22.62        63.81       125.79       135.75       178.32 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GE 
       18.18       125.19        30.84        79.59        23.61        26.43 
TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GN TCGA-D3-A8GP 
       58.52       241.38       170.20        89.13       161.00       152.75 
TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D9-A148 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 
       29.06       129.63       151.53         3.65         7.10        15.39 
TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW 
       18.44         9.90        66.25        22.95        48.89        36.03 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 
      117.21        20.38       194.83        35.93       107.34        61.18 
TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
       53.92        65.92        23.44        68.09        28.60        10.49 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG 
      215.44        15.68        13.87        10.36        20.35        68.25 
TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X 
       54.02        17.29        52.01         7.04        24.89        29.82 
TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 
       27.22         8.65        33.73        14.70        26.89        68.15 
TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C 
        4.96       151.27       168.26        63.35        85.08        78.97 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M 
       13.97        63.78        72.07        64.64         2.60        56.84 
TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V 
       18.61        66.74        14.47        61.28       369.93        25.87 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 
      195.02        17.92        46.82       102.90        36.82        39.29 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GJ 
       86.14        59.28       340.14       161.03        48.72       107.38 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP 
       54.74        79.66        75.48       102.12       126.81        13.91 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 
       81.21        44.88        94.82        21.67       129.27        28.83 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG 
       19.76        61.51        47.28       103.27       268.73       103.20 
TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP 
       16.96       204.66       216.66       167.90        47.54       248.65 
TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB 
       43.23       134.40        71.21        53.26       124.31       122.73 
TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J4 
       51.62        54.51        13.81        41.59       138.81       127.20 
TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JH 
       36.95        64.08        34.32       201.80        27.35       109.58 
TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 
      152.81        31.40        35.44        13.94        50.76         9.17 
TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G 
       77.75        98.40        12.59        13.02        26.37       268.93 
TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19Q 
      152.35         6.44       131.51        61.05        44.05        50.89 
TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
       37.25         8.88       148.18        79.99        43.82        23.34 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET 
       20.15        16.37        31.27        32.05       247.04        80.32 
TCGA-ER-A3EV TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 
       46.98         6.77        92.98       174.21        15.72       220.80 
TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YX 
       27.85        18.77        38.27        36.26       104.42        48.59 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC 
       20.91        28.08         7.79        27.72        48.85       357.37 
TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ 
       53.52        40.27        15.45         9.70        32.75        47.38 
TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS 
       23.93       101.26        74.73       133.55        11.41       148.80 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 
       53.16        26.56        49.48        27.09        27.02        77.82 
TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB 
       50.14        66.67        28.73       174.84        34.03        26.73 
TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV 
       54.41        80.68         0.20        22.92        55.59        13.51 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 
       19.30         9.90         7.23         2.04        15.78       139.89 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 
       84.72        10.13        62.79        32.48       121.91        39.35 
TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A8LL TCGA-GN-A9SD 
       10.42        48.89        22.13        50.10        21.37        59.41 
TCGA-LH-A9QB TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 
      368.78         7.23        18.05         0.33         0.69       228.16 
TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1V 
       63.02       121.08         4.01        69.07       111.09        42.08 
TCGA-W3-AA1W TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZM 
      219.16        24.03        49.05        61.15        15.98        98.89 
TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-A8ZY 
       58.98        67.63        59.77        11.80        32.58        49.51 
TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YD-A89C TCGA-YD-A9TA TCGA-YG-AA3O 
       35.01        19.73        22.29         6.90        49.18        37.94 
TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
       27.58        96.99        15.98 

  2P LOSS MUTATED 2P LOSS WILD-TYPE 
             0.23              0.20 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
           297.90            369.93 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
           66.655            49.050 
[1] "0.2 - 297.9 (66.7)" "0.2 - 369.9 (49.0)"
[1] "hr=" "1.3"
D44V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  2P LOSS MUTATED                   13             1
  2P LOSS WILD-TYPE                 52             4
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  2P LOSS MUTATED                                           9
  2P LOSS WILD-TYPE                                        63
                   vv
clus                REGIONAL LYMPH NODE
  2P LOSS MUTATED                    27
  2P LOSS WILD-TYPE                 188
D44V4, multiclass
                                           clus
vv                                          2P LOSS MUTATED 2P LOSS WILD-TYPE
  DISTANT METASTASIS                                     13                52
  PRIMARY TUMOR                                           1                 4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               9                63
  REGIONAL LYMPH NODE                                    27               188
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  2P LOSS MUTATED             1       0       5        1        4        4
  2P LOSS WILD-TYPE          11       7      23       17       23       20
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  2P LOSS MUTATED           1         4         2         6          3
  2P LOSS WILD-TYPE        13        15        10        31         12
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  2P LOSS MUTATED            3          5        3
  2P LOSS WILD-TYPE         29         55       17
D44V5, multiclass
             clus
vv            2P LOSS MUTATED 2P LOSS WILD-TYPE
  I OR II NOS               1                11
  STAGE 0                   0                 7
  STAGE I                   5                23
  STAGE IA                  1                17
  STAGE IB                  4                23
  STAGE II                  4                20
  STAGE IIA                 1                13
  STAGE IIB                 4                15
  STAGE IIC                 2                10
  STAGE III                 6                31
  STAGE IIIA                3                12
  STAGE IIIB                3                29
  STAGE IIIC                5                55
  STAGE IV                  3                17
[1] 14  2
[1] TRUE
[1] "dimension of contingency 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       7  8 12 14
  2P LOSS WILD-TYPE    57 64 65 54
D44V6, multiclass
       clus
vv      2P LOSS MUTATED 2P LOSS WILD-TYPE
  T0+T1               7                57
  T2                  8                64
  T3                 12                65
  T4                 14                54
[1] 4 2
[1] TRUE
[1] "dimension of 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    27   8   5   3
  2P LOSS WILD-TYPE 142  55  33  46
D44V7, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  N0              27               142
  N1               8                55
  N2               5                33
  N3               3                46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V8, binary
                   cls
clus                  0   1
  2P LOSS MUTATED    41   3
  2P LOSS WILD-TYPE 272  18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED     41    3
  2P LOSS WILD-TYPE  272   18
   clus
vv  2P LOSS MUTATED 2P LOSS WILD-TYPE
  0              41               272
  1               3                18
[1] 2 2
[1] FALSE
D44V9, binary
                   cls
clus                  0   1
  2P LOSS MUTATED    21  13
  2P LOSS WILD-TYPE 111  75
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED     21   13
  2P LOSS WILD-TYPE  111   75
     clus
vv    2P LOSS MUTATED 2P LOSS WILD-TYPE
  NO               21               111
  YES              13                75
[1] 2 2
[1] FALSE
D44V10, binary
                   cls
clus                  0   1
  2P LOSS MUTATED     3  47
  2P LOSS WILD-TYPE  41 266
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      3   47
  2P LOSS WILD-TYPE   41  266
     clus
vv    2P LOSS MUTATED 2P LOSS WILD-TYPE
  NO                3                41
  YES              47               266
[1] 2 2
[1] FALSE
D44V11, continuous
D44V12, binary
                   cls
clus                  0   1
  2P LOSS MUTATED    20  30
  2P LOSS WILD-TYPE 115 193
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED     20   30
  2P LOSS WILD-TYPE  115  193
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  FEMALE              20               115
  MALE                30               193
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  2P LOSS MUTATED       0                         0    47
  2P LOSS WILD-TYPE     5                         1   297
D44V13, multiclass
                           clus
vv                          2P LOSS MUTATED 2P LOSS WILD-TYPE
  ASIAN                                   0                 5
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  47               297
[1] 3 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     2  46
  2P LOSS WILD-TYPE   5 298
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      2   46
  2P LOSS WILD-TYPE    5  298
                        clus
vv                       2P LOSS MUTATED 2P LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                 5
  NOT HISPANIC OR LATINO              46               298
[1] 2 2
[1] FALSE

Clustering(45) Variable = 2Q LOSS MUTATION ANALYSIS
D45V1, survival
                   sevent
clus2                 0   1
  2Q LOSS MUTATED    10  23
  2Q LOSS WILD-TYPE 111  95
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               33               206 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               23                95 
$`2Q LOSS MUTATED`
TCGA-D3-A2JG TCGA-D3-A3C6 TCGA-D3-A3CF TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51T 
      107.61        58.06        16.96        90.21        23.67        11.34 
TCGA-D3-A8GM TCGA-D9-A1X3 TCGA-EE-A180 TCGA-EE-A20C TCGA-EE-A29D TCGA-EE-A29P 
       70.62        10.78        62.37        75.55        12.99        27.16 
TCGA-EE-A2GH TCGA-EE-A2GR TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2MS TCGA-EE-A3AF 
      189.40         0.20        63.25        67.50       143.93         6.28 
TCGA-EE-A3J3 TCGA-ER-A19C TCGA-ER-A19P TCGA-ER-A2ND TCGA-ER-A3PL TCGA-FR-A8YC 
       67.89        39.81       120.76         4.70        32.05        10.06 
TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1ZQ TCGA-GN-A267 TCGA-OD-A75X 
      171.78        49.74       195.98       130.95        17.06       297.01 
TCGA-W3-A828 TCGA-W3-AA21 TCGA-WE-AA9Y 
      120.07        92.84         1.94 

$`2Q LOSS WILD-TYPE`
TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
       60.46        12.99        14.83         8.42        15.72        31.89 
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB 
      110.93        49.35       133.25        19.04        76.41        62.60 
TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC 
       25.64        45.99        62.86        15.75       168.00        86.30 
TCGA-D3-A2JD TCGA-D3-A2JE TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
        7.27         9.76        36.30       171.58        64.83        66.08 
TCGA-D3-A2JP TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3ML 
       43.53        46.98       140.98        40.01        59.70        13.87 
TCGA-D3-A3MO TCGA-D3-A51E TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A5GL 
        9.34       173.85       144.46        31.76        62.70        42.05 
TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GJ 
       45.70       177.86       124.08        78.21        23.61       179.97 
TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GP TCGA-D3-A8GR TCGA-D9-A3Z1 TCGA-D9-A3Z3 
      120.00        69.53       135.12        36.53        15.02        16.90 
TCGA-D9-A4Z6 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 
       18.44        57.90        22.85        48.66       106.85        31.96 
TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 
      150.61        82.85        32.42        64.83        58.85        25.12 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN 
      214.59        14.96         3.91        33.24        50.07        45.50 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A184 
        6.64        13.15        24.89        20.38         0.00        67.50 
TCGA-EE-A20H TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H 
      155.90        75.22        76.14         0.26        44.28        63.12 
TCGA-EE-A29M TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A2 
       47.74        61.12       346.49       185.19       102.38         7.20 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GJ TCGA-EE-A2GK 
       77.98        26.14       239.11         0.20        68.65        10.62 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GS 
       32.48        18.35        31.00       118.32         0.76        71.31 
TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MF 
       81.99       103.13        15.25         5.75        23.77       209.79 
TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MR 
       94.19       171.85       104.78       145.45       227.01        25.08 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
       23.51        53.26       124.31       122.73        51.62         4.41 
TCGA-EE-A3AE TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JI 
       54.51       111.85        45.90         3.35       201.80       152.81 
TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A 
       14.56        34.45         1.58        47.31         7.82         4.54 
TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M 
       53.29        11.47       151.46       150.12        99.06        59.84 
TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
       42.48        49.71        34.95       146.63        47.97        22.36 
TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-FR-A44A 
       16.87        10.95       173.29        55.82        15.48       174.21 
TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZC 
      209.23        26.20         5.65         8.35        27.62       312.07 
TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM 
       32.78        35.90        12.92         7.82        36.33        78.61 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ 
      136.27        35.28         4.47        23.21         5.29         3.06 
TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TU 
       30.90        66.67       173.19        13.28        80.68        55.59 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 
       11.54        19.30         9.90         6.05         1.91        53.29 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 
      117.93        84.72        42.48         7.59       120.53        34.49 
TCGA-GN-A4U8 TCGA-GN-A8LK TCGA-GN-A9SD TCGA-LH-A9QB TCGA-QB-A6FS TCGA-QB-AA9O 
       46.92        43.23        59.41        85.05         7.23        18.05 
TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1V 
        0.33       174.12         1.97        44.05        79.99         8.09 
TCGA-W3-AA1W TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO 
      185.13         1.15        59.64        62.99        12.69        19.00 
TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 
       59.44        10.95        48.39        26.60        16.64        15.65 
TCGA-YG-AA3O TCGA-Z2-AA3S 
       28.21        91.23 

  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
              0.2               0.0 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
           297.01            346.49 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
            62.37             45.60 
[1] "0.2 - 297.0 (62.4)" "0.0 - 346.5 (45.6)"
[1] "hr=" "1.3"
D45V2, survival
                   sevent
clus2                 0   1
  2Q LOSS MUTATED    20  27
  2Q LOSS WILD-TYPE 149 153
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               47               302 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               27               153 
$`2Q LOSS MUTATED`
TCGA-D3-A2JG TCGA-D3-A3C6 TCGA-D3-A3CF TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51T 
      113.52        58.06        24.53       103.59        39.75        26.89 
TCGA-D3-A8GM TCGA-D3-A8GS TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1X3 TCGA-D9-A6EA 
      107.15       117.17       151.53        54.67        18.12        25.18 
TCGA-EE-A180 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29D 
       94.98       133.81       151.27        91.56        13.55        13.97 
TCGA-EE-A29P TCGA-EE-A2GC TCGA-EE-A2GH TCGA-EE-A2GR TCGA-EE-A2MJ TCGA-EE-A2MK 
       56.42        67.43       208.04        42.77        96.23       158.63 
TCGA-EE-A2MS TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3JA TCGA-EE-A3JE TCGA-ER-A19C 
      162.48        13.81       172.18        53.19        51.35        48.89 
TCGA-ER-A19P TCGA-ER-A2ND TCGA-ER-A3PL TCGA-FR-A8YC TCGA-FS-A1YW TCGA-FS-A1YY 
      162.08        23.34        33.21        34.82       216.92       228.59 
TCGA-FS-A1Z0 TCGA-FS-A1ZQ TCGA-GN-A267 TCGA-GN-A26D TCGA-HR-A2OG TCGA-HR-A2OH 
      202.65       133.55        64.44        39.58         0.23        65.88 
TCGA-OD-A75X TCGA-W3-A828 TCGA-W3-AA21 TCGA-WE-AA9Y TCGA-YG-AA3P 
      297.90       121.08       105.04        12.16        14.43 

$`2Q LOSS WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q3 
       17.03        66.48        12.99        14.93        16.57        16.67 
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 
      112.04       112.57        71.80       133.25        28.08        31.59 
TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 
       90.90        95.74        43.43       103.10        65.49        23.77 
TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JE TCGA-D3-A2JF 
      115.53       168.00        86.76        11.87        27.65        62.07 
TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP 
       42.08        12.10       171.58        66.48        66.08        59.57 
TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE 
      130.72        46.98        46.32       166.52        86.93        60.23 
TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
       13.87         9.34        45.30       174.84        55.73        56.35 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A5GL TCGA-D3-A5GN 
      145.12        32.94        22.62        63.81       125.79       135.75 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GC 
      137.92       178.32        18.18       125.19        30.84        79.59 
TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL 
       23.61        26.43        58.52       241.38       170.20        89.13 
TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D9-A1JW TCGA-D9-A1JX 
      161.00       152.75        29.06       129.63         3.65         7.10 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-D9-A6EG 
       15.39        22.29        18.44         9.90        66.25        22.95 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 
       48.89        36.03       117.21        20.38       194.83       176.55 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB 
       35.93       107.34        61.18        53.92        65.92        23.44 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q 
       68.09        28.60        10.49       215.44        15.68        13.87 
TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN 
       10.36        20.35        68.25        54.02        17.29        52.01 
TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A181 
        7.04        24.89        29.82        27.22         8.65        33.73 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20H TCGA-EE-A29A 
       14.70        26.89        68.15         4.96       168.26        63.35 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L 
       85.08        78.97        63.78        72.07        64.64         2.60 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T 
       56.84        18.61        66.74        14.47        61.28       369.93 
TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
       25.87       195.02        17.92        46.82       102.90        36.82 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GI 
       39.29        86.14        59.28       340.14       161.03        48.72 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO 
      107.38        54.74        79.66        75.48       102.12       126.81 
TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 
       13.91        81.21        44.88        94.82        21.67       129.27 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF 
       28.83        19.76        61.51        47.28       103.27       268.73 
TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN 
      103.20        16.96       204.66       216.66       167.90        47.54 
TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA 
      248.65        43.23       134.40        71.21        53.26       124.31 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AG TCGA-EE-A3AH 
      122.73        51.62        28.77        54.51        41.59       138.81 
TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JD 
      127.20        36.95        64.08        34.32       201.80        27.35 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
      109.58       152.81        31.40        35.44        13.94        50.76 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F 
        9.17        77.75        98.40        12.59        13.02        26.37 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
      268.93       152.35         6.44       131.51        61.05        44.05 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
       50.89        37.25         8.88       148.18        79.99        43.82 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET 
       20.15        16.37        31.27        32.05       247.04        80.32 
TCGA-ER-A3EV TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 
       46.98         6.77        92.98       174.21        15.72       220.80 
TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YX 
       27.85        18.77        38.27        36.26       104.42        48.59 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC 
       20.91        28.08         7.79        27.72        48.85       357.37 
TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ 
       53.52        40.27        15.45         9.70        32.75        47.38 
TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT 
       23.93       101.26        74.73        11.41       148.80        53.16 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 
       26.56        49.48        27.09        27.02        77.82        50.14 
TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC 
       66.67        28.73       174.84        34.03        26.73        54.41 
TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
       80.68         0.20        22.92        55.59        13.51        19.30 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 
        9.90         7.23         2.04        15.78       139.89       117.93 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 
       84.72        10.13        62.79        32.48       121.91        39.35 
TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A8LL TCGA-GN-A9SD 
       10.42        48.89        22.13        50.10        21.37        59.41 
TCGA-LH-A9QB TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 
      368.78         7.23        18.05         0.33         0.69       228.16 
TCGA-W3-A825 TCGA-W3-AA1O TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1V TCGA-W3-AA1W 
       63.02         4.01        69.07       111.09        42.08       219.16 
TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN 
       24.03        49.05        61.15        15.98        98.89        58.98 
TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AAA0 
       67.63        59.77        11.80        32.58        49.51        35.01 
TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YD-A89C TCGA-YD-A9TA TCGA-YG-AA3O TCGA-Z2-A8RT 
       19.73        22.29         6.90        49.18        37.94        27.58 
TCGA-Z2-AA3S TCGA-Z2-AA3V 
       96.99        15.98 

  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
             0.23              0.20 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
           297.90            369.93 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
           65.880            49.115 
[1] "0.2 - 297.9 (65.9)" "0.2 - 369.9 (49.1)"
[1] "hr=" "1.1"
D45V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  2Q LOSS MUTATED                   16             1
  2Q LOSS WILD-TYPE                 49             4
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  2Q LOSS MUTATED                                           9
  2Q LOSS WILD-TYPE                                        63
                   vv
clus                REGIONAL LYMPH NODE
  2Q LOSS MUTATED                    25
  2Q LOSS WILD-TYPE                 190
D45V4, multiclass
                                           clus
vv                                          2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  DISTANT METASTASIS                                     16                49
  PRIMARY TUMOR                                           1                 4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               9                63
  REGIONAL LYMPH NODE                                    25               190
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  2Q LOSS MUTATED             2       1       5        1        4        4
  2Q LOSS WILD-TYPE          10       6      23       17       23       20
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  2Q LOSS MUTATED           1         4         2         4          3
  2Q LOSS WILD-TYPE        13        15        10        33         12
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  2Q LOSS MUTATED            2          7        3
  2Q LOSS WILD-TYPE         30         53       17
D45V5, multiclass
             clus
vv            2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  I OR II NOS               2                10
  STAGE 0                   1                 6
  STAGE I                   5                23
  STAGE IA                  1                17
  STAGE IB                  4                23
  STAGE II                  4                20
  STAGE IIA                 1                13
  STAGE IIB                 4                15
  STAGE IIC                 2                10
  STAGE III                 4                33
  STAGE IIIA                3                12
  STAGE IIIB                2                30
  STAGE IIIC                7                53
  STAGE IV                  3                17
[1] 14  2
[1] TRUE
[1] "dimension of contingency 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       7  8 13 12
  2Q LOSS WILD-TYPE    57 64 64 56
D45V6, multiclass
       clus
vv      2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  T0+T1               7                57
  T2                  8                64
  T3                 13                64
  T4                 12                56
[1] 4 2
[1] TRUE
[1] "dimension of 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    29   7   3   6
  2Q LOSS WILD-TYPE 140  56  35  43
D45V7, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  N0              29               140
  N1               7                56
  N2               3                35
  N3               6                43
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V8, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED    42   4
  2Q LOSS WILD-TYPE 271  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED     42    4
  2Q LOSS WILD-TYPE  271   17
   clus
vv  2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  0              42               271
  1               4                17
[1] 2 2
[1] FALSE
D45V9, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED    21  13
  2Q LOSS WILD-TYPE 111  75
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED     21   13
  2Q LOSS WILD-TYPE  111   75
     clus
vv    2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  NO               21               111
  YES              13                75
[1] 2 2
[1] FALSE
D45V10, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED     2  49
  2Q LOSS WILD-TYPE  42 264
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      2   49
  2Q LOSS WILD-TYPE   42  264
     clus
vv    2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  NO                2                42
  YES              49               264
[1] 2 2
[1] FALSE
D45V11, continuous
D45V12, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED    20  31
  2Q LOSS WILD-TYPE 115 192
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED     20   31
  2Q LOSS WILD-TYPE  115  192
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  FEMALE              20               115
  MALE                31               192
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  2Q LOSS MUTATED       0                         0    48
  2Q LOSS WILD-TYPE     5                         1   296
D45V13, multiclass
                           clus
vv                          2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  ASIAN                                   0                 5
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  48               296
[1] 3 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     2  47
  2Q LOSS WILD-TYPE   5 297
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      2   47
  2Q LOSS WILD-TYPE    5  297
                        clus
vv                       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                 5
  NOT HISPANIC OR LATINO              47               297
[1] 2 2
[1] FALSE

Clustering(46) Variable = 3P LOSS MUTATION ANALYSIS
D46V1, survival
                   sevent
clus2                0  1
  3P LOSS MUTATED   23 24
  3P LOSS WILD-TYPE 98 94
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               47               192 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               24                94 
$`3P LOSS MUTATED`
TCGA-BF-AAP0 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A2J7 TCGA-D3-A2JA 
       14.83        31.89       110.93       133.25        45.99        15.75 
TCGA-D3-A2JG TCGA-D3-A2JN TCGA-D3-A3C6 TCGA-D3-A5GU TCGA-D3-A8GP TCGA-D9-A1X3 
      107.61        64.83        58.06       124.08       135.12        10.78 
TCGA-D9-A4Z6 TCGA-DA-A1HV TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-EE-A17Y 
       18.44        48.66       150.61        82.85        32.42        24.89 
TCGA-EE-A20C TCGA-EE-A29G TCGA-EE-A29P TCGA-EE-A2GH TCGA-EE-A2M6 TCGA-EE-A2MF 
       75.55        44.28        27.16       189.40       103.13       209.79 
TCGA-EE-A3AA TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-EE-A3JB TCGA-ER-A195 TCGA-ER-A197 
      124.31        67.89        45.90       201.80        34.45         1.58 
TCGA-ER-A19H TCGA-ER-A19S TCGA-ER-A2ND TCGA-ER-A2NG TCGA-FR-A8YC TCGA-FS-A1ZM 
      150.12        34.95         4.70        10.95        10.06        78.61 
TCGA-FS-A1ZQ TCGA-FS-A4F8 TCGA-FS-A4FD TCGA-FW-A3TU TCGA-GF-A6C8 TCGA-GN-A262 
      130.95       173.19        80.68        55.59         1.91        53.29 
TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 TCGA-WE-AAA4 TCGA-Z2-AA3S 
      117.93        17.06        42.48        15.65        91.23 

$`3P LOSS WILD-TYPE`
TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q6 TCGA-D3-A1Q8 
       60.46        12.99         8.42        15.72        49.35        19.04 
TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J8 TCGA-D3-A2JB TCGA-D3-A2JC 
       76.41        62.60        25.64        62.86       168.00        86.30 
TCGA-D3-A2JD TCGA-D3-A2JE TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JO TCGA-D3-A2JP 
        7.27         9.76        36.30       171.58        66.08        43.53 
TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML 
       46.98       140.98        40.01        59.70        16.96        13.87 
TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51J TCGA-D3-A51K 
        9.34        90.21        23.67       173.85       144.46        31.76 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A8GC 
       62.70        11.34        42.05        45.70       177.86        78.21 
TCGA-D3-A8GD TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GR 
       23.61       179.97       120.00        69.53        70.62        36.53 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HY TCGA-DA-A1I1 
       15.02        16.90        57.90        22.85       106.85        31.96 
TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q 
       64.83        58.85        25.12       214.59        14.96         3.91 
TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A180 
       33.24        50.07        45.50         6.64        13.15        62.37 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A184 TCGA-EE-A20H TCGA-EE-A29B TCGA-EE-A29C 
       20.38         0.00        67.50       155.90        75.22        76.14 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29Q TCGA-EE-A29T 
       12.99         0.26        63.12        47.74        61.12       346.49 
TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD 
      185.19       102.38         7.20        77.98        26.14       239.11 
TCGA-EE-A2GE TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN 
        0.20        68.65        10.62        32.48        18.35        31.00 
TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M7 
      118.32         0.76         0.20        71.31        81.99        15.25 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK 
        5.75        23.77        94.19       171.85        63.25        67.50 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT 
      104.78       145.45       227.01        25.08       143.93        23.51 
TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
       53.26       122.73        51.62         4.41        54.51         6.28 
TCGA-EE-A3J4 TCGA-EE-A3J8 TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A198 TCGA-ER-A199 
      111.85         3.35       152.81        14.56        47.31         7.82 
TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19L 
        4.54        53.29        39.81        11.47       151.46        99.06 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19W TCGA-ER-A1A1 
       59.84        42.48       120.76        49.71       146.63        47.97 
TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL 
       22.36        16.87       173.29        55.82        15.48        32.05 
TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FS-A1YW TCGA-FS-A1YY 
      174.21       209.23        26.20         5.65       171.78        49.74 
TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE 
      195.98         8.35        27.62       312.07        32.78        35.90 
TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU 
       12.92         7.82        36.33       136.27        35.28         4.47 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F9 
       23.21         5.29         3.06        30.90        66.67        13.28 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GN-A265 TCGA-GN-A26A 
       11.54        19.30         9.90         6.05        84.72         7.59 
TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-GN-A8LK TCGA-GN-A9SD TCGA-LH-A9QB 
      120.53        34.49        46.92        43.23        59.41        85.05 
TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A825 
      297.01         7.23        18.05         0.33       174.12         1.97 
TCGA-W3-A828 TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 
      120.07        44.05        79.99         8.09       185.13        92.84 
TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ 
        1.15        59.64        62.99        12.69        19.00        59.44 
TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-YG-AA3O 
       10.95        48.39         1.94        26.60        16.64        28.21 

  3P LOSS MUTATED 3P LOSS WILD-TYPE 
             1.58              0.00 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
           209.79            346.49 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
            55.59             43.79 
[1] "1.6 - 209.8 (55.6)" "0.0 - 346.5 (43.8)"
[1] "hr=" "1.1"
D46V2, survival
                   sevent
clus2                 0   1
  3P LOSS MUTATED    29  29
  3P LOSS WILD-TYPE 140 151
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               58               291 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               29               151 
$`3P LOSS MUTATED`
TCGA-BF-AAP0 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A2J7 TCGA-D3-A2JA 
       14.93       112.04       112.57       133.25       103.10       115.53 
TCGA-D3-A2JG TCGA-D3-A2JN TCGA-D3-A3C6 TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GP 
      113.52        66.48        58.06       125.19        30.84       152.75 
TCGA-D9-A1X3 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-DA-A1HV TCGA-DA-A1HW 
       18.12        18.44         9.90        25.18        48.89        36.03 
TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-EE-A17Y TCGA-EE-A20C TCGA-EE-A29G 
      176.55       107.34        61.18        27.22       151.27        72.07 
TCGA-EE-A29P TCGA-EE-A2GC TCGA-EE-A2GH TCGA-EE-A2M6 TCGA-EE-A2MF TCGA-EE-A3AA 
       56.42        67.43       208.04       129.27       268.73       124.31 
TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-EE-A3JB TCGA-ER-A195 TCGA-ER-A197 
       41.59       172.18        64.08       201.80        35.44        13.94 
TCGA-ER-A19H TCGA-ER-A19S TCGA-ER-A2ND TCGA-ER-A2NG TCGA-FR-A7U9 TCGA-FR-A8YC 
      152.35        37.25        23.34        31.27        18.77        34.82 
TCGA-FS-A1YX TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A4F8 TCGA-FS-A4FD TCGA-FW-A3TU 
       48.59       101.26       133.55       174.84        80.68        55.59 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A4U9 
        2.04       139.89       117.93        64.44        62.79        22.13 
TCGA-WE-A8ZX TCGA-WE-AAA4 TCGA-YG-AA3P TCGA-Z2-AA3S 
       32.58        22.29        14.43        96.99 

$`3P LOSS WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q6 
       17.03        66.48        12.99        16.57        16.67        71.80 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J8 
       28.08        31.59        90.90        95.74        43.43        65.49 
TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JE TCGA-D3-A2JF 
       23.77       168.00        86.76        11.87        27.65        62.07 
TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ 
       42.08        12.10       171.58        66.08        59.57       130.72 
TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF 
       46.98        46.32       166.52        86.93        60.23        24.53 
TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E 
       13.87         9.34       103.59        39.75        45.30       174.84 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R 
       55.73        56.35       145.12        32.94        22.62        63.81 
TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       26.89       125.79       135.75       137.92       178.32        18.18 
TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GK 
       79.59        23.61        26.43        58.52       241.38       170.20 
TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS 
       89.13       107.15       161.00        29.06       129.63       117.17 
TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 
      151.53        54.67         3.65         7.10        15.39        22.29 
TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I4 
       66.25        22.95       117.21        20.38       194.83        35.93 
TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
       53.92        65.92        23.44        68.09        28.60        10.49 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG 
      215.44        15.68        13.87        10.36        20.35        68.25 
TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X 
       54.02        17.29        52.01         7.04        24.89        29.82 
TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 
        8.65        94.98        33.73        14.70        26.89        68.15 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A 
        4.96       133.81        91.56       168.26        13.55        63.35 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L 
       85.08        78.97        13.97        63.78        64.64         2.60 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T 
       56.84        18.61        66.74        14.47        61.28       369.93 
TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
       25.87       195.02        17.92        46.82       102.90        36.82 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GI 
       39.29        86.14        59.28       340.14       161.03        48.72 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO 
      107.38        54.74        79.66        75.48       102.12       126.81 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 
       13.91        42.77        81.21        44.88        94.82        21.67 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG 
       28.83        19.76        61.51        47.28       103.27       103.20 
TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM 
       16.96       204.66        96.23       158.63       216.66       167.90 
TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT 
       47.54       248.65        43.23       134.40       162.48        71.21 
TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
       53.26       122.73        51.62        28.77        54.51        13.81 
TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD 
      138.81       127.20        36.95        34.32        53.19        27.35 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A198 TCGA-ER-A199 
       51.35       109.58       152.81        31.40        50.76         9.17 
TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F 
       77.75        98.40        48.89        12.59        13.02        26.37 
TCGA-ER-A19G TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P 
      268.93         6.44       131.51        61.05        44.05       162.08 
TCGA-ER-A19Q TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE 
       50.89         8.88       148.18        79.99        43.82        20.15 
TCGA-ER-A2NF TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL 
       16.37        32.05       247.04        80.32        46.98        33.21 
TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 
        6.77        92.98       174.21        15.72       220.80        27.85 
TCGA-FR-A7UA TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 
       38.27        36.26       104.42       216.92       228.59       202.65 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC 
       20.91        28.08         7.79        27.72        48.85       357.37 
TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ 
       53.52        40.27        15.45         9.70        32.75        47.38 
TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU 
       23.93        74.73        11.41       148.80        53.16        26.56 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 
       49.48        27.09        27.02        77.82        50.14        66.67 
TCGA-FS-A4F5 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FW-A3I3 TCGA-FW-A3R5 
       28.73        34.03        26.73        54.41         0.20        22.92 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C9 TCGA-GN-A265 
       13.51        19.30         9.90         7.23        15.78        84.72 
TCGA-GN-A266 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 
       10.13        32.48        39.58       121.91        39.35        10.42 
TCGA-GN-A4U8 TCGA-GN-A8LK TCGA-GN-A8LL TCGA-GN-A9SD TCGA-HR-A2OG TCGA-HR-A2OH 
       48.89        50.10        21.37        59.41         0.23        65.88 
TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 TCGA-RP-A694 
      368.78       297.90         7.23        18.05         0.33         0.69 
TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1Q TCGA-W3-AA1R 
      228.16        63.02       121.08         4.01        69.07       111.09 
TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K5 
       42.08       219.16       105.04        24.03        49.05        61.15 
TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT 
       15.98        98.89        58.98        67.63        59.77        11.80 
TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-YD-A89C TCGA-YD-A9TA 
       49.51        12.16        35.01        19.73         6.90        49.18 
TCGA-YG-AA3O TCGA-Z2-A8RT TCGA-Z2-AA3V 
       37.94        27.58        15.98 

  3P LOSS MUTATED 3P LOSS WILD-TYPE 
             2.04              0.20 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
           268.73            369.93 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
            64.26             49.18 
[1] "2.0 - 268.7 (64.3)" "0.2 - 369.9 (49.2)"
[1] "hr=" "1.2"
D46V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  3P LOSS MUTATED                   10             2
  3P LOSS WILD-TYPE                 55             3
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  3P LOSS MUTATED                                          14
  3P LOSS WILD-TYPE                                        58
                   vv
clus                REGIONAL LYMPH NODE
  3P LOSS MUTATED                    33
  3P LOSS WILD-TYPE                 182
D46V4, multiclass
                                           clus
vv                                          3P LOSS MUTATED 3P LOSS WILD-TYPE
  DISTANT METASTASIS                                     10                55
  PRIMARY TUMOR                                           2                 3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE              14                58
  REGIONAL LYMPH NODE                                    33               182
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  3P LOSS MUTATED             2       1       6        1        4        0
  3P LOSS WILD-TYPE          10       6      22       17       23       24
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  3P LOSS MUTATED           0         5         1         6          5
  3P LOSS WILD-TYPE        14        14        11        31         10
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  3P LOSS MUTATED            7         11        2
  3P LOSS WILD-TYPE         25         49       18
D46V5, multiclass
             clus
vv            3P LOSS MUTATED 3P LOSS WILD-TYPE
  I OR II NOS               2                10
  STAGE 0                   1                 6
  STAGE I                   6                22
  STAGE IA                  1                17
  STAGE IB                  4                23
  STAGE II                  0                24
  STAGE IIA                 0                14
  STAGE IIB                 5                14
  STAGE IIC                 1                11
  STAGE III                 6                31
  STAGE IIIA                5                10
  STAGE IIIB                7                25
  STAGE IIIC               11                49
  STAGE IV                  2                18
[1] 14  2
[1] TRUE
[1] "dimension of contingency 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      13 12 12 10
  3P LOSS WILD-TYPE    51 60 65 58
D46V6, multiclass
       clus
vv      3P LOSS MUTATED 3P LOSS WILD-TYPE
  T0+T1              13                51
  T2                 12                60
  T3                 12                65
  T4                 10                58
[1] 4 2
[1] TRUE
[1] "dimension of 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    22  14   9   7
  3P LOSS WILD-TYPE 147  49  29  42
D46V7, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  N0              22               147
  N1              14                49
  N2               9                29
  N3               7                42
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V8, binary
                   cls
clus                  0   1
  3P LOSS MUTATED    51   2
  3P LOSS WILD-TYPE 262  19
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     51    2
  3P LOSS WILD-TYPE  262   19
   clus
vv  3P LOSS MUTATED 3P LOSS WILD-TYPE
  0              51               262
  1               2                19
[1] 2 2
[1] FALSE
D46V9, binary
                   cls
clus                  0   1
  3P LOSS MUTATED    20  14
  3P LOSS WILD-TYPE 112  74
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     20   14
  3P LOSS WILD-TYPE  112   74
     clus
vv    3P LOSS MUTATED 3P LOSS WILD-TYPE
  NO               20               112
  YES              14                74
[1] 2 2
[1] FALSE
D46V10, binary
                   cls
clus                  0   1
  3P LOSS MUTATED     7  53
  3P LOSS WILD-TYPE  37 260
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      7   53
  3P LOSS WILD-TYPE   37  260
     clus
vv    3P LOSS MUTATED 3P LOSS WILD-TYPE
  NO                7                37
  YES              53               260
[1] 2 2
[1] FALSE
D46V11, continuous
D46V12, binary
                   cls
clus                  0   1
  3P LOSS MUTATED    27  33
  3P LOSS WILD-TYPE 108 190
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     27   33
  3P LOSS WILD-TYPE  108  190
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  FEMALE              27               108
  MALE                33               190
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3P LOSS MUTATED       1                         0    58
  3P LOSS WILD-TYPE     4                         1   286
D46V13, multiclass
                           clus
vv                          3P LOSS MUTATED 3P LOSS WILD-TYPE
  ASIAN                                   1                 4
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  58               286
[1] 3 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     1  58
  3P LOSS WILD-TYPE   6 286
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      1   58
  3P LOSS WILD-TYPE    6  286
                        clus
vv                       3P LOSS MUTATED 3P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 6
  NOT HISPANIC OR LATINO              58               286
[1] 2 2
[1] FALSE

Clustering(47) Variable = 3Q LOSS MUTATION ANALYSIS
D47V1, survival
                   sevent
clus2                 0   1
  3Q LOSS MUTATED    16  23
  3Q LOSS WILD-TYPE 105  95
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               39               200 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               23                95 
$`3Q LOSS MUTATED`
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A2JG TCGA-D3-A3C6 TCGA-D3-A5GU 
       31.89       110.93       133.25       107.61        58.06       124.08 
TCGA-D3-A8GP TCGA-D3-A8GR TCGA-D9-A1X3 TCGA-D9-A4Z6 TCGA-DA-A1HV TCGA-DA-A1I2 
      135.12        36.53        10.78        18.44        48.66       150.61 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-EE-A17Y TCGA-EE-A20C TCGA-EE-A29G TCGA-EE-A29H 
       82.85        32.42        24.89        75.55        44.28        63.12 
TCGA-EE-A29P TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A3J3 TCGA-EE-A3JI TCGA-ER-A195 
       27.16       189.40        68.65        67.89       152.81        34.45 
TCGA-ER-A197 TCGA-ER-A19H TCGA-ER-A19S TCGA-FR-A8YC TCGA-FS-A1ZM TCGA-FS-A1ZQ 
        1.58       150.12        34.95        10.06        78.61       130.95 
TCGA-FS-A4F8 TCGA-FS-A4FD TCGA-FW-A3TU TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A267 
      173.19        80.68        55.59        53.29       117.93        17.06 
TCGA-GN-A268 TCGA-WE-AAA4 TCGA-Z2-AA3S 
       42.48        15.65        91.23 

$`3Q LOSS WILD-TYPE`
TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q6 
       60.46        12.99        14.83         8.42        15.72        49.35 
TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 
       19.04        76.41        62.60        25.64        45.99        62.86 
TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JE TCGA-D3-A2JH 
       15.75       168.00        86.30         7.27         9.76        36.30 
TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C7 TCGA-D3-A3CB 
      171.58        64.83        66.08        43.53        46.98       140.98 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR 
       40.01        59.70        16.96        13.87         9.34        90.21 
TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T 
       23.67       173.85       144.46        31.76        62.70        11.34 
TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GJ 
       42.05        45.70       177.86        78.21        23.61       179.97 
TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6EC 
      120.00        69.53        70.62        15.02        16.90        57.90 
TCGA-D9-A6EG TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 
       22.85       106.85        31.96        64.83        58.85        25.12 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN 
      214.59        14.96         3.91        33.24        50.07        45.50 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A184 
        6.64        13.15        62.37        20.38         0.00        67.50 
TCGA-EE-A20H TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29M 
      155.90        75.22        76.14        12.99         0.26        47.74 
TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 
       61.12       346.49       185.19       102.38         7.20        77.98 
TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
       26.14       239.11         0.20        10.62        32.48        18.35 
TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU 
       31.00       118.32         0.76         0.20        71.31        81.99 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MG 
      103.13        15.25         5.75        23.77       209.79        94.19 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP 
      171.85        63.25        67.50       104.78       145.45       227.01 
TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB 
       25.08       143.93        23.51        53.26       124.31       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J4 TCGA-EE-A3J7 
       51.62         4.41        54.51         6.28       111.85        45.90 
TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-ER-A193 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A 
        3.35       201.80        14.56        47.31         7.82         4.54 
TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19L TCGA-ER-A19M 
       53.29        39.81        11.47       151.46        99.06        59.84 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
       42.48       120.76        49.71       146.63        47.97        22.36 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
        4.70        16.87        10.95       173.29        55.82        15.48 
TCGA-ER-A3PL TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FS-A1YW 
       32.05       174.21       209.23        26.20         5.65       171.78 
TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD 
       49.74       195.98         8.35        27.62       312.07        32.78 
TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZS TCGA-FS-A1ZT 
       35.90        12.92         7.82        36.33       136.27        35.28 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 
        4.47        23.21         5.29         3.06        30.90        66.67 
TCGA-FS-A4F9 TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 
       13.28        11.54        19.30         9.90         6.05         1.91 
TCGA-GN-A265 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-GN-A8LK 
       84.72         7.59       120.53        34.49        46.92        43.23 
TCGA-GN-A9SD TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 
       59.41        85.05       297.01         7.23        18.05         0.33 
TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1V 
      174.12         1.97       120.07        44.05        79.99         8.09 
TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8ZM TCGA-WE-A8ZN 
      185.13        92.84         1.15        59.64        62.99        12.69 
TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 
       19.00        59.44        10.95        48.39         1.94        26.60 
TCGA-WE-AAA3 TCGA-YG-AA3O 
       16.64        28.21 

  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
             1.58              0.00 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
           189.40            346.49 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
            63.12             43.79 
[1] "1.6 - 189.4 (63.1)" "0.0 - 346.5 (43.8)"
[1] "hr=" "1.1"
D47V2, survival
                   sevent
clus2                 0   1
  3Q LOSS MUTATED    22  28
  3Q LOSS WILD-TYPE 147 152
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               50               299 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               28               152 
$`3Q LOSS MUTATED`
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A2JG TCGA-D3-A3C6 TCGA-D3-A5GU 
      112.04       112.57       133.25       113.52        58.06       125.19 
TCGA-D3-A8GP TCGA-D3-A8GR TCGA-D9-A1X3 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EA 
      152.75       129.63        18.12        18.44         9.90        25.18 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-EE-A17Y 
       48.89        36.03       176.55       107.34        61.18        27.22 
TCGA-EE-A20C TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29P TCGA-EE-A2GC TCGA-EE-A2GH 
      151.27        72.07        64.64        56.42        67.43       208.04 
TCGA-EE-A2GJ TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 
      107.38        41.59       172.18       152.81        35.44        13.94 
TCGA-ER-A19H TCGA-ER-A19S TCGA-FR-A7U9 TCGA-FR-A8YC TCGA-FS-A1YX TCGA-FS-A1ZM 
      152.35        37.25        18.77        34.82        48.59       101.26 
TCGA-FS-A1ZQ TCGA-FS-A4F8 TCGA-FS-A4FD TCGA-FW-A3TU TCGA-GN-A262 TCGA-GN-A264 
      133.55       174.84        80.68        55.59       139.89       117.93 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A4U9 TCGA-GN-A8LL TCGA-WE-A8ZX TCGA-WE-AAA4 
       64.44        62.79        22.13        21.37        32.58        22.29 
TCGA-YG-AA3P TCGA-Z2-AA3S 
       14.43        96.99 

$`3Q LOSS WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q3 
       17.03        66.48        12.99        14.93        16.57        16.67 
TCGA-D3-A1Q6 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 
       71.80        28.08        31.59        90.90        95.74        43.43 
TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC 
      103.10        65.49        23.77       115.53       168.00        86.76 
TCGA-D3-A2JD TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL 
       11.87        27.65        62.07        42.08        12.10       171.58 
TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3C8 
       66.48        66.08        59.57       130.72        46.98        46.32 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO 
      166.52        86.93        60.23        24.53        13.87         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
      103.59        39.75        45.30       174.84        55.73        56.35 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL 
      145.12        32.94        22.62        63.81        26.89       125.79 
TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A8GB TCGA-D3-A8GC 
      135.75       137.92       178.32        18.18        30.84        79.59 
TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL 
       23.61        26.43        58.52       241.38       170.20        89.13 
TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GQ TCGA-D3-A8GS TCGA-D9-A148 TCGA-D9-A149 
      107.15       161.00        29.06       117.17       151.53        54.67 
TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6EC TCGA-D9-A6EG 
        3.65         7.10        15.39        22.29        66.25        22.95 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I4 TCGA-DA-A1I8 TCGA-DA-A1IA 
      117.21        20.38       194.83        35.93        53.92        65.92 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 
       23.44        68.09        28.60        10.49       215.44        15.68 
TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL 
       13.87        10.36        20.35        68.25        54.02        17.29 
TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A180 
       52.01         7.04        24.89        29.82         8.65        94.98 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B 
       33.73        14.70        26.89        68.15         4.96       133.81 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C 
       91.56       168.26        13.55        63.35        85.08        78.97 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29Q 
       13.97        63.78         2.60        56.84        18.61        66.74 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X 
       14.47        61.28       369.93        25.87       195.02        17.92 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
       46.82       102.90        36.82        39.29        86.14        59.28 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
      340.14       161.03        48.72        54.74        79.66        75.48 
TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT 
      102.12       126.81        13.91        42.77        81.21        44.88 
TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC 
       94.82        21.67       129.27        28.83        19.76        61.51 
TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
       47.28       103.27       268.73       103.20        16.96       204.66 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP 
       96.23       158.63       216.66       167.90        47.54       248.65 
TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA 
       43.23       134.40       162.48        71.21        53.26       124.31 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AH 
      122.73        51.62        28.77        54.51        13.81       138.81 
TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB 
      127.20        36.95        64.08        34.32        53.19       201.80 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A198 TCGA-ER-A199 
       27.35        51.35       109.58        31.40        50.76         9.17 
TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F 
       77.75        98.40        48.89        12.59        13.02        26.37 
TCGA-ER-A19G TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P 
      268.93         6.44       131.51        61.05        44.05       162.08 
TCGA-ER-A19Q TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
       50.89         8.88       148.18        79.99        43.82        23.34 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET 
       20.15        16.37        31.27        32.05       247.04        80.32 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       46.98        33.21         6.77        92.98       174.21        15.72 
TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW 
      220.80        27.85        38.27        36.26       104.42       216.92 
TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA 
      228.59       202.65        20.91        28.08         7.79        27.72 
TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG 
       48.85       357.37        53.52        40.27        15.45         9.70 
TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZS 
       32.75        47.38        23.93        74.73        11.41       148.80 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 
       53.16        26.56        49.48        27.09        27.02        77.82 
TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC 
       50.14        66.67        28.73        34.03        26.73        54.41 
TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
        0.20        22.92        13.51        19.30         9.90         7.23 
TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A26A TCGA-GN-A26D 
        2.04        15.78        84.72        10.13        32.48        39.58 
TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A8LK TCGA-GN-A9SD 
      121.91        39.35        10.42        48.89        50.10        59.41 
TCGA-HR-A2OG TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O 
        0.23        65.88       368.78       297.90         7.23        18.05 
TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O 
        0.33         0.69       228.16        63.02       121.08         4.01 
TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8JZ 
       69.07       111.09        42.08       219.16       105.04        24.03 
TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO 
       49.05        61.15        15.98        98.89        58.98        67.63 
TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 
       59.77        11.80        49.51        12.16        35.01        19.73 
TCGA-YD-A89C TCGA-YD-A9TA TCGA-YG-AA3O TCGA-Z2-A8RT TCGA-Z2-AA3V 
        6.90        49.18        37.94        27.58        15.98 

  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
              9.9               0.2 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
           208.04            369.93 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
            64.54             49.18 
[1] "9.9 - 208.0 (64.5)" "0.2 - 369.9 (49.2)"
[1] "hr=" "1.1"
D47V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  3Q LOSS MUTATED                    9             2
  3Q LOSS WILD-TYPE                 56             3
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  3Q LOSS MUTATED                                          11
  3Q LOSS WILD-TYPE                                        61
                   vv
clus                REGIONAL LYMPH NODE
  3Q LOSS MUTATED                    28
  3Q LOSS WILD-TYPE                 187
D47V4, multiclass
                                           clus
vv                                          3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  DISTANT METASTASIS                                      9                56
  PRIMARY TUMOR                                           2                 3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE              11                61
  REGIONAL LYMPH NODE                                    28               187
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  3Q LOSS MUTATED             2       2       4        3        4        0
  3Q LOSS WILD-TYPE          10       5      24       15       23       24
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  3Q LOSS MUTATED           0         4         2         3          4
  3Q LOSS WILD-TYPE        14        15        10        34         11
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  3Q LOSS MUTATED            6          8        1
  3Q LOSS WILD-TYPE         26         52       19
D47V5, multiclass
             clus
vv            3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  I OR II NOS               2                10
  STAGE 0                   2                 5
  STAGE I                   4                24
  STAGE IA                  3                15
  STAGE IB                  4                23
  STAGE II                  0                24
  STAGE IIA                 0                14
  STAGE IIB                 4                15
  STAGE IIC                 2                10
  STAGE III                 3                34
  STAGE IIIA                4                11
  STAGE IIIB                6                26
  STAGE IIIC                8                52
  STAGE IV                  1                19
[1] 14  2
[1] TRUE
[1] "dimension of contingency 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      11 10  7 10
  3Q LOSS WILD-TYPE    53 62 70 58
D47V6, multiclass
       clus
vv      3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  T0+T1              11                53
  T2                 10                62
  T3                  7                70
  T4                 10                58
[1] 4 2
[1] TRUE
[1] "dimension of 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    23   9   8   5
  3Q LOSS WILD-TYPE 146  54  30  44
D47V7, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  N0              23               146
  N1               9                54
  N2               8                30
  N3               5                44
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V8, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED    44   1
  3Q LOSS WILD-TYPE 269  20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED     44    1
  3Q LOSS WILD-TYPE  269   20
   clus
vv  3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  0              44               269
  1               1                20
[1] 2 2
[1] FALSE
D47V9, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED    18  11
  3Q LOSS WILD-TYPE 114  77
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED     18   11
  3Q LOSS WILD-TYPE  114   77
     clus
vv    3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  NO               18               114
  YES              11                77
[1] 2 2
[1] FALSE
D47V10, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED     5  46
  3Q LOSS WILD-TYPE  39 267
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      5   46
  3Q LOSS WILD-TYPE   39  267
     clus
vv    3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  NO                5                39
  YES              46               267
[1] 2 2
[1] FALSE
D47V11, continuous
D47V12, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED    22  29
  3Q LOSS WILD-TYPE 113 194
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED     22   29
  3Q LOSS WILD-TYPE  113  194
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  FEMALE              22               113
  MALE                29               194
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3Q LOSS MUTATED       1                         0    49
  3Q LOSS WILD-TYPE     4                         1   295
D47V13, multiclass
                           clus
vv                          3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  ASIAN                                   1                 4
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  49               295
[1] 3 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  49
  3Q LOSS WILD-TYPE   6 295
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      1   49
  3Q LOSS WILD-TYPE    6  295
                        clus
vv                       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 6
  NOT HISPANIC OR LATINO              49               295
[1] 2 2
[1] FALSE

Clustering(48) Variable = 4P LOSS MUTATION ANALYSIS
D48V1, survival
                   sevent
clus2                0  1
  4P LOSS MUTATED   23 27
  4P LOSS WILD-TYPE 98 91
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               50               189 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               27                91 
$`4P LOSS MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A2J6 TCGA-D3-A2JA TCGA-D3-A2JN TCGA-D3-A2JO 
        8.42        31.89        25.64        15.75        64.83        66.08 
TCGA-D3-A3CC TCGA-D3-A3MR TCGA-D3-A8GC TCGA-D3-A8GM TCGA-D9-A3Z3 TCGA-D9-A4Z6 
       40.01        90.21        78.21        70.62        16.90        18.44 
TCGA-D9-A6EC TCGA-DA-A3F8 TCGA-EE-A180 TCGA-EE-A20C TCGA-EE-A29B TCGA-EE-A29C 
       57.90        14.96        62.37        75.55        75.22        76.14 
TCGA-EE-A29D TCGA-EE-A29M TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2GH TCGA-EE-A2GM 
       12.99        47.74       346.49       185.19       189.40        18.35 
TCGA-EE-A2GO TCGA-EE-A2M6 TCGA-EE-A2MM TCGA-EE-A2MS TCGA-EE-A3J8 TCGA-ER-A193 
      118.32       103.13       145.45       143.93         3.35        14.56 
TCGA-ER-A197 TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19S TCGA-ER-A2ND TCGA-ER-A2NG 
        1.58        53.29        11.47        34.95         4.70        10.95 
TCGA-ER-A3EV TCGA-FR-A7U8 TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A4F8 TCGA-FW-A3TU 
       15.48        26.20       195.98        27.62       173.19        55.59 
TCGA-GF-A6C8 TCGA-GN-A4U3 TCGA-W3-A825 TCGA-W3-AA1R TCGA-W3-AA1V TCGA-WE-AA9Y 
        1.91       120.53         1.97        79.99         8.09         1.94 
TCGA-WE-AAA3 TCGA-YG-AA3O 
       16.64        28.21 

$`4P LOSS WILD-TYPE`
TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q3 TCGA-D3-A1Q5 TCGA-D3-A1Q6 
       60.46        12.99        14.83        15.72       110.93        49.35 
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J7 TCGA-D3-A2J8 
      133.25        19.04        76.41        62.60        45.99        62.86 
TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JE TCGA-D3-A2JG TCGA-D3-A2JH 
      168.00        86.30         7.27         9.76       107.61        36.30 
TCGA-D3-A2JL TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CE 
      171.58        43.53        58.06        46.98       140.98        59.70 
TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51J 
       16.96        13.87         9.34        23.67       173.85       144.46 
TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR 
       31.76        62.70        11.34        42.05        45.70       177.86 
TCGA-D3-A5GU TCGA-D3-A8GD TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GP 
      124.08        23.61       179.97       120.00        69.53       135.12 
TCGA-D3-A8GR TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY 
       36.53        10.78        15.02        22.85        48.66       106.85 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC 
       31.96       150.61        82.85        32.42        64.83        58.85 
TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-EB-A44Q TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN 
       25.12       214.59         3.91        33.24        50.07        45.50 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A184 
        6.64        13.15        24.89        20.38         0.00        67.50 
TCGA-EE-A20H TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29P TCGA-EE-A29Q 
      155.90         0.26        44.28        63.12        27.16        61.12 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE 
      102.38         7.20        77.98        26.14       239.11         0.20 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR 
       68.65        10.62        32.48        31.00         0.76         0.20 
TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MF 
       71.31        81.99        15.25         5.75        23.77       209.79 
TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MP 
       94.19       171.85        63.25        67.50       104.78       227.01 
TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC 
       25.08        23.51        53.26       124.31       122.73        51.62 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 
        4.41        54.51         6.28        67.89       111.85        45.90 
TCGA-EE-A3JB TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A 
      201.80       152.81        34.45        47.31         7.82         4.54 
TCGA-ER-A19C TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
       39.81       151.46       150.12        99.06        59.84        42.48 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE 
      120.76        49.71       146.63        47.97        22.36        16.87 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3PL TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7UA 
      173.29        55.82        32.05       174.21       209.23         5.65 
TCGA-FR-A8YC TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1ZC TCGA-FS-A1ZD 
       10.06       171.78        49.74         8.35       312.07        32.78 
TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ 
       35.90        12.92         7.82        36.33        78.61       130.95 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ 
      136.27        35.28         4.47        23.21         5.29         3.06 
TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TV TCGA-FW-A5DY 
       30.90        66.67        13.28        80.68        11.54        19.30 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 
        9.90         6.05        53.29       117.93        84.72        17.06 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-GN-A8LK TCGA-GN-A9SD 
       42.48         7.59        34.49        46.92        43.23        59.41 
TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 TCGA-W3-A824 
       85.05       297.01         7.23        18.05         0.33       174.12 
TCGA-W3-A828 TCGA-W3-AA1Q TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8K5 
      120.07        44.05       185.13        92.84         1.15        59.64 
TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZY 
       62.99        12.69        19.00        59.44        10.95        48.39 
TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-Z2-AA3S 
       26.60        15.65        91.23 

  4P LOSS MUTATED 4P LOSS WILD-TYPE 
             1.58              0.00 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
           346.49            312.07 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
            37.48             46.92 
[1] "1.6 - 346.5 (37.5)" "0.0 - 312.1 (46.9)"
[1] "hr=" "1.2"
D48V2, survival
                   sevent
clus2                 0   1
  4P LOSS MUTATED    37  39
  4P LOSS WILD-TYPE 132 141
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               76               273 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               39               141 
$`4P LOSS MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A2J6 TCGA-D3-A2JA TCGA-D3-A2JN TCGA-D3-A2JO 
       16.57       112.04        43.43       115.53        66.48        66.08 
TCGA-D3-A3CC TCGA-D3-A3MR TCGA-D3-A3MV TCGA-D3-A51F TCGA-D3-A51N TCGA-D3-A8GC 
       86.93       103.59        45.30        55.73        22.62        79.59 
TCGA-D3-A8GI TCGA-D3-A8GM TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A3Z3 TCGA-D9-A4Z6 
       58.52       107.15       151.53        54.67        22.29        18.44 
TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-DA-A1HW TCGA-DA-A3F8 TCGA-EB-A44R TCGA-EB-A5KH 
        9.90        66.25        36.03        15.68        10.36        20.35 
TCGA-EE-A180 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D 
       94.98       133.81       151.27        85.08        78.97        13.97 
TCGA-EE-A29M TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A5 TCGA-EE-A2GH TCGA-EE-A2GM 
       56.84       369.93       195.02        39.29       208.04        75.48 
TCGA-EE-A2GO TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2MM TCGA-EE-A2MQ TCGA-EE-A2MS 
      126.81        21.67       129.27       167.90        43.23       162.48 
TCGA-EE-A3AG TCGA-EE-A3J8 TCGA-EE-A3JE TCGA-ER-A193 TCGA-ER-A197 TCGA-ER-A19B 
       41.59        34.32        51.35        31.40        13.94        98.40 
TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A2ND TCGA-ER-A2NG 
       12.59        13.02        37.25         8.88        23.34        31.27 
TCGA-ER-A2NH TCGA-ER-A3EV TCGA-FR-A7U8 TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1ZA 
       32.05        46.98        27.85       202.65        28.08        27.72 
TCGA-FS-A4F8 TCGA-FW-A3TU TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A266 TCGA-GN-A4U3 
      174.84        55.59         2.04        15.78        10.13       121.91 
TCGA-W3-A825 TCGA-W3-AA1R TCGA-W3-AA1V TCGA-WE-A8JZ TCGA-WE-A8ZX TCGA-WE-AA9Y 
       63.02       111.09        42.08        24.03        32.58        12.16 
TCGA-WE-AAA3 TCGA-YD-A9TA TCGA-YG-AA3O TCGA-Z2-A8RT 
       19.73        49.18        37.94        27.58 

$`4P LOSS WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q3 TCGA-D3-A1Q5 
       17.03        66.48        12.99        14.93        16.67       112.57 
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB 
       71.80       133.25        28.08        31.59        90.90        95.74 
TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
      103.10        65.49        23.77       168.00        86.76        11.87 
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL 
       27.65        62.07       113.52        42.08        12.10       171.58 
TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB 
       59.57       130.72        58.06        46.98        46.32       166.52 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MU TCGA-D3-A51E 
       60.23        24.53        13.87         9.34        39.75       174.84 
TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL 
       56.35       145.12        32.94        63.81        26.89       125.79 
TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GB 
      135.75       137.92       178.32        18.18       125.19        30.84 
TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GN 
       23.61        26.43       241.38       170.20        89.13       161.00 
TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A1JW TCGA-D9-A1JX 
      152.75        29.06       129.63       117.17         3.65         7.10 
TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A6EA TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY 
       18.12        15.39        25.18        22.95        48.89       117.21 
TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 
       20.38       194.83       176.55        35.93       107.34        61.18 
TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
       53.92        65.92        23.44        68.09        28.60        10.49 
TCGA-DA-A3F5 TCGA-EB-A44Q TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN 
      215.44        13.87        68.25        54.02        17.29        52.01 
TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A181 
        7.04        24.89        29.82        27.22         8.65        33.73 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20F TCGA-EE-A20H 
       14.70        26.89        68.15         4.96        91.56       168.26 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L 
       13.55        63.35        63.78        72.07        64.64         2.60 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V 
       18.61        56.42        66.74        14.47        61.28        25.87 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB 
       17.92        46.82       102.90        36.82        86.14        59.28 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
       67.43       340.14       161.03        48.72       107.38        54.74 
TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT 
       79.66       102.12        13.91        42.77        81.21        44.88 
TCGA-EE-A2GU TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME 
       94.82        28.83        19.76        61.51        47.28       103.27 
TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK 
      268.73       103.20        16.96       204.66        96.23       158.63 
TCGA-EE-A2ML TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A2MU 
      216.66        47.54       248.65       134.40        71.21        53.26 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
      124.31       122.73        51.62        28.77        54.51        13.81 
TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3JA 
      138.81       172.18       127.20        36.95        64.08        53.19 
TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A198 
      201.80        27.35       109.58       152.81        35.44        50.76 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19C TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H 
        9.17        77.75        48.89        26.37       268.93       152.35 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
        6.44       131.51        61.05        44.05       162.08        50.89 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A3ES 
      148.18        79.99        43.82        20.15        16.37       247.04 
TCGA-ER-A3ET TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       80.32        33.21         6.77        92.98       174.21        15.72 
TCGA-FR-A729 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE 
      220.80        18.77        38.27        34.82        36.26       104.42 
TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1Z7 TCGA-FS-A1ZB 
      216.92        48.59       228.59        20.91         7.79        48.85 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH 
      357.37        53.52        40.27        15.45         9.70        32.75 
TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR 
       47.38        23.93       101.26        74.73       133.55        11.41 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ 
      148.80        53.16        26.56        49.48        27.09        27.02 
TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F9 TCGA-FS-A4FB 
       77.82        50.14        66.67        28.73        34.03        26.73 
TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TV TCGA-FW-A5DY 
       54.41        80.68         0.20        22.92        13.51        19.30 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 
        9.90         7.23       139.89       117.93        84.72        64.44 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 
       62.79        32.48        39.58        39.35        10.42        48.89 
TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A8LL TCGA-GN-A9SD TCGA-HR-A2OG TCGA-HR-A2OH 
       22.13        50.10        21.37        59.41         0.23        65.88 
TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 TCGA-RP-A694 
      368.78       297.90         7.23        18.05         0.33         0.69 
TCGA-W3-A824 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1Q TCGA-W3-AA1W TCGA-W3-AA21 
      228.16       121.08         4.01        69.07       219.16       105.04 
TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO 
       49.05        61.15        15.98        98.89        58.98        67.63 
TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-YD-A89C 
       59.77        11.80        49.51        35.01        22.29         6.90 
TCGA-YG-AA3P TCGA-Z2-AA3S TCGA-Z2-AA3V 
       14.43        96.99        15.98 

  4P LOSS MUTATED 4P LOSS WILD-TYPE 
             2.04              0.20 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
           369.93            368.78 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
           44.365            53.160 
[1] "2.0 - 369.9 (44.4)" "0.2 - 368.8 (53.2)"
[1] "hr=" "1.1"
D48V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  4P LOSS MUTATED                   15             3
  4P LOSS WILD-TYPE                 50             2
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  4P LOSS MUTATED                                          17
  4P LOSS WILD-TYPE                                        55
                   vv
clus                REGIONAL LYMPH NODE
  4P LOSS MUTATED                    42
  4P LOSS WILD-TYPE                 173
D48V4, multiclass
                                           clus
vv                                          4P LOSS MUTATED 4P LOSS WILD-TYPE
  DISTANT METASTASIS                                     15                50
  PRIMARY TUMOR                                           3                 2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE              17                55
  REGIONAL LYMPH NODE                                    42               173
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  4P LOSS MUTATED             1       2       6        2        5        6
  4P LOSS WILD-TYPE          11       5      22       16       22       18
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  4P LOSS MUTATED           0         6         2         7          5
  4P LOSS WILD-TYPE        14        13        10        30         10
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  4P LOSS MUTATED           11         13        3
  4P LOSS WILD-TYPE         21         47       17
D48V5, multiclass
             clus
vv            4P LOSS MUTATED 4P LOSS WILD-TYPE
  I OR II NOS               1                11
  STAGE 0                   2                 5
  STAGE I                   6                22
  STAGE IA                  2                16
  STAGE IB                  5                22
  STAGE II                  6                18
  STAGE IIA                 0                14
  STAGE IIB                 6                13
  STAGE IIC                 2                10
  STAGE III                 7                30
  STAGE IIIA                5                10
  STAGE IIIB               11                21
  STAGE IIIC               13                47
  STAGE IV                  3                17
[1] 14  2
[1] TRUE
[1] "dimension of contingency 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      13 14 21 12
  4P LOSS WILD-TYPE    51 58 56 56
D48V6, multiclass
       clus
vv      4P LOSS MUTATED 4P LOSS WILD-TYPE
  T0+T1              13                51
  T2                 14                58
  T3                 21                56
  T4                 12                56
[1] 4 2
[1] TRUE
[1] "dimension of 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    32  19   7  11
  4P LOSS WILD-TYPE 137  44  31  38
D48V7, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  N0              32               137
  N1              19                44
  N2               7                31
  N3              11                38
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V8, binary
                   cls
clus                  0   1
  4P LOSS MUTATED    68   4
  4P LOSS WILD-TYPE 245  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     68    4
  4P LOSS WILD-TYPE  245   17
   clus
vv  4P LOSS MUTATED 4P LOSS WILD-TYPE
  0              68               245
  1               4                17
[1] 2 2
[1] FALSE
D48V9, binary
                   cls
clus                  0   1
  4P LOSS MUTATED    31  18
  4P LOSS WILD-TYPE 101  70
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     31   18
  4P LOSS WILD-TYPE  101   70
     clus
vv    4P LOSS MUTATED 4P LOSS WILD-TYPE
  NO               31               101
  YES              18                70
[1] 2 2
[1] FALSE
D48V10, binary
                   cls
clus                  0   1
  4P LOSS MUTATED    10  68
  4P LOSS WILD-TYPE  34 245
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     10   68
  4P LOSS WILD-TYPE   34  245
     clus
vv    4P LOSS MUTATED 4P LOSS WILD-TYPE
  NO               10                34
  YES              68               245
[1] 2 2
[1] FALSE
D48V11, continuous
D48V12, binary
                   cls
clus                  0   1
  4P LOSS MUTATED    32  46
  4P LOSS WILD-TYPE 103 177
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     32   46
  4P LOSS WILD-TYPE  103  177
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  FEMALE              32               103
  MALE                46               177
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  4P LOSS MUTATED       2                         0    74
  4P LOSS WILD-TYPE     3                         1   270
D48V13, multiclass
                           clus
vv                          4P LOSS MUTATED 4P LOSS WILD-TYPE
  ASIAN                                   2                 3
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  74               270
[1] 3 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     1  76
  4P LOSS WILD-TYPE   6 268
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      1   76
  4P LOSS WILD-TYPE    6  268
                        clus
vv                       4P LOSS MUTATED 4P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 6
  NOT HISPANIC OR LATINO              76               268
[1] 2 2
[1] FALSE

Clustering(49) Variable = 4Q LOSS MUTATION ANALYSIS
D49V1, survival
                   sevent
clus2                0  1
  4Q LOSS MUTATED   23 29
  4Q LOSS WILD-TYPE 98 89
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               52               187 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               29                89 
$`4Q LOSS MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q8 TCGA-D3-A2JA TCGA-D3-A2JN TCGA-D3-A2JO 
        8.42        31.89        19.04        15.75        64.83        66.08 
TCGA-D3-A3C7 TCGA-D3-A3CC TCGA-D3-A3MR TCGA-D3-A8GC TCGA-D3-A8GM TCGA-D9-A3Z3 
       46.98        40.01        90.21        78.21        70.62        16.90 
TCGA-D9-A4Z6 TCGA-DA-A3F8 TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A20C 
       18.44        14.96        24.89        62.37        20.38        75.55 
TCGA-EE-A29C TCGA-EE-A29M TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2GH TCGA-EE-A2GM 
       76.14        47.74       346.49       185.19       189.40        18.35 
TCGA-EE-A2GO TCGA-EE-A2M6 TCGA-EE-A2MM TCGA-EE-A2MS TCGA-EE-A3J8 TCGA-ER-A193 
      118.32       103.13       145.45       143.93         3.35        14.56 
TCGA-ER-A197 TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19S TCGA-ER-A2ND TCGA-ER-A2NG 
        1.58        53.29        11.47        34.95         4.70        10.95 
TCGA-ER-A3EV TCGA-FR-A7U8 TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A4F8 TCGA-FW-A3TU 
       15.48        26.20       195.98        27.62       173.19        55.59 
TCGA-GF-A6C8 TCGA-GN-A4U3 TCGA-GN-A8LK TCGA-QB-AA9O TCGA-W3-A825 TCGA-W3-AA1R 
        1.91       120.53        43.23        18.05         1.97        79.99 
TCGA-W3-AA1V TCGA-WE-AA9Y TCGA-WE-AAA3 TCGA-YG-AA3O 
        8.09         1.94        16.64        28.21 

$`4Q LOSS WILD-TYPE`
TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q3 TCGA-D3-A1Q5 TCGA-D3-A1Q6 
       60.46        12.99        14.83        15.72       110.93        49.35 
TCGA-D3-A1Q7 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 
      133.25        76.41        62.60        25.64        45.99        62.86 
TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JE TCGA-D3-A2JG TCGA-D3-A2JH 
      168.00        86.30         7.27         9.76       107.61        36.30 
TCGA-D3-A2JL TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3CF 
      171.58        43.53        58.06       140.98        59.70        16.96 
TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51J TCGA-D3-A51K 
       13.87         9.34        23.67       173.85       144.46        31.76 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GU 
       62.70        11.34        42.05        45.70       177.86       124.08 
TCGA-D3-A8GD TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GP TCGA-D3-A8GR 
       23.61       179.97       120.00        69.53       135.12        36.53 
TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY 
       10.78        15.02        57.90        22.85        48.66       106.85 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC 
       31.96       150.61        82.85        32.42        64.83        58.85 
TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-EB-A44Q TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN 
       25.12       214.59         3.91        33.24        50.07        45.50 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A182 TCGA-EE-A184 TCGA-EE-A20H TCGA-EE-A29B 
        6.64        13.15         0.00        67.50       155.90        75.22 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29P TCGA-EE-A29Q 
       12.99         0.26        44.28        63.12        27.16        61.12 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE 
      102.38         7.20        77.98        26.14       239.11         0.20 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR 
       68.65        10.62        32.48        31.00         0.76         0.20 
TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MF 
       71.31        81.99        15.25         5.75        23.77       209.79 
TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MP 
       94.19       171.85        63.25        67.50       104.78       227.01 
TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC 
       25.08        23.51        53.26       124.31       122.73        51.62 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 
        4.41        54.51         6.28        67.89       111.85        45.90 
TCGA-EE-A3JB TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A 
      201.80       152.81        34.45        47.31         7.82         4.54 
TCGA-ER-A19C TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
       39.81       151.46       150.12        99.06        59.84        42.48 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE 
      120.76        49.71       146.63        47.97        22.36        16.87 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3PL TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7UA 
      173.29        55.82        32.05       174.21       209.23         5.65 
TCGA-FR-A8YC TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1ZC TCGA-FS-A1ZD 
       10.06       171.78        49.74         8.35       312.07        32.78 
TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ 
       35.90        12.92         7.82        36.33        78.61       130.95 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ 
      136.27        35.28         4.47        23.21         5.29         3.06 
TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TV TCGA-FW-A5DY 
       30.90        66.67        13.28        80.68        11.54        19.30 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 
        9.90         6.05        53.29       117.93        84.72        17.06 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-GN-A9SD TCGA-LH-A9QB 
       42.48         7.59        34.49        46.92        59.41        85.05 
TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A828 TCGA-W3-AA1Q 
      297.01         7.23         0.33       174.12       120.07        44.05 
TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8ZM TCGA-WE-A8ZN 
      185.13        92.84         1.15        59.64        62.99        12.69 
TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AAA0 TCGA-WE-AAA4 
       19.00        59.44        10.95        48.39        26.60        15.65 
TCGA-Z2-AA3S 
       91.23 

  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
             1.58              0.00 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
           346.49            312.07 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
            33.42             47.97 
[1] "1.6 - 346.5 (33.4)" "0.0 - 312.1 (48.0)"
[1] "hr=" "1.3"
D49V2, survival
                   sevent
clus2                 0   1
  4Q LOSS MUTATED    39  42
  4Q LOSS WILD-TYPE 130 138
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               81               268 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               42               138 
$`4Q LOSS MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q8 TCGA-D3-A2JA TCGA-D3-A2JN TCGA-D3-A2JO 
       16.57       112.04        28.08       115.53        66.48        66.08 
TCGA-D3-A3C7 TCGA-D3-A3CC TCGA-D3-A3MR TCGA-D3-A3MV TCGA-D3-A51F TCGA-D3-A51N 
       46.98        86.93       103.59        45.30        55.73        22.62 
TCGA-D3-A8GC TCGA-D3-A8GI TCGA-D3-A8GM TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A3Z3 
       79.59        58.52       107.15       151.53        54.67        22.29 
TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-DA-A1HW TCGA-DA-A3F8 TCGA-EB-A44R TCGA-EB-A5KH 
       18.44         9.90        36.03        15.68        10.36        20.35 
TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A29C 
       27.22        94.98        33.73       133.81       151.27        78.97 
TCGA-EE-A29M TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A5 TCGA-EE-A2GH TCGA-EE-A2GI 
       56.84       369.93       195.02        39.29       208.04        48.72 
TCGA-EE-A2GM TCGA-EE-A2GO TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2MM TCGA-EE-A2MQ 
       75.48       126.81        21.67       129.27       167.90        43.23 
TCGA-EE-A2MS TCGA-EE-A3AG TCGA-EE-A3J8 TCGA-EE-A3JE TCGA-ER-A193 TCGA-ER-A197 
      162.48        41.59        34.32        51.35        31.40        13.94 
TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A2ND 
       98.40        12.59        13.02        37.25         8.88        23.34 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3EV TCGA-FR-A7U8 TCGA-FS-A1Z0 TCGA-FS-A1Z4 
       31.27        32.05        46.98        27.85       202.65        28.08 
TCGA-FS-A1ZA TCGA-FS-A4F8 TCGA-FW-A3TU TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A266 
       27.72       174.84        55.59         2.04        15.78        10.13 
TCGA-GN-A4U3 TCGA-GN-A8LK TCGA-HR-A2OH TCGA-QB-AA9O TCGA-W3-A825 TCGA-W3-AA1R 
      121.91        50.10        65.88        18.05        63.02       111.09 
TCGA-W3-AA1V TCGA-WE-A8JZ TCGA-WE-A8K6 TCGA-WE-A8ZX TCGA-WE-AA9Y TCGA-WE-AAA3 
       42.08        24.03        15.98        32.58        12.16        19.73 
TCGA-YD-A9TA TCGA-YG-AA3O TCGA-Z2-A8RT 
       49.18        37.94        27.58 

$`4Q LOSS WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q3 TCGA-D3-A1Q5 
       17.03        66.48        12.99        14.93        16.67       112.57 
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 
       71.80       133.25        31.59        90.90        95.74        43.43 
TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
      103.10        65.49        23.77       168.00        86.76        11.87 
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL 
       27.65        62.07       113.52        42.08        12.10       171.58 
TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CE 
       59.57       130.72        58.06        46.32       166.52        60.23 
TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51H 
       24.53        13.87         9.34        39.75       174.84        56.35 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN 
      145.12        32.94        63.81        26.89       125.79       135.75 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GD 
      137.92       178.32        18.18       125.19        30.84        23.61 
TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GN TCGA-D3-A8GP 
       26.43       241.38       170.20        89.13       161.00       152.75 
TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A1X3 
       29.06       129.63       117.17         3.65         7.10        18.12 
TCGA-D9-A3Z1 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY 
       15.39        25.18        66.25        22.95        48.89       117.21 
TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 
       20.38       194.83       176.55        35.93       107.34        61.18 
TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
       53.92        65.92        23.44        68.09        28.60        10.49 
TCGA-DA-A3F5 TCGA-EB-A44Q TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN 
      215.44        13.87        68.25        54.02        17.29        52.01 
TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A182 TCGA-EE-A183 
        7.04        24.89        29.82         8.65        14.70        26.89 
TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A 
       68.15         4.96        91.56       168.26        13.55        63.35 
TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L 
       85.08        13.97        63.78        72.07        64.64         2.60 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V 
       18.61        56.42        66.74        14.47        61.28        25.87 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB 
       17.92        46.82       102.90        36.82        86.14        59.28 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
       67.43       340.14       161.03       107.38        54.74        79.66 
TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU 
      102.12        13.91        42.77        81.21        44.88        94.82 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF 
       28.83        19.76        61.51        47.28       103.27       268.73 
TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML 
      103.20        16.96       204.66        96.23       158.63       216.66 
TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA 
       47.54       248.65       134.40        71.21        53.26       124.31 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AH 
      122.73        51.62        28.77        54.51        13.81       138.81 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-EE-A3JB 
      172.18       127.20        36.95        64.08        53.19       201.80 
TCGA-EE-A3JD TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A199 
       27.35       109.58       152.81        35.44        50.76         9.17 
TCGA-ER-A19A TCGA-ER-A19C TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J 
       77.75        48.89        26.37       268.93       152.35         6.44 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19W 
      131.51        61.05        44.05       162.08        50.89       148.18 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A3ES TCGA-ER-A3ET 
       79.99        43.82        20.15        16.37       247.04        80.32 
TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 
       33.21         6.77        92.98       174.21        15.72       220.80 
TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW 
       18.77        38.27        34.82        36.26       104.42       216.92 
TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1Z7 TCGA-FS-A1ZB TCGA-FS-A1ZC 
       48.59       228.59        20.91         7.79        48.85       357.37 
TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ 
       53.52        40.27        15.45         9.70        32.75        47.38 
TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS 
       23.93       101.26        74.73       133.55        11.41       148.80 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 
       53.16        26.56        49.48        27.09        27.02        77.82 
TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC 
       50.14        66.67        28.73        34.03        26.73        54.41 
TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
       80.68         0.20        22.92        13.51        19.30         9.90 
TCGA-GF-A4EO TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 
        7.23       139.89       117.93        84.72        64.44        62.79 
TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A4U9 
       32.48        39.58        39.35        10.42        48.89        22.13 
TCGA-GN-A8LL TCGA-GN-A9SD TCGA-HR-A2OG TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS 
       21.37        59.41         0.23       368.78       297.90         7.23 
TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1Q 
        0.33         0.69       228.16       121.08         4.01        69.07 
TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8ZM TCGA-WE-A8ZN 
      219.16       105.04        49.05        61.15        98.89        58.98 
TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AAA0 TCGA-WE-AAA4 
       67.63        59.77        11.80        49.51        35.01        22.29 
TCGA-YD-A89C TCGA-YG-AA3P TCGA-Z2-AA3S TCGA-Z2-AA3V 
        6.90        14.43        96.99        15.98 

  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
             2.04              0.20 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
           369.93            368.78 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
            43.23             53.72 
[1] "2.0 - 369.9 (43.2)" "0.2 - 368.8 (53.7)"
[1] "hr=" "1.2"
D49V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  4Q LOSS MUTATED                   15             2
  4Q LOSS WILD-TYPE                 50             3
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  4Q LOSS MUTATED                                          18
  4Q LOSS WILD-TYPE                                        54
                   vv
clus                REGIONAL LYMPH NODE
  4Q LOSS MUTATED                    46
  4Q LOSS WILD-TYPE                 169
D49V4, multiclass
                                           clus
vv                                          4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  DISTANT METASTASIS                                     15                50
  PRIMARY TUMOR                                           2                 3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE              18                54
  REGIONAL LYMPH NODE                                    46               169
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  4Q LOSS MUTATED             0       2       6        3        6        7
  4Q LOSS WILD-TYPE          12       5      22       15       21       17
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  4Q LOSS MUTATED           0         4         2         8          4
  4Q LOSS WILD-TYPE        14        15        10        29         11
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  4Q LOSS MUTATED           14         13        4
  4Q LOSS WILD-TYPE         18         47       16
D49V5, multiclass
             clus
vv            4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  I OR II NOS               0                12
  STAGE 0                   2                 5
  STAGE I                   6                22
  STAGE IA                  3                15
  STAGE IB                  6                21
  STAGE II                  7                17
  STAGE IIA                 0                14
  STAGE IIB                 4                15
  STAGE IIC                 2                10
  STAGE III                 8                29
  STAGE IIIA                4                11
  STAGE IIIB               14                18
  STAGE IIIC               13                47
  STAGE IV                  4                16
[1] 14  2
[1] TRUE
[1] "dimension of contingency 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      17 13 20 12
  4Q LOSS WILD-TYPE    47 59 57 56
D49V6, multiclass
       clus
vv      4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  T0+T1              17                47
  T2                 13                59
  T3                 20                57
  T4                 12                56
[1] 4 2
[1] TRUE
[1] "dimension of 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    31  20   8  13
  4Q LOSS WILD-TYPE 138  43  30  36
D49V7, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  N0              31               138
  N1              20                43
  N2               8                30
  N3              13                36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V8, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED    70   5
  4Q LOSS WILD-TYPE 243  16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     70    5
  4Q LOSS WILD-TYPE  243   16
   clus
vv  4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  0              70               243
  1               5                16
[1] 2 2
[1] FALSE
D49V9, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED    32  17
  4Q LOSS WILD-TYPE 100  71
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     32   17
  4Q LOSS WILD-TYPE  100   71
     clus
vv    4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  NO               32               100
  YES              17                71
[1] 2 2
[1] FALSE
D49V10, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED    13  69
  4Q LOSS WILD-TYPE  31 244
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     13   69
  4Q LOSS WILD-TYPE   31  244
     clus
vv    4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  NO               13                31
  YES              69               244
[1] 2 2
[1] FALSE
D49V11, continuous
D49V12, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED    34  48
  4Q LOSS WILD-TYPE 101 175
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     34   48
  4Q LOSS WILD-TYPE  101  175
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  FEMALE              34               101
  MALE                48               175
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  4Q LOSS MUTATED       3                         0    76
  4Q LOSS WILD-TYPE     2                         1   268
D49V13, multiclass
                           clus
vv                          4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  ASIAN                                   3                 2
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  76               268
[1] 3 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     1  78
  4Q LOSS WILD-TYPE   6 266
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      1   78
  4Q LOSS WILD-TYPE    6  266
                        clus
vv                       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 6
  NOT HISPANIC OR LATINO              78               266
[1] 2 2
[1] FALSE

Clustering(50) Variable = 5P LOSS MUTATION ANALYSIS
D50V1, survival
                   sevent
clus2                0  1
  5P LOSS MUTATED   25 29
  5P LOSS WILD-TYPE 96 89
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               54               185 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               29                89 
$`5P LOSS MUTATED`
TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A2JB TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JL 
       12.99         8.42       168.00         7.27       107.61       171.58 
TCGA-D3-A2JO TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D9-A1X3 TCGA-D9-A4Z6 TCGA-DA-A1HV 
       66.08        40.01        16.96        10.78        18.44        48.66 
TCGA-DA-A3F5 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A184 TCGA-EE-A29C TCGA-EE-A29E 
      214.59        13.15        24.89        67.50        76.14         0.26 
TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A2A2 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE 
       47.74        27.16         7.20        26.14       239.11         0.20 
TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GR TCGA-EE-A2MM TCGA-EE-A2MU TCGA-EE-A3AD 
      189.40        68.65         0.20       145.45        53.26         4.41 
TCGA-EE-A3J7 TCGA-EE-A3JB TCGA-ER-A199 TCGA-ER-A2NE TCGA-ER-A2NG TCGA-FS-A1ZD 
       45.90       201.80         7.82        16.87        10.95        32.78 
TCGA-FS-A1ZG TCGA-FS-A1ZM TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F4 
        7.82        78.61        35.28        23.21         5.29        66.67 
TCGA-FS-A4F8 TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A4U3 
      173.19         1.91        53.29        17.06        42.48       120.53 
TCGA-GN-A8LK TCGA-OD-A75X TCGA-W3-AA1R TCGA-WE-A8ZM TCGA-WE-A8ZY TCGA-WE-AAA4 
       43.23       297.01        79.99        62.99        48.39        15.65 

$`5P LOSS WILD-TYPE`
TCGA-3N-A9WC TCGA-BF-AAP0 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 
       60.46        14.83        15.72        31.89       110.93        49.35 
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
      133.25        19.04        76.41        62.60        25.64        45.99 
TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JE TCGA-D3-A2JH TCGA-D3-A2JN 
       62.86        15.75        86.30         9.76        36.30        64.83 
TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3ML 
       43.53        58.06        46.98       140.98        59.70        13.87 
TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51J TCGA-D3-A51K 
        9.34        90.21        23.67       173.85       144.46        31.76 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GU 
       62.70        11.34        42.05        45.70       177.86       124.08 
TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM 
       78.21        23.61       179.97       120.00        69.53        70.62 
TCGA-D3-A8GP TCGA-D3-A8GR TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6EC TCGA-D9-A6EG 
      135.12        36.53        15.02        16.90        57.90        22.85 
TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA 
      106.85        31.96       150.61        82.85        32.42        64.83 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5SG TCGA-EB-A5SH 
       58.85        25.12        14.96         3.91        33.24        50.07 
TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A20C 
       45.50         6.64        62.37        20.38         0.00        75.55 
TCGA-EE-A20H TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29Q 
      155.90        75.22        12.99        44.28        63.12        61.12 
TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A6 TCGA-EE-A2GK TCGA-EE-A2GL 
      346.49       185.19       102.38        77.98        10.62        32.48 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2GU 
       18.35        31.00       118.32         0.76        71.31        81.99 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MG 
      103.13        15.25         5.75        23.77       209.79        94.19 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MP TCGA-EE-A2MR 
      171.85        63.25        67.50       104.78       227.01        25.08 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AE 
      143.93        23.51       124.31       122.73        51.62        54.51 
TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J8 TCGA-EE-A3JI TCGA-ER-A193 
        6.28        67.89       111.85         3.35       152.81        14.56 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C 
       34.45         1.58        47.31         4.54        53.29        39.81 
TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
       11.47       151.46       150.12        99.06        59.84        42.48 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
      120.76        49.71        34.95       146.63        47.97        22.36 
TCGA-ER-A2ND TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A44A 
        4.70       173.29        55.82        15.48        32.05       174.21 
TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FS-A1YW TCGA-FS-A1YY 
      209.23        26.20         5.65        10.06       171.78        49.74 
TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZE TCGA-FS-A1ZF 
      195.98         8.35        27.62       312.07        35.90        12.92 
TCGA-FS-A1ZJ TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZZ TCGA-FS-A4F0 
       36.33       130.95       136.27         4.47         3.06        30.90 
TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
       13.28        80.68        55.59        11.54        19.30         9.90 
TCGA-GF-A4EO TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A26A TCGA-GN-A4U4 TCGA-GN-A4U8 
        6.05       117.93        84.72         7.59        34.49        46.92 
TCGA-GN-A9SD TCGA-LH-A9QB TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 TCGA-W3-A824 
       59.41        85.05         7.23        18.05         0.33       174.12 
TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1Q TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 
        1.97       120.07        44.05         8.09       185.13        92.84 
TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT 
        1.15        59.64        12.69        19.00        59.44        10.95 
TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-YG-AA3O TCGA-Z2-AA3S 
        1.94        26.60        16.64        28.21        91.23 

  5P LOSS MUTATED 5P LOSS WILD-TYPE 
              0.2               0.0 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
           297.01            346.49 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
           41.245            47.310 
[1] "0.2 - 297.0 (41.2)" "0.0 - 346.5 (47.3)"
[1] "hr=" "1.2"
D50V2, survival
                   sevent
clus2                 0   1
  5P LOSS MUTATED    35  40
  5P LOSS WILD-TYPE 134 140
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               75               274 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               40               140 
$`5P LOSS MUTATED`
TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A2JB TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JL 
       12.99        16.57       168.00        11.87       113.52       171.58 
TCGA-D3-A2JO TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3MV TCGA-D3-A5GO TCGA-D3-A8GB 
       66.08        86.93        24.53        45.30       137.92        30.84 
TCGA-D3-A8GN TCGA-D9-A1X3 TCGA-D9-A4Z6 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A3F5 
      161.00        18.12        18.44        48.89        36.03       215.44 
TCGA-EB-A5KH TCGA-EB-A5UL TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A184 TCGA-EE-A185 
       20.35        17.29        29.82        27.22        68.15         4.96 
TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A2A2 TCGA-EE-A2GB 
       78.97        63.78        56.84        56.42        36.82        59.28 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GR 
      340.14       161.03       208.04        48.72       107.38        42.77 
TCGA-EE-A2GT TCGA-EE-A2MM TCGA-EE-A2MQ TCGA-EE-A2MU TCGA-EE-A3AD TCGA-EE-A3AH 
       44.88       167.90        43.23        53.26        28.77       138.81 
TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3JB TCGA-ER-A199 TCGA-ER-A2NE TCGA-ER-A2NG 
       36.95        64.08       201.80         9.17        20.15        31.27 
TCGA-ER-A2NH TCGA-FR-A69P TCGA-FS-A1ZD TCGA-FS-A1ZG TCGA-FS-A1ZM TCGA-FS-A1ZT 
       32.05        15.72        53.52         9.70       101.26        53.16 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4FB 
       49.48        27.09        50.14        66.67       174.84        26.73 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A4U3 
        2.04       139.89        10.13        64.44        62.79       121.91 
TCGA-GN-A8LK TCGA-HR-A2OG TCGA-HR-A2OH TCGA-OD-A75X TCGA-W3-AA1R TCGA-WE-A8ZM 
       50.10         0.23        65.88       297.90       111.09        98.89 
TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AAA4 
       32.58        49.51        22.29 

$`5P LOSS WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-BF-AAP0 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 
       17.03        66.48        14.93        16.67       112.04       112.57 
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB 
       71.80       133.25        28.08        31.59        90.90        95.74 
TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JC 
       43.43       103.10        65.49        23.77       115.53        86.76 
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JN TCGA-D3-A2JP 
       27.65        62.07        42.08        12.10        66.48        59.57 
TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CE 
      130.72        58.06        46.98        46.32       166.52        60.23 
TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F 
       13.87         9.34       103.59        39.75       174.84        55.73 
TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T 
       56.35       145.12        32.94        22.62        63.81        26.89 
TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GC 
      125.79       135.75       178.32        18.18       125.19        79.59 
TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL 
       23.61        26.43        58.52       241.38       170.20        89.13 
TCGA-D3-A8GM TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A148 
      107.15       152.75        29.06       129.63       117.17       151.53 
TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 
       54.67         3.65         7.10        15.39        22.29         9.90 
TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 
       25.18        66.25        22.95       117.21        20.38       194.83 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA 
      176.55        35.93       107.34        61.18        53.92        65.92 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EB-A44Q 
       23.44        68.09        28.60        10.49        15.68        13.87 
TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 
       10.36        68.25        54.02        52.01         7.04        24.89 
TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20B 
        8.65        94.98        33.73        14.70        26.89       133.81 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
      151.27        91.56       168.26        13.55        63.35        85.08 
TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29Q 
       13.97        72.07        64.64         2.60        18.61        66.74 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X 
       14.47        61.28       369.93        25.87       195.02        17.92 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GC TCGA-EE-A2GK 
       46.82       102.90        39.29        86.14        67.43        54.74 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GS 
       79.66        75.48       102.12       126.81        13.91        81.21 
TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC 
       94.82        21.67       129.27        28.83        19.76        61.51 
TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
       47.28       103.27       268.73       103.20        16.96       204.66 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MR 
       96.23       158.63       216.66        47.54       248.65       134.40 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AE 
      162.48        71.21       124.31       122.73        51.62        54.51 
TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J8 TCGA-EE-A3JA 
       13.81        41.59       172.18       127.20        34.32        53.19 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 
       27.35        51.35       109.58       152.81        31.40        35.44 
TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D 
       13.94        50.76        77.75        98.40        48.89        12.59 
TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L 
       13.02        26.37       268.93       152.35         6.44       131.51 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T 
       61.05        44.05       162.08        50.89        37.25         8.88 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NF TCGA-ER-A3ES 
      148.18        79.99        43.82        23.34        16.37       247.04 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A 
       80.32        46.98        33.21         6.77        92.98       174.21 
TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD 
      220.80        27.85        18.77        38.27        34.82        36.26 
TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
      104.42       216.92        48.59       228.59       202.65        20.91 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZE 
       28.08         7.79        27.72        48.85       357.37        40.27 
TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZQ 
       15.45        32.75        47.38        23.93        74.73       133.55 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F5 
       11.41       148.80        26.56        27.02        77.82        28.73 
TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU 
       34.03        54.41        80.68         0.20        22.92        55.59 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C9 TCGA-GN-A264 
       13.51        19.30         9.90         7.23        15.78       117.93 
TCGA-GN-A265 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 
       84.72        32.48        39.58        39.35        10.42        48.89 
TCGA-GN-A4U9 TCGA-GN-A8LL TCGA-GN-A9SD TCGA-LH-A9QB TCGA-QB-A6FS TCGA-QB-AA9O 
       22.13        21.37        59.41       368.78         7.23        18.05 
TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O 
        0.33         0.69       228.16        63.02       121.08         4.01 
TCGA-W3-AA1Q TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K1 
       69.07        42.08       219.16       105.04        24.03        49.05 
TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT 
       61.15        15.98        58.98        67.63        59.77        11.80 
TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-YD-A89C TCGA-YD-A9TA TCGA-YG-AA3O 
       12.16        35.01        19.73         6.90        49.18        37.94 
TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
       14.43        27.58        96.99        15.98 

  5P LOSS MUTATED 5P LOSS WILD-TYPE 
             0.23              0.20 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
           340.14            369.93 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
           50.100            51.485 
[1] "0.2 - 340.1 (50.1)" "0.2 - 369.9 (51.5)"
[1] "hr=" "1"  
D50V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  5P LOSS MUTATED                   13             0
  5P LOSS WILD-TYPE                 52             5
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  5P LOSS MUTATED                                          19
  5P LOSS WILD-TYPE                                        53
                   vv
clus                REGIONAL LYMPH NODE
  5P LOSS MUTATED                    46
  5P LOSS WILD-TYPE                 169
D50V4, multiclass
                                           clus
vv                                          5P LOSS MUTATED 5P LOSS WILD-TYPE
  DISTANT METASTASIS                                     13                52
  PRIMARY TUMOR                                           0                 5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE              19                53
  REGIONAL LYMPH NODE                                    46               169
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  5P LOSS MUTATED             4       2       5        4        4        5
  5P LOSS WILD-TYPE           8       5      23       14       23       19
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  5P LOSS MUTATED           3         4         3         9          4
  5P LOSS WILD-TYPE        11        15         9        28         11
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  5P LOSS MUTATED           11         14        0
  5P LOSS WILD-TYPE         21         46       20
D50V5, multiclass
             clus
vv            5P LOSS MUTATED 5P LOSS WILD-TYPE
  I OR II NOS               4                 8
  STAGE 0                   2                 5
  STAGE I                   5                23
  STAGE IA                  4                14
  STAGE IB                  4                23
  STAGE II                  5                19
  STAGE IIA                 3                11
  STAGE IIB                 4                15
  STAGE IIC                 3                 9
  STAGE III                 9                28
  STAGE IIIA                4                11
  STAGE IIIB               11                21
  STAGE IIIC               14                46
  STAGE IV                  0                20
[1] 14  2
[1] TRUE
[1] "dimension of contingency 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      12 16 17 17
  5P LOSS WILD-TYPE    52 56 60 51
D50V6, multiclass
       clus
vv      5P LOSS MUTATED 5P LOSS WILD-TYPE
  T0+T1              12                52
  T2                 16                56
  T3                 17                60
  T4                 17                51
[1] 4 2
[1] TRUE
[1] "dimension of 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    31  22   7  10
  5P LOSS WILD-TYPE 138  41  31  39
D50V7, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  N0              31               138
  N1              22                41
  N2               7                31
  N3              10                39
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V8, binary
                   cls
clus                  0   1
  5P LOSS MUTATED    71   0
  5P LOSS WILD-TYPE 242  21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED     71    0
  5P LOSS WILD-TYPE  242   21
   clus
vv  5P LOSS MUTATED 5P LOSS WILD-TYPE
  0              71               242
  1               0                21
[1] 2 2
[1] FALSE
D50V9, binary
                   cls
clus                  0   1
  5P LOSS MUTATED    25  23
  5P LOSS WILD-TYPE 107  65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED     25   23
  5P LOSS WILD-TYPE  107   65
     clus
vv    5P LOSS MUTATED 5P LOSS WILD-TYPE
  NO               25               107
  YES              23                65
[1] 2 2
[1] FALSE
D50V10, binary
                   cls
clus                  0   1
  5P LOSS MUTATED     6  72
  5P LOSS WILD-TYPE  38 241
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      6   72
  5P LOSS WILD-TYPE   38  241
     clus
vv    5P LOSS MUTATED 5P LOSS WILD-TYPE
  NO                6                38
  YES              72               241
[1] 2 2
[1] FALSE
D50V11, continuous
D50V12, binary
                   cls
clus                  0   1
  5P LOSS MUTATED    32  46
  5P LOSS WILD-TYPE 103 177
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED     32   46
  5P LOSS WILD-TYPE  103  177
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  FEMALE              32               103
  MALE                46               177
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  5P LOSS MUTATED       2                         1    73
  5P LOSS WILD-TYPE     3                         0   271
D50V13, multiclass
                           clus
vv                          5P LOSS MUTATED 5P LOSS WILD-TYPE
  ASIAN                                   2                 3
  BLACK OR AFRICAN AMERICAN               1                 0
  WHITE                                  73               271
[1] 3 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     0  73
  5P LOSS WILD-TYPE   7 271
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      0   73
  5P LOSS WILD-TYPE    7  271
                        clus
vv                       5P LOSS MUTATED 5P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 7
  NOT HISPANIC OR LATINO              73               271
[1] 2 2
[1] FALSE

Clustering(51) Variable = 5Q LOSS MUTATION ANALYSIS
D51V1, survival
                   sevent
clus2                0  1
  5Q LOSS MUTATED   33 35
  5Q LOSS WILD-TYPE 88 83
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               68               171 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               35                83 
$`5Q LOSS MUTATED`
TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q8 TCGA-D3-A2JB TCGA-D3-A2JD TCGA-D3-A2JG 
       12.99        14.83        19.04       168.00         7.27       107.61 
TCGA-D3-A2JL TCGA-D3-A2JO TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A5GL 
      171.58        66.08        58.06        40.01        16.96        42.05 
TCGA-D3-A5GN TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A4Z6 TCGA-D9-A6EC TCGA-DA-A1HV 
       45.70        10.78        15.02        18.44        57.90        48.66 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A3F5 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A20H 
       82.85        32.42       214.59        13.15        24.89       155.90 
TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A2A2 TCGA-EE-A2GB 
       76.14         0.26        47.74        27.16         7.20        26.14 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GM TCGA-EE-A2GR 
      239.11         0.20       189.40        68.65        18.35         0.20 
TCGA-EE-A2M6 TCGA-EE-A2MJ TCGA-EE-A2MM TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3J7 
      103.13        63.25       145.45       122.73         4.41        45.90 
TCGA-EE-A3JB TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A2NE TCGA-FR-A44A TCGA-FS-A1ZG 
      201.80         7.82        53.29        16.87       174.21         7.82 
TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F4 
       78.61       130.95        35.28        23.21         5.29        66.67 
TCGA-FS-A4F8 TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A4U3 
      173.19         1.91        53.29        17.06        42.48       120.53 
TCGA-GN-A8LK TCGA-OD-A75X TCGA-W3-A825 TCGA-W3-AA1R TCGA-W3-AA1V TCGA-WE-A8ZM 
       43.23       297.01         1.97        79.99         8.09        62.99 
TCGA-WE-A8ZY TCGA-WE-AAA4 
       48.39        15.65 

$`5Q LOSS WILD-TYPE`
TCGA-3N-A9WC TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 
       60.46         8.42        15.72        31.89       110.93        49.35 
TCGA-D3-A1Q7 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 
      133.25        76.41        62.60        25.64        45.99        62.86 
TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JE TCGA-D3-A2JH TCGA-D3-A2JN TCGA-D3-A2JP 
       15.75        86.30         9.76        36.30        64.83        43.53 
TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR 
       46.98       140.98        59.70        13.87         9.34        90.21 
TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T 
       23.67       173.85       144.46        31.76        62.70        11.34 
TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GJ TCGA-D3-A8GK 
      177.86       124.08        78.21        23.61       179.97       120.00 
TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GP TCGA-D3-A8GR TCGA-D9-A3Z3 TCGA-D9-A6EG 
       69.53        70.62       135.12        36.53        16.90        22.85 
TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 
      106.85        31.96       150.61        64.83        58.85        25.12 
TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A6L9 
       14.96         3.91        33.24        50.07        45.50         6.64 
TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A184 TCGA-EE-A20C TCGA-EE-A29B 
       62.37        20.38         0.00        67.50        75.55        75.22 
TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W 
       12.99        44.28        63.12        61.12       346.49       185.19 
TCGA-EE-A2A1 TCGA-EE-A2A6 TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GO 
      102.38        77.98        10.62        32.48        31.00       118.32 
TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC 
        0.76        71.31        81.99        15.25         5.75        23.77 
TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MP 
      209.79        94.19       171.85        67.50       104.78       227.01 
TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AC 
       25.08       143.93        23.51        53.26       124.31        51.62 
TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J8 TCGA-EE-A3JI 
       54.51         6.28        67.89       111.85         3.35       152.81 
TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19C 
       14.56        34.45         1.58        47.31         4.54        39.81 
TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
       11.47       151.46       150.12        99.06        59.84        42.48 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
      120.76        49.71        34.95       146.63        47.97        22.36 
TCGA-ER-A2ND TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL 
        4.70        10.95       173.29        55.82        15.48        32.05 
TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FS-A1YW TCGA-FS-A1YY 
      209.23        26.20         5.65        10.06       171.78        49.74 
TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE 
      195.98         8.35        27.62       312.07        32.78        35.90 
TCGA-FS-A1ZF TCGA-FS-A1ZJ TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZZ TCGA-FS-A4F0 
       12.92        36.33       136.27         4.47         3.06        30.90 
TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
       13.28        80.68        55.59        11.54        19.30         9.90 
TCGA-GF-A4EO TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A26A TCGA-GN-A4U4 TCGA-GN-A4U8 
        6.05       117.93        84.72         7.59        34.49        46.92 
TCGA-GN-A9SD TCGA-LH-A9QB TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 TCGA-W3-A824 
       59.41        85.05         7.23        18.05         0.33       174.12 
TCGA-W3-A828 TCGA-W3-AA1Q TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8K5 
      120.07        44.05       185.13        92.84         1.15        59.64 
TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-AA9Y TCGA-WE-AAA0 
       12.69        19.00        59.44        10.95         1.94        26.60 
TCGA-WE-AAA3 TCGA-YG-AA3O TCGA-Z2-AA3S 
       16.64        28.21        91.23 

  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
              0.2               0.0 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
           297.01            346.49 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
           44.465            46.980 
[1] "0.2 - 297.0 (44.5)" "0.0 - 346.5 (47.0)"
[1] "hr=" "1.1"
D51V2, survival
                   sevent
clus2                 0   1
  5Q LOSS MUTATED    42  52
  5Q LOSS WILD-TYPE 127 128
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               94               255 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               52               128 
$`5Q LOSS MUTATED`
TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q8 TCGA-D3-A2JB TCGA-D3-A2JD TCGA-D3-A2JG 
       12.99        14.93        28.08       168.00        11.87       113.52 
TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JO TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3CF 
       12.10       171.58        66.08        58.06        86.93        24.53 
TCGA-D3-A3MV TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A8GI TCGA-D9-A1JX 
       45.30       125.79       135.75       137.92        58.52         7.10 
TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A4Z6 TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW 
       18.12        15.39        18.44        66.25        48.89        36.03 
TCGA-DA-A1I0 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A3F5 TCGA-EB-A5KH TCGA-EB-A5UL 
       20.38       107.34        61.18       215.44        20.35        17.29 
TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A185 TCGA-EE-A20H TCGA-EE-A29C TCGA-EE-A29E 
       29.82        27.22         4.96       168.26        78.97        63.78 
TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29V TCGA-EE-A2A2 TCGA-EE-A2GB TCGA-EE-A2GD 
       56.84        56.42        25.87        36.82        59.28       340.14 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GM TCGA-EE-A2GR 
      161.03       208.04        48.72       107.38        75.48        42.77 
TCGA-EE-A2GT TCGA-EE-A2M6 TCGA-EE-A2MJ TCGA-EE-A2MM TCGA-EE-A2MQ TCGA-EE-A3AB 
       44.88       129.27        96.23       167.90        43.23       122.73 
TCGA-EE-A3AD TCGA-EE-A3AH TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3JB TCGA-ER-A199 
       28.77       138.81        36.95        64.08       201.80         9.17 
TCGA-ER-A19B TCGA-ER-A2NE TCGA-ER-A2NH TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YX 
       98.40        20.15        32.05       174.21        15.72        48.59 
TCGA-FS-A1ZB TCGA-FS-A1ZG TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZT TCGA-FS-A1ZW 
       48.85         9.70       101.26       133.55        53.16        49.48 
TCGA-FS-A1ZY TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4FB TCGA-GF-A6C8 
       27.09        50.14        66.67       174.84        26.73         2.04 
TCGA-GN-A262 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A4U3 TCGA-GN-A8LK 
      139.89        10.13        64.44        62.79       121.91        50.10 
TCGA-HR-A2OG TCGA-HR-A2OH TCGA-OD-A75X TCGA-W3-A825 TCGA-W3-AA1R TCGA-W3-AA1V 
        0.23        65.88       297.90        63.02       111.09        42.08 
TCGA-WE-A8ZM TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AAA4 
       98.89        32.58        49.51        22.29 

$`5Q LOSS WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 
       17.03        66.48        16.57        16.67       112.04       112.57 
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 
       71.80       133.25        31.59        90.90        95.74        43.43 
TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JE 
      103.10        65.49        23.77       115.53        86.76        27.65 
TCGA-D3-A2JF TCGA-D3-A2JH TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C7 
       62.07        42.08        66.48        59.57       130.72        46.98 
TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR 
       46.32       166.52        60.23        13.87         9.34       103.59 
TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K 
       39.75       174.84        55.73        56.35       145.12        32.94 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU 
       22.62        63.81        26.89       178.32        18.18       125.19 
TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GK 
       30.84        79.59        23.61        26.43       241.38       170.20 
TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR 
       89.13       107.15       161.00       152.75        29.06       129.63 
TCGA-D3-A8GS TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A3Z3 TCGA-D9-A6E9 
      117.17       151.53        54.67         3.65        22.29         9.90 
TCGA-D9-A6EA TCGA-D9-A6EG TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 
       25.18        22.95       117.21       194.83       176.55        35.93 
TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
       53.92        65.92        23.44        68.09        28.60        10.49 
TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN 
       15.68        13.87        10.36        68.25        54.02        52.01 
TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 
        7.04        24.89         8.65        94.98        33.73        14.70 
TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I 
       26.89        68.15       133.81       151.27        91.56        13.55 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L 
       63.35        85.08        13.97        72.07        64.64         2.60 
TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29W 
       18.61        66.74        14.47        61.28       369.93       195.02 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GC 
       17.92        46.82       102.90        39.29        86.14        67.43 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GS 
       54.74        79.66       102.12       126.81        13.91        81.21 
TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD 
       94.82        21.67        28.83        19.76        61.51        47.28 
TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK 
      103.27       268.73       103.20        16.96       204.66       158.63 
TCGA-EE-A2ML TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT 
      216.66        47.54       248.65       134.40       162.48        71.21 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG 
       53.26       124.31        51.62        54.51        13.81        41.59 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE 
      172.18       127.20        34.32        53.19        27.35        51.35 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
      109.58       152.81        31.40        35.44        13.94        50.76 
TCGA-ER-A19A TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G 
       77.75        48.89        12.59        13.02        26.37       268.93 
TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P 
      152.35         6.44       131.51        61.05        44.05       162.08 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
       50.89        37.25         8.88       148.18        79.99        43.82 
TCGA-ER-A2ND TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
       23.34        16.37        31.27       247.04        80.32        46.98 
TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 
       33.21         6.77        92.98       220.80        27.85        18.77 
TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YY 
       38.27        34.82        36.26       104.42       216.92       228.59 
TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZC 
      202.65        20.91        28.08         7.79        27.72       357.37 
TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK 
       53.52        40.27        15.45        32.75        47.38        23.93 
TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZZ TCGA-FS-A4F0 
       74.73        11.41       148.80        26.56        27.02        77.82 
TCGA-FS-A4F5 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 
       28.73        34.03        54.41        80.68         0.20        22.92 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C9 
       55.59        13.51        19.30         9.90         7.23        15.78 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U4 TCGA-GN-A4U7 
      117.93        84.72        32.48        39.58        39.35        10.42 
TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LL TCGA-GN-A9SD TCGA-LH-A9QB TCGA-QB-A6FS 
       48.89        22.13        21.37        59.41       368.78         7.23 
TCGA-QB-AA9O TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A828 TCGA-W3-AA1O 
       18.05         0.33         0.69       228.16       121.08         4.01 
TCGA-W3-AA1Q TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K5 
       69.07       219.16       105.04        24.03        49.05        61.15 
TCGA-WE-A8K6 TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-AA9Y 
       15.98        58.98        67.63        59.77        11.80        12.16 
TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-YD-A89C TCGA-YD-A9TA TCGA-YG-AA3O TCGA-YG-AA3P 
       35.01        19.73         6.90        49.18        37.94        14.43 
TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
       27.58        96.99        15.98 

  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
             0.23              0.20 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
           340.14            369.93 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
            54.79             50.76 
[1] "0.2 - 340.1 (54.8)" "0.2 - 369.9 (50.8)"
[1] "hr=" "1.1"
D51V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  5Q LOSS MUTATED                   17             1
  5Q LOSS WILD-TYPE                 48             4
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  5Q LOSS MUTATED                                          24
  5Q LOSS WILD-TYPE                                        48
                   vv
clus                REGIONAL LYMPH NODE
  5Q LOSS MUTATED                    56
  5Q LOSS WILD-TYPE                 159
D51V4, multiclass
                                           clus
vv                                          5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  DISTANT METASTASIS                                     17                48
  PRIMARY TUMOR                                           1                 4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE              24                48
  REGIONAL LYMPH NODE                                    56               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                I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  5Q LOSS MUTATED             4       3       9        4        5        9
  5Q LOSS WILD-TYPE           8       4      19       14       22       15
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  5Q LOSS MUTATED           2         4         4        11          5
  5Q LOSS WILD-TYPE        12        15         8        26         10
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  5Q LOSS MUTATED           11         15        4
  5Q LOSS WILD-TYPE         21         45       16
D51V5, multiclass
             clus
vv            5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  I OR II NOS               4                 8
  STAGE 0                   3                 4
  STAGE I                   9                19
  STAGE IA                  4                14
  STAGE IB                  5                22
  STAGE II                  9                15
  STAGE IIA                 2                12
  STAGE IIB                 4                15
  STAGE IIC                 4                 8
  STAGE III                11                26
  STAGE IIIA                5                10
  STAGE IIIB               11                21
  STAGE IIIC               15                45
  STAGE IV                  4                16
[1] 14  2
[1] TRUE
[1] "dimension of contingency 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      17 19 21 22
  5Q LOSS WILD-TYPE    47 53 56 46
D51V6, multiclass
       clus
vv      5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  T0+T1              17                47
  T2                 19                53
  T3                 21                56
  T4                 22                46
[1] 4 2
[1] TRUE
[1] "dimension of 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    44  23  10  11
  5Q LOSS WILD-TYPE 125  40  28  38
D51V7, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  N0              44               125
  N1              23                40
  N2              10                28
  N3              11                38
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V8, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED    87   4
  5Q LOSS WILD-TYPE 226  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     87    4
  5Q LOSS WILD-TYPE  226   17
   clus
vv  5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  0              87               226
  1               4                17
[1] 2 2
[1] FALSE
D51V9, binary
                   cls
clus                 0  1
  5Q LOSS MUTATED   33 25
  5Q LOSS WILD-TYPE 99 63
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     33   25
  5Q LOSS WILD-TYPE   99   63
     clus
vv    5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  NO               33                99
  YES              25                63
[1] 2 2
[1] FALSE
D51V10, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED     8  90
  5Q LOSS WILD-TYPE  36 223
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      8   90
  5Q LOSS WILD-TYPE   36  223
     clus
vv    5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  NO                8                36
  YES              90               223
[1] 2 2
[1] FALSE
D51V11, continuous
D51V12, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED    38  60
  5Q LOSS WILD-TYPE  97 163
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     38   60
  5Q LOSS WILD-TYPE   97  163
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  FEMALE              38                97
  MALE                60               163
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  5Q LOSS MUTATED       2                         1    93
  5Q LOSS WILD-TYPE     3                         0   251
D51V13, multiclass
                           clus
vv                          5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  ASIAN                                   2                 3
  BLACK OR AFRICAN AMERICAN               1                 0
  WHITE                                  93               251
[1] 3 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     0  93
  5Q LOSS WILD-TYPE   7 251
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      0   93
  5Q LOSS WILD-TYPE    7  251
                        clus
vv                       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 7
  NOT HISPANIC OR LATINO              93               251
[1] 2 2
[1] FALSE

Clustering(52) Variable = 6P LOSS MUTATION ANALYSIS
D52V1, survival
                   sevent
clus2                 0   1
  6P LOSS MUTATED    19  24
  6P LOSS WILD-TYPE 102  94
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               43               196 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               24                94 
$`6P LOSS MUTATED`
TCGA-D3-A1Q4 TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JH 
       31.89        25.64        45.99        86.30         7.27        36.30 
TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A3ML TCGA-D3-A5GR TCGA-D3-A8GC TCGA-D3-A8GD 
      171.58        64.83        13.87       177.86        78.21        23.61 
TCGA-D3-A8GM TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1IC 
       70.62        57.90        22.85       106.85        31.96        58.85 
TCGA-DA-A3F5 TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29Q 
      214.59        24.89        62.37        12.99        44.28        61.12 
TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2GL TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MC 
      185.19       102.38        32.48       103.13        15.25        23.77 
TCGA-EE-A3J4 TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A2NE TCGA-FR-A8YC TCGA-FS-A1ZG 
      111.85        53.29        11.47        16.87        10.06         7.82 
TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FW-A3TU TCGA-GN-A4U4 TCGA-QB-A6FS 
      130.95       136.27        35.28        55.59        34.49         7.23 
TCGA-WE-A8ZM 
       62.99 

$`6P LOSS WILD-TYPE`
TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q5 
       60.46        12.99        14.83         8.42        15.72       110.93 
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J8 
       49.35       133.25        19.04        76.41        62.60        62.86 
TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JE TCGA-D3-A2JG TCGA-D3-A2JO TCGA-D3-A2JP 
       15.75       168.00         9.76       107.61        66.08        43.53 
TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF 
       58.06        46.98       140.98        40.01        59.70        16.96 
TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51J TCGA-D3-A51K 
        9.34        90.21        23.67       173.85       144.46        31.76 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GU TCGA-D3-A8GJ 
       62.70        11.34        42.05        45.70       124.08       179.97 
TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GP TCGA-D3-A8GR TCGA-D9-A1X3 TCGA-D9-A3Z1 
      120.00        69.53       135.12        36.53        10.78        15.02 
TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-DA-A1HV TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 
       16.90        18.44        48.66       150.61        82.85        32.42 
TCGA-DA-A1IA TCGA-DA-A3F2 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5SG TCGA-EB-A5SH 
       64.83        25.12        14.96         3.91        33.24        50.07 
TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A184 
       45.50         6.64        13.15        20.38         0.00        67.50 
TCGA-EE-A20C TCGA-EE-A20H TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H 
       75.55       155.90        75.22        76.14         0.26        63.12 
TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29T TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB 
       47.74        27.16       346.49         7.20        77.98        26.14 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GM 
      239.11         0.20       189.40        68.65        10.62        18.35 
TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU 
       31.00       118.32         0.76         0.20        71.31        81.99 
TCGA-EE-A2M8 TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK 
        5.75       209.79        94.19       171.85        63.25        67.50 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT 
      104.78       145.45       227.01        25.08       143.93        23.51 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
       53.26       124.31       122.73        51.62         4.41        54.51 
TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JI 
        6.28        67.89        45.90         3.35       201.80       152.81 
TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A 
       14.56        34.45         1.58        47.31         7.82         4.54 
TCGA-ER-A19C TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
       39.81       151.46       150.12        99.06        59.84        42.48 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
      120.76        49.71        34.95       146.63        47.97        22.36 
TCGA-ER-A2ND TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL 
        4.70        10.95       173.29        55.82        15.48        32.05 
TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FS-A1YW TCGA-FS-A1YY 
      174.21       209.23        26.20         5.65       171.78        49.74 
TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE 
      195.98         8.35        27.62       312.07        32.78        35.90 
TCGA-FS-A1ZF TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY 
       12.92        36.33        78.61         4.47        23.21         5.29 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FD 
        3.06        30.90        66.67       173.19        13.28        80.68 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 
       11.54        19.30         9.90         6.05         1.91        53.29 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 
      117.93        84.72        17.06        42.48         7.59       120.53 
TCGA-GN-A4U8 TCGA-GN-A8LK TCGA-GN-A9SD TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-AA9O 
       46.92        43.23        59.41        85.05       297.01        18.05 
TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1Q TCGA-W3-AA1R 
        0.33       174.12         1.97       120.07        44.05        79.99 
TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8ZN 
        8.09       185.13        92.84         1.15        59.64        12.69 
TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 
       19.00        59.44        10.95        48.39         1.94        26.60 
TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-Z2-AA3S 
       16.64        15.65        28.21        91.23 

  6P LOSS MUTATED 6P LOSS WILD-TYPE 
             7.23              0.00 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
           214.59            346.49 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
            45.99             46.41 
[1] "7.2 - 214.6 (46.0)" "0.0 - 346.5 (46.4)"
[1] "hr=" "1.2"
D52V2, survival
                   sevent
clus2                 0   1
  6P LOSS MUTATED    27  37
  6P LOSS WILD-TYPE 142 143
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               64               285 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               37               143 
$`6P LOSS MUTATED`
TCGA-D3-A1Q4 TCGA-D3-A1Q9 TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2JC TCGA-D3-A2JD 
      112.04        31.59        43.43       103.10        86.76        11.87 
TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A3ML TCGA-D3-A3MV TCGA-D3-A51N 
       42.08       171.58        66.48        13.87        45.30        22.62 
TCGA-D3-A5GR TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GI TCGA-D3-A8GM TCGA-D3-A8GN 
      178.32        79.59        23.61        58.52       107.15       161.00 
TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I4 
       25.18        66.25        22.95       117.21       194.83        35.93 
TCGA-DA-A1I8 TCGA-DA-A1IC TCGA-DA-A3F5 TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A29A 
       53.92        68.09       215.44        27.22        94.98        63.35 
TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29Q TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 
       13.97        72.07        66.74       195.02        17.92        46.82 
TCGA-EE-A2A1 TCGA-EE-A2GL TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MC 
      102.90        79.66        21.67       129.27        28.83        61.51 
TCGA-EE-A3J4 TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19J TCGA-ER-A19T TCGA-ER-A2NE 
      127.20        98.40        12.59         6.44         8.88        20.15 
TCGA-FR-A69P TCGA-FR-A8YC TCGA-FS-A1YX TCGA-FS-A1ZB TCGA-FS-A1ZG TCGA-FS-A1ZQ 
       15.72        34.82        48.59        48.85         9.70       133.55 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FW-A3TU TCGA-GN-A4U4 TCGA-HR-A2OG 
       11.41       148.80        53.16        55.59        39.35         0.23 
TCGA-QB-A6FS TCGA-WE-A8JZ TCGA-WE-A8ZM TCGA-YG-AA3P 
        7.23        24.03        98.89        14.43 

$`6P LOSS WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q3 
       17.03        66.48        12.99        14.93        16.57        16.67 
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB 
      112.57        71.80       133.25        28.08        90.90        95.74 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JE TCGA-D3-A2JF 
       65.49        23.77       115.53       168.00        27.65        62.07 
TCGA-D3-A2JG TCGA-D3-A2JK TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 
      113.52        12.10        66.08        59.57       130.72        58.06 
TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF 
       46.98        46.32       166.52        86.93        60.23        24.53 
TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
        9.34       103.59        39.75       174.84        55.73        56.35 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN 
      145.12        32.94        63.81        26.89       125.79       135.75 
TCGA-D3-A5GO TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GE TCGA-D3-A8GJ 
      137.92        18.18       125.19        30.84        26.43       241.38 
TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS 
      170.20        89.13       152.75        29.06       129.63       117.17 
TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A1X3 TCGA-D9-A3Z1 
      151.53        54.67         3.65         7.10        18.12        15.39 
TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I0 
       22.29        18.44         9.90        48.89        36.03        20.38 
TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A3F2 
      176.55       107.34        61.18        65.92        23.44        28.60 
TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG 
       10.49        15.68        13.87        10.36        20.35        68.25 
TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X 
       54.02        17.29        52.01         7.04        24.89        29.82 
TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 
        8.65        33.73        14.70        26.89        68.15         4.96 
TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29B 
      133.81       151.27        91.56       168.26        13.55        85.08 
TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N 
       78.97        63.78        64.64         2.60        56.84        18.61 
TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A2A2 
       56.42        14.47        61.28       369.93        25.87        36.82 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE 
       39.29        86.14        59.28        67.43       340.14       161.03 
TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GM TCGA-EE-A2GN 
      208.04        48.72       107.38        54.74        75.48       102.12 
TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU 
      126.81        13.91        42.77        81.21        44.88        94.82 
TCGA-EE-A2M8 TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH 
       19.76        47.28       103.27       268.73       103.20        16.96 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN 
      204.66        96.23       158.63       216.66       167.90        47.54 
TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU 
      248.65        43.23       134.40       162.48        71.21        53.26 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
      124.31       122.73        51.62        28.77        54.51        13.81 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 
       41.59       138.81       172.18        36.95        64.08        34.32 
TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI 
       53.19       201.80        27.35        51.35       109.58       152.81 
TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A 
       31.40        35.44        13.94        50.76         9.17        77.75 
TCGA-ER-A19C TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L 
       48.89        13.02        26.37       268.93       152.35       131.51 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W 
       61.05        44.05       162.08        50.89        37.25       148.18 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH 
       79.99        43.82        23.34        16.37        31.27        32.05 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN 
      247.04        80.32        46.98        33.21         6.77        92.98 
TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YD 
      174.21       220.80        27.85        18.77        38.27        36.26 
TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 
      104.42       216.92       228.59       202.65        20.91        28.08 
TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF 
        7.79        27.72       357.37        53.52        40.27        15.45 
TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZU 
       32.75        47.38        23.93       101.26        74.73        26.56 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 
       49.48        27.09        27.02        77.82        50.14        66.67 
TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD 
       28.73       174.84        34.03        26.73        54.41        80.68 
TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
        0.20        22.92        13.51        19.30         9.90         7.23 
TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 
        2.04        15.78       139.89       117.93        84.72        10.13 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A4U7 
       64.44        62.79        32.48        39.58       121.91        10.42 
TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A8LL TCGA-GN-A9SD TCGA-HR-A2OH 
       48.89        22.13        50.10        21.37        59.41        65.88 
TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-AA9O TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 
      368.78       297.90        18.05         0.33         0.69       228.16 
TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1V 
       63.02       121.08         4.01        69.07       111.09        42.08 
TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZN 
      219.16       105.04        49.05        61.15        15.98        58.98 
TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AA9Y 
       67.63        59.77        11.80        32.58        49.51        12.16 
TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YD-A89C TCGA-YD-A9TA TCGA-YG-AA3O 
       35.01        19.73        22.29         6.90        49.18        37.94 
TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
       27.58        96.99        15.98 

  6P LOSS MUTATED 6P LOSS WILD-TYPE 
             0.23              0.20 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
           215.44            369.93 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
           51.005            50.890 
[1] "0.2 - 215.4 (51.0)" "0.2 - 369.9 (50.9)"
[1] "hr=" "1.3"
D52V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  6P LOSS MUTATED                   11             3
  6P LOSS WILD-TYPE                 54             2
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  6P LOSS MUTATED                                          16
  6P LOSS WILD-TYPE                                        56
                   vv
clus                REGIONAL LYMPH NODE
  6P LOSS MUTATED                    36
  6P LOSS WILD-TYPE                 179
D52V4, multiclass
                                           clus
vv                                          6P LOSS MUTATED 6P LOSS WILD-TYPE
  DISTANT METASTASIS                                     11                54
  PRIMARY TUMOR                                           3                 2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE              16                56
  REGIONAL LYMPH NODE                                    36               179
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  6P LOSS MUTATED             5       2       5        1        4        4
  6P LOSS WILD-TYPE           7       5      23       17       23       20
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  6P LOSS MUTATED           3         5         0         5          5
  6P LOSS WILD-TYPE        11        14        12        32         10
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  6P LOSS MUTATED            6         15        3
  6P LOSS WILD-TYPE         26         45       17
D52V5, multiclass
             clus
vv            6P LOSS MUTATED 6P LOSS WILD-TYPE
  I OR II NOS               5                 7
  STAGE 0                   2                 5
  STAGE I                   5                23
  STAGE IA                  1                17
  STAGE IB                  4                23
  STAGE II                  4                20
  STAGE IIA                 3                11
  STAGE IIB                 5                14
  STAGE IIC                 0                12
  STAGE III                 5                32
  STAGE IIIA                5                10
  STAGE IIIB                6                26
  STAGE IIIC               15                45
  STAGE IV                  3                17
[1] 14  2
[1] TRUE
[1] "dimension of contingency 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      10 13 17 12
  6P LOSS WILD-TYPE    54 59 60 56
D52V6, multiclass
       clus
vv      6P LOSS MUTATED 6P LOSS WILD-TYPE
  T0+T1              10                54
  T2                 13                59
  T3                 17                60
  T4                 12                56
[1] 4 2
[1] TRUE
[1] "dimension of 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    30  13   8  12
  6P LOSS WILD-TYPE 139  50  30  37
D52V7, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  N0              30               139
  N1              13                50
  N2               8                30
  N3              12                37
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V8, binary
                   cls
clus                  0   1
  6P LOSS MUTATED    60   3
  6P LOSS WILD-TYPE 253  18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     60    3
  6P LOSS WILD-TYPE  253   18
   clus
vv  6P LOSS MUTATED 6P LOSS WILD-TYPE
  0              60               253
  1               3                18
[1] 2 2
[1] FALSE
D52V9, binary
                   cls
clus                  0   1
  6P LOSS MUTATED    21  20
  6P LOSS WILD-TYPE 111  68
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     21   20
  6P LOSS WILD-TYPE  111   68
     clus
vv    6P LOSS MUTATED 6P LOSS WILD-TYPE
  NO               21               111
  YES              20                68
[1] 2 2
[1] FALSE
D52V10, binary
                   cls
clus                  0   1
  6P LOSS MUTATED     9  57
  6P LOSS WILD-TYPE  35 256
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      9   57
  6P LOSS WILD-TYPE   35  256
     clus
vv    6P LOSS MUTATED 6P LOSS WILD-TYPE
  NO                9                35
  YES              57               256
[1] 2 2
[1] FALSE
D52V11, continuous
D52V12, binary
                   cls
clus                  0   1
  6P LOSS MUTATED    22  44
  6P LOSS WILD-TYPE 113 179
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     22   44
  6P LOSS WILD-TYPE  113  179
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  FEMALE              22               113
  MALE                44               179
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  6P LOSS MUTATED       1                         0    62
  6P LOSS WILD-TYPE     4                         1   282
D52V13, multiclass
                           clus
vv                          6P LOSS MUTATED 6P LOSS WILD-TYPE
  ASIAN                                   1                 4
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  62               282
[1] 3 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     1  61
  6P LOSS WILD-TYPE   6 283
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      1   61
  6P LOSS WILD-TYPE    6  283
                        clus
vv                       6P LOSS MUTATED 6P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 6
  NOT HISPANIC OR LATINO              61               283
[1] 2 2
[1] FALSE

Clustering(53) Variable = 6Q LOSS MUTATION ANALYSIS
D53V1, survival
                   sevent
clus2                0  1
  6Q LOSS MUTATED   59 56
  6Q LOSS WILD-TYPE 62 62
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
              115               124 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               56                62 
$`6Q LOSS MUTATED`
TCGA-3N-A9WC TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A2J6 TCGA-D3-A2J7 
       60.46         8.42        31.89       110.93        25.64        45.99 
TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN 
      168.00        86.30         7.27        36.30       171.58        64.83 
TCGA-D3-A2JO TCGA-D3-A3C6 TCGA-D3-A3ML TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51J 
       66.08        58.06        13.87        90.21        23.67       144.46 
TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A8GC TCGA-D3-A8GD 
       11.34        42.05        45.70       177.86        78.21        23.61 
TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GP TCGA-D9-A3Z3 TCGA-D9-A6EC TCGA-D9-A6EG 
       69.53        70.62       135.12        16.90        57.90        22.85 
TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC 
       48.66       106.85        31.96        32.42        64.83        58.85 
TCGA-DA-A3F5 TCGA-EB-A5UN TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 
      214.59        45.50        24.89        62.37        20.38         0.00 
TCGA-EE-A184 TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M 
       67.50        76.14        12.99        44.28        63.12        47.74 
TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 
       61.12       346.49       185.19       102.38         7.20        77.98 
TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GO 
       26.14       239.11         0.20        32.48        31.00       118.32 
TCGA-EE-A2GP TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MC TCGA-EE-A2MF 
        0.76        81.99       103.13        15.25        23.77       209.79 
TCGA-EE-A2MP TCGA-EE-A2MT TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3J4 
      227.01        23.51        51.62         4.41         6.28       111.85 
TCGA-EE-A3J7 TCGA-EE-A3JB TCGA-ER-A195 TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19D 
       45.90       201.80        34.45         7.82        53.29        11.47 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A2NE TCGA-ER-A3PL TCGA-FR-A7U8 TCGA-FR-A8YC 
       42.48       120.76        16.87        32.05        26.20        10.06 
TCGA-FS-A1Z0 TCGA-FS-A1ZC TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM 
      195.98       312.07        12.92         7.82        36.33        78.61 
TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZZ 
      130.95       136.27        35.28         4.47        23.21         3.06 
TCGA-FW-A3TU TCGA-GF-A4EO TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
       55.59         6.05       117.93        17.06        42.48         7.59 
TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS 
      120.53        34.49        46.92        85.05       297.01         7.23 
TCGA-RP-A693 TCGA-W3-AA1R TCGA-WE-A8ZM TCGA-WE-A8ZQ TCGA-WE-AAA3 TCGA-WE-AAA4 
        0.33        79.99        62.99        59.44        16.64        15.65 
TCGA-YG-AA3O 
       28.21 

$`6Q LOSS WILD-TYPE`
TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q3 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       12.99        14.83        15.72        49.35       133.25        19.04 
TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JE TCGA-D3-A2JG 
       76.41        62.60        62.86        15.75         9.76       107.61 
TCGA-D3-A2JP TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF 
       43.53        46.98       140.98        40.01        59.70        16.96 
TCGA-D3-A3MO TCGA-D3-A51E TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A5GU TCGA-D3-A8GJ 
        9.34       173.85        31.76        62.70       124.08       179.97 
TCGA-D3-A8GK TCGA-D3-A8GR TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A4Z6 TCGA-DA-A1I2 
      120.00        36.53        10.78        15.02        18.44       150.61 
TCGA-DA-A1I5 TCGA-DA-A3F2 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5SG TCGA-EB-A5SH 
       82.85        25.12        14.96         3.91        33.24        50.07 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A20C TCGA-EE-A20H TCGA-EE-A29B TCGA-EE-A29E 
        6.64        13.15        75.55       155.90        75.22         0.26 
TCGA-EE-A29P TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GM TCGA-EE-A2GR 
       27.16       189.40        68.65        10.62        18.35         0.20 
TCGA-EE-A2GS TCGA-EE-A2M8 TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK 
       71.31         5.75        94.19       171.85        63.25        67.50 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AA 
      104.78       145.45        25.08       143.93        53.26       124.31 
TCGA-EE-A3AB TCGA-EE-A3AE TCGA-EE-A3J3 TCGA-EE-A3J8 TCGA-EE-A3JI TCGA-ER-A193 
      122.73        54.51        67.89         3.35       152.81        14.56 
TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19C TCGA-ER-A19G TCGA-ER-A19H 
        1.58        47.31         4.54        39.81       151.46       150.12 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 
       99.06        59.84        49.71        34.95       146.63        47.97 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
       22.36         4.70        10.95       173.29        55.82        15.48 
TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7UA TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z3 
      174.21       209.23         5.65       171.78        49.74         8.35 
TCGA-FS-A1Z4 TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZY TCGA-FS-A4F0 TCGA-FS-A4F4 
       27.62        32.78        35.90         5.29        30.90        66.67 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
      173.19        13.28        80.68        11.54        19.30         9.90 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A8LK TCGA-GN-A9SD TCGA-QB-AA9O 
        1.91        53.29        84.72        43.23        59.41        18.05 
TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1Q TCGA-W3-AA1V TCGA-W3-AA1W 
      174.12         1.97       120.07        44.05         8.09       185.13 
TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT 
       92.84         1.15        59.64        12.69        19.00        10.95 
TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-Z2-AA3S 
       48.39         1.94        26.60        91.23 

  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
              0.0               0.2 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
           346.49            209.23 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
           45.900            47.145 
[1] "0.0 - 346.5 (45.9)" "0.2 - 209.2 (47.1)"
[1] "hr=" "1.1"
D53V2, survival
                   sevent
clus2                0  1
  6Q LOSS MUTATED   76 86
  6Q LOSS WILD-TYPE 93 94
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
              162               187 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               86                94 
$`6Q LOSS MUTATED`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q9 
       17.03        66.48        16.57       112.04       112.57        31.59 
TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF 
       43.43       103.10       168.00        86.76        11.87        62.07 
TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A3C6 TCGA-D3-A3ML 
       42.08       171.58        66.48        66.08        58.06        13.87 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51J TCGA-D3-A51N TCGA-D3-A51T 
      103.59        39.75        45.30       145.12        22.62        26.89 
TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GI 
      125.79       135.75       178.32        79.59        23.61        58.52 
TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D9-A148 TCGA-D9-A1JW 
       89.13       107.15       161.00       152.75       151.53         3.65 
TCGA-D9-A1JX TCGA-D9-A3Z3 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV 
        7.10        22.29        25.18        66.25        22.95        48.89 
TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I4 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA 
      117.21       194.83        35.93        61.18        53.92        65.92 
TCGA-DA-A1IC TCGA-DA-A3F5 TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17Y TCGA-EE-A180 
       68.09       215.44        17.29        52.01        27.22        94.98 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B 
       33.73        14.70        26.89        68.15         4.96       133.81 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29H 
       13.55        63.35        78.97        13.97        72.07        64.64 
TCGA-EE-A29M TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W 
       56.84        66.74        61.28       369.93        25.87       195.02 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
       17.92        46.82       102.90        36.82        39.29        86.14 
TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GO 
       59.28       340.14       161.03        79.66       102.12       126.81 
TCGA-EE-A2GP TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MC 
       13.91        94.82        21.67       129.27        28.83        61.51 
TCGA-EE-A2MF TCGA-EE-A2MP TCGA-EE-A2MT TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AF 
      268.73       248.65        71.21        51.62        28.77        13.81 
TCGA-EE-A3AG TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3JB TCGA-EE-A3JH TCGA-ER-A195 
       41.59       127.20        64.08       201.80       109.58        35.44 
TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19N 
        9.17        98.40        12.59        26.37         6.44        44.05 
TCGA-ER-A19P TCGA-ER-A19T TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A3PL TCGA-ER-A42K 
      162.08         8.88        20.15        16.37        33.21         6.77 
TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FS-A1YX TCGA-FS-A1Z0 
       15.72        27.85        34.82        36.26        48.59       202.65 
TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ 
       48.85       357.37        15.45         9.70        32.75        47.38 
TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU 
      101.26       133.55        11.41       148.80        53.16        26.56 
TCGA-FS-A1ZW TCGA-FS-A1ZZ TCGA-FS-A4F5 TCGA-FS-A4FB TCGA-FW-A3R5 TCGA-FW-A3TU 
       49.48        27.02        28.73        26.73        22.92        55.59 
TCGA-GF-A4EO TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 
        7.23       117.93        64.44        62.79        32.48       121.91 
TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LL TCGA-HR-A2OG 
       39.35        10.42        48.89        22.13        21.37         0.23 
TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A693 TCGA-W3-AA1R TCGA-WE-A8JZ 
      368.78       297.90         7.23         0.33       111.09        24.03 
TCGA-WE-A8ZM TCGA-WE-A8ZQ TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-YG-AA3P 
       98.89        59.77        19.73        22.29        37.94        14.43 

$`6Q LOSS WILD-TYPE`
TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q3 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       12.99        14.93        16.67        71.80       133.25        28.08 
TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JE 
       90.90        95.74        65.49        23.77       115.53        27.65 
TCGA-D3-A2JG TCGA-D3-A2JK TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3C8 
      113.52        12.10        59.57       130.72        46.98        46.32 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A51E 
      166.52        86.93        60.23        24.53         9.34       174.84 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A5GO TCGA-D3-A5GS 
       55.73        56.35        32.94        63.81       137.92        18.18 
TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GQ 
      125.19        30.84        26.43       241.38       170.20        29.06 
TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A149 TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A4Z6 
      129.63       117.17        54.67        18.12        15.39        18.44 
TCGA-D9-A6E9 TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1IB 
        9.90        36.03        20.38       176.55       107.34        23.44 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH 
       28.60        10.49        15.68        13.87        10.36        20.35 
TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Z 
       68.25        54.02         7.04        24.89        29.82         8.65 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29B TCGA-EE-A29E TCGA-EE-A29L 
      151.27        91.56       168.26        85.08        63.78         2.60 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A2GC TCGA-EE-A2GH TCGA-EE-A2GI 
       18.61        56.42        14.47        67.43       208.04        48.72 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GM TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT 
      107.38        54.74        75.48        42.77        81.21        44.88 
TCGA-EE-A2M8 TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
       19.76        47.28       103.27       103.20        16.96       204.66 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MQ 
       96.23       158.63       216.66       167.90        47.54        43.23 
TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AE 
      134.40       162.48        53.26       124.31       122.73        54.51 
TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J5 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD 
      138.81       172.18        36.95        34.32        53.19        27.35 
TCGA-EE-A3JE TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A19A 
       51.35       152.81        31.40        13.94        50.76        77.75 
TCGA-ER-A19C TCGA-ER-A19E TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M 
       48.89        13.02       268.93       152.35       131.51        61.05 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
       50.89        37.25       148.18        79.99        43.82        23.34 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-FR-A3YN 
       31.27        32.05       247.04        80.32        46.98        92.98 
TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YE TCGA-FS-A1YW 
      174.21       220.80        18.77        38.27       104.42       216.92 
TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZD 
      228.59        20.91        28.08         7.79        27.72        53.52 
TCGA-FS-A1ZE TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZY TCGA-FS-A4F0 TCGA-FS-A4F2 
       40.27        23.93        74.73        27.09        77.82        50.14 
TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 
       66.67       174.84        34.03        54.41        80.68         0.20 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 
       13.51        19.30         9.90         2.04        15.78       139.89 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A26D TCGA-GN-A8LK TCGA-GN-A9SD TCGA-HR-A2OH 
       84.72        10.13        39.58        50.10        59.41        65.88 
TCGA-QB-AA9O TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O 
       18.05         0.69       228.16        63.02       121.08         4.01 
TCGA-W3-AA1Q TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8K5 
       69.07        42.08       219.16       105.04        49.05        61.15 
TCGA-WE-A8K6 TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-A8ZY 
       15.98        58.98        67.63        11.80        32.58        49.51 
TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-YD-A89C TCGA-YD-A9TA TCGA-Z2-A8RT TCGA-Z2-AA3S 
       12.16        35.01         6.90        49.18        27.58        96.99 
TCGA-Z2-AA3V 
       15.98 

  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
             0.23              0.20 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
           369.93            268.93 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
            50.55             50.89 
[1] "0.2 - 369.9 (50.5)" "0.2 - 268.9 (50.9)"
[1] "hr=" "1"  
D53V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  6Q LOSS MUTATED                   32             4
  6Q LOSS WILD-TYPE                 33             1
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  6Q LOSS MUTATED                                          36
  6Q LOSS WILD-TYPE                                        36
                   vv
clus                REGIONAL LYMPH NODE
  6Q LOSS MUTATED                    95
  6Q LOSS WILD-TYPE                 120
D53V4, multiclass
                                           clus
vv                                          6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  DISTANT METASTASIS                                     32                33
  PRIMARY TUMOR                                           4                 1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE              36                36
  REGIONAL LYMPH NODE                                    95               120
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  6Q LOSS MUTATED             7       4      11        7       13        8
  6Q LOSS WILD-TYPE           5       3      17       11       14       16
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  6Q LOSS MUTATED           7         8         5        17          8
  6Q LOSS WILD-TYPE         7        11         7        20          7
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  6Q LOSS MUTATED           15         32        7
  6Q LOSS WILD-TYPE         17         28       13
D53V5, multiclass
             clus
vv            6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  I OR II NOS               7                 5
  STAGE 0                   4                 3
  STAGE I                  11                17
  STAGE IA                  7                11
  STAGE IB                 13                14
  STAGE II                  8                16
  STAGE IIA                 7                 7
  STAGE IIB                 8                11
  STAGE IIC                 5                 7
  STAGE III                17                20
  STAGE IIIA                8                 7
  STAGE IIIB               15                17
  STAGE IIIC               32                28
  STAGE IV                  7                13
[1] 14  2
[1] TRUE
[1] "dimension of contingency 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      28 38 33 29
  6Q LOSS WILD-TYPE    36 34 44 39
D53V6, multiclass
       clus
vv      6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  T0+T1              28                36
  T2                 38                34
  T3                 33                44
  T4                 29                39
[1] 4 2
[1] TRUE
[1] "dimension of 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   72 33 19 25
  6Q LOSS WILD-TYPE 97 30 19 24
D53V7, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  N0              72                97
  N1              33                30
  N2              19                19
  N3              25                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V8, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED   149   8
  6Q LOSS WILD-TYPE 164  13
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED    149    8
  6Q LOSS WILD-TYPE  164   13
   clus
vv  6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  0             149               164
  1               8                13
[1] 2 2
[1] FALSE
D53V9, binary
                   cls
clus                 0  1
  6Q LOSS MUTATED   55 47
  6Q LOSS WILD-TYPE 77 41
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     55   47
  6Q LOSS WILD-TYPE   77   41
     clus
vv    6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  NO               55                77
  YES              47                41
[1] 2 2
[1] FALSE
D53V10, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED    21 145
  6Q LOSS WILD-TYPE  23 168
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     21  145
  6Q LOSS WILD-TYPE   23  168
     clus
vv    6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  NO               21                23
  YES             145               168
[1] 2 2
[1] FALSE
D53V11, continuous
D53V12, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED    68  99
  6Q LOSS WILD-TYPE  67 124
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     68   99
  6Q LOSS WILD-TYPE   67  124
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  FEMALE              68                67
  MALE                99               124
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  6Q LOSS MUTATED       1                         1   160
  6Q LOSS WILD-TYPE     4                         0   184
D53V13, multiclass
                           clus
vv                          6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  ASIAN                                   1                 4
  BLACK OR AFRICAN AMERICAN               1                 0
  WHITE                                 160               184
[1] 3 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     3 160
  6Q LOSS WILD-TYPE   4 184
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      3  160
  6Q LOSS WILD-TYPE    4  184
                        clus
vv                       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   3                 4
  NOT HISPANIC OR LATINO             160               184
[1] 2 2
[1] FALSE

Clustering(54) Variable = 7P LOSS MUTATION ANALYSIS
D54V1, survival
                   sevent
clus2                 0   1
  7P LOSS MUTATED     6   6
  7P LOSS WILD-TYPE 115 112
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               12               227 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                6               112 
$`7P LOSS MUTATED`
TCGA-D3-A1QA TCGA-D3-A3CE TCGA-DA-A3F8 TCGA-EE-A20C TCGA-EE-A29M TCGA-EE-A3JI 
       76.41        59.70        14.96        75.55        47.74       152.81 
TCGA-ER-A198 TCGA-FR-A7U8 TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-W3-A828 
       47.31        26.20       136.27        35.28         4.47       120.07 

$`7P LOSS WILD-TYPE`
TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
       60.46        12.99        14.83         8.42        15.72        31.89 
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QB TCGA-D3-A2J6 
      110.93        49.35       133.25        19.04        62.60        25.64 
TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
       45.99        62.86        15.75       168.00        86.30         7.27 
TCGA-D3-A2JE TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
        9.76       107.61        36.30       171.58        64.83        66.08 
TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CF 
       43.53        58.06        46.98       140.98        40.01        16.96 
TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51J 
       13.87         9.34        90.21        23.67       173.85       144.46 
TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR 
       31.76        62.70        11.34        42.05        45.70       177.86 
TCGA-D3-A5GU TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL 
      124.08        78.21        23.61       179.97       120.00        69.53 
TCGA-D3-A8GM TCGA-D3-A8GP TCGA-D3-A8GR TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       70.62       135.12        36.53        10.78        15.02        16.90 
TCGA-D9-A4Z6 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 
       18.44        57.90        22.85        48.66       106.85        31.96 
TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 
      150.61        82.85        32.42        64.83        58.85        25.12 
TCGA-DA-A3F5 TCGA-EB-A44Q TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A6L9 
      214.59         3.91        33.24        50.07        45.50         6.64 
TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A184 
       13.15        24.89        62.37        20.38         0.00        67.50 
TCGA-EE-A20H TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G 
      155.90        75.22        76.14        12.99         0.26        44.28 
TCGA-EE-A29H TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 
       63.12        27.16        61.12       346.49       185.19       102.38 
TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
        7.20        77.98        26.14       239.11         0.20       189.40 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO 
       68.65        10.62        32.48        18.35        31.00       118.32 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 
        0.76         0.20        71.31        81.99       103.13        15.25 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ 
        5.75        23.77       209.79        94.19       171.85        63.25 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MR TCGA-EE-A2MS 
       67.50       104.78       145.45       227.01        25.08       143.93 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
       23.51        53.26       124.31       122.73        51.62         4.41 
TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 
       54.51         6.28        67.89       111.85        45.90         3.35 
TCGA-EE-A3JB TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A 
      201.80        14.56        34.45         1.58         7.82         4.54 
TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L 
       53.29        39.81        11.47       151.46       150.12        99.06 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W 
       59.84        42.48       120.76        49.71        34.95       146.63 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A3ES 
       47.97        22.36         4.70        16.87        10.95       173.29 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7UA 
       55.82        15.48        32.05       174.21       209.23         5.65 
TCGA-FR-A8YC TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 
       10.06       171.78        49.74       195.98         8.35        27.62 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZJ 
      312.07        32.78        35.90        12.92         7.82        36.33 
TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 
       78.61       130.95        23.21         5.29         3.06        30.90 
TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV 
       66.67       173.19        13.28        80.68        55.59        11.54 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 
       19.30         9.90         6.05         1.91        53.29       117.93 
TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 
       84.72        17.06        42.48         7.59       120.53        34.49 
TCGA-GN-A4U8 TCGA-GN-A8LK TCGA-GN-A9SD TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS 
       46.92        43.23        59.41        85.05       297.01         7.23 
TCGA-QB-AA9O TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-AA1Q TCGA-W3-AA1R 
       18.05         0.33       174.12         1.97        44.05        79.99 
TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8ZM 
        8.09       185.13        92.84         1.15        59.64        62.99 
TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AA9Y 
       12.69        19.00        59.44        10.95        48.39         1.94 
TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-Z2-AA3S 
       26.60        16.64        15.65        28.21        91.23 

  7P LOSS MUTATED 7P LOSS WILD-TYPE 
             4.47              0.00 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
           152.81            346.49 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
            53.72             45.70 
[1] "4.5 - 152.8 (53.7)" "0.0 - 346.5 (45.7)"
[1] "hr=" "1"  
D54V2, survival
                   sevent
clus2                 0   1
  7P LOSS MUTATED     7  11
  7P LOSS WILD-TYPE 162 169
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               18               331 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               11               169 
$`7P LOSS MUTATED`
TCGA-D3-A1QA TCGA-D3-A3CE TCGA-D3-A3MV TCGA-D3-A8GI TCGA-DA-A3F8 TCGA-EB-A44R 
       90.90        60.23        45.30        58.52        15.68        10.36 
TCGA-EE-A20C TCGA-EE-A29M TCGA-EE-A2A5 TCGA-EE-A3JA TCGA-EE-A3JI TCGA-ER-A198 
      151.27        56.84        39.29        53.19       152.81        50.76 
TCGA-FR-A7U8 TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-GN-A8LL TCGA-W3-A828 
       27.85       148.80        53.16        26.56        21.37       121.08 

$`7P LOSS WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q3 
       17.03        66.48        12.99        14.93        16.57        16.67 
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 
      112.04       112.57        71.80       133.25        28.08        31.59 
TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA 
       95.74        43.43       103.10        65.49        23.77       115.53 
TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A2JG 
      168.00        86.76        11.87        27.65        62.07       113.52 
TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP 
       42.08        12.10       171.58        66.48        66.08        59.57 
TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC 
      130.72        58.06        46.98        46.32       166.52        86.93 
TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E 
       24.53        13.87         9.34       103.59        39.75       174.84 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R 
       55.73        56.35       145.12        32.94        22.62        63.81 
TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       26.89       125.79       135.75       137.92       178.32        18.18 
TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GJ 
      125.19        30.84        79.59        23.61        26.43       241.38 
TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GQ 
      170.20        89.13       107.15       161.00       152.75        29.06 
TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX 
      129.63       117.17       151.53        54.67         3.65         7.10 
TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EA 
       18.12        15.39        22.29        18.44         9.90        25.18 
TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 
       66.25        22.95        48.89        36.03       117.21        20.38 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
      194.83       176.55        35.93       107.34        61.18        53.92 
TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 
       65.92        23.44        68.09        28.60        10.49       215.44 
TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN 
       13.87        20.35        68.25        54.02        17.29        52.01 
TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 
        7.04        24.89        29.82        27.22         8.65        94.98 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B 
       33.73        14.70        26.89        68.15         4.96       133.81 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C 
       91.56       168.26        13.55        63.35        85.08        78.97 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N 
       13.97        63.78        72.07        64.64         2.60        18.61 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V 
       56.42        66.74        14.47        61.28       369.93        25.87 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 
      195.02        17.92        46.82       102.90        36.82        86.14 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
       59.28        67.43       340.14       161.03       208.04        48.72 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO 
      107.38        54.74        79.66        75.48       102.12       126.81 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 
       13.91        42.77        81.21        44.88        94.82        21.67 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME 
      129.27        28.83        19.76        61.51        47.28       103.27 
TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK 
      268.73       103.20        16.96       204.66        96.23       158.63 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR 
      216.66       167.90        47.54       248.65        43.23       134.40 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC 
      162.48        71.21        53.26       124.31       122.73        51.62 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 
       28.77        54.51        13.81        41.59       138.81       172.18 
TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JD 
      127.20        36.95        64.08        34.32       201.80        27.35 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 
       51.35       109.58        31.40        35.44        13.94         9.17 
TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F 
       77.75        98.40        48.89        12.59        13.02        26.37 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
      268.93       152.35         6.44       131.51        61.05        44.05 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 
      162.08        50.89        37.25         8.88       148.18        79.99 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH 
       43.82        23.34        20.15        16.37        31.27        32.05 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN 
      247.04        80.32        46.98        33.21         6.77        92.98 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC 
      174.21        15.72       220.80        18.77        38.27        34.82 
TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
       36.26       104.42       216.92        48.59       228.59       202.65 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC 
       20.91        28.08         7.79        27.72        48.85       357.37 
TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ 
       53.52        40.27        15.45         9.70        32.75        47.38 
TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZW 
       23.93       101.26        74.73       133.55        11.41        49.48 
TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 
       27.09        27.02        77.82        50.14        66.67        28.73 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 
      174.84        34.03        26.73        54.41        80.68         0.20 
TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
       22.92        55.59        13.51        19.30         9.90         7.23 
TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 
        2.04        15.78       139.89       117.93        84.72        10.13 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A4U4 
       64.44        62.79        32.48        39.58       121.91        39.35 
TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A9SD TCGA-HR-A2OG 
       10.42        48.89        22.13        50.10        59.41         0.23 
TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 
       65.88       368.78       297.90         7.23        18.05         0.33 
TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-AA1O TCGA-W3-AA1Q TCGA-W3-AA1R 
        0.69       228.16        63.02         4.01        69.07       111.09 
TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K5 
       42.08       219.16       105.04        24.03        49.05        61.15 
TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT 
       15.98        98.89        58.98        67.63        59.77        11.80 
TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 
       32.58        49.51        12.16        35.01        19.73        22.29 
TCGA-YD-A89C TCGA-YD-A9TA TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S 
        6.90        49.18        37.94        14.43        27.58        96.99 
TCGA-Z2-AA3V 
       15.98 

  7P LOSS MUTATED 7P LOSS WILD-TYPE 
            10.36              0.20 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
           152.81            369.93 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
           53.175            50.140 
[1] "10.4 - 152.8 (53.2)" "0.2 - 369.9 (50.1)" 
[1] "hr=" "1.3"
D54V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  7P LOSS MUTATED                    5             0
  7P LOSS WILD-TYPE                 60             5
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  7P LOSS MUTATED                                           3
  7P LOSS WILD-TYPE                                        69
                   vv
clus                REGIONAL LYMPH NODE
  7P LOSS MUTATED                    10
  7P LOSS WILD-TYPE                 205
D54V4, multiclass
                                           clus
vv                                          7P LOSS MUTATED 7P LOSS WILD-TYPE
  DISTANT METASTASIS                                      5                60
  PRIMARY TUMOR                                           0                 5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               3                69
  REGIONAL LYMPH NODE                                    10               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"
                   vv
clus                I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  7P LOSS MUTATED             0       1       2        1        4        1
  7P LOSS WILD-TYPE          12       6      26       17       23       23
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  7P LOSS MUTATED           0         0         2         2          0
  7P LOSS WILD-TYPE        14        19        10        35         15
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  7P LOSS MUTATED            3          1        0
  7P LOSS WILD-TYPE         29         59       20
D54V5, multiclass
             clus
vv            7P LOSS MUTATED 7P LOSS WILD-TYPE
  I OR II NOS               0                12
  STAGE 0                   1                 6
  STAGE I                   2                26
  STAGE IA                  1                17
  STAGE IB                  4                23
  STAGE II                  1                23
  STAGE IIA                 0                14
  STAGE IIB                 0                19
  STAGE IIC                 2                10
  STAGE III                 2                35
  STAGE IIIA                0                15
  STAGE IIIB                3                29
  STAGE IIIC                1                59
  STAGE IV                  0                20
[1] 14  2
[1] TRUE
[1] "dimension of contingency 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       2  9  1  2
  7P LOSS WILD-TYPE    62 63 76 66
D54V6, multiclass
       clus
vv      7P LOSS MUTATED 7P LOSS WILD-TYPE
  T0+T1               2                62
  T2                  9                63
  T3                  1                76
  T4                  2                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
  7P LOSS MUTATED    10   2   3   1
  7P LOSS WILD-TYPE 159  61  35  48
D54V7, multiclass
    clus
vv   7P LOSS MUTATED 7P LOSS WILD-TYPE
  N0              10               159
  N1               2                61
  N2               3                35
  N3               1                48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V8, binary
                   cls
clus                  0   1
  7P LOSS MUTATED    18   0
  7P LOSS WILD-TYPE 295  21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED     18    0
  7P LOSS WILD-TYPE  295   21
   clus
vv  7P LOSS MUTATED 7P LOSS WILD-TYPE
  0              18               295
  1               0                21
[1] 2 2
[1] FALSE
D54V9, binary
                   cls
clus                  0   1
  7P LOSS MUTATED     7   4
  7P LOSS WILD-TYPE 125  84
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      7    4
  7P LOSS WILD-TYPE  125   84
     clus
vv    7P LOSS MUTATED 7P LOSS WILD-TYPE
  NO                7               125
  YES               4                84
[1] 2 2
[1] FALSE
D54V10, binary
                   cls
clus                  0   1
  7P LOSS MUTATED     2  16
  7P LOSS WILD-TYPE  42 297
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      2   16
  7P LOSS WILD-TYPE   42  297
     clus
vv    7P LOSS MUTATED 7P LOSS WILD-TYPE
  NO                2                42
  YES              16               297
[1] 2 2
[1] FALSE
D54V11, continuous
D54V12, binary
                   cls
clus                  0   1
  7P LOSS MUTATED     5  13
  7P LOSS WILD-TYPE 130 210
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      5   13
  7P LOSS WILD-TYPE  130  210
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  FEMALE               5               130
  MALE                13               210
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  7P LOSS MUTATED       1                         0    17
  7P LOSS WILD-TYPE     4                         1   327
D54V13, multiclass
                           clus
vv                          7P LOSS MUTATED 7P LOSS WILD-TYPE
  ASIAN                                   1                 4
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  17               327
[1] 3 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     0  18
  7P LOSS WILD-TYPE   7 326
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      0   18
  7P LOSS WILD-TYPE    7  326
                        clus
vv                       7P LOSS MUTATED 7P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 7
  NOT HISPANIC OR LATINO              18               326
[1] 2 2
[1] FALSE

Clustering(55) Variable = 7Q LOSS MUTATION ANALYSIS
D55V1, survival
                   sevent
clus2                 0   1
  7Q LOSS MUTATED     6   7
  7Q LOSS WILD-TYPE 115 111
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               13               226 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                7               111 
$`7Q LOSS MUTATED`
TCGA-D3-A1QA TCGA-D3-A3CE TCGA-EE-A29D TCGA-EE-A29M TCGA-EE-A2GN TCGA-EE-A3JI 
       76.41        59.70        12.99        47.74        31.00       152.81 
TCGA-ER-A19W TCGA-FS-A1ZE TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A4F0 TCGA-W3-A828 
      146.63        35.90        35.28         4.47        30.90       120.07 
TCGA-WE-A8ZM 
       62.99 

$`7Q LOSS WILD-TYPE`
TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
       60.46        12.99        14.83         8.42        15.72        31.89 
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QB TCGA-D3-A2J6 
      110.93        49.35       133.25        19.04        62.60        25.64 
TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
       45.99        62.86        15.75       168.00        86.30         7.27 
TCGA-D3-A2JE TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
        9.76       107.61        36.30       171.58        64.83        66.08 
TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CF 
       43.53        58.06        46.98       140.98        40.01        16.96 
TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51J 
       13.87         9.34        90.21        23.67       173.85       144.46 
TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR 
       31.76        62.70        11.34        42.05        45.70       177.86 
TCGA-D3-A5GU TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL 
      124.08        78.21        23.61       179.97       120.00        69.53 
TCGA-D3-A8GM TCGA-D3-A8GP TCGA-D3-A8GR TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       70.62       135.12        36.53        10.78        15.02        16.90 
TCGA-D9-A4Z6 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 
       18.44        57.90        22.85        48.66       106.85        31.96 
TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 
      150.61        82.85        32.42        64.83        58.85        25.12 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN 
      214.59        14.96         3.91        33.24        50.07        45.50 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 
        6.64        13.15        24.89        62.37        20.38         0.00 
TCGA-EE-A184 TCGA-EE-A20C TCGA-EE-A20H TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E 
       67.50        75.55       155.90        75.22        76.14         0.26 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W 
       44.28        63.12        27.16        61.12       346.49       185.19 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE 
      102.38         7.20        77.98        26.14       239.11         0.20 
TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GO 
      189.40        68.65        10.62        32.48        18.35       118.32 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 
        0.76         0.20        71.31        81.99       103.13        15.25 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ 
        5.75        23.77       209.79        94.19       171.85        63.25 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MR TCGA-EE-A2MS 
       67.50       104.78       145.45       227.01        25.08       143.93 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
       23.51        53.26       124.31       122.73        51.62         4.41 
TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 
       54.51         6.28        67.89       111.85        45.90         3.35 
TCGA-EE-A3JB TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 
      201.80        14.56        34.45         1.58        47.31         7.82 
TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19H 
        4.54        53.29        39.81        11.47       151.46       150.12 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S 
       99.06        59.84        42.48       120.76        49.71        34.95 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A3ES 
       47.97        22.36         4.70        16.87        10.95       173.29 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7U8 
       55.82        15.48        32.05       174.21       209.23        26.20 
TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
        5.65        10.06       171.78        49.74       195.98         8.35 
TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZJ 
       27.62       312.07        32.78        12.92         7.82        36.33 
TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ 
       78.61       130.95       136.27        23.21         5.29         3.06 
TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV 
       66.67       173.19        13.28        80.68        55.59        11.54 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 
       19.30         9.90         6.05         1.91        53.29       117.93 
TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 
       84.72        17.06        42.48         7.59       120.53        34.49 
TCGA-GN-A4U8 TCGA-GN-A8LK TCGA-GN-A9SD TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS 
       46.92        43.23        59.41        85.05       297.01         7.23 
TCGA-QB-AA9O TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-AA1Q TCGA-W3-AA1R 
       18.05         0.33       174.12         1.97        44.05        79.99 
TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8ZN 
        8.09       185.13        92.84         1.15        59.64        12.69 
TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 
       19.00        59.44        10.95        48.39         1.94        26.60 
TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-Z2-AA3S 
       16.64        15.65        28.21        91.23 

  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
             4.47              0.00 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
           152.81            346.49 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
           47.740            45.945 
[1] "4.5 - 152.8 (47.7)" "0.0 - 346.5 (45.9)"
[1] "hr=" "1.2"
D55V2, survival
                   sevent
clus2                 0   1
  7Q LOSS MUTATED     6  11
  7Q LOSS WILD-TYPE 163 169
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               17               332 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               11               169 
$`7Q LOSS MUTATED`
TCGA-D3-A1QA TCGA-D3-A3CE TCGA-EB-A44R TCGA-EE-A29D TCGA-EE-A29M TCGA-EE-A2A5 
       90.90        60.23        10.36        13.97        56.84        39.29 
TCGA-EE-A2GN TCGA-EE-A3JA TCGA-EE-A3JI TCGA-ER-A19W TCGA-FS-A1ZE TCGA-FS-A1ZT 
      102.12        53.19       152.81       148.18        40.27        53.16 
TCGA-FS-A1ZU TCGA-FS-A4F0 TCGA-GN-A8LL TCGA-W3-A828 TCGA-WE-A8ZM 
       26.56        77.82        21.37       121.08        98.89 

$`7Q LOSS WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q3 
       17.03        66.48        12.99        14.93        16.57        16.67 
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 
      112.04       112.57        71.80       133.25        28.08        31.59 
TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA 
       95.74        43.43       103.10        65.49        23.77       115.53 
TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A2JG 
      168.00        86.76        11.87        27.65        62.07       113.52 
TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP 
       42.08        12.10       171.58        66.48        66.08        59.57 
TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC 
      130.72        58.06        46.98        46.32       166.52        86.93 
TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV 
       24.53        13.87         9.34       103.59        39.75        45.30 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
      174.84        55.73        56.35       145.12        32.94        22.62 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR 
       63.81        26.89       125.79       135.75       137.92       178.32 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GE 
       18.18       125.19        30.84        79.59        23.61        26.43 
TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GN 
       58.52       241.38       170.20        89.13       107.15       161.00 
TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A148 TCGA-D9-A149 
      152.75        29.06       129.63       117.17       151.53        54.67 
TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 
        3.65         7.10        18.12        15.39        22.29        18.44 
TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW 
        9.90        25.18        66.25        22.95        48.89        36.03 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
      117.21        20.38       194.83       176.55        35.93       107.34 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
       61.18        53.92        65.92        23.44        68.09        28.60 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5SG 
       10.49       215.44        15.68        13.87        20.35        68.25 
TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X 
       54.02        17.29        52.01         7.04        24.89        29.82 
TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
       27.22         8.65        94.98        33.73        14.70        26.89 
TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H 
       68.15         4.96       133.81       151.27        91.56       168.26 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G 
       13.55        63.35        85.08        78.97        63.78        72.07 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
       64.64         2.60        18.61        56.42        66.74        14.47 
TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 
       61.28       369.93        25.87       195.02        17.92        46.82 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD 
      102.90        36.82        86.14        59.28        67.43       340.14 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
      161.03       208.04        48.72       107.38        54.74        79.66 
TCGA-EE-A2GM TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT 
       75.48       126.81        13.91        42.77        81.21        44.88 
TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC 
       94.82        21.67       129.27        28.83        19.76        61.51 
TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
       47.28       103.27       268.73       103.20        16.96       204.66 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP 
       96.23       158.63       216.66       167.90        47.54       248.65 
TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA 
       43.23       134.40       162.48        71.21        53.26       124.31 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG 
      122.73        51.62        28.77        54.51        13.81        41.59 
TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 
      138.81       172.18       127.20        36.95        64.08        34.32 
TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 
      201.80        27.35        51.35       109.58        31.40        35.44 
TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C 
       13.94        50.76         9.17        77.75        98.40        48.89 
TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J 
       12.59        13.02        26.37       268.93       152.35         6.44 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S 
      131.51        61.05        44.05       162.08        50.89        37.25 
TCGA-ER-A19T TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF 
        8.88        79.99        43.82        23.34        20.15        16.37 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL 
       31.27        32.05       247.04        80.32        46.98        33.21 
TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 
        6.77        92.98       174.21        15.72       220.80        27.85 
TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW 
       18.77        38.27        34.82        36.26       104.42       216.92 
TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 
       48.59       228.59       202.65        20.91        28.08         7.79 
TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZG 
       27.72        48.85       357.37        53.52        15.45         9.70 
TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ 
       32.75        47.38        23.93       101.26        74.73       133.55 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F2 
       11.41       148.80        49.48        27.09        27.02        50.14 
TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC 
       66.67        28.73       174.84        34.03        26.73        54.41 
TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
       80.68         0.20        22.92        55.59        13.51        19.30 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 
        9.90         7.23         2.04        15.78       139.89       117.93 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
       84.72        10.13        64.44        62.79        32.48        39.58 
TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK 
      121.91        39.35        10.42        48.89        22.13        50.10 
TCGA-GN-A9SD TCGA-HR-A2OG TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS 
       59.41         0.23        65.88       368.78       297.90         7.23 
TCGA-QB-AA9O TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-AA1O 
       18.05         0.33         0.69       228.16        63.02         4.01 
TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8JZ 
       69.07       111.09        42.08       219.16       105.04        24.03 
TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ 
       49.05        61.15        15.98        58.98        67.63        59.77 
TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 
       11.80        32.58        49.51        12.16        35.01        19.73 
TCGA-WE-AAA4 TCGA-YD-A89C TCGA-YD-A9TA TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-A8RT 
       22.29         6.90        49.18        37.94        14.43        27.58 
TCGA-Z2-AA3S TCGA-Z2-AA3V 
       96.99        15.98 

  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
            10.36              0.20 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
           152.81            369.93 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
            56.84             50.12 
[1] "10.4 - 152.8 (56.8)" "0.2 - 369.9 (50.1)" 
[1] "hr=" "1.3"
D55V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  7Q LOSS MUTATED                    4             0
  7Q LOSS WILD-TYPE                 61             5
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  7Q LOSS MUTATED                                           5
  7Q LOSS WILD-TYPE                                        67
                   vv
clus                REGIONAL LYMPH NODE
  7Q LOSS MUTATED                     8
  7Q LOSS WILD-TYPE                 207
D55V4, multiclass
                                           clus
vv                                          7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  DISTANT METASTASIS                                      4                61
  PRIMARY TUMOR                                           0                 5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               5                67
  REGIONAL LYMPH NODE                                     8               207
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  7Q LOSS MUTATED             0       0       1        0        4        1
  7Q LOSS WILD-TYPE          12       7      27       18       23       23
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  7Q LOSS MUTATED           1         1         3         2          0
  7Q LOSS WILD-TYPE        13        18         9        35         15
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  7Q LOSS MUTATED            2          1        0
  7Q LOSS WILD-TYPE         30         59       20
D55V5, multiclass
             clus
vv            7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  I OR II NOS               0                12
  STAGE 0                   0                 7
  STAGE I                   1                27
  STAGE IA                  0                18
  STAGE IB                  4                23
  STAGE II                  1                23
  STAGE IIA                 1                13
  STAGE IIB                 1                18
  STAGE IIC                 3                 9
  STAGE III                 2                35
  STAGE IIIA                0                15
  STAGE IIIB                2                30
  STAGE IIIC                1                59
  STAGE IV                  0                20
[1] 14  2
[1] TRUE
[1] "dimension of contingency 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  7  2  4
  7Q LOSS WILD-TYPE    63 65 75 64
D55V6, multiclass
       clus
vv      7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  T0+T1               1                63
  T2                  7                65
  T3                  2                75
  T4                  4                64
[1] 4 2
[1] TRUE
[1] "dimension of 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    10   4   1   0
  7Q LOSS WILD-TYPE 159  59  37  49
D55V7, multiclass
    clus
vv   7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  N0              10               159
  N1               4                59
  N2               1                37
  N3               0                49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V8, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED    16   0
  7Q LOSS WILD-TYPE 297  21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED     16    0
  7Q LOSS WILD-TYPE  297   21
   clus
vv  7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  0              16               297
  1               0                21
[1] 2 2
[1] FALSE
D55V9, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED     7   5
  7Q LOSS WILD-TYPE 125  83
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      7    5
  7Q LOSS WILD-TYPE  125   83
     clus
vv    7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  NO                7               125
  YES               5                83
[1] 2 2
[1] FALSE
D55V10, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED     1  16
  7Q LOSS WILD-TYPE  43 297
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      1   16
  7Q LOSS WILD-TYPE   43  297
     clus
vv    7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  NO                1                43
  YES              16               297
[1] 2 2
[1] FALSE
D55V11, continuous
D55V12, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED     6  11
  7Q LOSS WILD-TYPE 129 212
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      6   11
  7Q LOSS WILD-TYPE  129  212
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  FEMALE               6               129
  MALE                11               212
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  7Q LOSS MUTATED       1                         0    16
  7Q LOSS WILD-TYPE     4                         1   328
D55V13, multiclass
                           clus
vv                          7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  ASIAN                                   1                 4
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  16               328
[1] 3 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     0  17
  7Q LOSS WILD-TYPE   7 327
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      0   17
  7Q LOSS WILD-TYPE    7  327
                        clus
vv                       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 7
  NOT HISPANIC OR LATINO              17               327
[1] 2 2
[1] FALSE

Clustering(56) Variable = 8P LOSS MUTATION ANALYSIS
D56V1, survival
                   sevent
clus2                 0   1
  8P LOSS MUTATED    19  33
  8P LOSS WILD-TYPE 102  85
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               52               187 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               33                85 
$`8P LOSS MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A2J6 TCGA-D3-A2JA TCGA-D3-A2JD TCGA-D3-A2JE TCGA-D3-A2JG 
        8.42        25.64        15.75         7.27         9.76       107.61 
TCGA-D3-A2JL TCGA-D3-A3C6 TCGA-D3-A3MO TCGA-D3-A5GN TCGA-D3-A8GC TCGA-D3-A8GM 
      171.58        58.06         9.34        45.70        78.21        70.62 
TCGA-DA-A1IA TCGA-EB-A6L9 TCGA-EE-A180 TCGA-EE-A20C TCGA-EE-A29C TCGA-EE-A29H 
       64.83         6.64        62.37        75.55        76.14        63.12 
TCGA-EE-A29M TCGA-EE-A2GS TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MM 
       47.74        71.31       209.79        94.19       171.85       145.45 
TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3J3 
      227.01       143.93        53.26       124.31        51.62        67.89 
TCGA-EE-A3JI TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19S TCGA-ER-A2ND TCGA-ER-A2NE 
      152.81         1.58         7.82        34.95         4.70        16.87 
TCGA-ER-A3PL TCGA-FR-A8YC TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1ZC TCGA-FS-A1ZT 
       32.05        10.06        49.74       195.98       312.07        35.28 
TCGA-GN-A264 TCGA-GN-A265 TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O TCGA-W3-AA1R 
      117.93        84.72       297.01         7.23        18.05        79.99 
TCGA-WE-A8ZY TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-Z2-AA3S 
       48.39        26.60        16.64        91.23 

$`8P LOSS WILD-TYPE`
TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 
       60.46        12.99        14.83        15.72        31.89       110.93 
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J7 
       49.35       133.25        19.04        76.41        62.60        45.99 
TCGA-D3-A2J8 TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JH TCGA-D3-A2JN TCGA-D3-A2JO 
       62.86       168.00        86.30        36.30        64.83        66.08 
TCGA-D3-A2JP TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF 
       43.53        46.98       140.98        40.01        59.70        16.96 
TCGA-D3-A3ML TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51J TCGA-D3-A51K 
       13.87        90.21        23.67       173.85       144.46        31.76 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D3-A8GD 
       62.70        11.34        42.05       177.86       124.08        23.61 
TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GP TCGA-D3-A8GR TCGA-D9-A1X3 
      179.97       120.00        69.53       135.12        36.53        10.78 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV 
       15.02        16.90        18.44        57.90        22.85        48.66 
TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IC 
      106.85        31.96       150.61        82.85        32.42        58.85 
TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5SG TCGA-EB-A5SH 
       25.12       214.59        14.96         3.91        33.24        50.07 
TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A184 
       45.50        13.15        24.89        20.38         0.00        67.50 
TCGA-EE-A20H TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29P 
      155.90        75.22        12.99         0.26        44.28        27.16 
TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 
       61.12       346.49       185.19       102.38         7.20        77.98 
TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK 
       26.14       239.11         0.20       189.40        68.65        10.62 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR 
       32.48        18.35        31.00       118.32         0.76         0.20 
TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MJ 
       81.99       103.13        15.25         5.75        23.77        63.25 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A3AB TCGA-EE-A3AD 
       67.50       104.78        25.08        23.51       122.73         4.41 
TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB 
       54.51         6.28       111.85        45.90         3.35       201.80 
TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C 
       14.56        34.45        47.31         4.54        53.29        39.81 
TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
       11.47       151.46       150.12        99.06        59.84        42.48 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NG 
      120.76        49.71       146.63        47.97        22.36        10.95 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7U8 
      173.29        55.82        15.48       174.21       209.23        26.20 
TCGA-FR-A7UA TCGA-FS-A1YW TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZD TCGA-FS-A1ZE 
        5.65       171.78         8.35        27.62        32.78        35.90 
TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS 
       12.92         7.82        36.33        78.61       130.95       136.27 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 
        4.47        23.21         5.29         3.06        30.90        66.67 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
      173.19        13.28        80.68        55.59        11.54        19.30 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A267 TCGA-GN-A268 
        9.90         6.05         1.91        53.29        17.06        42.48 
TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-GN-A8LK TCGA-GN-A9SD 
        7.59       120.53        34.49        46.92        43.23        59.41 
TCGA-LH-A9QB TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1Q 
       85.05         0.33       174.12         1.97       120.07        44.05 
TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8ZM 
        8.09       185.13        92.84         1.15        59.64        62.99 
TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-AA9Y TCGA-WE-AAA4 
       12.69        19.00        59.44        10.95         1.94        15.65 
TCGA-YG-AA3O 
       28.21 

  8P LOSS MUTATED 8P LOSS WILD-TYPE 
             1.58              0.00 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
           312.07            346.49 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
           60.215            43.230 
[1] "1.6 - 312.1 (60.2)" "0.0 - 346.5 (43.2)"
[1] "hr=" "1.1"
D56V2, survival
                   sevent
clus2                 0   1
  8P LOSS MUTATED    28  39
  8P LOSS WILD-TYPE 141 141
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               67               282 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               39               141 
$`8P LOSS MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A2J6 TCGA-D3-A2JA TCGA-D3-A2JD TCGA-D3-A2JE TCGA-D3-A2JG 
       16.57        43.43       115.53        11.87        27.65       113.52 
TCGA-D3-A2JL TCGA-D3-A3C6 TCGA-D3-A3MO TCGA-D3-A51N TCGA-D3-A5GN TCGA-D3-A8GC 
      171.58        58.06         9.34        22.62       135.75        79.59 
TCGA-D3-A8GM TCGA-D9-A148 TCGA-D9-A1JW TCGA-D9-A6EA TCGA-DA-A1IA TCGA-EB-A6L9 
      107.15       151.53         3.65        25.18        65.92        24.89 
TCGA-EE-A180 TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A29C TCGA-EE-A29H TCGA-EE-A29M 
       94.98        26.89       151.27        78.97        64.64        56.84 
TCGA-EE-A29V TCGA-EE-A2A5 TCGA-EE-A2GI TCGA-EE-A2GS TCGA-EE-A2MF TCGA-EE-A2MG 
       25.87        39.29        48.72        81.21       268.73       103.20 
TCGA-EE-A2MI TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MU 
      204.66       167.90        47.54       248.65       162.48        53.26 
TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3J3 TCGA-EE-A3JI TCGA-ER-A197 TCGA-ER-A199 
      124.31        51.62       172.18       152.81        13.94         9.17 
TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A3PL TCGA-FR-A8YC 
       37.25         8.88        23.34        20.15        33.21        34.82 
TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1ZA TCGA-FS-A1ZC TCGA-FS-A1ZT TCGA-FW-A3R5 
      228.59       202.65        27.72       357.37        53.16        22.92 
TCGA-GN-A264 TCGA-GN-A265 TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O TCGA-W3-AA1R 
      117.93        84.72       297.90         7.23        18.05       111.09 
TCGA-WE-A8JZ TCGA-WE-A8ZY TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-YD-A9TA TCGA-YG-AA3P 
       24.03        49.51        35.01        19.73        49.18        14.43 
TCGA-Z2-AA3S 
       96.99 

$`8P LOSS WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
       17.03        66.48        12.99        14.93        16.67       112.04 
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA 
      112.57        71.80       133.25        28.08        31.59        90.90 
TCGA-D3-A1QB TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JC 
       95.74       103.10        65.49        23.77       168.00        86.76 
TCGA-D3-A2JF TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP 
       62.07        42.08        12.10        66.48        66.08        59.57 
TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE 
      130.72        46.98        46.32       166.52        86.93        60.23 
TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E 
       24.53        13.87       103.59        39.75        45.30       174.84 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T 
       55.73        56.35       145.12        32.94        63.81        26.89 
TCGA-D3-A5GL TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GB 
      125.79       137.92       178.32        18.18       125.19        30.84 
TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL 
       23.61        26.43        58.52       241.38       170.20        89.13 
TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A149 
      161.00       152.75        29.06       129.63       117.17        54.67 
TCGA-D9-A1JX TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 
        7.10        18.12        15.39        22.29        18.44         9.90 
TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 
       66.25        22.95        48.89        36.03       117.21        20.38 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
      194.83       176.55        35.93       107.34        61.18        53.92 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 
       23.44        68.09        28.60        10.49       215.44        15.68 
TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL 
       13.87        10.36        20.35        68.25        54.02        17.29 
TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A181 
       52.01         7.04        29.82        27.22         8.65        33.73 
TCGA-EE-A182 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H 
       14.70        68.15         4.96       133.81        91.56       168.26 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G 
       13.55        63.35        85.08        13.97        63.78        72.07 
TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
        2.60        18.61        56.42        66.74        14.47        61.28 
TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
      369.93       195.02        17.92        46.82       102.90        36.82 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
       86.14        59.28        67.43       340.14       161.03       208.04 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO 
      107.38        54.74        79.66        75.48       102.12       126.81 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 
       13.91        42.77        44.88        94.82        21.67       129.27 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MH 
       28.83        19.76        61.51        47.28       103.27        16.96 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MT 
       96.23       158.63       216.66        43.23       134.40        71.21 
TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH 
      122.73        28.77        54.51        13.81        41.59       138.81 
TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB 
      127.20        36.95        64.08        34.32        53.19       201.80 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A198 
       27.35        51.35       109.58        31.40        35.44        50.76 
TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F 
       77.75        98.40        48.89        12.59        13.02        26.37 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
      268.93       152.35         6.44       131.51        61.05        44.05 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NF 
      162.08        50.89       148.18        79.99        43.82        16.37 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A42K 
       31.27        32.05       247.04        80.32        46.98         6.77 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 
       92.98       174.21        15.72       220.80        27.85        18.77 
TCGA-FR-A7UA TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1Z3 
       38.27        36.26       104.42       216.92        48.59        20.91 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZB TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF 
       28.08         7.79        48.85        53.52        40.27        15.45 
TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP 
        9.70        32.75        47.38        23.93       101.26        74.73 
TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY 
      133.55        11.41       148.80        26.56        49.48        27.09 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 
       27.02        77.82        50.14        66.67        28.73       174.84 
TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU 
       34.03        26.73        54.41        80.68         0.20        55.59 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 
       13.51        19.30         9.90         7.23         2.04        15.78 
TCGA-GN-A262 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
      139.89        10.13        64.44        62.79        32.48        39.58 
TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK 
      121.91        39.35        10.42        48.89        22.13        50.10 
TCGA-GN-A8LL TCGA-GN-A9SD TCGA-HR-A2OG TCGA-HR-A2OH TCGA-LH-A9QB TCGA-RP-A693 
       21.37        59.41         0.23        65.88       368.78         0.33 
TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1Q 
        0.69       228.16        63.02       121.08         4.01        69.07 
TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8K6 
       42.08       219.16       105.04        49.05        61.15        15.98 
TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX 
       98.89        58.98        67.63        59.77        11.80        32.58 
TCGA-WE-AA9Y TCGA-WE-AAA4 TCGA-YD-A89C TCGA-YG-AA3O TCGA-Z2-A8RT TCGA-Z2-AA3V 
       12.16        22.29         6.90        37.94        27.58        15.98 

  8P LOSS MUTATED 8P LOSS WILD-TYPE 
             3.65              0.20 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
           357.37            369.93 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
            53.16             50.45 
[1] "3.6 - 357.4 (53.2)" "0.2 - 369.9 (50.5)"
[1] "hr=" "1"  
D56V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  8P LOSS MUTATED                   15             2
  8P LOSS WILD-TYPE                 50             3
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  8P LOSS MUTATED                                           8
  8P LOSS WILD-TYPE                                        64
                   vv
clus                REGIONAL LYMPH NODE
  8P LOSS MUTATED                    41
  8P LOSS WILD-TYPE                 174
D56V4, multiclass
                                           clus
vv                                          8P LOSS MUTATED 8P LOSS WILD-TYPE
  DISTANT METASTASIS                                     15                50
  PRIMARY TUMOR                                           2                 3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               8                64
  REGIONAL LYMPH NODE                                    41               174
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  8P LOSS MUTATED             2       3       7        6        6        2
  8P LOSS WILD-TYPE          10       4      21       12       21       22
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  8P LOSS MUTATED           2         5         0         6          2
  8P LOSS WILD-TYPE        12        14        12        31         13
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  8P LOSS MUTATED            4         12        3
  8P LOSS WILD-TYPE         28         48       17
D56V5, multiclass
             clus
vv            8P LOSS MUTATED 8P LOSS WILD-TYPE
  I OR II NOS               2                10
  STAGE 0                   3                 4
  STAGE I                   7                21
  STAGE IA                  6                12
  STAGE IB                  6                21
  STAGE II                  2                22
  STAGE IIA                 2                12
  STAGE IIB                 5                14
  STAGE IIC                 0                12
  STAGE III                 6                31
  STAGE IIIA                2                13
  STAGE IIIB                4                28
  STAGE IIIC               12                48
  STAGE IV                  3                17
[1] 14  2
[1] TRUE
[1] "dimension of contingency 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      14 15 10 11
  8P LOSS WILD-TYPE    50 57 67 57
D56V6, multiclass
       clus
vv      8P LOSS MUTATED 8P LOSS WILD-TYPE
  T0+T1              14                50
  T2                 15                57
  T3                 10                67
  T4                 11                57
[1] 4 2
[1] TRUE
[1] "dimension of 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    34   8   7  12
  8P LOSS WILD-TYPE 135  55  31  37
D56V7, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  N0              34               135
  N1               8                55
  N2               7                31
  N3              12                37
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V8, binary
                   cls
clus                  0   1
  8P LOSS MUTATED    59   4
  8P LOSS WILD-TYPE 254  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     59    4
  8P LOSS WILD-TYPE  254   17
   clus
vv  8P LOSS MUTATED 8P LOSS WILD-TYPE
  0              59               254
  1               4                17
[1] 2 2
[1] FALSE
D56V9, binary
                   cls
clus                  0   1
  8P LOSS MUTATED    28  12
  8P LOSS WILD-TYPE 104  76
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     28   12
  8P LOSS WILD-TYPE  104   76
     clus
vv    8P LOSS MUTATED 8P LOSS WILD-TYPE
  NO               28               104
  YES              12                76
[1] 2 2
[1] FALSE
D56V10, binary
                   cls
clus                  0   1
  8P LOSS MUTATED     8  59
  8P LOSS WILD-TYPE  36 254
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      8   59
  8P LOSS WILD-TYPE   36  254
     clus
vv    8P LOSS MUTATED 8P LOSS WILD-TYPE
  NO                8                36
  YES              59               254
[1] 2 2
[1] FALSE
D56V11, continuous
D56V12, binary
                   cls
clus                  0   1
  8P LOSS MUTATED    23  44
  8P LOSS WILD-TYPE 112 179
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     23   44
  8P LOSS WILD-TYPE  112  179
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  FEMALE              23               112
  MALE                44               179
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  8P LOSS MUTATED       1                         0    64
  8P LOSS WILD-TYPE     4                         1   280
D56V13, multiclass
                           clus
vv                          8P LOSS MUTATED 8P LOSS WILD-TYPE
  ASIAN                                   1                 4
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  64               280
[1] 3 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     1  65
  8P LOSS WILD-TYPE   6 279
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      1   65
  8P LOSS WILD-TYPE    6  279
                        clus
vv                       8P LOSS MUTATED 8P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 6
  NOT HISPANIC OR LATINO              65               279
[1] 2 2
[1] FALSE

Clustering(57) Variable = 8Q LOSS MUTATION ANALYSIS
D57V1, survival
                   sevent
clus2                 0   1
  8Q LOSS MUTATED     6  15
  8Q LOSS WILD-TYPE 115 103
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               21               218 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               15               103 
$`8Q LOSS MUTATED`
TCGA-D3-A2JD TCGA-D3-A2JL TCGA-D3-A8GC TCGA-D3-A8GM TCGA-DA-A1IA TCGA-EE-A180 
        7.27       171.58        78.21        70.62        64.83        62.37 
TCGA-EE-A20C TCGA-EE-A29M TCGA-EE-A2MF TCGA-EE-A2MI TCGA-EE-A2MM TCGA-EE-A2MP 
       75.55        47.74       209.79       171.85       145.45       227.01 
TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3JI TCGA-ER-A199 TCGA-ER-A2NE TCGA-ER-A3PL 
      143.93        53.26       152.81         7.82        16.87        32.05 
TCGA-FS-A1ZC TCGA-W3-AA1R TCGA-WE-A8ZY 
      312.07        79.99        48.39 

$`8Q LOSS WILD-TYPE`
TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
       60.46        12.99        14.83         8.42        15.72        31.89 
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB 
      110.93        49.35       133.25        19.04        76.41        62.60 
TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC 
       25.64        45.99        62.86        15.75       168.00        86.30 
TCGA-D3-A2JE TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP 
        9.76       107.61        36.30        64.83        66.08        43.53 
TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF 
       58.06        46.98       140.98        40.01        59.70        16.96 
TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51J 
       13.87         9.34        90.21        23.67       173.85       144.46 
TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR 
       31.76        62.70        11.34        42.05        45.70       177.86 
TCGA-D3-A5GU TCGA-D3-A8GD TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GP 
      124.08        23.61       179.97       120.00        69.53       135.12 
TCGA-D3-A8GR TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6EC 
       36.53        10.78        15.02        16.90        18.44        57.90 
TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 
       22.85        48.66       106.85        31.96       150.61        82.85 
TCGA-DA-A1I7 TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q 
       32.42        58.85        25.12       214.59        14.96         3.91 
TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y 
       33.24        50.07        45.50         6.64        13.15        24.89 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A184 TCGA-EE-A20H TCGA-EE-A29B TCGA-EE-A29C 
       20.38         0.00        67.50       155.90        75.22        76.14 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29P TCGA-EE-A29Q 
       12.99         0.26        44.28        63.12        27.16        61.12 
TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB 
      346.49       185.19       102.38         7.20        77.98        26.14 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
      239.11         0.20       189.40        68.65        10.62        32.48 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
       18.35        31.00       118.32         0.76         0.20        71.31 
TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MG 
       81.99       103.13        15.25         5.75        23.77        94.19 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A3AA 
       63.25        67.50       104.78        25.08        23.51       124.31 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J3 
      122.73        51.62         4.41        54.51         6.28        67.89 
TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-ER-A193 TCGA-ER-A195 
      111.85        45.90         3.35       201.80        14.56        34.45 
TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D 
        1.58        47.31         4.54        53.29        39.81        11.47 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P 
      151.46       150.12        99.06        59.84        42.48       120.76 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
       49.71        34.95       146.63        47.97        22.36         4.70 
TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-FR-A44A TCGA-FR-A729 
       10.95       173.29        55.82        15.48       174.21       209.23 
TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 
       26.20         5.65        10.06       171.78        49.74       195.98 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG 
        8.35        27.62        32.78        35.90        12.92         7.82 
TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU 
       36.33        78.61       130.95       136.27        35.28         4.47 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 
       23.21         5.29         3.06        30.90        66.67       173.19 
TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
       13.28        80.68        55.59        11.54        19.30         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 
        6.05         1.91        53.29       117.93        84.72        17.06 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-GN-A8LK 
       42.48         7.59       120.53        34.49        46.92        43.23 
TCGA-GN-A9SD TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 
       59.41        85.05       297.01         7.23        18.05         0.33 
TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1Q TCGA-W3-AA1V TCGA-W3-AA1W 
      174.12         1.97       120.07        44.05         8.09       185.13 
TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO 
       92.84         1.15        59.64        62.99        12.69        19.00 
TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 
       59.44        10.95         1.94        26.60        16.64        15.65 
TCGA-YG-AA3O TCGA-Z2-AA3S 
       28.21        91.23 

  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
             7.27              0.00 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
           312.07            346.49 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
            75.55             43.38 
[1] "7.3 - 312.1 (75.5)" "0.0 - 346.5 (43.4)"
[1] "hr=" "1.1"
D57V2, survival
                   sevent
clus2                 0   1
  8Q LOSS MUTATED    10  17
  8Q LOSS WILD-TYPE 159 163
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               27               322 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               17               163 
$`8Q LOSS MUTATED`
TCGA-D3-A2JD TCGA-D3-A2JL TCGA-D3-A8GC TCGA-D3-A8GM TCGA-D9-A6EA TCGA-DA-A1IA 
       11.87       171.58        79.59       107.15        25.18        65.92 
TCGA-EE-A180 TCGA-EE-A20C TCGA-EE-A29M TCGA-EE-A2MF TCGA-EE-A2MI TCGA-EE-A2MM 
       94.98       151.27        56.84       268.73       204.66       167.90 
TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3JI TCGA-ER-A199 TCGA-ER-A19E 
      248.65       162.48        53.26       152.81         9.17        13.02 
TCGA-ER-A2NE TCGA-ER-A3PL TCGA-FS-A1ZA TCGA-FS-A1ZC TCGA-FW-A3R5 TCGA-W3-AA1R 
       20.15        33.21        27.72       357.37        22.92       111.09 
TCGA-WE-A8JZ TCGA-WE-A8ZY TCGA-YG-AA3P 
       24.03        49.51        14.43 

$`8Q LOSS WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q3 
       17.03        66.48        12.99        14.93        16.57        16.67 
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 
      112.04       112.57        71.80       133.25        28.08        31.59 
TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 
       90.90        95.74        43.43       103.10        65.49        23.77 
TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A2JG 
      115.53       168.00        86.76        27.65        62.07       113.52 
TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ 
       42.08        12.10        66.48        66.08        59.57       130.72 
TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE 
       58.06        46.98        46.32       166.52        86.93        60.23 
TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV 
       24.53        13.87         9.34       103.59        39.75        45.30 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
      174.84        55.73        56.35       145.12        32.94        22.62 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR 
       63.81        26.89       125.79       135.75       137.92       178.32 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GI 
       18.18       125.19        30.84        23.61        26.43        58.52 
TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GQ 
      241.38       170.20        89.13       161.00       152.75        29.06 
TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX 
      129.63       117.17       151.53        54.67         3.65         7.10 
TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EC 
       18.12        15.39        22.29        18.44         9.90        66.25 
TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 
       22.95        48.89        36.03       117.21        20.38       194.83 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IB 
      176.55        35.93       107.34        61.18        53.92        23.44 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q 
       68.09        28.60        10.49       215.44        15.68        13.87 
TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN 
       10.36        20.35        68.25        54.02        17.29        52.01 
TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A181 
        7.04        24.89        29.82        27.22         8.65        33.73 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F 
       14.70        26.89        68.15         4.96       133.81        91.56 
TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D 
      168.26        13.55        63.35        85.08        78.97        13.97 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P 
       63.78        72.07        64.64         2.60        18.61        56.42 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W 
       66.74        14.47        61.28       369.93        25.87       195.02 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
       17.92        46.82       102.90        36.82        39.29        86.14 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
       59.28        67.43       340.14       161.03       208.04        48.72 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO 
      107.38        54.74        79.66        75.48       102.12       126.81 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 
       13.91        42.77        81.21        44.88        94.82        21.67 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME 
      129.27        28.83        19.76        61.51        47.28       103.27 
TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MN 
      103.20        16.96        96.23       158.63       216.66        47.54 
TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC 
       43.23       134.40        71.21       124.31       122.73        51.62 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 
       28.77        54.51        13.81        41.59       138.81       172.18 
TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB 
      127.20        36.95        64.08        34.32        53.19       201.80 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
       27.35        51.35       109.58        31.40        35.44        13.94 
TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19F 
       50.76        77.75        98.40        48.89        12.59        26.37 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
      268.93       152.35         6.44       131.51        61.05        44.05 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 
      162.08        50.89        37.25         8.88       148.18        79.99 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES 
       43.82        23.34        16.37        31.27        32.05       247.04 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       80.32        46.98         6.77        92.98       174.21        15.72 
TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD 
      220.80        27.85        18.77        38.27        34.82        36.26 
TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
      104.42       216.92        48.59       228.59       202.65        20.91 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZB TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF 
       28.08         7.79        48.85        53.52        40.27        15.45 
TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP 
        9.70        32.75        47.38        23.93       101.26        74.73 
TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW 
      133.55        11.41       148.80        53.16        26.56        49.48 
TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 
       27.09        27.02        77.82        50.14        66.67        28.73 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 
      174.84        34.03        26.73        54.41        80.68         0.20 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 
       55.59        13.51        19.30         9.90         7.23         2.04 
TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 
       15.78       139.89       117.93        84.72        10.13        64.44 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 
       62.79        32.48        39.58       121.91        39.35        10.42 
TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A8LL TCGA-GN-A9SD TCGA-HR-A2OG 
       48.89        22.13        50.10        21.37        59.41         0.23 
TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 
       65.88       368.78       297.90         7.23        18.05         0.33 
TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1Q 
        0.69       228.16        63.02       121.08         4.01        69.07 
TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8K6 
       42.08       219.16       105.04        49.05        61.15        15.98 
TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX 
       98.89        58.98        67.63        59.77        11.80        32.58 
TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YD-A89C TCGA-YD-A9TA 
       12.16        35.01        19.73        22.29         6.90        49.18 
TCGA-YG-AA3O TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
       37.94        27.58        96.99        15.98 

  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
             9.17              0.20 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
           357.37            369.93 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
            65.92             50.12 
[1] "9.2 - 357.4 (65.9)" "0.2 - 369.9 (50.1)"
[1] "hr=" "1.1"
D57V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  8Q LOSS MUTATED                    7             1
  8Q LOSS WILD-TYPE                 58             4
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  8Q LOSS MUTATED                                           3
  8Q LOSS WILD-TYPE                                        69
                   vv
clus                REGIONAL LYMPH NODE
  8Q LOSS MUTATED                    16
  8Q LOSS WILD-TYPE                 199
D57V4, multiclass
                                           clus
vv                                          8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  DISTANT METASTASIS                                      7                58
  PRIMARY TUMOR                                           1                 4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               3                69
  REGIONAL LYMPH NODE                                    16               199
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  8Q LOSS MUTATED             2       2       4        1        2        2
  8Q LOSS WILD-TYPE          10       5      24       17       25       22
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  8Q LOSS MUTATED           1         3         0         2          0
  8Q LOSS WILD-TYPE        13        16        12        35         15
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  8Q LOSS MUTATED            3          4        1
  8Q LOSS WILD-TYPE         29         56       19
D57V5, multiclass
             clus
vv            8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  I OR II NOS               2                10
  STAGE 0                   2                 5
  STAGE I                   4                24
  STAGE IA                  1                17
  STAGE IB                  2                25
  STAGE II                  2                22
  STAGE IIA                 1                13
  STAGE IIB                 3                16
  STAGE IIC                 0                12
  STAGE III                 2                35
  STAGE IIIA                0                15
  STAGE IIIB                3                29
  STAGE IIIC                4                56
  STAGE IV                  1                19
[1] 14  2
[1] TRUE
[1] "dimension of contingency 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       1  7  5  8
  8Q LOSS WILD-TYPE    63 65 72 60
D57V6, multiclass
       clus
vv      8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  T0+T1               1                63
  T2                  7                65
  T3                  5                72
  T4                  8                60
[1] 4 2
[1] TRUE
[1] "dimension of 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    18   3   2   3
  8Q LOSS WILD-TYPE 151  60  36  46
D57V7, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  N0              18               151
  N1               3                60
  N2               2                36
  N3               3                46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V8, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED    26   1
  8Q LOSS WILD-TYPE 287  20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED     26    1
  8Q LOSS WILD-TYPE  287   20
   clus
vv  8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  0              26               287
  1               1                20
[1] 2 2
[1] FALSE
D57V9, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED    10   6
  8Q LOSS WILD-TYPE 122  82
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED     10    6
  8Q LOSS WILD-TYPE  122   82
     clus
vv    8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  NO               10               122
  YES               6                82
[1] 2 2
[1] FALSE
D57V10, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED     1  26
  8Q LOSS WILD-TYPE  43 287
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      1   26
  8Q LOSS WILD-TYPE   43  287
     clus
vv    8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  NO                1                43
  YES              26               287
[1] 2 2
[1] FALSE
D57V11, continuous
D57V12, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED    10  17
  8Q LOSS WILD-TYPE 125 206
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED     10   17
  8Q LOSS WILD-TYPE  125  206
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  FEMALE              10               125
  MALE                17               206
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  8Q LOSS MUTATED       0                         0    25
  8Q LOSS WILD-TYPE     5                         1   319
D57V13, multiclass
                           clus
vv                          8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  ASIAN                                   0                 5
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  25               319
[1] 3 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  25
  8Q LOSS WILD-TYPE   6 319
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      1   25
  8Q LOSS WILD-TYPE    6  319
                        clus
vv                       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 6
  NOT HISPANIC OR LATINO              25               319
[1] 2 2
[1] FALSE

Clustering(58) Variable = 9P LOSS MUTATION ANALYSIS
D58V1, survival
                   sevent
clus2                0  1
  9P LOSS MUTATED   71 85
  9P LOSS WILD-TYPE 50 33
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              156                83 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               85                33 
$`9P LOSS MUTATED`
TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q8 
       14.83         8.42        31.89       110.93        49.35        19.04 
TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JL TCGA-D3-A2JN 
       25.64        45.99       168.00        86.30       171.58        64.83 
TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3ML 
       43.53        58.06        46.98        40.01        16.96        13.87 
TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51J TCGA-D3-A51T 
        9.34        90.21        23.67       173.85       144.46        11.34 
TCGA-D3-A5GL TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D3-A8GD TCGA-D3-A8GL TCGA-D3-A8GP 
       42.05       177.86       124.08        23.61        69.53       135.12 
TCGA-D3-A8GR TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6EG 
       36.53        10.78        15.02        16.90        18.44        22.85 
TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1IA 
       48.66       106.85        31.96       150.61        82.85        64.83 
TCGA-DA-A1IC TCGA-DA-A3F5 TCGA-EB-A44Q TCGA-EB-A5SG TCGA-EB-A5UN TCGA-EE-A17X 
       58.85       214.59         3.91        33.24        45.50        13.15 
TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A20C TCGA-EE-A20H 
       24.89        62.37        20.38         0.00        75.55       155.90 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29P TCGA-EE-A29Q 
       76.14        12.99         0.26        44.28        27.16        61.12 
TCGA-EE-A29W TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GL 
      185.19        26.14       239.11         0.20       189.40        32.48 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
       18.35        31.00       118.32         0.76         0.20        71.31 
TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M8 TCGA-EE-A2MF TCGA-EE-A2MK TCGA-EE-A2ML 
       81.99       103.13         5.75       209.79        67.50       104.78 
TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A3AA TCGA-EE-A3AB 
      145.45       227.01        25.08       143.93       124.31       122.73 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-EE-A3J8 
        4.41        54.51         6.28        67.89        45.90         3.35 
TCGA-EE-A3JB TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 
      201.80       152.81        14.56        34.45         1.58         7.82 
TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M 
       53.29        39.81        11.47       150.12        99.06        59.84 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A2ND TCGA-ER-A2NG 
      120.76        49.71        34.95       146.63         4.70        10.95 
TCGA-ER-A3ES TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A8YC 
      173.29        15.48        32.05       174.21       209.23        10.06 
TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZF 
      171.78        49.74         8.35       312.07        32.78        12.92 
TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F0 
       78.61       130.95       136.27        23.21         5.29        30.90 
TCGA-FS-A4F4 TCGA-FS-A4F9 TCGA-FW-A3TU TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 
       66.67        13.28        55.59         6.05         1.91        53.29 
TCGA-GN-A265 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A8LK TCGA-GN-A9SD 
       84.72        42.48         7.59       120.53        43.23        59.41 
TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A693 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1R 
      297.01         7.23         0.33         1.97       120.07        79.99 
TCGA-W3-AA1V TCGA-W3-AA21 TCGA-WE-A8K5 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO 
        8.09        92.84        59.64        62.99        12.69        19.00 
TCGA-WE-A8ZQ TCGA-WE-A8ZY TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-Z2-AA3S 
       59.44        48.39        16.64        15.65        28.21        91.23 

$`9P LOSS WILD-TYPE`
TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q3 TCGA-D3-A1Q7 TCGA-D3-A1QA TCGA-D3-A1QB 
       60.46        12.99        15.72       133.25        76.41        62.60 
TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JD TCGA-D3-A2JE TCGA-D3-A2JG TCGA-D3-A2JH 
       62.86        15.75         7.27         9.76       107.61        36.30 
TCGA-D3-A2JO TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A5GN 
       66.08       140.98        59.70        31.76        62.70        45.70 
TCGA-D3-A8GC TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GM TCGA-D9-A6EC TCGA-DA-A1I7 
       78.21       179.97       120.00        70.62        57.90        32.42 
TCGA-DA-A3F2 TCGA-DA-A3F8 TCGA-EB-A5SH TCGA-EB-A6L9 TCGA-EE-A184 TCGA-EE-A29B 
       25.12        14.96        50.07         6.64        67.50        75.22 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29T TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 
       63.12        47.74       346.49       102.38         7.20        77.98 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2M7 TCGA-EE-A2MC TCGA-EE-A2MG TCGA-EE-A2MI 
       68.65        10.62        15.25        23.77        94.19       171.85 
TCGA-EE-A2MJ TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AC TCGA-EE-A3J4 TCGA-ER-A198 
       63.25        23.51        53.26        51.62       111.85        47.31 
TCGA-ER-A19A TCGA-ER-A19G TCGA-ER-A19N TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE 
        4.54       151.46        42.48        47.97        22.36        16.87 
TCGA-ER-A3ET TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1ZE 
       55.82        26.20         5.65       195.98        27.62        35.90 
TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZZ TCGA-FS-A4F8 
        7.82        36.33        35.28         4.47         3.06       173.19 
TCGA-FS-A4FD TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GN-A264 TCGA-GN-A267 
       80.68        11.54        19.30         9.90       117.93        17.06 
TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-LH-A9QB TCGA-QB-AA9O TCGA-W3-A824 TCGA-W3-AA1Q 
       34.49        46.92        85.05        18.05       174.12        44.05 
TCGA-W3-AA1W TCGA-WE-A8K1 TCGA-WE-A8ZT TCGA-WE-AA9Y TCGA-WE-AAA0 
      185.13         1.15        10.95         1.94        26.60 

  9P LOSS MUTATED 9P LOSS WILD-TYPE 
             0.00              1.15 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
           312.07            346.49 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
           45.945            46.920 
[1] "0.0 - 312.1 (45.9)" "1.1 - 346.5 (46.9)"
[1] "hr=" "1.2"
D58V2, survival
                   sevent
clus2                 0   1
  9P LOSS MUTATED    99 125
  9P LOSS WILD-TYPE  70  55
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              224               125 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              125                55 
$`9P LOSS MUTATED`
TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q8 
       14.93        16.57       112.04       112.57        71.80        28.08 
TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JF TCGA-D3-A2JK 
       43.43       103.10       168.00        86.76        62.07        12.10 
TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CC 
      171.58        66.48        59.57        58.06        46.98        86.93 
TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV 
       24.53        13.87         9.34       103.59        39.75        45.30 
TCGA-D3-A51E TCGA-D3-A51J TCGA-D3-A51N TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GO 
      174.84       145.12        22.62        26.89       125.79       137.92 
TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GD TCGA-D3-A8GI TCGA-D3-A8GL 
      178.32       125.19        30.84        23.61        58.52        89.13 
TCGA-D3-A8GP TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1X3 
      152.75       129.63       117.17       151.53        54.67        18.12 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EG TCGA-DA-A1HV 
       15.39        22.29        18.44         9.90        22.95        48.89 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
       36.03       117.21       194.83       176.55        35.93       107.34 
TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F5 TCGA-EB-A44Q TCGA-EB-A44R 
       53.92        65.92        68.09       215.44        13.87        10.36 
TCGA-EB-A5SG TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A180 
       68.25        17.29        52.01        29.82        27.22        94.98 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F 
       33.73        14.70         4.96       133.81       151.27        91.56 
TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G 
      168.26        13.55        78.97        13.97        63.78        72.07 
TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29V 
        2.60        18.61        56.42        66.74        61.28        25.87 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A5 TCGA-EE-A2GB TCGA-EE-A2GC 
      195.02        17.92        46.82        39.29        59.28        67.43 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GL TCGA-EE-A2GM 
      340.14       161.03       208.04        48.72        79.66        75.48 
TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU 
      102.12       126.81        13.91        42.77        81.21        94.82 
TCGA-EE-A2M6 TCGA-EE-A2M8 TCGA-EE-A2MD TCGA-EE-A2MF TCGA-EE-A2MH TCGA-EE-A2MK 
      129.27        19.76        47.28       268.73        16.96       158.63 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MR TCGA-EE-A2MS 
      216.66       167.90        47.54       248.65       134.40       162.48 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG 
      124.31       122.73        28.77        54.51        13.81        41.59 
TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB 
      138.81       172.18        64.08        34.32        53.19       201.80 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 
      109.58       152.81        31.40        35.44        13.94         9.17 
TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19H 
       98.40        48.89        12.59        13.02        26.37       152.35 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T 
      131.51        61.05       162.08        50.89        37.25         8.88 
TCGA-ER-A19W TCGA-ER-A2ND TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3EV 
      148.18        23.34        31.27        32.05       247.04        46.98 
TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 
       33.21         6.77        92.98       174.21        15.72       220.80 
TCGA-FR-A8YC TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1Z7 
       34.82       216.92        48.59       228.59        20.91         7.79 
TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZH 
       27.72        48.85       357.37        53.52        15.45        32.75 
TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZW TCGA-FS-A1ZY 
      101.26       133.55        11.41       148.80        49.48        27.09 
TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F9 TCGA-FS-A4FB 
       77.82        50.14        66.67        28.73        34.03        26.73 
TCGA-FS-A4FC TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-GF-A4EO TCGA-GF-A6C8 
       54.41         0.20        22.92        55.59         7.23         2.04 
TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
       15.78       139.89        84.72        62.79        32.48        39.58 
TCGA-GN-A4U3 TCGA-GN-A4U7 TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A8LL TCGA-GN-A9SD 
      121.91        10.42        22.13        50.10        21.37        59.41 
TCGA-HR-A2OG TCGA-HR-A2OH TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 
        0.23        65.88       297.90         7.23         0.33         0.69 
TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1R TCGA-W3-AA1V TCGA-W3-AA21 TCGA-WE-A8JZ 
       63.02       121.08       111.09        42.08       105.04        24.03 
TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ 
       61.15        15.98        98.89        58.98        67.63        59.77 
TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-Z2-A8RT 
       32.58        49.51        19.73        22.29        37.94        27.58 
TCGA-Z2-AA3S TCGA-Z2-AA3V 
       96.99        15.98 

$`9P LOSS WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q3 TCGA-D3-A1Q7 TCGA-D3-A1Q9 
       17.03        66.48        12.99        16.67       133.25        31.59 
TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JD 
       90.90        95.74        65.49        23.77       115.53        11.87 
TCGA-D3-A2JE TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JO TCGA-D3-A3BZ TCGA-D3-A3C8 
       27.65       113.52        42.08        66.08       130.72        46.32 
TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51K TCGA-D3-A51R 
      166.52        60.23        55.73        56.35        32.94        63.81 
TCGA-D3-A5GN TCGA-D3-A5GS TCGA-D3-A8GC TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GK 
      135.75        18.18        79.59        26.43       241.38       170.20 
TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GQ TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A6EA 
      107.15       161.00        29.06         3.65         7.10        25.18 
TCGA-D9-A6EC TCGA-DA-A1I0 TCGA-DA-A1I7 TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-DA-A3F3 
       66.25        20.38        61.18        23.44        28.60        10.49 
TCGA-DA-A3F8 TCGA-EB-A5KH TCGA-EB-A5SH TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17Z 
       15.68        20.35        54.02         7.04        24.89         8.65 
TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29H TCGA-EE-A29M 
       26.89        68.15        63.35        85.08        64.64        56.84 
TCGA-EE-A29R TCGA-EE-A29T TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GJ 
       14.47       369.93       102.90        36.82        86.14       107.38 
TCGA-EE-A2GK TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2M7 TCGA-EE-A2MC TCGA-EE-A2ME 
       54.74        44.88        21.67        28.83        61.51       103.27 
TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MQ TCGA-EE-A2MT TCGA-EE-A2MU 
      103.20       204.66        96.23        43.23        71.21        53.26 
TCGA-EE-A3AC TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3JD TCGA-EE-A3JE TCGA-ER-A198 
       51.62       127.20        36.95        27.35        51.35        50.76 
TCGA-ER-A19A TCGA-ER-A19G TCGA-ER-A19J TCGA-ER-A19N TCGA-ER-A1A1 TCGA-ER-A2NC 
       77.75       268.93         6.44        44.05        79.99        43.82 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A3ET TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA 
       20.15        16.37        80.32        27.85        18.77        38.27 
TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1ZE TCGA-FS-A1ZG 
       36.26       104.42       202.65        28.08        40.27         9.70 
TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZZ 
       47.38        23.93        74.73        53.16        26.56        27.02 
TCGA-FS-A4F8 TCGA-FS-A4FD TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GN-A264 
      174.84        80.68        13.51        19.30         9.90       117.93 
TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-LH-A9QB TCGA-QB-AA9O 
       10.13        64.44        39.35        48.89       368.78        18.05 
TCGA-W3-A824 TCGA-W3-AA1O TCGA-W3-AA1Q TCGA-W3-AA1W TCGA-WE-A8K1 TCGA-WE-A8ZT 
      228.16         4.01        69.07       219.16        49.05        11.80 
TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-YD-A89C TCGA-YD-A9TA TCGA-YG-AA3P 
       12.16        35.01         6.90        49.18        14.43 

  9P LOSS MUTATED 9P LOSS WILD-TYPE 
             0.20              3.65 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
           357.37            369.93 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
            53.72             48.89 
[1] "0.2 - 357.4 (53.7)" "3.6 - 369.9 (48.9)"
[1] "hr=" "1.1"
D58V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  9P LOSS MUTATED                   41             2
  9P LOSS WILD-TYPE                 24             3
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  9P LOSS MUTATED                                          54
  9P LOSS WILD-TYPE                                        18
                   vv
clus                REGIONAL LYMPH NODE
  9P LOSS MUTATED                   134
  9P LOSS WILD-TYPE                  81
D58V4, multiclass
                                           clus
vv                                          9P LOSS MUTATED 9P LOSS WILD-TYPE
  DISTANT METASTASIS                                     41                24
  PRIMARY TUMOR                                           2                 3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE              54                18
  REGIONAL LYMPH NODE                                   134                81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  9P LOSS MUTATED            10       4      18        9       17       17
  9P LOSS WILD-TYPE           2       3      10        9       10        7
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  9P LOSS MUTATED           9        12         8        24          7
  9P LOSS WILD-TYPE         5         7         4        13          8
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  9P LOSS MUTATED           24         37       14
  9P LOSS WILD-TYPE          8         23        6
D58V5, multiclass
             clus
vv            9P LOSS MUTATED 9P LOSS WILD-TYPE
  I OR II NOS              10                 2
  STAGE 0                   4                 3
  STAGE I                  18                10
  STAGE IA                  9                 9
  STAGE IB                 17                10
  STAGE II                 17                 7
  STAGE IIA                 9                 5
  STAGE IIB                12                 7
  STAGE IIC                 8                 4
  STAGE III                24                13
  STAGE IIIA                7                 8
  STAGE IIIB               24                 8
  STAGE IIIC               37                23
  STAGE IV                 14                 6
[1] 14  2
[1] TRUE
[1] "dimension of contingency 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      39 48 52 45
  9P LOSS WILD-TYPE    25 24 25 23
D58V6, multiclass
       clus
vv      9P LOSS MUTATED 9P LOSS WILD-TYPE
  T0+T1              39                25
  T2                 48                24
  T3                 52                25
  T4                 45                23
[1] 4 2
[1] TRUE
[1] "dimension of 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   111  42  23  30
  9P LOSS WILD-TYPE  58  21  15  19
D58V7, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  N0             111                58
  N1              42                21
  N2              23                15
  N3              30                19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V8, binary
                   cls
clus                  0   1
  9P LOSS MUTATED   200  15
  9P LOSS WILD-TYPE 113   6
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED    200   15
  9P LOSS WILD-TYPE  113    6
   clus
vv  9P LOSS MUTATED 9P LOSS WILD-TYPE
  0             200               113
  1              15                 6
[1] 2 2
[1] FALSE
D58V9, binary
                   cls
clus                 0  1
  9P LOSS MUTATED   83 58
  9P LOSS WILD-TYPE 49 30
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     83   58
  9P LOSS WILD-TYPE   49   30
     clus
vv    9P LOSS MUTATED 9P LOSS WILD-TYPE
  NO               83                49
  YES              58                30
[1] 2 2
[1] FALSE
D58V10, binary
                   cls
clus                  0   1
  9P LOSS MUTATED    26 205
  9P LOSS WILD-TYPE  18 108
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     26  205
  9P LOSS WILD-TYPE   18  108
     clus
vv    9P LOSS MUTATED 9P LOSS WILD-TYPE
  NO               26                18
  YES             205               108
[1] 2 2
[1] FALSE
D58V11, continuous
D58V12, binary
                   cls
clus                  0   1
  9P LOSS MUTATED    99 133
  9P LOSS WILD-TYPE  36  90
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     99  133
  9P LOSS WILD-TYPE   36   90
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  FEMALE              99                36
  MALE               133                90
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  9P LOSS MUTATED       3                         1   221
  9P LOSS WILD-TYPE     2                         0   123
D58V13, multiclass
                           clus
vv                          9P LOSS MUTATED 9P LOSS WILD-TYPE
  ASIAN                                   3                 2
  BLACK OR AFRICAN AMERICAN               1                 0
  WHITE                                 221               123
[1] 3 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     2 224
  9P LOSS WILD-TYPE   5 120
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      2  224
  9P LOSS WILD-TYPE    5  120
                        clus
vv                       9P LOSS MUTATED 9P LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                 5
  NOT HISPANIC OR LATINO             224               120
[1] 2 2
[1] FALSE

Clustering(59) Variable = 9Q LOSS MUTATION ANALYSIS
D59V1, survival
                   sevent
clus2                0  1
  9Q LOSS MUTATED   58 67
  9Q LOSS WILD-TYPE 63 51
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
              125               114 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               67                51 
$`9Q LOSS MUTATED`
TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q8 TCGA-D3-A1QA 
       14.83         8.42       110.93        49.35        19.04        76.41 
TCGA-D3-A2J7 TCGA-D3-A2JC TCGA-D3-A2JL TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3C7 
       45.99        86.30       171.58        43.53        58.06        46.98 
TCGA-D3-A3CC TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51J TCGA-D3-A51T TCGA-D3-A5GL 
       40.01        90.21        23.67       144.46        11.34        42.05 
TCGA-D3-A5GU TCGA-D3-A8GD TCGA-D3-A8GL TCGA-D3-A8GP TCGA-D3-A8GR TCGA-D9-A1X3 
      124.08        23.61        69.53       135.12        36.53        10.78 
TCGA-DA-A1HV TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1IA TCGA-DA-A1IC 
       48.66        31.96       150.61        82.85        64.83        58.85 
TCGA-DA-A3F5 TCGA-EB-A5SG TCGA-EB-A5UN TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A181 
      214.59        33.24        45.50        24.89        62.37        20.38 
TCGA-EE-A20C TCGA-EE-A20H TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29P TCGA-EE-A29Q 
       75.55       155.90        12.99        44.28        27.16        61.12 
TCGA-EE-A29W TCGA-EE-A2A2 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
      185.19         7.20        26.14       239.11         0.20       189.40 
TCGA-EE-A2GJ TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GS 
       68.65        32.48        18.35        31.00         0.76        71.31 
TCGA-EE-A2M6 TCGA-EE-A2M8 TCGA-EE-A2MF TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM 
      103.13         5.75       209.79        67.50       104.78       145.45 
TCGA-EE-A2MP TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AD 
      227.01        25.08       143.93       124.31       122.73         4.41 
TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JI TCGA-ER-A193 
       54.51         6.28         3.35       201.80       152.81        14.56 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D 
       34.45         1.58         7.82        53.29        39.81        11.47 
TCGA-ER-A19H TCGA-ER-A19M TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19W TCGA-ER-A2NG 
      150.12        59.84       120.76        49.71       146.63        10.95 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A729 TCGA-FR-A8YC TCGA-FS-A1YW TCGA-FS-A1YY 
       15.48        32.05       209.23        10.06       171.78        49.74 
TCGA-FS-A1Z3 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZM TCGA-FS-A1ZQ 
        8.35       312.07        32.78        12.92        78.61       130.95 
TCGA-FS-A1ZS TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FW-A3TV 
      136.27        23.21         5.29         3.06        30.90        11.54 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A268 TCGA-GN-A26A 
        6.05         1.91        53.29        84.72        42.48         7.59 
TCGA-GN-A4U3 TCGA-GN-A8LK TCGA-GN-A9SD TCGA-OD-A75X TCGA-RP-A693 TCGA-W3-A825 
      120.53        43.23        59.41       297.01         0.33         1.97 
TCGA-W3-A828 TCGA-W3-AA1R TCGA-W3-AA1V TCGA-W3-AA21 TCGA-WE-A8ZM TCGA-WE-A8ZN 
      120.07        79.99         8.09        92.84        62.99        12.69 
TCGA-WE-A8ZO TCGA-WE-A8ZY TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-Z2-AA3S 
       19.00        48.39        15.65        28.21        91.23 

$`9Q LOSS WILD-TYPE`
TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q7 TCGA-D3-A1QB 
       60.46        12.99        15.72        31.89       133.25        62.60 
TCGA-D3-A2J6 TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JD TCGA-D3-A2JE 
       25.64        62.86        15.75       168.00         7.27         9.76 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A3CB TCGA-D3-A3CE 
      107.61        36.30        64.83        66.08       140.98        59.70 
TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A51E TCGA-D3-A51K TCGA-D3-A51R 
       16.96        13.87         9.34       173.85        31.76        62.70 
TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A8GC TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GM 
       45.70       177.86        78.21       179.97       120.00        70.62 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HY 
       15.02        16.90        18.44        57.90        22.85       106.85 
TCGA-DA-A1I7 TCGA-DA-A3F2 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5SH TCGA-EB-A6L9 
       32.42        25.12        14.96         3.91        50.07         6.64 
TCGA-EE-A17X TCGA-EE-A182 TCGA-EE-A184 TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E 
       13.15         0.00        67.50        75.22        76.14         0.26 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29T TCGA-EE-A2A1 TCGA-EE-A2A6 TCGA-EE-A2GK 
       63.12        47.74       346.49       102.38        77.98        10.62 
TCGA-EE-A2GO TCGA-EE-A2GR TCGA-EE-A2GU TCGA-EE-A2M7 TCGA-EE-A2MC TCGA-EE-A2MG 
      118.32         0.20        81.99        15.25        23.77        94.19 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AC TCGA-EE-A3J3 
      171.85        63.25        23.51        53.26        51.62        67.89 
TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19G TCGA-ER-A19L 
      111.85        45.90        47.31         4.54       151.46        99.06 
TCGA-ER-A19N TCGA-ER-A19S TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
       42.48        34.95        47.97        22.36         4.70        16.87 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-FR-A44A TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FS-A1Z0 
      173.29        55.82       174.21        26.20         5.65       195.98 
TCGA-FS-A1Z4 TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZT TCGA-FS-A1ZU 
       27.62        35.90         7.82        36.33        35.28         4.47 
TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A5DY 
       66.67       173.19        13.28        80.68        55.59        19.30 
TCGA-GF-A3OT TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-LH-A9QB 
        9.90       117.93        17.06        34.49        46.92        85.05 
TCGA-QB-A6FS TCGA-QB-AA9O TCGA-W3-A824 TCGA-W3-AA1Q TCGA-W3-AA1W TCGA-WE-A8K1 
        7.23        18.05       174.12        44.05       185.13         1.15 
TCGA-WE-A8K5 TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 
       59.64        59.44        10.95         1.94        26.60        16.64 

  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
              0.2               0.0 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
           312.07            346.49 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
            46.98             45.80 
[1] "0.2 - 312.1 (47.0)" "0.0 - 346.5 (45.8)"
[1] "hr=" "1.1"
D59V2, survival
                   sevent
clus2                0  1
  9Q LOSS MUTATED   79 98
  9Q LOSS WILD-TYPE 90 82
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
              177               172 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               98                82 
$`9Q LOSS MUTATED`
TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q8 TCGA-D3-A1QA 
       14.93        16.57       112.57        71.80        28.08        90.90 
TCGA-D3-A2J7 TCGA-D3-A2JC TCGA-D3-A2JL TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3C7 
      103.10        86.76       171.58        59.57        58.06        46.98 
TCGA-D3-A3CC TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51J TCGA-D3-A51N 
       86.93       103.59        39.75        45.30       145.12        22.62 
TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GO TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GD 
       26.89       125.79       137.92       125.19        30.84        23.61 
TCGA-D3-A8GI TCGA-D3-A8GL TCGA-D3-A8GP TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A148 
       58.52        89.13       152.75       129.63       117.17       151.53 
TCGA-D9-A149 TCGA-D9-A1X3 TCGA-D9-A6E9 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I1 
       54.67        18.12         9.90        48.89        36.03       194.83 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IC 
      176.55        35.93       107.34        53.92        65.92        68.09 
TCGA-DA-A3F5 TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5UN TCGA-EE-A17Y TCGA-EE-A180 
      215.44        10.36        68.25        52.01        27.22        94.98 
TCGA-EE-A181 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I 
       33.73       133.81       151.27        91.56       168.26        13.55 
TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
       13.97        72.07         2.60        18.61        56.42        66.74 
TCGA-EE-A29S TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A2 TCGA-EE-A2GB 
       61.28       195.02        17.92        46.82        36.82        59.28 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       67.43       340.14       161.03       208.04        48.72       107.38 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2M6 
       79.66        75.48       102.12        13.91        81.21       129.27 
TCGA-EE-A2M8 TCGA-EE-A2MF TCGA-EE-A2MH TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM 
       19.76       268.73        16.96       158.63       216.66       167.90 
TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A3AA TCGA-EE-A3AB 
      248.65        43.23       134.40       162.48       124.31       122.73 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3J5 TCGA-EE-A3J8 
       28.77        54.51        13.81        41.59        36.95        34.32 
TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 
       53.19       201.80        51.35       109.58       152.81        31.40 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D 
       35.44        13.94         9.17        98.40        48.89        12.59 
TCGA-ER-A19F TCGA-ER-A19H TCGA-ER-A19M TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19T 
       26.37       152.35        61.05       162.08        50.89         8.88 
TCGA-ER-A19W TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A69P 
      148.18        31.27        32.05        46.98        33.21        15.72 
TCGA-FR-A729 TCGA-FR-A8YC TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1ZA 
      220.80        34.82       216.92       228.59        20.91        27.72 
TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-FS-A1ZM 
       48.85       357.37        53.52        15.45        32.75       101.26 
TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ 
      133.55        11.41       148.80        49.48        27.09        27.02 
TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F5 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FW-A3I3 
       77.82        50.14        28.73        26.73        54.41         0.20 
TCGA-FW-A3R5 TCGA-FW-A3TV TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 
       22.92        13.51         7.23         2.04        15.78       139.89 
TCGA-GN-A265 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A4U7 
       84.72        62.79        32.48        39.58       121.91        10.42 
TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A9SD TCGA-HR-A2OG TCGA-HR-A2OH TCGA-OD-A75X 
       22.13        50.10        59.41         0.23        65.88       297.90 
TCGA-RP-A693 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1R TCGA-W3-AA1V TCGA-W3-AA21 
        0.33        63.02       121.08       111.09        42.08       105.04 
TCGA-WE-A8JZ TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZX TCGA-WE-A8ZY 
       24.03        98.89        58.98        67.63        32.58        49.51 
TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-Z2-AA3S 
       22.29        37.94        96.99 

$`9Q LOSS WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q7 
       17.03        66.48        12.99        16.67       112.04       133.25 
TCGA-D3-A1Q9 TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA 
       31.59        95.74        43.43        65.49        23.77       115.53 
TCGA-D3-A2JB TCGA-D3-A2JD TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH 
      168.00        11.87        27.65        62.07       113.52        42.08 
TCGA-D3-A2JK TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A3BZ TCGA-D3-A3C8 TCGA-D3-A3CB 
       12.10        66.48        66.08       130.72        46.32       166.52 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A51E TCGA-D3-A51F 
       60.23        24.53        13.87         9.34       174.84        55.73 
TCGA-D3-A51H TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS 
       56.35        32.94        63.81       135.75       178.32        18.18 
TCGA-D3-A8GC TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GM TCGA-D3-A8GN 
       79.59        26.43       241.38       170.20       107.15       161.00 
TCGA-D3-A8GQ TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 
       29.06         3.65         7.10        15.39        22.29        18.44 
TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I7 
       25.18        66.25        22.95       117.21        20.38        61.18 
TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH 
       23.44        28.60        10.49        15.68        13.87        20.35 
TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Z 
       54.02        17.29         7.04        24.89        29.82         8.65 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A29A TCGA-EE-A29B 
       14.70        26.89        68.15         4.96        63.35        85.08 
TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29R TCGA-EE-A29T 
       78.97        63.78        64.64        56.84        14.47       369.93 
TCGA-EE-A29V TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GK TCGA-EE-A2GO 
       25.87       102.90        39.29        86.14        54.74       126.81 
TCGA-EE-A2GR TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M7 TCGA-EE-A2MC 
       42.77        44.88        94.82        21.67        28.83        61.51 
TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MN 
       47.28       103.27       103.20       204.66        96.23        47.54 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AC TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 
       71.21        53.26        51.62       138.81       172.18       127.20 
TCGA-EE-A3J7 TCGA-EE-A3JD TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19E TCGA-ER-A19G 
       64.08        27.35        50.76        77.75        13.02       268.93 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A19S TCGA-ER-A1A1 TCGA-ER-A2NC 
        6.44       131.51        44.05        37.25        79.99        43.82 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A42K 
       23.34        20.15        16.37       247.04        80.32         6.77 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YD 
       92.98       174.21        27.85        18.77        38.27        36.26 
TCGA-FR-A8YE TCGA-FS-A1YX TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZE 
      104.42        48.59       202.65        28.08         7.79        40.27 
TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZT TCGA-FS-A1ZU 
        9.70        47.38        23.93        74.73        53.16        26.56 
TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A5DY 
       66.67       174.84        34.03        80.68        55.59        19.30 
TCGA-GF-A3OT TCGA-GN-A264 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A4U4 TCGA-GN-A4U8 
        9.90       117.93        10.13        64.44        39.35        48.89 
TCGA-GN-A8LL TCGA-LH-A9QB TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A694 TCGA-W3-A824 
       21.37       368.78         7.23        18.05         0.69       228.16 
TCGA-W3-AA1O TCGA-W3-AA1Q TCGA-W3-AA1W TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8K6 
        4.01        69.07       219.16        49.05        61.15        15.98 
TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-YD-A89C 
       59.77        11.80        12.16        35.01        19.73         6.90 
TCGA-YD-A9TA TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3V 
       49.18        14.43        27.58        15.98 

  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
             0.20              0.69 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
           357.37            369.93 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
            54.67             46.80 
[1] "0.2 - 357.4 (54.7)" "0.7 - 369.9 (46.8)"
[1] "hr=" "1"  
D59V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  9Q LOSS MUTATED                   35             2
  9Q LOSS WILD-TYPE                 30             3
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  9Q LOSS MUTATED                                          44
  9Q LOSS WILD-TYPE                                        28
                   vv
clus                REGIONAL LYMPH NODE
  9Q LOSS MUTATED                   101
  9Q LOSS WILD-TYPE                 114
D59V4, multiclass
                                           clus
vv                                          9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  DISTANT METASTASIS                                     35                30
  PRIMARY TUMOR                                           2                 3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE              44                28
  REGIONAL LYMPH NODE                                   101               114
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  9Q LOSS MUTATED             8       3      15        6       13       11
  9Q LOSS WILD-TYPE           4       4      13       12       14       13
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  9Q LOSS MUTATED           8        11         7        22          6
  9Q LOSS WILD-TYPE         6         8         5        15          9
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  9Q LOSS MUTATED           21         22       12
  9Q LOSS WILD-TYPE         11         38        8
D59V5, multiclass
             clus
vv            9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  I OR II NOS               8                 4
  STAGE 0                   3                 4
  STAGE I                  15                13
  STAGE IA                  6                12
  STAGE IB                 13                14
  STAGE II                 11                13
  STAGE IIA                 8                 6
  STAGE IIB                11                 8
  STAGE IIC                 7                 5
  STAGE III                22                15
  STAGE IIIA                6                 9
  STAGE IIIB               21                11
  STAGE IIIC               22                38
  STAGE IV                 12                 8
[1] 14  2
[1] TRUE
[1] "dimension of contingency 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      33 36 41 36
  9Q LOSS WILD-TYPE    31 36 36 32
D59V6, multiclass
       clus
vv      9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  T0+T1              33                31
  T2                 36                36
  T3                 41                36
  T4                 36                32
[1] 4 2
[1] TRUE
[1] "dimension of 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   90 32 21 20
  9Q LOSS WILD-TYPE 79 31 17 29
D59V7, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  N0              90                79
  N1              32                31
  N2              21                17
  N3              20                29
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V8, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED   157  13
  9Q LOSS WILD-TYPE 156   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED    157   13
  9Q LOSS WILD-TYPE  156    8
   clus
vv  9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  0             157               156
  1              13                 8
[1] 2 2
[1] FALSE
D59V9, binary
                   cls
clus                 0  1
  9Q LOSS MUTATED   68 42
  9Q LOSS WILD-TYPE 64 46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     68   42
  9Q LOSS WILD-TYPE   64   46
     clus
vv    9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  NO               68                64
  YES              42                46
[1] 2 2
[1] FALSE
D59V10, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED    22 161
  9Q LOSS WILD-TYPE  22 152
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     22  161
  9Q LOSS WILD-TYPE   22  152
     clus
vv    9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  NO               22                22
  YES             161               152
[1] 2 2
[1] FALSE
D59V11, continuous
D59V12, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED    79 104
  9Q LOSS WILD-TYPE  56 119
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     79  104
  9Q LOSS WILD-TYPE   56  119
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  FEMALE              79                56
  MALE               104               119
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  9Q LOSS MUTATED       2                         0   175
  9Q LOSS WILD-TYPE     3                         1   169
D59V13, multiclass
                           clus
vv                          9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  ASIAN                                   2                 3
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                 175               169
[1] 3 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     3 176
  9Q LOSS WILD-TYPE   4 168
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      3  176
  9Q LOSS WILD-TYPE    4  168
                        clus
vv                       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   3                 4
  NOT HISPANIC OR LATINO             176               168
[1] 2 2
[1] FALSE

Clustering(60) Variable = 10P LOSS MUTATION ANALYSIS
D60V1, survival
                    sevent
clus2                 0  1
  10P LOSS MUTATED   68 69
  10P LOSS WILD-TYPE 53 49
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
               137                102 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                69                 49 
$`10P LOSS MUTATED`
TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 
       60.46        12.99        14.83         8.42        31.89       110.93 
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JD 
       49.35       133.25        19.04        15.75        86.30         7.27 
TCGA-D3-A2JG TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C7 TCGA-D3-A3CE 
      107.61        64.83        66.08        43.53        46.98        59.70 
TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MU TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51T 
       16.96         9.34        23.67       144.46        31.76        11.34 
TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GJ 
       45.70       177.86       124.08        78.21        23.61       179.97 
TCGA-D3-A8GP TCGA-D3-A8GR TCGA-D9-A1X3 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6EG 
      135.12        36.53        10.78        16.90        18.44        22.85 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A3F5 
       31.96       150.61        82.85        32.42        64.83       214.59 
TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A20H TCGA-EE-A29G 
       50.07        45.50        62.37        20.38       155.90        44.28 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W 
       63.12        47.74        27.16        61.12       346.49       185.19 
TCGA-EE-A2A2 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GM 
        7.20        26.14         0.20       189.40        68.65        18.35 
TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU 
       31.00       118.32         0.76         0.20        71.31        81.99 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MG TCGA-EE-A2MK TCGA-EE-A2MM 
      103.13        15.25         5.75        94.19        67.50       145.45 
TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AD 
      227.01       143.93        53.26       124.31       122.73         4.41 
TCGA-EE-A3AE TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB 
       54.51        67.89       111.85        45.90         3.35       201.80 
TCGA-EE-A3JI TCGA-ER-A199 TCGA-ER-A19D TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19P 
      152.81         7.82        11.47       150.12        99.06       120.76 
TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NG 
       34.95       146.63        22.36         4.70        16.87        10.95 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7U8 
       55.82        15.48        32.05       174.21       209.23        26.20 
TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZG 
      195.98         8.35       312.07        32.78        12.92         7.82 
TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY 
       36.33        78.61       130.95         4.47        23.21         5.29 
TCGA-FS-A4F4 TCGA-FS-A4FD TCGA-FW-A3TV TCGA-GF-A4EO TCGA-GN-A264 TCGA-GN-A267 
       66.67        80.68        11.54         6.05       117.93        17.06 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A8LK TCGA-GN-A9SD TCGA-OD-A75X 
       42.48         7.59       120.53        43.23        59.41       297.01 
TCGA-RP-A693 TCGA-W3-A825 TCGA-W3-AA21 TCGA-WE-A8ZM TCGA-WE-A8ZQ TCGA-WE-A8ZY 
        0.33         1.97        92.84        62.99        59.44        48.39 
TCGA-WE-AA9Y TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-Z2-AA3S 
        1.94        16.64        15.65        28.21        91.23 

$`10P LOSS WILD-TYPE`
TCGA-D3-A1Q3 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 
       15.72        76.41        62.60        25.64        45.99        62.86 
TCGA-D3-A2JB TCGA-D3-A2JE TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A3C6 TCGA-D3-A3CB 
      168.00         9.76        36.30       171.58        58.06       140.98 
TCGA-D3-A3CC TCGA-D3-A3ML TCGA-D3-A3MR TCGA-D3-A51E TCGA-D3-A51R TCGA-D3-A5GL 
       40.01        13.87        90.21       173.85        62.70        42.05 
TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D9-A3Z1 TCGA-D9-A6EC TCGA-DA-A1HV 
      120.00        69.53        70.62        15.02        57.90        48.66 
TCGA-DA-A1HY TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5SG 
      106.85        58.85        25.12        14.96         3.91        33.24 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A182 TCGA-EE-A184 TCGA-EE-A20C 
        6.64        13.15        24.89         0.00        67.50        75.55 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A2A1 TCGA-EE-A2A6 
       75.22        76.14        12.99         0.26       102.38        77.98 
TCGA-EE-A2GD TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MI 
      239.11        10.62        32.48        23.77       209.79       171.85 
TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A3AC TCGA-EE-A3AF 
       63.25       104.78        25.08        23.51        51.62         6.28 
TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19B 
       14.56        34.45         1.58        47.31         4.54        53.29 
TCGA-ER-A19C TCGA-ER-A19G TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A1A1 
       39.81       151.46        59.84        42.48        49.71        47.97 
TCGA-ER-A3ES TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z4 
      173.29         5.65        10.06       171.78        49.74        27.62 
TCGA-FS-A1ZE TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F8 
       35.90       136.27        35.28         3.06        30.90       173.19 
TCGA-FS-A4F9 TCGA-FW-A3TU TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GN-A262 
       13.28        55.59        19.30         9.90         1.91        53.29 
TCGA-GN-A265 TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-LH-A9QB TCGA-QB-A6FS TCGA-QB-AA9O 
       84.72        34.49        46.92        85.05         7.23        18.05 
TCGA-W3-A824 TCGA-W3-A828 TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1V TCGA-W3-AA1W 
      174.12       120.07        44.05        79.99         8.09       185.13 
TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-AAA0 
        1.15        59.64        12.69        19.00        10.95        26.60 

  10P LOSS MUTATED 10P LOSS WILD-TYPE 
               0.2                0.0 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
            346.49             239.11 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
             46.98              45.02 
[1] "0.2 - 346.5 (47.0)" "0.0 - 239.1 (45.0)"
[1] "hr=" "1.1"
D60V2, survival
                    sevent
clus2                  0   1
  10P LOSS MUTATED    93 100
  10P LOSS WILD-TYPE  76  80
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
               193                156 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
               100                 80 
$`10P LOSS MUTATED`
TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 
       66.48        12.99        14.93        16.57       112.04       112.57 
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A2JA TCGA-D3-A2JC 
       71.80       133.25        28.08        31.59       115.53        86.76 
TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JK TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP 
       11.87       113.52        12.10        66.48        66.08        59.57 
TCGA-D3-A3C7 TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MU TCGA-D3-A3MV 
       46.98        60.23        24.53         9.34        39.75        45.30 
TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO 
       55.73       145.12        32.94        26.89       135.75       137.92 
TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GI TCGA-D3-A8GJ 
      178.32       125.19        79.59        23.61        58.52       241.38 
TCGA-D3-A8GP TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A149 TCGA-D9-A1X3 TCGA-D9-A3Z3 
      152.75       129.63       117.17        54.67        18.12        22.29 
TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EG TCGA-DA-A1HW TCGA-DA-A1I1 
       18.44         9.90        25.18        22.95        36.03       194.83 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA 
      176.55        35.93       107.34        61.18        53.92        65.92 
TCGA-DA-A3F5 TCGA-EB-A44R TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17Z 
      215.44        10.36        54.02        17.29        52.01         8.65 
TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H 
       94.98        33.73         4.96       133.81        91.56       168.26 
TCGA-EE-A20I TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29P 
       13.55        72.07        64.64         2.60        56.84        56.42 
TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A2 TCGA-EE-A2A5 
       66.74       369.93       195.02        17.92        36.82        39.29 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       59.28        67.43       161.03       208.04        48.72       107.38 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
       75.48       102.12       126.81        13.91        42.77        81.21 
TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MG TCGA-EE-A2MH 
       94.82       129.27        28.83        19.76       103.20        16.96 
TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AA 
      158.63       167.90       248.65       162.48        53.26       124.31 
TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 
      122.73        28.77        54.51       138.81       172.18       127.20 
TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JE 
       36.95        64.08        34.32        53.19       201.80        51.35 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A199 TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19H 
      109.58       152.81         9.17        12.59        13.02       152.35 
TCGA-ER-A19L TCGA-ER-A19P TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A2NC 
      131.51       162.08        37.25         8.88       148.18        43.82 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ET TCGA-ER-A3EV 
       23.34        20.15        31.27        32.05        80.32        46.98 
TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 
       33.21         6.77        92.98       174.21        15.72       220.80 
TCGA-FR-A7U8 TCGA-FR-A8YE TCGA-FS-A1YX TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z7 
       27.85       104.42        48.59       202.65        20.91         7.79 
TCGA-FS-A1ZA TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH 
       27.72       357.37        53.52        15.45         9.70        32.75 
TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZU TCGA-FS-A1ZW 
       47.38       101.26       133.55        11.41        26.56        49.48 
TCGA-FS-A1ZY TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4FD TCGA-FW-A3TV TCGA-GF-A4EO 
       27.09        66.67        28.73        80.68        13.51         7.23 
TCGA-GN-A264 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 
      117.93        10.13        64.44        62.79        32.48       121.91 
TCGA-GN-A4U7 TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A8LL TCGA-GN-A9SD TCGA-HR-A2OG 
       10.42        22.13        50.10        21.37        59.41         0.23 
TCGA-HR-A2OH TCGA-OD-A75X TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A825 TCGA-W3-AA21 
       65.88       297.90         0.33         0.69        63.02       105.04 
TCGA-WE-A8JZ TCGA-WE-A8ZM TCGA-WE-A8ZQ TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AA9Y 
       24.03        98.89        59.77        32.58        49.51        12.16 
TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YD-A9TA TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-AA3S 
       19.73        22.29        49.18        37.94        14.43        96.99 
TCGA-Z2-AA3V 
       15.98 

$`10P LOSS WILD-TYPE`
TCGA-3N-A9WB TCGA-D3-A1Q3 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       17.03        16.67        90.90        95.74        43.43       103.10 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A2JH 
       65.49        23.77       168.00        27.65        62.07        42.08 
TCGA-D3-A2JL TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC 
      171.58       130.72        58.06        46.32       166.52        86.93 
TCGA-D3-A3ML TCGA-D3-A3MR TCGA-D3-A51E TCGA-D3-A51H TCGA-D3-A51N TCGA-D3-A51R 
       13.87       103.59       174.84        56.35        22.62        63.81 
TCGA-D3-A5GL TCGA-D3-A5GS TCGA-D3-A8GB TCGA-D3-A8GE TCGA-D3-A8GK TCGA-D3-A8GL 
      125.79        18.18        30.84        26.43       170.20        89.13 
TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GQ TCGA-D9-A148 TCGA-D9-A1JW TCGA-D9-A1JX 
      107.15       161.00        29.06       151.53         3.65         7.10 
TCGA-D9-A3Z1 TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1IB 
       15.39        66.25        48.89       117.21        20.38        23.44 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH 
       68.09        28.60        10.49        15.68        13.87        20.35 
TCGA-EB-A5SG TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A182 
       68.25         7.04        24.89        29.82        27.22        14.70 
TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A20C TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C 
       26.89        68.15       151.27        63.35        85.08        78.97 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29N TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V 
       13.97        63.78        18.61        14.47        61.28        25.87 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A6 TCGA-EE-A2GD TCGA-EE-A2GK TCGA-EE-A2GL 
       46.82       102.90        86.14       340.14        54.74        79.66 
TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF 
       44.88        21.67        61.51        47.28       103.27       268.73 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MR 
      204.66        96.23       216.66        47.54        43.23       134.40 
TCGA-EE-A2MT TCGA-EE-A3AC TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3JD TCGA-ER-A193 
       71.21        51.62        13.81        41.59        27.35        31.40 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C 
       35.44        13.94        50.76        77.75        98.40        48.89 
TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19J TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19Q 
       26.37       268.93         6.44        61.05        44.05        50.89 
TCGA-ER-A1A1 TCGA-ER-A2NF TCGA-ER-A3ES TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC 
       79.99        16.37       247.04        18.77        38.27        34.82 
TCGA-FR-A8YD TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z4 TCGA-FS-A1ZB TCGA-FS-A1ZE 
       36.26       216.92       228.59        28.08        48.85        40.27 
TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZZ TCGA-FS-A4F0 
       23.93        74.73       148.80        53.16        27.02        77.82 
TCGA-FS-A4F2 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FW-A3I3 
       50.14       174.84        34.03        26.73        54.41         0.20 
TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GF-A6C9 
       22.92        55.59        19.30         9.90         2.04        15.78 
TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A26D TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-LH-A9QB 
      139.89        84.72        39.58        39.35        48.89       368.78 
TCGA-QB-A6FS TCGA-QB-AA9O TCGA-W3-A824 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1Q 
        7.23        18.05       228.16       121.08         4.01        69.07 
TCGA-W3-AA1R TCGA-W3-AA1V TCGA-W3-AA1W TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8K6 
      111.09        42.08       219.16        49.05        61.15        15.98 
TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-AAA0 TCGA-YD-A89C TCGA-Z2-A8RT 
       58.98        67.63        11.80        35.01         6.90        27.58 

  10P LOSS MUTATED 10P LOSS WILD-TYPE 
              0.23               0.20 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
            369.93             368.78 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
             53.92              48.89 
[1] "0.2 - 369.9 (53.9)" "0.2 - 368.8 (48.9)"
[1] "hr=" "1"  
D60V3, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  10P LOSS MUTATED                   35             3
  10P LOSS WILD-TYPE                 30             2
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  10P LOSS MUTATED                                          48
  10P LOSS WILD-TYPE                                        24
                    vv
clus                 REGIONAL LYMPH NODE
  10P LOSS MUTATED                   113
  10P LOSS WILD-TYPE                 102
D60V4, multiclass
                                           clus
vv                                          10P LOSS MUTATED 10P LOSS WILD-TYPE
  DISTANT METASTASIS                                      35                 30
  PRIMARY TUMOR                                            3                  2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               48                 24
  REGIONAL LYMPH NODE                                    113                102
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  10P LOSS MUTATED             7       4      16       12       15       14
  10P LOSS WILD-TYPE           5       3      12        6       12       10
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  10P LOSS MUTATED           5         6         6        24         11
  10P LOSS WILD-TYPE         9        13         6        13          4
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  10P LOSS MUTATED           17         37       10
  10P LOSS WILD-TYPE         15         23       10
D60V5, multiclass
             clus
vv            10P LOSS MUTATED 10P LOSS WILD-TYPE
  I OR II NOS                7                  5
  STAGE 0                    4                  3
  STAGE I                   16                 12
  STAGE IA                  12                  6
  STAGE IB                  15                 12
  STAGE II                  14                 10
  STAGE IIA                  5                  9
  STAGE IIB                  6                 13
  STAGE IIC                  6                  6
  STAGE III                 24                 13
  STAGE IIIA                11                  4
  STAGE IIIB                17                 15
  STAGE IIIC                37                 23
  STAGE IV                  10                 10
[1] 14  2
[1] TRUE
[1] "dimension of contingency 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      40 42 32 47
  10P LOSS WILD-TYPE    24 30 45 21
D60V6, multiclass
       clus
vv      10P LOSS MUTATED 10P LOSS WILD-TYPE
  T0+T1               40                 24
  T2                  42                 30
  T3                  32                 45
  T4                  47                 21
[1] 4 2
[1] TRUE
[1] "dimension of 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   90 39 23 27
  10P LOSS WILD-TYPE 79 24 15 22
D60V7, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  N0               90                 79
  N1               39                 24
  N2               23                 15
  N3               27                 22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V8, binary
                    cls
clus                   0   1
  10P LOSS MUTATED   177  10
  10P LOSS WILD-TYPE 136  11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED    177   10
  10P LOSS WILD-TYPE  136   11
   clus
vv  10P LOSS MUTATED 10P LOSS WILD-TYPE
  0              177                136
  1               10                 11
[1] 2 2
[1] FALSE
D60V9, binary
                    cls
clus                  0  1
  10P LOSS MUTATED   71 51
  10P LOSS WILD-TYPE 61 37
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     71   51
  10P LOSS WILD-TYPE   61   37
     clus
vv    10P LOSS MUTATED 10P LOSS WILD-TYPE
  NO                71                 61
  YES               51                 37
[1] 2 2
[1] FALSE
D60V10, binary
                    cls
clus                   0   1
  10P LOSS MUTATED    22 176
  10P LOSS WILD-TYPE  22 137
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     22  176
  10P LOSS WILD-TYPE   22  137
     clus
vv    10P LOSS MUTATED 10P LOSS WILD-TYPE
  NO                22                 22
  YES              176                137
[1] 2 2
[1] FALSE
D60V11, continuous
D60V12, binary
                    cls
clus                   0   1
  10P LOSS MUTATED    85 114
  10P LOSS WILD-TYPE  50 109
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     85  114
  10P LOSS WILD-TYPE   50  109
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  FEMALE               85                 50
  MALE                114                109
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  10P LOSS MUTATED       1                         0   192
  10P LOSS WILD-TYPE     4                         1   152
D60V13, multiclass
                           clus
vv                          10P LOSS MUTATED 10P LOSS WILD-TYPE
  ASIAN                                    1                  4
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                  192                152
[1] 3 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     4 191
  10P LOSS WILD-TYPE   3 153
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      4  191
  10P LOSS WILD-TYPE    3  153
                        clus
vv                       10P LOSS MUTATED 10P LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                  3
  NOT HISPANIC OR LATINO              191                153
[1] 2 2
[1] FALSE

Clustering(61) Variable = 10Q LOSS MUTATION ANALYSIS
D61V1, survival
                    sevent
clus2                 0  1
  10Q LOSS MUTATED   73 75
  10Q LOSS WILD-TYPE 48 43
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
               148                 91 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                75                 43 
$`10Q LOSS MUTATED`
TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 
       12.99        14.83         8.42        31.89       110.93        49.35 
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG 
      133.25        19.04        15.75        86.30         7.27       107.61 
TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3C7 
      171.58        64.83        66.08        43.53        58.06        46.98 
TCGA-D3-A3CE TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51J TCGA-D3-A51K 
       59.70         9.34        90.21        23.67       144.46        31.76 
TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D3-A8GC TCGA-D3-A8GD 
       11.34        45.70       177.86       124.08        78.21        23.61 
TCGA-D3-A8GM TCGA-D3-A8GP TCGA-D9-A1X3 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6EC 
       70.62       135.12        10.78        16.90        18.44        57.90 
TCGA-D9-A6EG TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA 
       22.85        31.96       150.61        82.85        32.42        64.83 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EE-A180 TCGA-EE-A181 
      214.59        14.96        50.07        45.50        62.37        20.38 
TCGA-EE-A20H TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P 
      155.90        12.99        44.28        63.12        47.74        27.16 
TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB 
       61.12       346.49       185.19         7.20        77.98        26.14 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GM TCGA-EE-A2GN 
      239.11         0.20       189.40        68.65        18.35        31.00 
TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 
      118.32         0.76         0.20        71.31        81.99       103.13 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MK 
       15.25         5.75       209.79        94.19       171.85        67.50 
TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AD 
      145.45       227.01        53.26       124.31       122.73         4.41 
TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 
       54.51         6.28        67.89       111.85        45.90         3.35 
TCGA-EE-A3JB TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A199 TCGA-ER-A19C TCGA-ER-A19D 
      201.80       152.81        14.56         7.82        39.81        11.47 
TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19P TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A2NC 
      150.12        99.06       120.76        34.95       146.63        22.36 
TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A44A TCGA-FR-A729 
       16.87        10.95        15.48        32.05       174.21       209.23 
TCGA-FR-A7U8 TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1ZC TCGA-FS-A1ZD 
       26.20        49.74       195.98         8.35       312.07        32.78 
TCGA-FS-A1ZF TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZU TCGA-FS-A1ZW 
       12.92        36.33        78.61       130.95         4.47        23.21 
TCGA-FS-A1ZY TCGA-FS-A4F4 TCGA-FS-A4FD TCGA-FW-A3TV TCGA-GF-A4EO TCGA-GF-A6C8 
        5.29        66.67        80.68        11.54         6.05         1.91 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U8 
       53.29       117.93        17.06         7.59       120.53        46.92 
TCGA-GN-A8LK TCGA-GN-A9SD TCGA-OD-A75X TCGA-RP-A693 TCGA-W3-A825 TCGA-W3-AA21 
       43.23        59.41       297.01         0.33         1.97        92.84 
TCGA-WE-A8K5 TCGA-WE-A8ZM TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AA9Y 
       59.64        62.99        59.44        10.95        48.39         1.94 
TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-Z2-AA3S 
       16.64        15.65        28.21        91.23 

$`10Q LOSS WILD-TYPE`
TCGA-3N-A9WC TCGA-D3-A1Q3 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       60.46        15.72        76.41        62.60        25.64        45.99 
TCGA-D3-A2J8 TCGA-D3-A2JB TCGA-D3-A2JE TCGA-D3-A2JH TCGA-D3-A3CB TCGA-D3-A3CC 
       62.86       168.00         9.76        36.30       140.98        40.01 
TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A51E TCGA-D3-A51R TCGA-D3-A5GL TCGA-D3-A8GJ 
       16.96        13.87       173.85        62.70        42.05       179.97 
TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GR TCGA-D9-A3Z1 TCGA-DA-A1HV TCGA-DA-A1HY 
      120.00        69.53        36.53        15.02        48.66       106.85 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-EB-A44Q TCGA-EB-A5SG TCGA-EB-A6L9 TCGA-EE-A17X 
       58.85        25.12         3.91        33.24         6.64        13.15 
TCGA-EE-A17Y TCGA-EE-A182 TCGA-EE-A184 TCGA-EE-A20C TCGA-EE-A29B TCGA-EE-A29C 
       24.89         0.00        67.50        75.55        75.22        76.14 
TCGA-EE-A29E TCGA-EE-A2A1 TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2MC TCGA-EE-A2MJ 
        0.26       102.38        10.62        32.48        23.77        63.25 
TCGA-EE-A2ML TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AC TCGA-ER-A195 
      104.78        25.08       143.93        23.51        51.62        34.45 
TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19G TCGA-ER-A19M 
        1.58        47.31         4.54        53.29       151.46        59.84 
TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A1A1 TCGA-ER-A2ND TCGA-ER-A3ES TCGA-ER-A3ET 
       42.48        49.71        47.97         4.70       173.29        55.82 
TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FS-A1YW TCGA-FS-A1Z4 TCGA-FS-A1ZE TCGA-FS-A1ZG 
        5.65        10.06       171.78        27.62        35.90         7.82 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F8 TCGA-FS-A4F9 
      136.27        35.28         3.06        30.90       173.19        13.28 
TCGA-FW-A3TU TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GN-A265 TCGA-GN-A268 TCGA-GN-A4U4 
       55.59        19.30         9.90        84.72        42.48        34.49 
TCGA-LH-A9QB TCGA-QB-A6FS TCGA-QB-AA9O TCGA-W3-A824 TCGA-W3-A828 TCGA-W3-AA1Q 
       85.05         7.23        18.05       174.12       120.07        44.05 
TCGA-W3-AA1R TCGA-W3-AA1V TCGA-W3-AA1W TCGA-WE-A8K1 TCGA-WE-A8ZN TCGA-WE-A8ZO 
       79.99         8.09       185.13         1.15        12.69        19.00 
TCGA-WE-AAA0 
       26.60 

  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
               0.2                0.0 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
            346.49             185.13 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
             48.87              42.05 
[1] "0.2 - 346.5 (48.9)" "0.0 - 185.1 (42.0)"
[1] "hr=" "1.2"
D61V2, survival
                    sevent
clus2                  0   1
  10Q LOSS MUTATED   103 109
  10Q LOSS WILD-TYPE  66  71
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
               212                137 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
               109                 71 
$`10Q LOSS MUTATED`
TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 
       12.99        14.93        16.57       112.04       112.57        71.80 
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JD 
      133.25        28.08        31.59       115.53        86.76        11.87 
TCGA-D3-A2JG TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP 
      113.52        12.10       171.58        66.48        66.08        59.57 
TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CE TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU 
       58.06        46.98        60.23         9.34       103.59        39.75 
TCGA-D3-A3MV TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51T 
       45.30        55.73       145.12        32.94        22.62        26.89 
TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GB 
      135.75       137.92       178.32        18.18       125.19        30.84 
TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GI TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GP 
       79.59        23.61        58.52       107.15       161.00       152.75 
TCGA-D3-A8GS TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1X3 TCGA-D9-A3Z3 TCGA-D9-A4Z6 
      117.17       151.53        54.67        18.12        22.29        18.44 
TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HW TCGA-DA-A1I1 
        9.90        25.18        66.25        22.95        36.03       194.83 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA 
      176.55        35.93       107.34        61.18        53.92        65.92 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44R TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN 
      215.44        15.68        10.36        54.02        17.29        52.01 
TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F 
        8.65        94.98        33.73         4.96       133.81        91.56 
TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L 
      168.26        13.55        13.97        72.07        64.64         2.60 
TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A29X 
       56.84        56.42        66.74       369.93       195.02        17.92 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD 
       36.82        39.29        86.14        59.28        67.43       340.14 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GM TCGA-EE-A2GN 
      161.03       208.04        48.72       107.38        75.48       102.12 
TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 
      126.81        13.91        42.77        81.21        94.82       129.27 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MD TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH 
       28.83        19.76        47.28       268.73       103.20        16.96 
TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MU TCGA-EE-A3AA 
      204.66       158.63       167.90       248.65        53.26       124.31 
TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH 
      122.73        28.77        54.51        13.81        41.59       138.81 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA 
      172.18       127.20        36.95        64.08        34.32        53.19 
TCGA-EE-A3JB TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A199 
      201.80        51.35       109.58       152.81        31.40         9.17 
TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19P 
       48.89        12.59        13.02       152.35       131.51       162.08 
TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NG 
       37.25         8.88       148.18        43.82        20.15        31.27 
TCGA-ER-A2NH TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A 
       32.05        46.98        33.21         6.77        92.98       174.21 
TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A8YE TCGA-FS-A1YX TCGA-FS-A1YY 
       15.72       220.80        27.85       104.42        48.59       228.59 
TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZC TCGA-FS-A1ZD 
      202.65        20.91         7.79        27.72       357.37        53.52 
TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZR 
       15.45        32.75        47.38       101.26       133.55        11.41 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4FB 
       26.56        49.48        27.09        66.67        28.73        26.73 
TCGA-FS-A4FD TCGA-FW-A3TV TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 
       80.68        13.51         7.23         2.04       139.89       117.93 
TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U7 TCGA-GN-A4U8 
       10.13        64.44        32.48       121.91        10.42        48.89 
TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A9SD TCGA-HR-A2OG TCGA-HR-A2OH TCGA-OD-A75X 
       22.13        50.10        59.41         0.23        65.88       297.90 
TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A825 TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K5 
        0.33         0.69        63.02       105.04        24.03        61.15 
TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-A8ZY 
       15.98        98.89        59.77        11.80        32.58        49.51 
TCGA-WE-AA9Y TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YD-A9TA TCGA-YG-AA3O TCGA-YG-AA3P 
       12.16        19.73        22.29        49.18        37.94        14.43 
TCGA-Z2-AA3S TCGA-Z2-AA3V 
       96.99        15.98 

$`10Q LOSS WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-D3-A1Q3 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 
       17.03        66.48        16.67        90.90        95.74        43.43 
TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JE TCGA-D3-A2JF 
      103.10        65.49        23.77       168.00        27.65        62.07 
TCGA-D3-A2JH TCGA-D3-A3BZ TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CF 
       42.08       130.72        46.32       166.52        86.93        24.53 
TCGA-D3-A3ML TCGA-D3-A51E TCGA-D3-A51H TCGA-D3-A51R TCGA-D3-A5GL TCGA-D3-A8GE 
       13.87       174.84        56.35        63.81       125.79        26.43 
TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D9-A1JW 
      241.38       170.20        89.13        29.06       129.63         3.65 
TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1IB 
        7.10        15.39        48.89       117.21        20.38        23.44 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5SG 
       68.09        28.60        10.49        13.87        20.35        68.25 
TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A182 TCGA-EE-A183 
        7.04        24.89        29.82        27.22        14.70        26.89 
TCGA-EE-A184 TCGA-EE-A20C TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E 
       68.15       151.27        63.35        85.08        78.97        63.78 
TCGA-EE-A29N TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A2A0 TCGA-EE-A2A1 
       18.61        14.47        61.28        25.87        46.82       102.90 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2MC TCGA-EE-A2ME 
       54.74        79.66        44.88        21.67        61.51       103.27 
TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS 
       96.23       216.66        47.54        43.23       134.40       162.48 
TCGA-EE-A2MT TCGA-EE-A3AC TCGA-EE-A3JD TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
       71.21        51.62        27.35        35.44        13.94        50.76 
TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19J TCGA-ER-A19M 
       77.75        98.40        26.37       268.93         6.44        61.05 
TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A1A1 TCGA-ER-A2ND TCGA-ER-A2NF TCGA-ER-A3ES 
       44.05        50.89        79.99        23.34        16.37       247.04 
TCGA-ER-A3ET TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FS-A1YW 
       80.32        18.77        38.27        34.82        36.26       216.92 
TCGA-FS-A1Z4 TCGA-FS-A1ZB TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZK TCGA-FS-A1ZP 
       28.08        48.85        40.27         9.70        23.93        74.73 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F8 
      148.80        53.16        27.02        77.82        50.14       174.84 
TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A5DY 
       34.03        54.41         0.20        22.92        55.59        19.30 
TCGA-GF-A3OT TCGA-GF-A6C9 TCGA-GN-A265 TCGA-GN-A268 TCGA-GN-A26D TCGA-GN-A4U4 
        9.90        15.78        84.72        62.79        39.58        39.35 
TCGA-GN-A8LL TCGA-LH-A9QB TCGA-QB-A6FS TCGA-QB-AA9O TCGA-W3-A824 TCGA-W3-A828 
       21.37       368.78         7.23        18.05       228.16       121.08 
TCGA-W3-AA1O TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1V TCGA-W3-AA1W TCGA-WE-A8K1 
        4.01        69.07       111.09        42.08       219.16        49.05 
TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-AAA0 TCGA-YD-A89C TCGA-Z2-A8RT 
       58.98        67.63        35.01         6.90        27.58 

  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
              0.23               0.20 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
            369.93             368.78 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
             53.39              48.89 
[1] "0.2 - 369.9 (53.4)" "0.2 - 368.8 (48.9)"
[1] "hr=" "1.1"
D61V3, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  10Q LOSS MUTATED                   35             4
  10Q LOSS WILD-TYPE                 30             1
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  10Q LOSS MUTATED                                          52
  10Q LOSS WILD-TYPE                                        20
                    vv
clus                 REGIONAL LYMPH NODE
  10Q LOSS MUTATED                   128
  10Q LOSS WILD-TYPE                  87
D61V4, multiclass
                                           clus
vv                                          10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  DISTANT METASTASIS                                      35                 30
  PRIMARY TUMOR                                            4                  1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               52                 20
  REGIONAL LYMPH NODE                                    128                 87
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  10Q LOSS MUTATED             9       3      18       13       16       13
  10Q LOSS WILD-TYPE           3       4      10        5       11       11
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  10Q LOSS MUTATED           5        10         5        27         11
  10Q LOSS WILD-TYPE         9         9         7        10          4
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  10Q LOSS MUTATED           20         36       14
  10Q LOSS WILD-TYPE         12         24        6
D61V5, multiclass
             clus
vv            10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  I OR II NOS                9                  3
  STAGE 0                    3                  4
  STAGE I                   18                 10
  STAGE IA                  13                  5
  STAGE IB                  16                 11
  STAGE II                  13                 11
  STAGE IIA                  5                  9
  STAGE IIB                 10                  9
  STAGE IIC                  5                  7
  STAGE III                 27                 10
  STAGE IIIA                11                  4
  STAGE IIIB                20                 12
  STAGE IIIC                36                 24
  STAGE IV                  14                  6
[1] 14  2
[1] TRUE
[1] "dimension of contingency 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      45 47 38 45
  10Q LOSS WILD-TYPE    19 25 39 23
D61V6, multiclass
       clus
vv      10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  T0+T1               45                 19
  T2                  47                 25
  T3                  38                 39
  T4                  45                 23
[1] 4 2
[1] TRUE
[1] "dimension of 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   97 46 24 29
  10Q LOSS WILD-TYPE 72 17 14 20
D61V7, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  N0               97                 72
  N1               46                 17
  N2               24                 14
  N3               29                 20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V8, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED   189  15
  10Q LOSS WILD-TYPE 124   6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED    189   15
  10Q LOSS WILD-TYPE  124    6
   clus
vv  10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  0              189                124
  1               15                  6
[1] 2 2
[1] FALSE
D61V9, binary
                    cls
clus                  0  1
  10Q LOSS MUTATED   79 53
  10Q LOSS WILD-TYPE 53 35
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     79   53
  10Q LOSS WILD-TYPE   53   35
     clus
vv    10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  NO                79                 53
  YES               53                 35
[1] 2 2
[1] FALSE
D61V10, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED    27 191
  10Q LOSS WILD-TYPE  17 122
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     27  191
  10Q LOSS WILD-TYPE   17  122
     clus
vv    10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  NO                27                 17
  YES              191                122
[1] 2 2
[1] FALSE
D61V11, continuous
D61V12, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED    91 128
  10Q LOSS WILD-TYPE  44  95
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     91  128
  10Q LOSS WILD-TYPE   44   95
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  FEMALE               91                 44
  MALE                128                 95
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  10Q LOSS MUTATED       1                         0   212
  10Q LOSS WILD-TYPE     4                         1   132
D61V13, multiclass
                           clus
vv                          10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  ASIAN                                    1                  4
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                  212                132
[1] 3 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     4 211
  10Q LOSS WILD-TYPE   3 133
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      4  211
  10Q LOSS WILD-TYPE    3  133
                        clus
vv                       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                  3
  NOT HISPANIC OR LATINO              211                133
[1] 2 2
[1] FALSE

Clustering(62) Variable = 11P LOSS MUTATION ANALYSIS
D62V1, survival
                    sevent
clus2                 0  1
  11P LOSS MUTATED   41 41
  11P LOSS WILD-TYPE 80 77
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                82                157 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                41                 77 
$`11P LOSS MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2JB TCGA-D3-A2JD 
        8.42       110.93        25.64        45.99       168.00         7.27 
TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CC TCGA-D3-A3MO 
      171.58        64.83        58.06        46.98        40.01         9.34 
TCGA-D3-A51E TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D3-A8GC TCGA-D3-A8GD 
      173.85        45.70       177.86       124.08        78.21        23.61 
TCGA-D3-A8GM TCGA-D3-A8GP TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6EG TCGA-DA-A1HV 
       70.62       135.12        16.90        18.44        22.85        48.66 
TCGA-DA-A1I1 TCGA-DA-A1I5 TCGA-DA-A3F5 TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A182 
       31.96        82.85       214.59        33.24        50.07         0.00 
TCGA-EE-A20C TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29Q 
       75.55        76.14        12.99        47.74        27.16        61.12 
TCGA-EE-A2A2 TCGA-EE-A2GE TCGA-EE-A2GM TCGA-EE-A2M6 TCGA-EE-A2MJ TCGA-EE-A2MP 
        7.20         0.20        18.35       103.13        63.25       227.01 
TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3J7 
      143.93        53.26       122.73         4.41        54.51        45.90 
TCGA-EE-A3J8 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19L 
        3.35         1.58         7.82        39.81        11.47        99.06 
TCGA-ER-A19S TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL 
       34.95         4.70        16.87        55.82        15.48        32.05 
TCGA-FR-A7UA TCGA-FS-A1Z3 TCGA-FS-A1ZF TCGA-FS-A1ZM TCGA-FS-A1ZW TCGA-FS-A4F4 
        5.65         8.35        12.92        78.61        23.21        66.67 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A26A 
      173.19        13.28        53.29       117.93        17.06         7.59 
TCGA-GN-A9SD TCGA-QB-AA9O TCGA-W3-AA1R TCGA-WE-A8K5 TCGA-WE-A8ZM TCGA-WE-A8ZN 
       59.41        18.05        79.99        59.64        62.99        12.69 
TCGA-WE-A8ZO TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O 
       19.00        16.64        15.65        28.21 

$`11P LOSS WILD-TYPE`
TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q6 
       60.46        12.99        14.83        15.72        31.89        49.35 
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J8 TCGA-D3-A2JA 
      133.25        19.04        76.41        62.60        62.86        15.75 
TCGA-D3-A2JC TCGA-D3-A2JE TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JO TCGA-D3-A2JP 
       86.30         9.76       107.61        36.30        66.08        43.53 
TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MR TCGA-D3-A3MU 
      140.98        59.70        16.96        13.87        90.21        23.67 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A8GJ 
      144.46        31.76        62.70        11.34        42.05       179.97 
TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GR TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A6EC 
      120.00        69.53        36.53        10.78        15.02        57.90 
TCGA-DA-A1HY TCGA-DA-A1I2 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 
      106.85       150.61        32.42        64.83        58.85        25.12 
TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y 
       14.96         3.91        45.50         6.64        13.15        24.89 
TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A184 TCGA-EE-A20H TCGA-EE-A29B TCGA-EE-A29E 
       62.37        20.38        67.50       155.90        75.22         0.26 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A6 
       44.28        63.12       346.49       185.19       102.38        77.98 
TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
       26.14       239.11       189.40        68.65        10.62        32.48 
TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU 
       31.00       118.32         0.76         0.20        71.31        81.99 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI 
       15.25         5.75        23.77       209.79        94.19       171.85 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A3AA 
       67.50       104.78       145.45        25.08        23.51       124.31 
TCGA-EE-A3AC TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3JB TCGA-EE-A3JI 
       51.62         6.28        67.89       111.85       201.80       152.81 
TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19G 
       14.56        34.45        47.31         4.54        53.29       151.46 
TCGA-ER-A19H TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19W 
      150.12        59.84        42.48       120.76        49.71       146.63 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NG TCGA-ER-A3ES TCGA-FR-A44A TCGA-FR-A729 
       47.97        22.36        10.95       173.29       174.21       209.23 
TCGA-FR-A7U8 TCGA-FR-A8YC TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z4 
       26.20        10.06       171.78        49.74       195.98        27.62 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZQ 
      312.07        32.78        35.90         7.82        36.33       130.95 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 
      136.27        35.28         4.47         5.29         3.06        30.90 
TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
       80.68        55.59        11.54        19.30         9.90         6.05 
TCGA-GF-A6C8 TCGA-GN-A265 TCGA-GN-A268 TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 
        1.91        84.72        42.48       120.53        34.49        46.92 
TCGA-GN-A8LK TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A693 TCGA-W3-A824 
       43.23        85.05       297.01         7.23         0.33       174.12 
TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1Q TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 
        1.97       120.07        44.05         8.09       185.13        92.84 
TCGA-WE-A8K1 TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 
        1.15        59.44        10.95        48.39         1.94        26.60 
TCGA-Z2-AA3S 
       91.23 

  11P LOSS MUTATED 11P LOSS WILD-TYPE 
               0.0                0.2 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
            227.01             346.49 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
            42.855             47.970 
[1] "0.0 - 227.0 (42.9)" "0.2 - 346.5 (48.0)"
[1] "hr=" "1.3"
D62V2, survival
                    sevent
clus2                  0   1
  11P LOSS MUTATED    58  64
  11P LOSS WILD-TYPE 111 116
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
               122                227 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                64                116 
$`11P LOSS MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q9 TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2JB 
       16.57       112.57        31.59        43.43       103.10       168.00 
TCGA-D3-A2JD TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CC 
       11.87       171.58        66.48        58.06        46.98        86.93 
TCGA-D3-A3MO TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS 
        9.34        45.30       174.84       135.75       178.32        18.18 
TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GI TCGA-D3-A8GM 
      125.19        30.84        79.59        23.61        58.52       107.15 
TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D9-A149 TCGA-D9-A1JX TCGA-D9-A3Z3 TCGA-D9-A4Z6 
      161.00       152.75        54.67         7.10        22.29        18.44 
TCGA-D9-A6EA TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I1 TCGA-DA-A1I5 
       25.18        22.95        48.89        36.03       194.83       107.34 
TCGA-DA-A1I8 TCGA-DA-A3F5 TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL 
       53.92       215.44        10.36        68.25        54.02        17.29 
TCGA-EE-A182 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20I TCGA-EE-A29C TCGA-EE-A29D 
       14.70       133.81       151.27        13.55        78.97        13.97 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
        2.60        56.84        18.61        56.42        66.74        14.47 
TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2GC TCGA-EE-A2GE 
       25.87        17.92        36.82        39.29        67.43       161.03 
TCGA-EE-A2GM TCGA-EE-A2M6 TCGA-EE-A2MJ TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MS 
       75.48       129.27        96.23        47.54       248.65       162.48 
TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3J5 TCGA-EE-A3J7 
       53.26       122.73        28.77        54.51        36.95        64.08 
TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JH TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19C 
       34.32        53.19       109.58        13.94         9.17        48.89 
TCGA-ER-A19D TCGA-ER-A19L TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A2ND TCGA-ER-A2NE 
       12.59       131.51        37.25         8.88        23.34        20.15 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A69P TCGA-FR-A7UA 
       80.32        46.98        33.21        92.98        15.72        38.27 
TCGA-FS-A1Z3 TCGA-FS-A1ZA TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-FS-A1ZM TCGA-FS-A1ZW 
       20.91        27.72        15.45        32.75       101.26        49.48 
TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FW-A3I3 TCGA-GN-A262 
       66.67        28.73       174.84        34.03         0.20       139.89 
TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A4U7 TCGA-GN-A4U9 TCGA-GN-A9SD 
      117.93        64.44        32.48        10.42        22.13        59.41 
TCGA-HR-A2OH TCGA-QB-AA9O TCGA-W3-AA1R TCGA-WE-A8JZ TCGA-WE-A8K5 TCGA-WE-A8ZM 
       65.88        18.05       111.09        24.03        61.15        98.89 
TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YD-A9TA TCGA-YG-AA3O 
       58.98        67.63        19.73        22.29        49.18        37.94 
TCGA-YG-AA3P TCGA-Z2-A8RT 
       14.43        27.58 

$`11P LOSS WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
       17.03        66.48        12.99        14.93        16.67       112.04 
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J8 
       71.80       133.25        28.08        90.90        95.74        65.49 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A2JG 
       23.77       115.53        86.76        27.65        62.07       113.52 
TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C8 
       42.08        12.10        66.08        59.57       130.72        46.32 
TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MR TCGA-D3-A3MU 
      166.52        60.23        24.53        13.87       103.59        39.75 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R 
       55.73        56.35       145.12        32.94        22.62        63.81 
TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GO TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GK 
       26.89       125.79       137.92        26.43       241.38       170.20 
TCGA-D3-A8GL TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A148 TCGA-D9-A1JW 
       89.13        29.06       129.63       117.17       151.53         3.65 
TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-DA-A1HY TCGA-DA-A1I0 
       18.12        15.39         9.90        66.25       117.21        20.38 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
      176.55        35.93        61.18        65.92        23.44        68.09 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN 
       28.60        10.49        15.68        13.87        20.35        52.01 
TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 
        7.04        24.89        29.82        27.22         8.65        94.98 
TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20F TCGA-EE-A20H 
       33.73        26.89        68.15         4.96        91.56       168.26 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29S 
       63.35        85.08        63.78        72.07        64.64        61.28 
TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A6 TCGA-EE-A2GB 
      369.93       195.02        46.82       102.90        86.14        59.28 
TCGA-EE-A2GD TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
      340.14       208.04        48.72       107.38        54.74        79.66 
TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT 
      102.12       126.81        13.91        42.77        81.21        44.88 
TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD 
       94.82        21.67        28.83        19.76        61.51        47.28 
TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK 
      103.27       268.73       103.20        16.96       204.66       158.63 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A3AA 
      216.66       167.90        43.23       134.40        71.21       124.31 
TCGA-EE-A3AC TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 
       51.62        13.81        41.59       138.81       172.18       127.20 
TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 
      201.80        27.35        51.35       152.81        31.40        35.44 
TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G 
       50.76        77.75        98.40        13.02        26.37       268.93 
TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
      152.35         6.44        61.05        44.05       162.08        50.89 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH 
      148.18        79.99        43.82        16.37        31.27        32.05 
TCGA-ER-A3ES TCGA-ER-A42K TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 
      247.04         6.77       174.21       220.80        27.85        18.77 
TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY 
       34.82        36.26       104.42       216.92        48.59       228.59 
TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD 
      202.65        28.08         7.79        48.85       357.37        53.52 
TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZQ 
       40.27         9.70        47.38        23.93        74.73       133.55 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A1ZZ 
       11.41       148.80        53.16        26.56        27.09        27.02 
TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3R5 
       77.82        50.14        26.73        54.41        80.68        22.92 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 
       55.59        13.51        19.30         9.90         7.23         2.04 
TCGA-GF-A6C9 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A268 TCGA-GN-A26D TCGA-GN-A4U3 
       15.78        84.72        10.13        62.79        39.58       121.91 
TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-GN-A8LK TCGA-GN-A8LL TCGA-HR-A2OG TCGA-LH-A9QB 
       39.35        48.89        50.10        21.37         0.23       368.78 
TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 
      297.90         7.23         0.33         0.69       228.16        63.02 
TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1Q TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 
      121.08         4.01        69.07        42.08       219.16       105.04 
TCGA-WE-A8K1 TCGA-WE-A8K6 TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-A8ZY 
       49.05        15.98        59.77        11.80        32.58        49.51 
TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-YD-A89C TCGA-Z2-AA3S TCGA-Z2-AA3V 
       12.16        35.01         6.90        96.99        15.98 

  11P LOSS MUTATED 11P LOSS WILD-TYPE 
              0.20               0.23 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
            248.65             369.93 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
             48.89              52.01 
[1] "0.2 - 248.7 (48.9)" "0.2 - 369.9 (52.0)"
[1] "hr=" "1.2"
D62V3, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  11P LOSS MUTATED                   18             2
  11P LOSS WILD-TYPE                 47             3
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  11P LOSS MUTATED                                          30
  11P LOSS WILD-TYPE                                        42
                    vv
clus                 REGIONAL LYMPH NODE
  11P LOSS MUTATED                    73
  11P LOSS WILD-TYPE                 142
D62V4, multiclass
                                           clus
vv                                          11P LOSS MUTATED 11P LOSS WILD-TYPE
  DISTANT METASTASIS                                      18                 47
  PRIMARY TUMOR                                            2                  3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               30                 42
  REGIONAL LYMPH NODE                                     73                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                 I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  11P LOSS MUTATED             6       3       8        4       12        4
  11P LOSS WILD-TYPE           6       4      20       14       15       20
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  11P LOSS MUTATED           0         7         4        13          5
  11P LOSS WILD-TYPE        14        12         8        24         10
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  11P LOSS MUTATED           14         25       10
  11P LOSS WILD-TYPE         18         35       10
D62V5, multiclass
             clus
vv            11P LOSS MUTATED 11P LOSS WILD-TYPE
  I OR II NOS                6                  6
  STAGE 0                    3                  4
  STAGE I                    8                 20
  STAGE IA                   4                 14
  STAGE IB                  12                 15
  STAGE II                   4                 20
  STAGE IIA                  0                 14
  STAGE IIB                  7                 12
  STAGE IIC                  4                  8
  STAGE III                 13                 24
  STAGE IIIA                 5                 10
  STAGE IIIB                14                 18
  STAGE IIIC                25                 35
  STAGE IV                  10                 10
[1] 14  2
[1] TRUE
[1] "dimension of contingency 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      21 25 22 29
  11P LOSS WILD-TYPE    43 47 55 39
D62V6, multiclass
       clus
vv      11P LOSS MUTATED 11P LOSS WILD-TYPE
  T0+T1               21                 43
  T2                  25                 47
  T3                  22                 55
  T4                  29                 39
[1] 4 2
[1] TRUE
[1] "dimension of 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    53  29  12  18
  11P LOSS WILD-TYPE 116  34  26  31
D62V7, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  N0               53                116
  N1               29                 34
  N2               12                 26
  N3               18                 31
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V8, binary
                    cls
clus                   0   1
  11P LOSS MUTATED   106  10
  11P LOSS WILD-TYPE 207  11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED    106   10
  11P LOSS WILD-TYPE  207   11
   clus
vv  11P LOSS MUTATED 11P LOSS WILD-TYPE
  0              106                207
  1               10                 11
[1] 2 2
[1] FALSE
D62V9, binary
                    cls
clus                  0  1
  11P LOSS MUTATED   43 37
  11P LOSS WILD-TYPE 89 51
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     43   37
  11P LOSS WILD-TYPE   89   51
     clus
vv    11P LOSS MUTATED 11P LOSS WILD-TYPE
  NO                43                 89
  YES               37                 51
[1] 2 2
[1] FALSE
D62V10, binary
                    cls
clus                   0   1
  11P LOSS MUTATED    13 111
  11P LOSS WILD-TYPE  31 202
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     13  111
  11P LOSS WILD-TYPE   31  202
     clus
vv    11P LOSS MUTATED 11P LOSS WILD-TYPE
  NO                13                 31
  YES              111                202
[1] 2 2
[1] FALSE
D62V11, continuous
D62V12, binary
                    cls
clus                   0   1
  11P LOSS MUTATED    57  67
  11P LOSS WILD-TYPE  78 156
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     57   67
  11P LOSS WILD-TYPE   78  156
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  FEMALE               57                 78
  MALE                 67                156
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  11P LOSS MUTATED       1                         1   116
  11P LOSS WILD-TYPE     4                         0   228
D62V13, multiclass
                           clus
vv                          11P LOSS MUTATED 11P LOSS WILD-TYPE
  ASIAN                                    1                  4
  BLACK OR AFRICAN AMERICAN                1                  0
  WHITE                                  116                228
[1] 3 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     2 119
  11P LOSS WILD-TYPE   5 225
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      2  119
  11P LOSS WILD-TYPE    5  225
                        clus
vv                       11P LOSS MUTATED 11P LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  5
  NOT HISPANIC OR LATINO              119                225
[1] 2 2
[1] FALSE

Clustering(63) Variable = 11Q LOSS MUTATION ANALYSIS
D63V1, survival
                    sevent
clus2                 0  1
  11Q LOSS MUTATED   55 47
  11Q LOSS WILD-TYPE 66 71
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
               102                137 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                47                 71 
$`11Q LOSS MUTATED`
TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1QB TCGA-D3-A2J6 
       14.83         8.42       110.93       133.25        62.60        25.64 
TCGA-D3-A2J7 TCGA-D3-A2JB TCGA-D3-A2JD TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
       45.99       168.00         7.27       171.58        64.83        66.08 
TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CC TCGA-D3-A3MO TCGA-D3-A51E TCGA-D3-A5GN 
       58.06        46.98        40.01         9.34       173.85        45.70 
TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GJ TCGA-D3-A8GM 
      177.86       124.08        78.21        23.61       179.97        70.62 
TCGA-D3-A8GP TCGA-D3-A8GR TCGA-D9-A3Z3 TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1I1 
      135.12        36.53        16.90        22.85        48.66        31.96 
TCGA-DA-A1I5 TCGA-DA-A3F5 TCGA-EB-A44Q TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A180 
       82.85       214.59         3.91        33.24        50.07        62.37 
TCGA-EE-A182 TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29Q 
        0.00        76.14        12.99        47.74        27.16        61.12 
TCGA-EE-A29T TCGA-EE-A2A2 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GM TCGA-EE-A2M6 
      346.49         7.20        26.14         0.20        18.35       103.13 
TCGA-EE-A2MJ TCGA-EE-A2MP TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AD 
       63.25       227.01        23.51        53.26       122.73         4.41 
TCGA-EE-A3AE TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-ER-A193 TCGA-ER-A197 TCGA-ER-A199 
       54.51        45.90         3.35        14.56         1.58         7.82 
TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19L TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A2ND 
       39.81        11.47        99.06        34.95       146.63         4.70 
TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A7UA 
       16.87        10.95        55.82        15.48        32.05         5.65 
TCGA-FS-A1Z3 TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZW 
        8.35        35.90        12.92        36.33        78.61        23.21 
TCGA-FS-A1ZZ TCGA-FS-A4F4 TCGA-FS-A4FD TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A26A 
        3.06        66.67        80.68       117.93        17.06         7.59 
TCGA-GN-A4U3 TCGA-GN-A9SD TCGA-LH-A9QB TCGA-QB-A6FS TCGA-QB-AA9O TCGA-W3-AA1R 
      120.53        59.41        85.05         7.23        18.05        79.99 
TCGA-W3-AA1V TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO 
        8.09         1.15        59.64        62.99        12.69        19.00 
TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O 
       48.39         1.94        26.60        16.64        15.65        28.21 

$`11Q LOSS WILD-TYPE`
TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q6 TCGA-D3-A1Q8 
       60.46        12.99        15.72        31.89        49.35        19.04 
TCGA-D3-A1QA TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JE TCGA-D3-A2JG 
       76.41        62.86        15.75        86.30         9.76       107.61 
TCGA-D3-A2JH TCGA-D3-A2JP TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML 
       36.30        43.53       140.98        59.70        16.96        13.87 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T 
       90.21        23.67       144.46        31.76        62.70        11.34 
TCGA-D3-A5GL TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A4Z6 
       42.05       120.00        69.53        10.78        15.02        18.44 
TCGA-D9-A6EC TCGA-DA-A1HY TCGA-DA-A1I2 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC 
       57.90       106.85       150.61        32.42        64.83        58.85 
TCGA-DA-A3F2 TCGA-DA-A3F8 TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y 
       25.12        14.96        45.50         6.64        13.15        24.89 
TCGA-EE-A181 TCGA-EE-A184 TCGA-EE-A20C TCGA-EE-A20H TCGA-EE-A29B TCGA-EE-A29E 
       20.38        67.50        75.55       155.90        75.22         0.26 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A6 TCGA-EE-A2GD 
       44.28        63.12       185.19       102.38        77.98       239.11 
TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GO 
      189.40        68.65        10.62        32.48        31.00       118.32 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M7 TCGA-EE-A2M8 
        0.76         0.20        71.31        81.99        15.25         5.75 
TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML 
       23.77       209.79        94.19       171.85        67.50       104.78 
TCGA-EE-A2MM TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AF 
      145.45        25.08       143.93       124.31        51.62         6.28 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3JB TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A198 
       67.89       111.85       201.80       152.81        34.45        47.31 
TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19M TCGA-ER-A19N 
        4.54        53.29       151.46       150.12        59.84        42.48 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A3ES TCGA-FR-A44A 
      120.76        49.71        47.97        22.36       173.29       174.21 
TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A8YC TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 
      209.23        26.20        10.06       171.78        49.74       195.98 
TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZG TCGA-FS-A1ZQ TCGA-FS-A1ZS 
       27.62       312.07        32.78         7.82       130.95       136.27 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A4F0 TCGA-FS-A4F8 TCGA-FS-A4F9 
       35.28         4.47         5.29        30.90       173.19        13.28 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 
       55.59        11.54        19.30         9.90         6.05         1.91 
TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A268 TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-GN-A8LK 
       53.29        84.72        42.48        34.49        46.92        43.23 
TCGA-OD-A75X TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1Q 
      297.01         0.33       174.12         1.97       120.07        44.05 
TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-Z2-AA3S 
      185.13        92.84        59.44        10.95        91.23 

  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
               0.0                0.2 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
            346.49             312.07 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
             36.43              49.74 
[1] "0.0 - 346.5 (36.4)" "0.2 - 312.1 (49.7)"
[1] "hr=" "1.1"
D63V2, survival
                    sevent
clus2                  0   1
  11Q LOSS MUTATED    72  71
  11Q LOSS WILD-TYPE  97 109
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
               143                206 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                71                109 
$`11Q LOSS MUTATED`
TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A1QB 
       14.93        16.57       112.57       133.25        31.59        95.74 
TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2JB TCGA-D3-A2JD TCGA-D3-A2JL TCGA-D3-A2JN 
       43.43       103.10       168.00        11.87       171.58        66.48 
TCGA-D3-A2JO TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CC TCGA-D3-A3MO TCGA-D3-A3MV 
       66.08        58.06        46.98        86.93         9.34        45.30 
TCGA-D3-A51E TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GB 
      174.84       135.75       178.32        18.18       125.19        30.84 
TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GM TCGA-D3-A8GN 
       79.59        23.61        58.52       241.38       107.15       161.00 
TCGA-D3-A8GP TCGA-D3-A8GR TCGA-D9-A149 TCGA-D9-A1JX TCGA-D9-A3Z3 TCGA-D9-A6EA 
      152.75       129.63        54.67         7.10        22.29        25.18 
TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I1 TCGA-DA-A1I5 TCGA-DA-A1I8 
       22.95        48.89        36.03       194.83       107.34        53.92 
TCGA-DA-A3F5 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL 
      215.44        13.87        10.36        68.25        54.02        17.29 
TCGA-EE-A180 TCGA-EE-A182 TCGA-EE-A20B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29L 
       94.98        14.70       133.81        78.97        13.97         2.60 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29T 
       56.84        18.61        56.42        66.74        14.47       369.93 
TCGA-EE-A29V TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GE 
       25.87        36.82        39.29        59.28        67.43       161.03 
TCGA-EE-A2GM TCGA-EE-A2M6 TCGA-EE-A2MD TCGA-EE-A2MJ TCGA-EE-A2MN TCGA-EE-A2MP 
       75.48       129.27        47.28        96.23        47.54       248.65 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3J5 
       71.21        53.26       122.73        28.77        54.51        36.95 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A197 
       64.08        34.32        53.19       109.58        31.40        13.94 
TCGA-ER-A199 TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19L TCGA-ER-A19S TCGA-ER-A19T 
        9.17        48.89        12.59       131.51        37.25         8.88 
TCGA-ER-A19W TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A3ET TCGA-ER-A3EV 
      148.18        23.34        20.15        31.27        80.32        46.98 
TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A69P TCGA-FR-A7UA TCGA-FS-A1Z3 TCGA-FS-A1Z7 
       33.21        92.98        15.72        38.27        20.91         7.79 
TCGA-FS-A1ZA TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZM 
       27.72        40.27        15.45        32.75        47.38       101.26 
TCGA-FS-A1ZW TCGA-FS-A1ZZ TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4FD TCGA-FW-A3I3 
       49.48        27.02        66.67        28.73        80.68         0.20 
TCGA-GN-A264 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U3 
      117.93        10.13        64.44        32.48        39.58       121.91 
TCGA-GN-A4U7 TCGA-GN-A4U9 TCGA-GN-A9SD TCGA-HR-A2OH TCGA-LH-A9QB TCGA-QB-A6FS 
       10.42        22.13        59.41        65.88       368.78         7.23 
TCGA-QB-AA9O TCGA-W3-AA1R TCGA-W3-AA1V TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K5 
       18.05       111.09        42.08        24.03        49.05        61.15 
TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 
       98.89        58.98        67.63        49.51        12.16        35.01 
TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-A8RT 
       19.73        22.29        37.94        14.43        27.58 

$`11Q LOSS WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q6 
       17.03        66.48        12.99        16.67       112.04        71.80 
TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JC 
       28.08        90.90        65.49        23.77       115.53        86.76 
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JP 
       27.65        62.07       113.52        42.08        12.10        59.57 
TCGA-D3-A3BZ TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML 
      130.72        46.32       166.52        60.23        24.53        13.87 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K 
      103.59        39.75        55.73        56.35       145.12        32.94 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GO TCGA-D3-A8GE 
       22.62        63.81        26.89       125.79       137.92        26.43 
TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GQ TCGA-D3-A8GS TCGA-D9-A148 TCGA-D9-A1JW 
      170.20        89.13        29.06       117.17       151.53         3.65 
TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-DA-A1HY 
       18.12        15.39        18.44         9.90        66.25       117.21 
TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IB 
       20.38       176.55        35.93        61.18        65.92        23.44 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EB-A5KH TCGA-EB-A5UN 
       68.09        28.60        10.49        15.68        20.35        52.01 
TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A181 
        7.04        24.89        29.82        27.22         8.65        33.73 
TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H 
       26.89        68.15         4.96       151.27        91.56       168.26 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H 
       13.55        63.35        85.08        63.78        72.07        64.64 
TCGA-EE-A29S TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A6 
       61.28       195.02        17.92        46.82       102.90        86.14 
TCGA-EE-A2GD TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
      340.14       208.04        48.72       107.38        54.74        79.66 
TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT 
      102.12       126.81        13.91        42.77        81.21        44.88 
TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2ME 
       94.82        21.67        28.83        19.76        61.51       103.27 
TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML 
      268.73       103.20        16.96       204.66       158.63       216.66 
TCGA-EE-A2MM TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A3AA TCGA-EE-A3AC 
      167.90        43.23       134.40       162.48       124.31        51.62 
TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3JB 
       13.81        41.59       138.81       172.18       127.20       201.80 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A19A 
       27.35        51.35       152.81        35.44        50.76        77.75 
TCGA-ER-A19B TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J 
       98.40        13.02        26.37       268.93       152.35         6.44 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A1A1 TCGA-ER-A2NC 
       61.05        44.05       162.08        50.89        79.99        43.82 
TCGA-ER-A2NF TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A42K TCGA-FR-A44A TCGA-FR-A729 
       16.37        32.05       247.04         6.77       174.21       220.80 
TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW 
       27.85        18.77        34.82        36.26       104.42       216.92 
TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1ZB TCGA-FS-A1ZC 
       48.59       228.59       202.65        28.08        48.85       357.37 
TCGA-FS-A1ZD TCGA-FS-A1ZG TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR 
       53.52         9.70        23.93        74.73       133.55        11.41 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A4F0 TCGA-FS-A4F2 
      148.80        53.16        26.56        27.09        77.82        50.14 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FW-A3R5 TCGA-FW-A3TU 
      174.84        34.03        26.73        54.41        22.92        55.59 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 
       13.51        19.30         9.90         7.23         2.04        15.78 
TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A268 TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-GN-A8LK 
      139.89        84.72        62.79        39.35        48.89        50.10 
TCGA-GN-A8LL TCGA-HR-A2OG TCGA-OD-A75X TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 
       21.37         0.23       297.90         0.33         0.69       228.16 
TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1Q TCGA-W3-AA1W TCGA-W3-AA21 
       63.02       121.08         4.01        69.07       219.16       105.04 
TCGA-WE-A8K6 TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-YD-A89C TCGA-YD-A9TA 
       15.98        59.77        11.80        32.58         6.90        49.18 
TCGA-Z2-AA3S TCGA-Z2-AA3V 
       96.99        15.98 

  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
              0.20               0.23 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
            369.93             357.37 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
             48.89              53.34 
[1] "0.2 - 369.9 (48.9)" "0.2 - 357.4 (53.3)"
[1] "hr=" "1.1"
D63V3, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  11Q LOSS MUTATED                   24             2
  11Q LOSS WILD-TYPE                 41             3
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  11Q LOSS MUTATED                                          33
  11Q LOSS WILD-TYPE                                        39
                    vv
clus                 REGIONAL LYMPH NODE
  11Q LOSS MUTATED                    86
  11Q LOSS WILD-TYPE                 129
D63V4, multiclass
                                           clus
vv                                          11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  DISTANT METASTASIS                                      24                 41
  PRIMARY TUMOR                                            2                  3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               33                 39
  REGIONAL LYMPH NODE                                     86                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                 I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  11Q LOSS MUTATED             6       3       8        5       13        6
  11Q LOSS WILD-TYPE           6       4      20       13       14       18
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  11Q LOSS MUTATED           1         9         6        16          5
  11Q LOSS WILD-TYPE        13        10         6        21         10
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  11Q LOSS MUTATED           15         31       10
  11Q LOSS WILD-TYPE         17         29       10
D63V5, multiclass
             clus
vv            11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  I OR II NOS                6                  6
  STAGE 0                    3                  4
  STAGE I                    8                 20
  STAGE IA                   5                 13
  STAGE IB                  13                 14
  STAGE II                   6                 18
  STAGE IIA                  1                 13
  STAGE IIB                  9                 10
  STAGE IIC                  6                  6
  STAGE III                 16                 21
  STAGE IIIA                 5                 10
  STAGE IIIB                15                 17
  STAGE IIIC                31                 29
  STAGE IV                  10                 10
[1] 14  2
[1] TRUE
[1] "dimension of contingency 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      24 29 29 33
  11Q LOSS WILD-TYPE    40 43 48 35
D63V6, multiclass
       clus
vv      11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  T0+T1               24                 40
  T2                  29                 43
  T3                  29                 48
  T4                  33                 35
[1] 4 2
[1] TRUE
[1] "dimension of 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    61  31  13  24
  11Q LOSS WILD-TYPE 108  32  25  25
D63V7, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  N0               61                108
  N1               31                 32
  N2               13                 25
  N3               24                 25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V8, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED   125  10
  11Q LOSS WILD-TYPE 188  11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED    125   10
  11Q LOSS WILD-TYPE  188   11
   clus
vv  11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  0              125                188
  1               10                 11
[1] 2 2
[1] FALSE
D63V9, binary
                    cls
clus                  0  1
  11Q LOSS MUTATED   53 45
  11Q LOSS WILD-TYPE 79 43
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     53   45
  11Q LOSS WILD-TYPE   79   43
     clus
vv    11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  NO                53                 79
  YES               45                 43
[1] 2 2
[1] FALSE
D63V10, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED    16 130
  11Q LOSS WILD-TYPE  28 183
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     16  130
  11Q LOSS WILD-TYPE   28  183
     clus
vv    11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  NO                16                 28
  YES              130                183
[1] 2 2
[1] FALSE
D63V11, continuous
D63V12, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED    69  77
  11Q LOSS WILD-TYPE  66 146
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     69   77
  11Q LOSS WILD-TYPE   66  146
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  FEMALE               69                 66
  MALE                 77                146
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  11Q LOSS MUTATED       2                         1   137
  11Q LOSS WILD-TYPE     3                         0   207
D63V13, multiclass
                           clus
vv                          11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  ASIAN                                    2                  3
  BLACK OR AFRICAN AMERICAN                1                  0
  WHITE                                  137                207
[1] 3 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     3 140
  11Q LOSS WILD-TYPE   4 204
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      3  140
  11Q LOSS WILD-TYPE    4  204
                        clus
vv                       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  4
  NOT HISPANIC OR LATINO              140                204
[1] 2 2
[1] FALSE

Clustering(64) Variable = 12P LOSS MUTATION ANALYSIS
D64V1, survival
                    sevent
clus2                  0   1
  12P LOSS MUTATED    20  12
  12P LOSS WILD-TYPE 101 106
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                32                207 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                12                106 
$`12P LOSS MUTATED`
TCGA-D3-A2J6 TCGA-D3-A2JL TCGA-D3-A2JO TCGA-D3-A5GR TCGA-D3-A8GD TCGA-D9-A1X3 
       25.64       171.58        66.08       177.86        23.61        10.78 
TCGA-DA-A1I1 TCGA-EB-A5SH TCGA-EE-A20C TCGA-EE-A29G TCGA-EE-A29Q TCGA-EE-A2A2 
       31.96        50.07        75.55        44.28        61.12         7.20 
TCGA-EE-A2GP TCGA-EE-A2MG TCGA-EE-A2MK TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MU 
        0.76        94.19        67.50       227.01       143.93        53.26 
TCGA-EE-A3AE TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-ER-A19S TCGA-ER-A2NG TCGA-FS-A1Z4 
       54.51        67.89        45.90        34.95        10.95        27.62 
TCGA-FS-A1ZQ TCGA-FS-A1ZT TCGA-GN-A4U3 TCGA-LH-A9QB TCGA-OD-A75X TCGA-RP-A693 
      130.95        35.28       120.53        85.05       297.01         0.33 
TCGA-W3-AA1V TCGA-WE-A8ZY 
        8.09        48.39 

$`12P LOSS WILD-TYPE`
TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
       60.46        12.99        14.83         8.42        15.72        31.89 
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB 
      110.93        49.35       133.25        19.04        76.41        62.60 
TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
       45.99        62.86        15.75       168.00        86.30         7.27 
TCGA-D3-A2JE TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3C6 
        9.76       107.61        36.30        64.83        43.53        58.06 
TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML 
       46.98       140.98        40.01        59.70        16.96        13.87 
TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51J TCGA-D3-A51K 
        9.34        90.21        23.67       173.85       144.46        31.76 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GU TCGA-D3-A8GC 
       62.70        11.34        42.05        45.70       124.08        78.21 
TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GP TCGA-D3-A8GR 
      179.97       120.00        69.53        70.62       135.12        36.53 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV 
       15.02        16.90        18.44        57.90        22.85        48.66 
TCGA-DA-A1HY TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC 
      106.85       150.61        82.85        32.42        64.83        58.85 
TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5SG TCGA-EB-A5UN 
       25.12       214.59        14.96         3.91        33.24        45.50 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 
        6.64        13.15        24.89        62.37        20.38         0.00 
TCGA-EE-A184 TCGA-EE-A20H TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
       67.50       155.90        75.22        76.14        12.99         0.26 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 
       63.12        47.74        27.16       346.49       185.19       102.38 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ 
       77.98        26.14       239.11         0.20       189.40        68.65 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GR 
       10.62        32.48        18.35        31.00       118.32         0.20 
TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC 
       71.31        81.99       103.13        15.25         5.75        23.77 
TCGA-EE-A2MF TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MR 
      209.79       171.85        63.25       104.78       145.45        25.08 
TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AF 
       23.51       124.31       122.73        51.62         4.41         6.28 
TCGA-EE-A3J4 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 
      111.85         3.35       201.80       152.81        14.56        34.45 
TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C 
        1.58        47.31         7.82         4.54        53.29        39.81 
TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
       11.47       151.46       150.12        99.06        59.84        42.48 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
      120.76        49.71       146.63        47.97        22.36         4.70 
TCGA-ER-A2NE TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A44A 
       16.87       173.29        55.82        15.48        32.05       174.21 
TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FS-A1YW TCGA-FS-A1YY 
      209.23        26.20         5.65        10.06       171.78        49.74 
TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF 
      195.98         8.35       312.07        32.78        35.90        12.92 
TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZW 
        7.82        36.33        78.61       136.27         4.47        23.21 
TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 
        5.29         3.06        30.90        66.67       173.19        13.28 
TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
       80.68        55.59        11.54        19.30         9.90         6.05 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 
        1.91        53.29       117.93        84.72        17.06        42.48 
TCGA-GN-A26A TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-GN-A8LK TCGA-GN-A9SD TCGA-QB-A6FS 
        7.59        34.49        46.92        43.23        59.41         7.23 
TCGA-QB-AA9O TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1Q TCGA-W3-AA1R 
       18.05       174.12         1.97       120.07        44.05        79.99 
TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8ZM TCGA-WE-A8ZN 
      185.13        92.84         1.15        59.64        62.99        12.69 
TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 
       19.00        59.44        10.95         1.94        26.60        16.64 
TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-Z2-AA3S 
       15.65        28.21        91.23 

  12P LOSS MUTATED 12P LOSS WILD-TYPE 
              0.33               0.00 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
            297.01             346.49 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
            51.665             45.500 
[1] "0.3 - 297.0 (51.7)" "0.0 - 346.5 (45.5)"
[1] "hr=" "1.5"
D64V2, survival
                    sevent
clus2                  0   1
  12P LOSS MUTATED    30  24
  12P LOSS WILD-TYPE 139 156
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                54                295 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                24                156 
$`12P LOSS MUTATED`
TCGA-D3-A2J6 TCGA-D3-A2JL TCGA-D3-A2JO TCGA-D3-A51N TCGA-D3-A5GO TCGA-D3-A5GR 
       43.43       171.58        66.08        22.62       137.92       178.32 
TCGA-D3-A5GS TCGA-D3-A8GB TCGA-D3-A8GD TCGA-D3-A8GI TCGA-D3-A8GN TCGA-D9-A1X3 
       18.18        30.84        23.61        58.52       161.00        18.12 
TCGA-D9-A6EA TCGA-DA-A1I1 TCGA-EB-A5SH TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A29G 
       25.18       194.83        54.02       133.81       151.27        72.07 
TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A2A2 TCGA-EE-A2GP TCGA-EE-A2MG TCGA-EE-A2MK 
       66.74        61.28        36.82        13.91       103.20       158.63 
TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AE TCGA-EE-A3J3 TCGA-EE-A3J7 
      248.65       162.48        53.26        54.51       172.18        64.08 
TCGA-EE-A3JA TCGA-ER-A19E TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A2NG TCGA-ER-A42K 
       53.19        13.02        37.25         8.88        31.27         6.77 
TCGA-FS-A1YX TCGA-FS-A1Z4 TCGA-FS-A1ZA TCGA-FS-A1ZH TCGA-FS-A1ZQ TCGA-FS-A1ZT 
       48.59        28.08        27.72        32.75       133.55        53.16 
TCGA-FS-A4F5 TCGA-FW-A3R5 TCGA-GN-A4U3 TCGA-GN-A8LL TCGA-HR-A2OH TCGA-LH-A9QB 
       28.73        22.92       121.91        21.37        65.88       368.78 
TCGA-OD-A75X TCGA-RP-A693 TCGA-W3-AA1V TCGA-WE-A8JZ TCGA-WE-A8ZY TCGA-YD-A9TA 
      297.90         0.33        42.08        24.03        49.51        49.18 

$`12P LOSS WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q3 
       17.03        66.48        12.99        14.93        16.57        16.67 
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 
      112.04       112.57        71.80       133.25        28.08        31.59 
TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA 
       90.90        95.74       103.10        65.49        23.77       115.53 
TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A2JG 
      168.00        86.76        11.87        27.65        62.07       113.52 
TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 
       42.08        12.10        66.48        59.57       130.72        58.06 
TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF 
       46.98        46.32       166.52        86.93        60.23        24.53 
TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E 
       13.87         9.34       103.59        39.75        45.30       174.84 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T 
       55.73        56.35       145.12        32.94        63.81        26.89 
TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GU TCGA-D3-A8GC TCGA-D3-A8GE TCGA-D3-A8GJ 
      125.79       135.75       125.19        79.59        26.43       241.38 
TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR 
      170.20        89.13       107.15       152.75        29.06       129.63 
TCGA-D3-A8GS TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 
      117.17       151.53        54.67         3.65         7.10        15.39 
TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV 
       22.29        18.44         9.90        66.25        22.95        48.89 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
       36.03       117.21        20.38       176.55        35.93       107.34 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
       61.18        53.92        65.92        23.44        68.09        28.60 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH 
       10.49       215.44        15.68        13.87        10.36        20.35 
TCGA-EB-A5SG TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X 
       68.25        17.29        52.01         7.04        24.89        29.82 
TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
       27.22         8.65        94.98        33.73        14.70        26.89 
TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A 
       68.15         4.96        91.56       168.26        13.55        63.35 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L 
       85.08        78.97        13.97        63.78        64.64         2.60 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A29T TCGA-EE-A29V 
       56.84        18.61        56.42        14.47       369.93        25.87 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-EE-A2A6 
      195.02        17.92        46.82       102.90        39.29        86.14 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
       59.28        67.43       340.14       161.03       208.04        48.72 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO 
      107.38        54.74        79.66        75.48       102.12       126.81 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 
       42.77        81.21        44.88        94.82        21.67       129.27 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF 
       28.83        19.76        61.51        47.28       103.27       268.73 
TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN 
       16.96       204.66        96.23       216.66       167.90        47.54 
TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC 
       43.23       134.40        71.21       124.31       122.73        51.62 
TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J5 
       28.77        13.81        41.59       138.81       127.20        36.95 
TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI 
       34.32       201.80        27.35        51.35       109.58       152.81 
TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A 
       31.40        35.44        13.94        50.76         9.17        77.75 
TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H 
       98.40        48.89        12.59        26.37       268.93       152.35 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
        6.44       131.51        61.05        44.05       162.08        50.89 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF 
      148.18        79.99        43.82        23.34        20.15        16.37 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN 
       32.05       247.04        80.32        46.98        33.21        92.98 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA 
      174.21        15.72       220.80        27.85        18.77        38.27 
TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 
       34.82        36.26       104.42       216.92       228.59       202.65 
TCGA-FS-A1Z3 TCGA-FS-A1Z7 TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE 
       20.91         7.79        48.85       357.37        53.52        40.27 
TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP 
       15.45         9.70        47.38        23.93       101.26        74.73 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ 
       11.41       148.80        26.56        49.48        27.09        27.02 
TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB 
       77.82        50.14        66.67       174.84        34.03        26.73 
TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
       54.41        80.68         0.20        55.59        13.51        19.30 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 
        9.90         7.23         2.04        15.78       139.89       117.93 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
       84.72        10.13        64.44        62.79        32.48        39.58 
TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A9SD 
       39.35        10.42        48.89        22.13        50.10        59.41 
TCGA-HR-A2OG TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 
        0.23         7.23        18.05         0.69       228.16        63.02 
TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1W TCGA-W3-AA21 
      121.08         4.01        69.07       111.09       219.16       105.04 
TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO 
       49.05        61.15        15.98        98.89        58.98        67.63 
TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 
       59.77        11.80        32.58        12.16        35.01        19.73 
TCGA-WE-AAA4 TCGA-YD-A89C TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S 
       22.29         6.90        37.94        14.43        27.58        96.99 
TCGA-Z2-AA3V 
       15.98 

  12P LOSS MUTATED 12P LOSS WILD-TYPE 
              0.33               0.20 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
            368.78             369.93 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
            53.175             50.760 
[1] "0.3 - 368.8 (53.2)" "0.2 - 369.9 (50.8)"
[1] "hr=" "1.4"
D64V3, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  12P LOSS MUTATED                   15             2
  12P LOSS WILD-TYPE                 50             3
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  12P LOSS MUTATED                                          13
  12P LOSS WILD-TYPE                                        59
                    vv
clus                 REGIONAL LYMPH NODE
  12P LOSS MUTATED                    28
  12P LOSS WILD-TYPE                 187
D64V4, multiclass
                                           clus
vv                                          12P LOSS MUTATED 12P LOSS WILD-TYPE
  DISTANT METASTASIS                                      15                 50
  PRIMARY TUMOR                                            2                  3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               13                 59
  REGIONAL LYMPH NODE                                     28                187
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  12P LOSS MUTATED             4       1       5        3        4        4
  12P LOSS WILD-TYPE           8       6      23       15       23       20
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  12P LOSS MUTATED           2         2         1         6          1
  12P LOSS WILD-TYPE        12        17        11        31         14
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  12P LOSS MUTATED            5          7        6
  12P LOSS WILD-TYPE         27         53       14
D64V5, multiclass
             clus
vv            12P LOSS MUTATED 12P LOSS WILD-TYPE
  I OR II NOS                4                  8
  STAGE 0                    1                  6
  STAGE I                    5                 23
  STAGE IA                   3                 15
  STAGE IB                   4                 23
  STAGE II                   4                 20
  STAGE IIA                  2                 12
  STAGE IIB                  2                 17
  STAGE IIC                  1                 11
  STAGE III                  6                 31
  STAGE IIIA                 1                 14
  STAGE IIIB                 5                 27
  STAGE IIIC                 7                 53
  STAGE IV                   6                 14
[1] 14  2
[1] TRUE
[1] "dimension of contingency 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       8  9 12 14
  12P LOSS WILD-TYPE    56 63 65 54
D64V6, multiclass
       clus
vv      12P LOSS MUTATED 12P LOSS WILD-TYPE
  T0+T1                8                 56
  T2                   9                 63
  T3                  12                 65
  T4                  14                 54
[1] 4 2
[1] TRUE
[1] "dimension of 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    26   8   6   8
  12P LOSS WILD-TYPE 143  55  32  41
D64V7, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  N0               26                143
  N1                8                 55
  N2                6                 32
  N3                8                 41
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V8, binary
                    cls
clus                   0   1
  12P LOSS MUTATED    46   6
  12P LOSS WILD-TYPE 267  15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     46    6
  12P LOSS WILD-TYPE  267   15
   clus
vv  12P LOSS MUTATED 12P LOSS WILD-TYPE
  0               46                267
  1                6                 15
[1] 2 2
[1] FALSE
D64V9, binary
                    cls
clus                   0   1
  12P LOSS MUTATED    20  16
  12P LOSS WILD-TYPE 112  72
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     20   16
  12P LOSS WILD-TYPE  112   72
     clus
vv    12P LOSS MUTATED 12P LOSS WILD-TYPE
  NO                20                112
  YES               16                 72
[1] 2 2
[1] FALSE
D64V10, binary
                    cls
clus                   0   1
  12P LOSS MUTATED     5  52
  12P LOSS WILD-TYPE  39 261
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      5   52
  12P LOSS WILD-TYPE   39  261
     clus
vv    12P LOSS MUTATED 12P LOSS WILD-TYPE
  NO                 5                 39
  YES               52                261
[1] 2 2
[1] FALSE
D64V11, continuous
D64V12, binary
                    cls
clus                   0   1
  12P LOSS MUTATED    25  33
  12P LOSS WILD-TYPE 110 190
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     25   33
  12P LOSS WILD-TYPE  110  190
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  FEMALE               25                110
  MALE                 33                190
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  12P LOSS MUTATED       0                         0    56
  12P LOSS WILD-TYPE     5                         1   288
D64V13, multiclass
                           clus
vv                          12P LOSS MUTATED 12P LOSS WILD-TYPE
  ASIAN                                    0                  5
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   56                288
[1] 3 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     0  56
  12P LOSS WILD-TYPE   7 288
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      0   56
  12P LOSS WILD-TYPE    7  288
                        clus
vv                       12P LOSS MUTATED 12P LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  7
  NOT HISPANIC OR LATINO               56                288
[1] 2 2
[1] FALSE

Clustering(65) Variable = 12Q LOSS MUTATION ANALYSIS
D65V1, survival
                    sevent
clus2                  0   1
  12Q LOSS MUTATED    23  18
  12Q LOSS WILD-TYPE  98 100
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                41                198 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                18                100 
$`12Q LOSS MUTATED`
TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A2J6 TCGA-D3-A2JL TCGA-D3-A3CC TCGA-D3-A5GR 
       12.99         8.42        25.64       171.58        40.01       177.86 
TCGA-D3-A8GC TCGA-D9-A1X3 TCGA-D9-A6EC TCGA-DA-A1I1 TCGA-EB-A5SH TCGA-EE-A20C 
       78.21        10.78        57.90        31.96        50.07        75.55 
TCGA-EE-A29G TCGA-EE-A29Q TCGA-EE-A2A2 TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GU 
       44.28        61.12         7.20         0.76         0.20        81.99 
TCGA-EE-A2MG TCGA-EE-A2MK TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AA 
       94.19        67.50       227.01       143.93        53.26       124.31 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-ER-A199 TCGA-ER-A19S 
        4.41        54.51        67.89        45.90         7.82        34.95 
TCGA-ER-A3PL TCGA-FS-A1Z4 TCGA-FS-A1ZQ TCGA-FS-A1ZT TCGA-GN-A4U3 TCGA-LH-A9QB 
       32.05        27.62       130.95        35.28       120.53        85.05 
TCGA-OD-A75X TCGA-RP-A693 TCGA-W3-AA1R TCGA-WE-A8ZM TCGA-WE-A8ZY 
      297.01         0.33        79.99        62.99        48.39 

$`12Q LOSS WILD-TYPE`
TCGA-3N-A9WC TCGA-BF-AAP0 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 
       60.46        14.83        15.72        31.89       110.93        49.35 
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J7 TCGA-D3-A2J8 
      133.25        19.04        76.41        62.60        45.99        62.86 
TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JE TCGA-D3-A2JG 
       15.75       168.00        86.30         7.27         9.76       107.61 
TCGA-D3-A2JH TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3C7 
       36.30        64.83        66.08        43.53        58.06        46.98 
TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR 
      140.98        59.70        16.96        13.87         9.34        90.21 
TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T 
       23.67       173.85       144.46        31.76        62.70        11.34 
TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GU TCGA-D3-A8GD TCGA-D3-A8GJ TCGA-D3-A8GK 
       42.05        45.70       124.08        23.61       179.97       120.00 
TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GP TCGA-D3-A8GR TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       69.53        70.62       135.12        36.53        15.02        16.90 
TCGA-D9-A4Z6 TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I2 TCGA-DA-A1I5 
       18.44        22.85        48.66       106.85       150.61        82.85 
TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 
       32.42        64.83        58.85        25.12       214.59        14.96 
TCGA-EB-A44Q TCGA-EB-A5SG TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y 
        3.91        33.24        45.50         6.64        13.15        24.89 
TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A184 TCGA-EE-A20H TCGA-EE-A29B 
       62.37        20.38         0.00        67.50       155.90        75.22 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P 
       76.14        12.99         0.26        63.12        47.74        27.16 
TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD 
      346.49       185.19       102.38        77.98        26.14       239.11 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
        0.20       189.40        68.65        10.62        32.48        18.35 
TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GS TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 
       31.00       118.32        71.31       103.13        15.25         5.75 
TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MM 
       23.77       209.79       171.85        63.25       104.78       145.45 
TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AF TCGA-EE-A3J4 
       25.08        23.51       122.73        51.62         6.28       111.85 
TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
        3.35       201.80       152.81        14.56        34.45         1.58 
TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19G 
       47.31         4.54        53.29        39.81        11.47       151.46 
TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
      150.12        99.06        59.84        42.48       120.76        49.71 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NG 
      146.63        47.97        22.36         4.70        16.87        10.95 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7U8 
      173.29        55.82        15.48       174.21       209.23        26.20 
TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
        5.65        10.06       171.78        49.74       195.98         8.35 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZJ 
      312.07        32.78        35.90        12.92         7.82        36.33 
TCGA-FS-A1ZM TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ 
       78.61       136.27         4.47        23.21         5.29         3.06 
TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TU 
       30.90        66.67       173.19        13.28        80.68        55.59 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 
       11.54        19.30         9.90         6.05         1.91        53.29 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U4 
      117.93        84.72        17.06        42.48         7.59        34.49 
TCGA-GN-A4U8 TCGA-GN-A8LK TCGA-GN-A9SD TCGA-QB-A6FS TCGA-QB-AA9O TCGA-W3-A824 
       46.92        43.23        59.41         7.23        18.05       174.12 
TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1Q TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 
        1.97       120.07        44.05         8.09       185.13        92.84 
TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT 
        1.15        59.64        12.69        19.00        59.44        10.95 
TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-Z2-AA3S 
        1.94        26.60        16.64        15.65        28.21        91.23 

  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
               0.2                0.0 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
            297.01             346.49 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
            53.260             44.775 
[1] "0.2 - 297.0 (53.3)" "0.0 - 346.5 (44.8)"
[1] "hr=" "1.2"
D65V2, survival
                    sevent
clus2                  0   1
  12Q LOSS MUTATED    32  31
  12Q LOSS WILD-TYPE 137 149
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                63                286 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                31                149 
$`12Q LOSS MUTATED`
TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A2J6 TCGA-D3-A2JL TCGA-D3-A3CC TCGA-D3-A51N 
       12.99        16.57        43.43       171.58        86.93        22.62 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A8GC TCGA-D3-A8GI TCGA-D3-A8GN TCGA-D9-A1X3 
      137.92       178.32        79.59        58.52       161.00        18.12 
TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1I1 TCGA-EB-A5SH TCGA-EE-A20B TCGA-EE-A20C 
       25.18        66.25       194.83        54.02       133.81       151.27 
TCGA-EE-A29G TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29X TCGA-EE-A2A2 TCGA-EE-A2A5 
       72.07        66.74        61.28        17.92        36.82        39.29 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GU TCGA-EE-A2MG TCGA-EE-A2MK TCGA-EE-A2MP 
       13.91        42.77        94.82       103.20       158.63       248.65 
TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3J3 
      162.48        53.26       124.31        28.77        54.51       172.18 
TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-ER-A199 TCGA-ER-A19E TCGA-ER-A19S TCGA-ER-A3PL 
       64.08        53.19         9.17        13.02        37.25        33.21 
TCGA-ER-A42K TCGA-FS-A1YX TCGA-FS-A1Z4 TCGA-FS-A1ZA TCGA-FS-A1ZH TCGA-FS-A1ZQ 
        6.77        48.59        28.08        27.72        32.75       133.55 
TCGA-FS-A1ZT TCGA-FS-A4F2 TCGA-FS-A4F5 TCGA-FW-A3R5 TCGA-GN-A4U3 TCGA-GN-A8LL 
       53.16        50.14        28.73        22.92       121.91        21.37 
TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X TCGA-RP-A693 TCGA-W3-AA1R TCGA-WE-A8JZ 
       65.88       368.78       297.90         0.33       111.09        24.03 
TCGA-WE-A8ZM TCGA-WE-A8ZY TCGA-YD-A9TA 
       98.89        49.51        49.18 

$`12Q LOSS WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-BF-AAP0 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 
       17.03        66.48        14.93        16.67       112.04       112.57 
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB 
       71.80       133.25        28.08        31.59        90.90        95.74 
TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC 
      103.10        65.49        23.77       115.53       168.00        86.76 
TCGA-D3-A2JD TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK 
       11.87        27.65        62.07       113.52        42.08        12.10 
TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 
       66.48        66.08        59.57       130.72        58.06        46.98 
TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO 
       46.32       166.52        60.23        24.53        13.87         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
      103.59        39.75        45.30       174.84        55.73        56.35 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN 
      145.12        32.94        63.81        26.89       125.79       135.75 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GJ 
       18.18       125.19        30.84        23.61        26.43       241.38 
TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR 
      170.20        89.13       107.15       152.75        29.06       129.63 
TCGA-D3-A8GS TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 
      117.17       151.53        54.67         3.65         7.10        15.39 
TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW 
       22.29        18.44         9.90        22.95        48.89        36.03 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 
      117.21        20.38       176.55        35.93       107.34        61.18 
TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
       53.92        65.92        23.44        68.09        28.60        10.49 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG 
      215.44        15.68        13.87        10.36        20.35        68.25 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y 
       17.29        52.01         7.04        24.89        29.82        27.22 
TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 
        8.65        94.98        33.73        14.70        26.89        68.15 
TCGA-EE-A185 TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
        4.96        91.56       168.26        13.55        63.35        85.08 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M 
       78.97        13.97        63.78        64.64         2.60        56.84 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W 
       18.61        56.42        14.47       369.93        25.87       195.02 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD 
       46.82       102.90        86.14        59.28        67.43       340.14 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
      161.03       208.04        48.72       107.38        54.74        79.66 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2M5 
       75.48       102.12       126.81        81.21        44.88        21.67 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME 
      129.27        28.83        19.76        61.51        47.28       103.27 
TCGA-EE-A2MF TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MM 
      268.73        16.96       204.66        96.23       216.66       167.90 
TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A3AB TCGA-EE-A3AC 
       47.54        43.23       134.40        71.21       122.73        51.62 
TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J8 
       13.81        41.59       138.81       127.20        36.95        34.32 
TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 
      201.80        27.35        51.35       109.58       152.81        31.40 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C 
       35.44        13.94        50.76        77.75        98.40        48.89 
TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L 
       12.59        26.37       268.93       152.35         6.44       131.51 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19T TCGA-ER-A19W 
       61.05        44.05       162.08        50.89         8.88       148.18 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
       79.99        43.82        23.34        20.15        16.37        31.27 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-FR-A3YN TCGA-FR-A44A 
       32.05       247.04        80.32        46.98        92.98       174.21 
TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC 
       15.72       220.80        27.85        18.77        38.27        34.82 
TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
       36.26       104.42       216.92       228.59       202.65        20.91 
TCGA-FS-A1Z7 TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF 
        7.79        48.85       357.37        53.52        40.27        15.45 
TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZR 
        9.70        47.38        23.93       101.26        74.73        11.41 
TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 
      148.80        26.56        49.48        27.09        27.02        77.82 
TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD 
       66.67       174.84        34.03        26.73        54.41        80.68 
TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
        0.20        55.59        13.51        19.30         9.90         7.23 
TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 
        2.04        15.78       139.89       117.93        84.72        10.13 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U4 TCGA-GN-A4U7 
       64.44        62.79        32.48        39.58        39.35        10.42 
TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A9SD TCGA-HR-A2OG TCGA-QB-A6FS 
       48.89        22.13        50.10        59.41         0.23         7.23 
TCGA-QB-AA9O TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O 
       18.05         0.69       228.16        63.02       121.08         4.01 
TCGA-W3-AA1Q TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8K5 
       69.07        42.08       219.16       105.04        49.05        61.15 
TCGA-WE-A8K6 TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX 
       15.98        58.98        67.63        59.77        11.80        32.58 
TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YD-A89C TCGA-YG-AA3O 
       12.16        35.01        19.73        22.29         6.90        37.94 
TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
       14.43        27.58        96.99        15.98 

  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
              0.33               0.20 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
            368.78             369.93 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
             53.26              49.79 
[1] "0.3 - 368.8 (53.3)" "0.2 - 369.9 (49.8)"
[1] "hr=" "1.2"
D65V3, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  12Q LOSS MUTATED                   14             2
  12Q LOSS WILD-TYPE                 51             3
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  12Q LOSS MUTATED                                          18
  12Q LOSS WILD-TYPE                                        54
                    vv
clus                 REGIONAL LYMPH NODE
  12Q LOSS MUTATED                    32
  12Q LOSS WILD-TYPE                 183
D65V4, multiclass
                                           clus
vv                                          12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  DISTANT METASTASIS                                      14                 51
  PRIMARY TUMOR                                            2                  3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               18                 54
  REGIONAL LYMPH NODE                                     32                183
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  12Q LOSS MUTATED             4       1       5        4        6        5
  12Q LOSS WILD-TYPE           8       6      23       14       21       19
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  12Q LOSS MUTATED           2         2         3         8          3
  12Q LOSS WILD-TYPE        12        17         9        29         12
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  12Q LOSS MUTATED            5          7        4
  12Q LOSS WILD-TYPE         27         53       16
D65V5, multiclass
             clus
vv            12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  I OR II NOS                4                  8
  STAGE 0                    1                  6
  STAGE I                    5                 23
  STAGE IA                   4                 14
  STAGE IB                   6                 21
  STAGE II                   5                 19
  STAGE IIA                  2                 12
  STAGE IIB                  2                 17
  STAGE IIC                  3                  9
  STAGE III                  8                 29
  STAGE IIIA                 3                 12
  STAGE IIIB                 5                 27
  STAGE IIIC                 7                 53
  STAGE IV                   4                 16
[1] 14  2
[1] TRUE
[1] "dimension of contingency 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      11 12 12 16
  12Q LOSS WILD-TYPE    53 60 65 52
D65V6, multiclass
       clus
vv      12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  T0+T1               11                 53
  T2                  12                 60
  T3                  12                 65
  T4                  16                 52
[1] 4 2
[1] TRUE
[1] "dimension of 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    33  10   7   7
  12Q LOSS WILD-TYPE 136  53  31  42
D65V7, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  N0               33                136
  N1               10                 53
  N2                7                 31
  N3                7                 42
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V8, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED    56   4
  12Q LOSS WILD-TYPE 257  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED     56    4
  12Q LOSS WILD-TYPE  257   17
   clus
vv  12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  0               56                257
  1                4                 17
[1] 2 2
[1] FALSE
D65V9, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED    22  17
  12Q LOSS WILD-TYPE 110  71
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED     22   17
  12Q LOSS WILD-TYPE  110   71
     clus
vv    12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  NO                22                110
  YES               17                 71
[1] 2 2
[1] FALSE
D65V10, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED     8  57
  12Q LOSS WILD-TYPE  36 256
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      8   57
  12Q LOSS WILD-TYPE   36  256
     clus
vv    12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  NO                 8                 36
  YES               57                256
[1] 2 2
[1] FALSE
D65V11, continuous
D65V12, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED    28  38
  12Q LOSS WILD-TYPE 107 185
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED     28   38
  12Q LOSS WILD-TYPE  107  185
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  FEMALE               28                107
  MALE                 38                185
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  12Q LOSS MUTATED       0                         0    64
  12Q LOSS WILD-TYPE     5                         1   280
D65V13, multiclass
                           clus
vv                          12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  ASIAN                                    0                  5
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   64                280
[1] 3 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     0  64
  12Q LOSS WILD-TYPE   7 280
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      0   64
  12Q LOSS WILD-TYPE    7  280
                        clus
vv                       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  7
  NOT HISPANIC OR LATINO               64                280
[1] 2 2
[1] FALSE

Clustering(66) Variable = 13Q LOSS MUTATION ANALYSIS
D66V1, survival
                    sevent
clus2                 0  1
  13Q LOSS MUTATED   30 22
  13Q LOSS WILD-TYPE 91 96
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                52                187 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                22                 96 
$`13Q LOSS MUTATED`
TCGA-BF-AAP0 TCGA-D3-A1Q8 TCGA-D3-A2J7 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JL 
       14.83        19.04        45.99        15.75        86.30       171.58 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A8GD 
       90.21        23.67        42.05        45.70       177.86        23.61 
TCGA-D3-A8GK TCGA-D3-A8GR TCGA-D9-A3Z3 TCGA-DA-A1HV TCGA-DA-A1I2 TCGA-DA-A1I5 
      120.00        36.53        16.90        48.66       150.61        82.85 
TCGA-DA-A1IC TCGA-EB-A5UN TCGA-EE-A181 TCGA-EE-A184 TCGA-EE-A29C TCGA-EE-A29D 
       58.85        45.50        20.38        67.50        76.14        12.99 
TCGA-EE-A29M TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A6 TCGA-EE-A2GE 
       47.74        61.12       346.49       185.19        77.98         0.20 
TCGA-EE-A2GJ TCGA-EE-A2MG TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AB 
       68.65        94.19        25.08       143.93        53.26       122.73 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3JB TCGA-ER-A193 TCGA-ER-A19B TCGA-ER-A19H 
        4.41        54.51       201.80        14.56        53.29       150.12 
TCGA-ER-A2NG TCGA-FS-A4F4 TCGA-GN-A8LK TCGA-GN-A9SD TCGA-RP-A693 TCGA-W3-AA1V 
       10.95        66.67        43.23        59.41         0.33         8.09 
TCGA-WE-A8ZM TCGA-WE-A8ZQ TCGA-WE-A8ZY TCGA-YG-AA3O 
       62.99        59.44        48.39        28.21 

$`13Q LOSS WILD-TYPE`
TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 
       60.46        12.99         8.42        15.72        31.89       110.93 
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J8 
       49.35       133.25        76.41        62.60        25.64        62.86 
TCGA-D3-A2JB TCGA-D3-A2JD TCGA-D3-A2JE TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JN 
      168.00         7.27         9.76       107.61        36.30        64.83 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CC 
       66.08        43.53        58.06        46.98       140.98        40.01 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A51E TCGA-D3-A51J 
       59.70        16.96        13.87         9.34       173.85       144.46 
TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GU TCGA-D3-A8GC TCGA-D3-A8GJ 
       31.76        62.70        11.34       124.08        78.21       179.97 
TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GP TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A4Z6 
       69.53        70.62       135.12        10.78        15.02        18.44 
TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I7 TCGA-DA-A1IA 
       57.90        22.85       106.85        31.96        32.42        64.83 
TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5SG TCGA-EB-A5SH 
       25.12       214.59        14.96         3.91        33.24        50.07 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A182 TCGA-EE-A20C 
        6.64        13.15        24.89        62.37         0.00        75.55 
TCGA-EE-A20H TCGA-EE-A29B TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29P 
      155.90        75.22         0.26        44.28        63.12        27.16 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GH TCGA-EE-A2GK 
      102.38         7.20        26.14       239.11       189.40        10.62 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR 
       32.48        18.35        31.00       118.32         0.76         0.20 
TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC 
       71.31        81.99       103.13        15.25         5.75        23.77 
TCGA-EE-A2MF TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM 
      209.79       171.85        63.25        67.50       104.78       145.45 
TCGA-EE-A2MP TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AF TCGA-EE-A3J3 
      227.01        23.51       124.31        51.62         6.28        67.89 
TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 
      111.85        45.90         3.35       152.81        34.45         1.58 
TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19G 
       47.31         7.82         4.54        39.81        11.47       151.46 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S 
       99.06        59.84        42.48       120.76        49.71        34.95 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A3ES 
      146.63        47.97        22.36         4.70        16.87       173.29 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7U8 
       55.82        15.48        32.05       174.21       209.23        26.20 
TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
        5.65        10.06       171.78        49.74       195.98         8.35 
TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG 
       27.62       312.07        32.78        35.90        12.92         7.82 
TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU 
       36.33        78.61       130.95       136.27        35.28         4.47 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F8 TCGA-FS-A4F9 
       23.21         5.29         3.06        30.90       173.19        13.28 
TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
       80.68        55.59        11.54        19.30         9.90         6.05 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 
        1.91        53.29       117.93        84.72        17.06        42.48 
TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-LH-A9QB TCGA-OD-A75X 
        7.59       120.53        34.49        46.92        85.05       297.01 
TCGA-QB-A6FS TCGA-QB-AA9O TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1Q 
        7.23        18.05       174.12         1.97       120.07        44.05 
TCGA-W3-AA1R TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8ZN 
       79.99       185.13        92.84         1.15        59.64        12.69 
TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 
       19.00        10.95         1.94        26.60        16.64        15.65 
TCGA-Z2-AA3S 
       91.23 

  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
               0.2                0.0 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
            346.49             312.07 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
            53.275             42.480 
[1] "0.2 - 346.5 (53.3)" "0.0 - 312.1 (42.5)"
[1] "hr=" "1.3"
D66V2, survival
                    sevent
clus2                  0   1
  13Q LOSS MUTATED    39  38
  13Q LOSS WILD-TYPE 130 142
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                77                272 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                38                142 
$`13Q LOSS MUTATED`
TCGA-BF-AAP0 TCGA-D3-A1Q8 TCGA-D3-A2J7 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JL 
       14.93        28.08       103.10       115.53        86.76       171.58 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A8GB 
      103.59        39.75       125.79       135.75       178.32        30.84 
TCGA-D3-A8GD TCGA-D3-A8GK TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A148 TCGA-D9-A149 
       23.61       170.20       129.63       117.17       151.53        54.67 
TCGA-D9-A3Z3 TCGA-D9-A6EA TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I2 TCGA-DA-A1I4 
       22.29        25.18        48.89        36.03       176.55        35.93 
TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A1IC TCGA-EB-A5UN TCGA-EE-A181 TCGA-EE-A184 
      107.34        53.92        68.09        52.01        33.73        68.15 
TCGA-EE-A20I TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29Q 
       13.55        78.97        13.97        56.84        18.61        66.74 
TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A6 TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GJ 
      369.93       195.02        86.14       161.03        48.72       107.38 
TCGA-EE-A2M5 TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MU 
       21.67       103.20        16.96       134.40       162.48        53.26 
TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AH TCGA-EE-A3J5 TCGA-EE-A3JB 
      122.73        28.77        54.51       138.81        36.95       201.80 
TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A19B TCGA-ER-A19H TCGA-ER-A19T TCGA-ER-A2NG 
      109.58        31.40        98.40       152.35         8.88        31.27 
TCGA-FR-A3YN TCGA-FR-A7U9 TCGA-FS-A1ZA TCGA-FS-A1ZH TCGA-FS-A4F4 TCGA-GN-A266 
       92.98        18.77        27.72        32.75        66.67        10.13 
TCGA-GN-A26D TCGA-GN-A4U7 TCGA-GN-A8LK TCGA-GN-A9SD TCGA-RP-A693 TCGA-W3-AA1V 
       39.58        10.42        50.10        59.41         0.33        42.08 
TCGA-WE-A8ZM TCGA-WE-A8ZQ TCGA-WE-A8ZY TCGA-YG-AA3O TCGA-YG-AA3P 
       98.89        59.77        49.51        37.94        14.43 

$`13Q LOSS WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
       17.03        66.48        12.99        16.57        16.67       112.04 
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB 
      112.57        71.80       133.25        31.59        90.90        95.74 
TCGA-D3-A2J6 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JD TCGA-D3-A2JE 
       43.43        65.49        23.77       168.00        11.87        27.65 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JN TCGA-D3-A2JO 
       62.07       113.52        42.08        12.10        66.48        66.08 
TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB 
       59.57       130.72        58.06        46.98        46.32       166.52 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MV 
       86.93        60.23        24.53        13.87         9.34        45.30 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
      174.84        55.73        56.35       145.12        32.94        22.62 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GO TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GC 
       63.81        26.89       137.92        18.18       125.19        79.59 
TCGA-D3-A8GE TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GN 
       26.43        58.52       241.38        89.13       107.15       161.00 
TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A1X3 TCGA-D9-A3Z1 
      152.75        29.06         3.65         7.10        18.12        15.39 
TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HY TCGA-DA-A1I0 
       18.44         9.90        66.25        22.95       117.21        20.38 
TCGA-DA-A1I1 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-DA-A3F3 
      194.83        61.18        65.92        23.44        28.60        10.49 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG 
      215.44        15.68        13.87        10.36        20.35        68.25 
TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y 
       54.02        17.29         7.04        24.89        29.82        27.22 
TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B 
        8.65        94.98        14.70        26.89         4.96       133.81 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29E 
      151.27        91.56       168.26        63.35        85.08        63.78 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A29S 
       72.07        64.64         2.60        56.42        14.47        61.28 
TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 
       25.87        17.92        46.82       102.90        36.82        39.29 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GH TCGA-EE-A2GK TCGA-EE-A2GL 
       59.28        67.43       340.14       208.04        54.74        79.66 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
       75.48       102.12       126.81        13.91        42.77        81.21 
TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC 
       44.88        94.82       129.27        28.83        19.76        61.51 
TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK 
       47.28       103.27       268.73       204.66        96.23       158.63 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MT 
      216.66       167.90        47.54       248.65        43.23        71.21 
TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3J4 
      124.31        51.62        13.81        41.59       172.18       127.20 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JI 
       64.08        34.32        53.19        27.35        51.35       152.81 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19C 
       35.44        13.94        50.76         9.17        77.75        48.89 
TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19J TCGA-ER-A19L 
       12.59        13.02        26.37       268.93         6.44       131.51 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W 
       61.05        44.05       162.08        50.89        37.25       148.18 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NH 
       79.99        43.82        23.34        20.15        16.37        32.05 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A44A 
      247.04        80.32        46.98        33.21         6.77       174.21 
TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD 
       15.72       220.80        27.85        38.27        34.82        36.26 
TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
      104.42       216.92        48.59       228.59       202.65        20.91 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE 
       28.08         7.79        48.85       357.37        53.52        40.27 
TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP 
       15.45         9.70        47.38        23.93       101.26        74.73 
TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW 
      133.55        11.41       148.80        53.16        26.56        49.48 
TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F5 TCGA-FS-A4F8 
       27.09        27.02        77.82        50.14        28.73       174.84 
TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 
       34.03        26.73        54.41        80.68         0.20        22.92 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 
       55.59        13.51        19.30         9.90         7.23         2.04 
TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 
       15.78       139.89       117.93        84.72        64.44        62.79 
TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LL 
       32.48       121.91        39.35        48.89        22.13        21.37 
TCGA-HR-A2OG TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O 
        0.23        65.88       368.78       297.90         7.23        18.05 
TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1Q 
        0.69       228.16        63.02       121.08         4.01        69.07 
TCGA-W3-AA1R TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K5 
      111.09       219.16       105.04        24.03        49.05        61.15 
TCGA-WE-A8K6 TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-AA9Y 
       15.98        58.98        67.63        11.80        32.58        12.16 
TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YD-A89C TCGA-YD-A9TA TCGA-Z2-A8RT 
       35.01        19.73        22.29         6.90        49.18        27.58 
TCGA-Z2-AA3S TCGA-Z2-AA3V 
       96.99        15.98 

  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
              0.33               0.20 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
            369.93             368.78 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
            54.670             49.115 
[1] "0.3 - 369.9 (54.7)" "0.2 - 368.8 (49.1)"
[1] "hr=" "1.2"
D66V3, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  13Q LOSS MUTATED                   10             2
  13Q LOSS WILD-TYPE                 55             3
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  13Q LOSS MUTATED                                          17
  13Q LOSS WILD-TYPE                                        55
                    vv
clus                 REGIONAL LYMPH NODE
  13Q LOSS MUTATED                    48
  13Q LOSS WILD-TYPE                 167
D66V4, multiclass
                                           clus
vv                                          13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  DISTANT METASTASIS                                      10                 55
  PRIMARY TUMOR                                            2                  3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               17                 55
  REGIONAL LYMPH NODE                                     48                167
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  13Q LOSS MUTATED             2       2       6        6        7        5
  13Q LOSS WILD-TYPE          10       5      22       12       20       19
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  13Q LOSS MUTATED           3         3         2         8          2
  13Q LOSS WILD-TYPE        11        16        10        29         13
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  13Q LOSS MUTATED            7         10        7
  13Q LOSS WILD-TYPE         25         50       13
D66V5, multiclass
             clus
vv            13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  I OR II NOS                2                 10
  STAGE 0                    2                  5
  STAGE I                    6                 22
  STAGE IA                   6                 12
  STAGE IB                   7                 20
  STAGE II                   5                 19
  STAGE IIA                  3                 11
  STAGE IIB                  3                 16
  STAGE IIC                  2                 10
  STAGE III                  8                 29
  STAGE IIIA                 2                 13
  STAGE IIIB                 7                 25
  STAGE IIIC                10                 50
  STAGE IV                   7                 13
[1] 14  2
[1] TRUE
[1] "dimension of contingency 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      18 12 21 12
  13Q LOSS WILD-TYPE    46 60 56 56
D66V6, multiclass
       clus
vv      13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  T0+T1               18                 46
  T2                  12                 60
  T3                  21                 56
  T4                  12                 56
[1] 4 2
[1] TRUE
[1] "dimension of 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    37  13   9   9
  13Q LOSS WILD-TYPE 132  50  29  40
D66V7, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  N0               37                132
  N1               13                 50
  N2                9                 29
  N3                9                 40
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V8, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED    65   8
  13Q LOSS WILD-TYPE 248  13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     65    8
  13Q LOSS WILD-TYPE  248   13
   clus
vv  13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  0               65                248
  1                8                 13
[1] 2 2
[1] FALSE
D66V9, binary
                    cls
clus                  0  1
  13Q LOSS MUTATED   37 15
  13Q LOSS WILD-TYPE 95 73
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     37   15
  13Q LOSS WILD-TYPE   95   73
     clus
vv    13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  NO                37                 95
  YES               15                 73
[1] 2 2
[1] FALSE
D66V10, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED     8  69
  13Q LOSS WILD-TYPE  36 244
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      8   69
  13Q LOSS WILD-TYPE   36  244
     clus
vv    13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  NO                 8                 36
  YES               69                244
[1] 2 2
[1] FALSE
D66V11, continuous
D66V12, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED    27  50
  13Q LOSS WILD-TYPE 108 173
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     27   50
  13Q LOSS WILD-TYPE  108  173
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  FEMALE               27                108
  MALE                 50                173
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  13Q LOSS MUTATED       0                         0    74
  13Q LOSS WILD-TYPE     5                         1   270
D66V13, multiclass
                           clus
vv                          13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  ASIAN                                    0                  5
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   74                270
[1] 3 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     2  74
  13Q LOSS WILD-TYPE   5 270
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      2   74
  13Q LOSS WILD-TYPE    5  270
                        clus
vv                       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  5
  NOT HISPANIC OR LATINO               74                270
[1] 2 2
[1] FALSE

Clustering(67) Variable = 14Q LOSS MUTATION ANALYSIS
D67V1, survival
                    sevent
clus2                 0  1
  14Q LOSS MUTATED   36 35
  14Q LOSS WILD-TYPE 85 83
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                71                168 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                35                 83 
$`14Q LOSS MUTATED`
TCGA-3N-A9WC TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A2J6 TCGA-D3-A2JN TCGA-D3-A2JO 
       60.46         8.42        31.89        25.64        64.83        66.08 
TCGA-D3-A2JP TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3MR TCGA-D3-A51J TCGA-D3-A5GN 
       43.53        40.01        59.70        90.21       144.46        45.70 
TCGA-D3-A5GR TCGA-D3-A8GC TCGA-D9-A4Z6 TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 
      177.86        78.21        18.44        48.66       106.85        31.96 
TCGA-DA-A1I5 TCGA-DA-A3F5 TCGA-EE-A181 TCGA-EE-A29C TCGA-EE-A29G TCGA-EE-A2A2 
       82.85       214.59        20.38        76.14        44.28         7.20 
TCGA-EE-A2A6 TCGA-EE-A2GE TCGA-EE-A2GP TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 
       77.98         0.20         0.76       103.13        15.25         5.75 
TCGA-EE-A2MG TCGA-EE-A2MK TCGA-EE-A2MS TCGA-EE-A3AA TCGA-EE-A3J3 TCGA-EE-A3J7 
       94.19        67.50       143.93       124.31        67.89        45.90 
TCGA-EE-A3JB TCGA-EE-A3JI TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19G 
      201.80       152.81         1.58         7.82        53.29       151.46 
TCGA-ER-A19H TCGA-ER-A19S TCGA-ER-A2ND TCGA-ER-A3PL TCGA-FR-A44A TCGA-FS-A1Z4 
      150.12        34.95         4.70        32.05       174.21        27.62 
TCGA-FS-A1ZC TCGA-FS-A1ZE TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZT TCGA-FS-A4F8 
      312.07        35.90        78.61       130.95        35.28       173.19 
TCGA-FS-A4F9 TCGA-FW-A3TU TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A264 TCGA-GN-A267 
       13.28        55.59         6.05         1.91       117.93        17.06 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A8LK TCGA-LH-A9QB TCGA-OD-A75X 
       42.48         7.59       120.53        43.23        85.05       297.01 
TCGA-W3-A825 TCGA-W3-AA1V TCGA-WE-A8ZM TCGA-WE-A8ZY TCGA-YG-AA3O 
        1.97         8.09        62.99        48.39        28.21 

$`14Q LOSS WILD-TYPE`
TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q3 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       12.99        14.83        15.72       110.93        49.35       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA 
       19.04        76.41        62.60        45.99        62.86        15.75 
TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JE TCGA-D3-A2JG TCGA-D3-A2JH 
      168.00        86.30         7.27         9.76       107.61        36.30 
TCGA-D3-A2JL TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CF TCGA-D3-A3ML 
      171.58        58.06        46.98       140.98        16.96        13.87 
TCGA-D3-A3MO TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T 
        9.34        23.67       173.85        31.76        62.70        11.34 
TCGA-D3-A5GL TCGA-D3-A5GU TCGA-D3-A8GD TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL 
       42.05       124.08        23.61       179.97       120.00        69.53 
TCGA-D3-A8GM TCGA-D3-A8GP TCGA-D3-A8GR TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       70.62       135.12        36.53        10.78        15.02        16.90 
TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1I2 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC 
       57.90        22.85       150.61        32.42        64.83        58.85 
TCGA-DA-A3F2 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN 
       25.12        14.96         3.91        33.24        50.07        45.50 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A182 TCGA-EE-A184 
        6.64        13.15        24.89        62.37         0.00        67.50 
TCGA-EE-A20C TCGA-EE-A20H TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H 
       75.55       155.90        75.22        12.99         0.26        63.12 
TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 
       47.74        27.16        61.12       346.49       185.19       102.38 
TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
       26.14       239.11       189.40        68.65        10.62        32.48 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU 
       18.35        31.00       118.32         0.20        71.31        81.99 
TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MM 
       23.77       209.79       171.85        63.25       104.78       145.45 
TCGA-EE-A2MP TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC 
      227.01        25.08        23.51        53.26       122.73        51.62 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J4 TCGA-EE-A3J8 TCGA-ER-A193 
        4.41        54.51         6.28       111.85         3.35        14.56 
TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19L 
       34.45        47.31         4.54        39.81        11.47        99.06 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19W TCGA-ER-A1A1 
       59.84        42.48       120.76        49.71       146.63        47.97 
TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
       22.36        16.87        10.95       173.29        55.82        15.48 
TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FS-A1YW TCGA-FS-A1YY 
      209.23        26.20         5.65        10.06       171.78        49.74 
TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZJ 
      195.98         8.35        32.78        12.92         7.82        36.33 
TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 
      136.27         4.47        23.21         5.29         3.06        30.90 
TCGA-FS-A4F4 TCGA-FS-A4FD TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GN-A262 
       66.67        80.68        11.54        19.30         9.90        53.29 
TCGA-GN-A265 TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-GN-A9SD TCGA-QB-A6FS TCGA-QB-AA9O 
       84.72        34.49        46.92        59.41         7.23        18.05 
TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A828 TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1W 
        0.33       174.12       120.07        44.05        79.99       185.13 
TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ 
       92.84         1.15        59.64        12.69        19.00        59.44 
TCGA-WE-A8ZT TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-Z2-AA3S 
       10.95         1.94        26.60        16.64        15.65        91.23 

  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               0.2                0.0 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
            312.07             346.49 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
            48.660             44.775 
[1] "0.2 - 312.1 (48.7)" "0.0 - 346.5 (44.8)"
[1] "hr=" "1.2"
D67V2, survival
                    sevent
clus2                  0   1
  14Q LOSS MUTATED    52  57
  14Q LOSS WILD-TYPE 117 123
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               109                240 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                57                123 
$`14Q LOSS MUTATED`
TCGA-3N-A9WC TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A2J6 TCGA-D3-A2JF TCGA-D3-A2JN 
       66.48        16.57       112.04        43.43        62.07        66.48 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3MR TCGA-D3-A3MV 
       66.08        59.57        86.93        60.23       103.59        45.30 
TCGA-D3-A51J TCGA-D3-A51N TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A8GC 
      145.12        22.62       135.75       137.92       178.32        79.59 
TCGA-D3-A8GI TCGA-D3-A8GN TCGA-D3-A8GS TCGA-D9-A149 TCGA-D9-A4Z6 TCGA-D9-A6EA 
       58.52       161.00       117.17        54.67        18.44        25.18 
TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A3F5 
       48.89       117.21       194.83       107.34        53.92       215.44 
TCGA-EB-A44R TCGA-EB-A5UL TCGA-EE-A181 TCGA-EE-A29C TCGA-EE-A29G TCGA-EE-A29V 
       10.36        17.29        33.73        78.97        72.07        25.87 
TCGA-EE-A29X TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GE TCGA-EE-A2GP 
       17.92        36.82        39.29        86.14       161.03        13.91 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MD TCGA-EE-A2MG TCGA-EE-A2MH 
      129.27        28.83        19.76        47.28       103.20        16.96 
TCGA-EE-A2MK TCGA-EE-A2MN TCGA-EE-A2MS TCGA-EE-A3AA TCGA-EE-A3AH TCGA-EE-A3J3 
      158.63        47.54       162.48       124.31       138.81       172.18 
TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JE TCGA-EE-A3JI 
       36.95        64.08        53.19       201.80        51.35       152.81 
TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19E TCGA-ER-A19G TCGA-ER-A19H 
       13.94         9.17        98.40        13.02       268.93       152.35 
TCGA-ER-A19S TCGA-ER-A2ND TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A44A TCGA-FS-A1YX 
       37.25        23.34        33.21         6.77       174.21        48.59 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZC TCGA-FS-A1ZE TCGA-FS-A1ZH 
       28.08         7.79        27.72       357.37        40.27        32.75 
TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZT TCGA-FS-A4F2 TCGA-FS-A4F5 
      101.26       133.55        11.41        53.16        50.14        28.73 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FW-A3TU TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 
      174.84        34.03        55.59         7.23         2.04        15.78 
TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U9 
      117.93        64.44        62.79        32.48       121.91        22.13 
TCGA-GN-A8LK TCGA-HR-A2OG TCGA-LH-A9QB TCGA-OD-A75X TCGA-W3-A825 TCGA-W3-AA1V 
       50.10         0.23       368.78       297.90        63.02        42.08 
TCGA-WE-A8JZ TCGA-WE-A8ZM TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-YG-AA3O TCGA-YG-AA3P 
       24.03        98.89        32.58        49.51        37.94        14.43 
TCGA-Z2-A8RT 
       27.58 

$`14Q LOSS WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q3 TCGA-D3-A1Q5 TCGA-D3-A1Q6 
       17.03        12.99        14.93        16.67       112.57        71.80 
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J7 
      133.25        28.08        31.59        90.90        95.74       103.10 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
       65.49        23.77       115.53       168.00        86.76        11.87 
TCGA-D3-A2JE TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A3BZ 
       27.65       113.52        42.08        12.10       171.58       130.72 
TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CF TCGA-D3-A3ML 
       58.06        46.98        46.32       166.52        24.53        13.87 
TCGA-D3-A3MO TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51K 
        9.34        39.75       174.84        55.73        56.35        32.94 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GB 
       63.81        26.89       125.79        18.18       125.19        30.84 
TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM 
       23.61        26.43       241.38       170.20        89.13       107.15 
TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D9-A148 TCGA-D9-A1JW TCGA-D9-A1JX 
      152.75        29.06       129.63       151.53         3.65         7.10 
TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-D9-A6EG 
       18.12        15.39        22.29         9.90        66.25        22.95 
TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I7 TCGA-DA-A1IA 
       36.03        20.38       176.55        35.93        61.18        65.92 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EB-A44Q 
       23.44        68.09        28.60        10.49        15.68        13.87 
TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 
       20.35        68.25        54.02        52.01         7.04        24.89 
TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A182 TCGA-EE-A183 
       29.82        27.22         8.65        94.98        14.70        26.89 
TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H 
       68.15         4.96       133.81       151.27        91.56       168.26 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H 
       13.55        63.35        85.08        13.97        63.78        64.64 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
        2.60        56.84        18.61        56.42        66.74        14.47 
TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2GB 
       61.28       369.93       195.02        46.82       102.90        59.28 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
       67.43       340.14       208.04        48.72       107.38        54.74 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GR TCGA-EE-A2GS 
       79.66        75.48       102.12       126.81        42.77        81.21 
TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2MC TCGA-EE-A2ME TCGA-EE-A2MF 
       44.88        94.82        21.67        61.51       103.27       268.73 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MQ 
      204.66        96.23       216.66       167.90       248.65        43.23 
TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
      134.40        71.21        53.26       122.73        51.62        28.77 
TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3J4 TCGA-EE-A3J8 TCGA-EE-A3JD 
       54.51        13.81        41.59       127.20        34.32        27.35 
TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19C 
      109.58        31.40        35.44        50.76        77.75        48.89 
TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
       12.59        26.37         6.44       131.51        61.05        44.05 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
      162.08        50.89         8.88       148.18        79.99        43.82 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET 
       20.15        16.37        31.27        32.05       247.04        80.32 
TCGA-ER-A3EV TCGA-FR-A3YN TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 
       46.98        92.98        15.72       220.80        27.85        18.77 
TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YY 
       38.27        34.82        36.26       104.42       216.92       228.59 
TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1ZB TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZG 
      202.65        20.91        48.85        53.52        15.45         9.70 
TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZW 
       47.38        23.93        74.73       148.80        26.56        49.48 
TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4FB TCGA-FS-A4FC 
       27.09        27.02        77.82        66.67        26.73        54.41 
TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
       80.68         0.20        22.92        13.51        19.30         9.90 
TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A26D TCGA-GN-A4U4 TCGA-GN-A4U7 
      139.89        84.72        10.13        39.58        39.35        10.42 
TCGA-GN-A4U8 TCGA-GN-A8LL TCGA-GN-A9SD TCGA-HR-A2OH TCGA-QB-A6FS TCGA-QB-AA9O 
       48.89        21.37        59.41        65.88         7.23        18.05 
TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1Q 
        0.33         0.69       228.16       121.08         4.01        69.07 
TCGA-W3-AA1R TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8K6 
      111.09       219.16       105.04        49.05        61.15        15.98 
TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-AA9Y TCGA-WE-AAA0 
       58.98        67.63        59.77        11.80        12.16        35.01 
TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YD-A89C TCGA-YD-A9TA TCGA-Z2-AA3S TCGA-Z2-AA3V 
       19.73        22.29         6.90        49.18        96.99        15.98 

  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
              0.23               0.20 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
            368.78             369.93 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
             53.19              49.33 
[1] "0.2 - 368.8 (53.2)" "0.2 - 369.9 (49.3)"
[1] "hr=" "1.1"
D67V3, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  14Q LOSS MUTATED                   22             1
  14Q LOSS WILD-TYPE                 43             4
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  14Q LOSS MUTATED                                          28
  14Q LOSS WILD-TYPE                                        44
                    vv
clus                 REGIONAL LYMPH NODE
  14Q LOSS MUTATED                    59
  14Q LOSS WILD-TYPE                 156
D67V4, multiclass
                                           clus
vv                                          14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  DISTANT METASTASIS                                      22                 43
  PRIMARY TUMOR                                            1                  4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               28                 44
  REGIONAL LYMPH NODE                                     59                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                 I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  14Q LOSS MUTATED             5       0      11        3        8       10
  14Q LOSS WILD-TYPE           7       7      17       15       19       14
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  14Q LOSS MUTATED           2         5         3        15          3
  14Q LOSS WILD-TYPE        12        14         9        22         12
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  14Q LOSS MUTATED           11         20        4
  14Q LOSS WILD-TYPE         21         40       16
D67V5, multiclass
             clus
vv            14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  I OR II NOS                5                  7
  STAGE 0                    0                  7
  STAGE I                   11                 17
  STAGE IA                   3                 15
  STAGE IB                   8                 19
  STAGE II                  10                 14
  STAGE IIA                  2                 12
  STAGE IIB                  5                 14
  STAGE IIC                  3                  9
  STAGE III                 15                 22
  STAGE IIIA                 3                 12
  STAGE IIIB                11                 21
  STAGE IIIC                20                 40
  STAGE IV                   4                 16
[1] 14  2
[1] TRUE
[1] "dimension of contingency 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      24 23 21 22
  14Q LOSS WILD-TYPE    40 49 56 46
D67V6, multiclass
       clus
vv      14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  T0+T1               24                 40
  T2                  23                 49
  T3                  21                 56
  T4                  22                 46
[1] 4 2
[1] TRUE
[1] "dimension of 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    50  25   8  16
  14Q LOSS WILD-TYPE 119  38  30  33
D67V7, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  N0               50                119
  N1               25                 38
  N2                8                 30
  N3               16                 33
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V8, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED    99   4
  14Q LOSS WILD-TYPE 214  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     99    4
  14Q LOSS WILD-TYPE  214   17
   clus
vv  14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  0               99                214
  1                4                 17
[1] 2 2
[1] FALSE
D67V9, binary
                    cls
clus                  0  1
  14Q LOSS MUTATED   38 28
  14Q LOSS WILD-TYPE 94 60
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     38   28
  14Q LOSS WILD-TYPE   94   60
     clus
vv    14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  NO                38                 94
  YES               28                 60
[1] 2 2
[1] FALSE
D67V10, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED    15  95
  14Q LOSS WILD-TYPE  29 218
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     15   95
  14Q LOSS WILD-TYPE   29  218
     clus
vv    14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  NO                15                 29
  YES               95                218
[1] 2 2
[1] FALSE
D67V11, continuous
D67V12, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED    45  66
  14Q LOSS WILD-TYPE  90 157
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     45   66
  14Q LOSS WILD-TYPE   90  157
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  FEMALE               45                 90
  MALE                 66                157
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  14Q LOSS MUTATED       1                         0   106
  14Q LOSS WILD-TYPE     4                         1   238
D67V13, multiclass
                           clus
vv                          14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  ASIAN                                    1                  4
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                  106                238
[1] 3 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     3 106
  14Q LOSS WILD-TYPE   4 238
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      3  106
  14Q LOSS WILD-TYPE    4  238
                        clus
vv                       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  4
  NOT HISPANIC OR LATINO              106                238
[1] 2 2
[1] FALSE

Clustering(68) Variable = 15Q LOSS MUTATION ANALYSIS
D68V1, survival
                    sevent
clus2                  0   1
  15Q LOSS MUTATED    14  17
  15Q LOSS WILD-TYPE 107 101
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                31                208 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                17                101 
$`15Q LOSS MUTATED`
TCGA-3N-A9WD TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3MU TCGA-D3-A5GN TCGA-D3-A8GC 
       12.99        58.06        40.01        23.67        45.70        78.21 
TCGA-D9-A6EC TCGA-DA-A1I1 TCGA-DA-A1IA TCGA-EB-A5SH TCGA-EE-A180 TCGA-EE-A29P 
       57.90        31.96        64.83        50.07        62.37        27.16 
TCGA-EE-A29Q TCGA-EE-A2GH TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MK TCGA-EE-A2MM 
       61.12       189.40        23.77       209.79        67.50       145.45 
TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3J7 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A3EV 
       53.26       122.73        45.90         1.58         7.82        15.48 
TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1ZM TCGA-FS-A1ZT TCGA-GN-A8LK TCGA-W3-AA1R 
      195.98        27.62        78.61        35.28        43.23        79.99 
TCGA-W3-AA1V 
        8.09 

$`15Q LOSS WILD-TYPE`
TCGA-3N-A9WC TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 
       60.46        14.83         8.42        15.72        31.89       110.93 
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 
       49.35       133.25        19.04        76.41        62.60        25.64 
TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
       45.99        62.86        15.75       168.00        86.30         7.27 
TCGA-D3-A2JE TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
        9.76       107.61        36.30       171.58        64.83        66.08 
TCGA-D3-A2JP TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML 
       43.53        46.98       140.98        59.70        16.96        13.87 
TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A51E TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R 
        9.34        90.21       173.85       144.46        31.76        62.70 
TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D3-A8GD TCGA-D3-A8GJ 
       11.34        42.05       177.86       124.08        23.61       179.97 
TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GP TCGA-D3-A8GR TCGA-D9-A1X3 
      120.00        69.53        70.62       135.12        36.53        10.78 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY 
       15.02        16.90        18.44        22.85        48.66       106.85 
TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 
      150.61        82.85        32.42        58.85        25.12       214.59 
TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5SG TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X 
       14.96         3.91        33.24        45.50         6.64        13.15 
TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A184 TCGA-EE-A20C TCGA-EE-A20H 
       24.89        20.38         0.00        67.50        75.55       155.90 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H 
       75.22        76.14        12.99         0.26        44.28        63.12 
TCGA-EE-A29M TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 
       47.74       346.49       185.19       102.38         7.20        77.98 
TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
       26.14       239.11         0.20        68.65        10.62        32.48 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
       18.35        31.00       118.32         0.76         0.20        71.31 
TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MG TCGA-EE-A2MI 
       81.99       103.13        15.25         5.75        94.19       171.85 
TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MP TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT 
       63.25       104.78       227.01        25.08       143.93        23.51 
TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J3 
      124.31        51.62         4.41        54.51         6.28        67.89 
TCGA-EE-A3J4 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 
      111.85         3.35       201.80       152.81        14.56        34.45 
TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19G 
       47.31         4.54        53.29        39.81        11.47       151.46 
TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
      150.12        99.06        59.84        42.48       120.76        49.71 
TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
       34.95       146.63        47.97        22.36         4.70        16.87 
TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3PL TCGA-FR-A44A TCGA-FR-A729 
       10.95       173.29        55.82        32.05       174.21       209.23 
TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z3 
       26.20         5.65        10.06       171.78        49.74         8.35 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZJ 
      312.07        32.78        35.90        12.92         7.82        36.33 
TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ 
      130.95       136.27         4.47        23.21         5.29         3.06 
TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TU 
       30.90        66.67       173.19        13.28        80.68        55.59 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 
       11.54        19.30         9.90         6.05         1.91        53.29 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 
      117.93        84.72        17.06        42.48         7.59       120.53 
TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-GN-A9SD TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS 
       34.49        46.92        59.41        85.05       297.01         7.23 
TCGA-QB-AA9O TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1Q 
       18.05         0.33       174.12         1.97       120.07        44.05 
TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8ZM TCGA-WE-A8ZN 
      185.13        92.84         1.15        59.64        62.99        12.69 
TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 
       19.00        59.44        10.95        48.39         1.94        26.60 
TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-Z2-AA3S 
       16.64        15.65        28.21        91.23 

  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
              1.58               0.00 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
            209.79             346.49 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
            50.070             45.745 
[1] "1.6 - 209.8 (50.1)" "0.0 - 346.5 (45.7)"
[1] "hr=" "1.1"
D68V2, survival
                    sevent
clus2                  0   1
  15Q LOSS MUTATED    19  30
  15Q LOSS WILD-TYPE 150 150
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                49                300 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                30                150 
$`15Q LOSS MUTATED`
TCGA-3N-A9WD TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3MU TCGA-D3-A5GN TCGA-D3-A5GO 
       12.99        58.06        86.93        39.75       135.75       137.92 
TCGA-D3-A8GC TCGA-D3-A8GN TCGA-D9-A148 TCGA-D9-A6EC TCGA-DA-A1I1 TCGA-DA-A1I8 
       79.59       161.00       151.53        66.25       194.83        53.92 
TCGA-DA-A1IA TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SH TCGA-EE-A180 TCGA-EE-A29L 
       65.92        10.36        20.35        54.02        94.98         2.60 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A2A5 TCGA-EE-A2GH TCGA-EE-A2M5 TCGA-EE-A2MC 
       56.42        66.74        39.29       208.04        21.67        61.51 
TCGA-EE-A2MF TCGA-EE-A2MH TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MU TCGA-EE-A3AB 
      268.73        16.96       158.63       167.90        53.26       122.73 
TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-EE-A3JE TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19E 
       64.08        53.19        51.35        13.94         9.17        13.02 
TCGA-ER-A3EV TCGA-FS-A1YX TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1ZM TCGA-FS-A1ZT 
       46.98        48.59       202.65        28.08       101.26        53.16 
TCGA-GN-A266 TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A8LL TCGA-W3-AA1R TCGA-W3-AA1V 
       10.13        22.13        50.10        21.37       111.09        42.08 
TCGA-WE-A8JZ 
       24.03 

$`15Q LOSS WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
       17.03        66.48        14.93        16.57        16.67       112.04 
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA 
      112.57        71.80       133.25        28.08        31.59        90.90 
TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA 
       95.74        43.43       103.10        65.49        23.77       115.53 
TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A2JG 
      168.00        86.76        11.87        27.65        62.07       113.52 
TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP 
       42.08        12.10       171.58        66.48        66.08        59.57 
TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3CF 
      130.72        46.98        46.32       166.52        60.23        24.53 
TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F 
       13.87         9.34       103.59        45.30       174.84        55.73 
TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T 
       56.35       145.12        32.94        22.62        63.81        26.89 
TCGA-D3-A5GL TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GD 
      125.79       178.32        18.18       125.19        30.84        23.61 
TCGA-D3-A8GE TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM 
       26.43        58.52       241.38       170.20        89.13       107.15 
TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A149 TCGA-D9-A1JW 
      152.75        29.06       129.63       117.17        54.67         3.65 
TCGA-D9-A1JX TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 
        7.10        18.12        15.39        22.29        18.44         9.90 
TCGA-D9-A6EA TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 
       25.18        22.95        48.89        36.03       117.21        20.38 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IB TCGA-DA-A1IC 
      176.55        35.93       107.34        61.18        23.44        68.09 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5SG 
       28.60        10.49       215.44        15.68        13.87        68.25 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y 
       17.29        52.01         7.04        24.89        29.82        27.22 
TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 
        8.65        33.73        14.70        26.89        68.15         4.96 
TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A 
      133.81       151.27        91.56       168.26        13.55        63.35 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H 
       85.08        78.97        13.97        63.78        72.07        64.64 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V 
       56.84        18.61        14.47        61.28       369.93        25.87 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 
      195.02        17.92        46.82       102.90        36.82        86.14 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GJ 
       59.28        67.43       340.14       161.03        48.72       107.38 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP 
       54.74        79.66        75.48       102.12       126.81        13.91 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 
       42.77        81.21        44.88        94.82       129.27        28.83 
TCGA-EE-A2M8 TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ 
       19.76        47.28       103.27       103.20       204.66        96.23 
TCGA-EE-A2ML TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS 
      216.66        47.54       248.65        43.23       134.40       162.48 
TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
       71.21       124.31        51.62        28.77        54.51        13.81 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J8 
       41.59       138.81       172.18       127.20        36.95        34.32 
TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 
      201.80        27.35       109.58       152.81        31.40        35.44 
TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19F 
       50.76        77.75        98.40        48.89        12.59        26.37 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
      268.93       152.35         6.44       131.51        61.05        44.05 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 
      162.08        50.89        37.25         8.88       148.18        79.99 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH 
       43.82        23.34        20.15        16.37        31.27        32.05 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A 
      247.04        80.32        33.21         6.77        92.98       174.21 
TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC 
       15.72       220.80        27.85        18.77        38.27        34.82 
TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1Z7 
       36.26       104.42       216.92       228.59        20.91         7.79 
TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF 
       27.72        48.85       357.37        53.52        40.27        15.45 
TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZQ 
        9.70        32.75        47.38        23.93        74.73       133.55 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ 
       11.41       148.80        26.56        49.48        27.09        27.02 
TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 
       77.82        50.14        66.67        28.73       174.84        34.03 
TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU 
       26.73        54.41        80.68         0.20        22.92        55.59 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 
       13.51        19.30         9.90         7.23         2.04        15.78 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
      139.89       117.93        84.72        64.44        62.79        32.48 
TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A9SD 
       39.58       121.91        39.35        10.42        48.89        59.41 
TCGA-HR-A2OG TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O 
        0.23        65.88       368.78       297.90         7.23        18.05 
TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O 
        0.33         0.69       228.16        63.02       121.08         4.01 
TCGA-W3-AA1Q TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8K6 
       69.07       219.16       105.04        49.05        61.15        15.98 
TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX 
       98.89        58.98        67.63        59.77        11.80        32.58 
TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YD-A89C 
       49.51        12.16        35.01        19.73        22.29         6.90 
TCGA-YD-A9TA TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
       49.18        37.94        14.43        27.58        96.99        15.98 

  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
               2.6                0.2 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
            268.73             369.93 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
             53.92              49.33 
[1] "2.6 - 268.7 (53.9)" "0.2 - 369.9 (49.3)"
[1] "hr=" "1.2"
D68V3, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  15Q LOSS MUTATED                    8             1
  15Q LOSS WILD-TYPE                 57             4
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  15Q LOSS MUTATED                                          12
  15Q LOSS WILD-TYPE                                        60
                    vv
clus                 REGIONAL LYMPH NODE
  15Q LOSS MUTATED                    28
  15Q LOSS WILD-TYPE                 187
D68V4, multiclass
                                           clus
vv                                          15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  DISTANT METASTASIS                                       8                 57
  PRIMARY TUMOR                                            1                  4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               12                 60
  REGIONAL LYMPH NODE                                     28                187
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  15Q LOSS MUTATED             1       1       9        2        5        3
  15Q LOSS WILD-TYPE          11       6      19       16       22       21
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  15Q LOSS MUTATED           0         1         3         9          3
  15Q LOSS WILD-TYPE        14        18         9        28         12
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  15Q LOSS MUTATED            5          6        0
  15Q LOSS WILD-TYPE         27         54       20
D68V5, multiclass
             clus
vv            15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  I OR II NOS                1                 11
  STAGE 0                    1                  6
  STAGE I                    9                 19
  STAGE IA                   2                 16
  STAGE IB                   5                 22
  STAGE II                   3                 21
  STAGE IIA                  0                 14
  STAGE IIB                  1                 18
  STAGE IIC                  3                  9
  STAGE III                  9                 28
  STAGE IIIA                 3                 12
  STAGE IIIB                 5                 27
  STAGE IIIC                 6                 54
  STAGE IV                   0                 20
[1] 14  2
[1] TRUE
[1] "dimension of contingency 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       8 16  6 14
  15Q LOSS WILD-TYPE    56 56 71 54
D68V6, multiclass
       clus
vv      15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  T0+T1                8                 56
  T2                  16                 56
  T3                   6                 71
  T4                  14                 54
[1] 4 2
[1] TRUE
[1] "dimension of 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    28   8   4   7
  15Q LOSS WILD-TYPE 141  55  34  42
D68V7, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  N0               28                141
  N1                8                 55
  N2                4                 34
  N3                7                 42
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V8, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED    47   1
  15Q LOSS WILD-TYPE 266  20
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED     47    1
  15Q LOSS WILD-TYPE  266   20
   clus
vv  15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  0               47                266
  1                1                 20
[1] 2 2
[1] FALSE
D68V9, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED    20  13
  15Q LOSS WILD-TYPE 112  75
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED     20   13
  15Q LOSS WILD-TYPE  112   75
     clus
vv    15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  NO                20                112
  YES               13                 75
[1] 2 2
[1] FALSE
D68V10, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED     5  45
  15Q LOSS WILD-TYPE  39 268
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      5   45
  15Q LOSS WILD-TYPE   39  268
     clus
vv    15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  NO                 5                 39
  YES               45                268
[1] 2 2
[1] FALSE
D68V11, continuous
D68V12, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED    18  32
  15Q LOSS WILD-TYPE 117 191
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED     18   32
  15Q LOSS WILD-TYPE  117  191
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  FEMALE               18                117
  MALE                 32                191
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  15Q LOSS MUTATED       2                         0    47
  15Q LOSS WILD-TYPE     3                         1   297
D68V13, multiclass
                           clus
vv                          15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  ASIAN                                    2                  3
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   47                297
[1] 3 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     0  49
  15Q LOSS WILD-TYPE   7 295
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      0   49
  15Q LOSS WILD-TYPE    7  295
                        clus
vv                       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  7
  NOT HISPANIC OR LATINO               49                295
[1] 2 2
[1] FALSE

Clustering(69) Variable = 16P LOSS MUTATION ANALYSIS
D69V1, survival
                    sevent
clus2                  0   1
  16P LOSS MUTATED    20  23
  16P LOSS WILD-TYPE 101  95
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                43                196 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                23                 95 
$`16P LOSS MUTATED`
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1QA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JL 
       31.89       110.93        76.41       168.00        86.30       171.58 
TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A3CC TCGA-D3-A8GD TCGA-D3-A8GM TCGA-D9-A6EC 
       64.83        66.08        40.01        23.61        70.62        57.90 
TCGA-DA-A1I2 TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A29D TCGA-EE-A29M TCGA-EE-A29W 
      150.61        62.37        20.38        12.99        47.74       185.19 
TCGA-EE-A2GO TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3JI 
      118.32        67.50       145.45        53.26       122.73       152.81 
TCGA-ER-A193 TCGA-ER-A197 TCGA-ER-A2ND TCGA-FR-A8YC TCGA-FS-A1Z0 TCGA-FS-A1ZT 
       14.56         1.58         4.70        10.06       195.98        35.28 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FW-A3TU TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A267 
        4.47        23.21        55.59        53.29       117.93        17.06 
TCGA-GN-A268 TCGA-GN-A4U3 TCGA-OD-A75X TCGA-WE-A8K5 TCGA-WE-A8ZQ TCGA-YG-AA3O 
       42.48       120.53       297.01        59.64        59.44        28.21 
TCGA-Z2-AA3S 
       91.23 

$`16P LOSS WILD-TYPE`
TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q6 
       60.46        12.99        14.83         8.42        15.72        49.35 
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 
      133.25        19.04        62.60        25.64        45.99        62.86 
TCGA-D3-A2JA TCGA-D3-A2JD TCGA-D3-A2JE TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JP 
       15.75         7.27         9.76       107.61        36.30        43.53 
TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML 
       58.06        46.98       140.98        59.70        16.96        13.87 
TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51J TCGA-D3-A51K 
        9.34        90.21        23.67       173.85       144.46        31.76 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GU 
       62.70        11.34        42.05        45.70       177.86       124.08 
TCGA-D3-A8GC TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GP TCGA-D3-A8GR 
       78.21       179.97       120.00        69.53       135.12        36.53 
TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6EG TCGA-DA-A1HV 
       10.78        15.02        16.90        18.44        22.85        48.66 
TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC 
      106.85        31.96        82.85        32.42        64.83        58.85 
TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5SG TCGA-EB-A5SH 
       25.12       214.59        14.96         3.91        33.24        50.07 
TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A182 TCGA-EE-A184 
       45.50         6.64        13.15        24.89         0.00        67.50 
TCGA-EE-A20C TCGA-EE-A20H TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G 
       75.55       155.90        75.22        76.14         0.26        44.28 
TCGA-EE-A29H TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A2A1 TCGA-EE-A2A2 
       63.12        27.16        61.12       346.49       102.38         7.20 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ 
       77.98        26.14       239.11         0.20       189.40        68.65 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR 
       10.62        32.48        18.35        31.00         0.76         0.20 
TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC 
       71.31        81.99       103.13        15.25         5.75        23.77 
TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MP 
      209.79        94.19       171.85        63.25       104.78       227.01 
TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AD 
       25.08       143.93        23.51       124.31        51.62         4.41 
TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 
       54.51         6.28        67.89       111.85        45.90         3.35 
TCGA-EE-A3JB TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B 
      201.80        34.45        47.31         7.82         4.54        53.29 
TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M 
       39.81        11.47       151.46       150.12        99.06        59.84 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 
       42.48       120.76        49.71        34.95       146.63        47.97 
TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
       22.36        16.87        10.95       173.29        55.82        15.48 
TCGA-ER-A3PL TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FS-A1YW 
       32.05       174.21       209.23        26.20         5.65       171.78 
TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE 
       49.74         8.35        27.62       312.07        32.78        35.90 
TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS 
       12.92         7.82        36.33        78.61       130.95       136.27 
TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 
        5.29         3.06        30.90        66.67       173.19        13.28 
TCGA-FS-A4FD TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 
       80.68        11.54        19.30         9.90         6.05         1.91 
TCGA-GN-A265 TCGA-GN-A26A TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-GN-A8LK TCGA-GN-A9SD 
       84.72         7.59        34.49        46.92        43.23        59.41 
TCGA-LH-A9QB TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A825 
       85.05         7.23        18.05         0.33       174.12         1.97 
TCGA-W3-A828 TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 
      120.07        44.05        79.99         8.09       185.13        92.84 
TCGA-WE-A8K1 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-A8ZY 
        1.15        62.99        12.69        19.00        10.95        48.39 
TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 
        1.94        26.60        16.64        15.65 

  16P LOSS MUTATED 16P LOSS WILD-TYPE 
              1.58               0.00 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
            297.01             346.49 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
             59.64              43.38 
[1] "1.6 - 297.0 (59.6)" "0.0 - 346.5 (43.4)"
[1] "hr=" "1.1"
D69V2, survival
                    sevent
clus2                  0   1
  16P LOSS MUTATED    29  36
  16P LOSS WILD-TYPE 140 144
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                65                284 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                36                144 
$`16P LOSS MUTATED`
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1QA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JL 
      112.04       112.57        90.90       168.00        86.76       171.58 
TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A3BZ TCGA-D3-A3CC TCGA-D3-A51N TCGA-D3-A8GD 
       66.48        66.08       130.72        86.93        22.62        23.61 
TCGA-D3-A8GM TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HW TCGA-DA-A1I2 TCGA-EB-A44R 
      107.15        25.18        66.25        36.03       176.55        10.36 
TCGA-EB-A5UL TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A20I TCGA-EE-A29D 
       17.29         8.65        94.98        33.73        13.55        13.97 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2GC 
        2.60        56.84       195.02        17.92        46.82        67.43 
TCGA-EE-A2GO TCGA-EE-A2M5 TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MQ TCGA-EE-A2MU 
      126.81        21.67       158.63       167.90        43.23        53.26 
TCGA-EE-A3AB TCGA-EE-A3J5 TCGA-EE-A3JA TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A197 
      122.73        36.95        53.19       152.81        31.40        13.94 
TCGA-ER-A19E TCGA-ER-A19T TCGA-ER-A2ND TCGA-FR-A8YC TCGA-FS-A1Z0 TCGA-FS-A1ZT 
       13.02         8.88        23.34        34.82       202.65        53.16 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-GN-A262 TCGA-GN-A264 
       26.56        49.48        22.92        55.59       139.89       117.93 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26D TCGA-GN-A4U3 TCGA-OD-A75X TCGA-WE-A8JZ 
       64.44        62.79        39.58       121.91       297.90        24.03 
TCGA-WE-A8K5 TCGA-WE-A8ZQ TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-AA3S 
       61.15        59.77        37.94        14.43        96.99 

$`16P LOSS WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q3 
       17.03        66.48        12.99        14.93        16.57        16.67 
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QB TCGA-D3-A2J6 
       71.80       133.25        28.08        31.59        95.74        43.43 
TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JD TCGA-D3-A2JE 
      103.10        65.49        23.77       115.53        11.87        27.65 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JP TCGA-D3-A3C6 
       62.07       113.52        42.08        12.10        59.57        58.06 
TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML 
       46.98        46.32       166.52        60.23        24.53        13.87 
TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F 
        9.34       103.59        39.75        45.30       174.84        55.73 
TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL 
       56.35       145.12        32.94        63.81        26.89       125.79 
TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GB 
      135.75       137.92       178.32        18.18       125.19        30.84 
TCGA-D3-A8GC TCGA-D3-A8GE TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL 
       79.59        26.43        58.52       241.38       170.20        89.13 
TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A148 
      161.00       152.75        29.06       129.63       117.17       151.53 
TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       54.67         3.65         7.10        18.12        15.39        22.29 
TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I0 
       18.44         9.90        22.95        48.89       117.21        20.38 
TCGA-DA-A1I1 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA 
      194.83        35.93       107.34        61.18        53.92        65.92 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 
       23.44        68.09        28.60        10.49       215.44        15.68 
TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A5VV 
       13.87        20.35        68.25        54.02        52.01         7.04 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 
       24.89        29.82        27.22        14.70        26.89        68.15 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A 
        4.96       133.81       151.27        91.56       168.26        63.35 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29N 
       85.08        78.97        63.78        72.07        64.64        18.61 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V 
       56.42        66.74        14.47        61.28       369.93        25.87 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD 
      102.90        36.82        39.29        86.14        59.28       340.14 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
      161.03       208.04        48.72       107.38        54.74        79.66 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT 
       75.48       102.12        13.91        42.77        81.21        44.88 
TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD 
       94.82       129.27        28.83        19.76        61.51        47.28 
TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ 
      103.27       268.73       103.20        16.96       204.66        96.23 
TCGA-EE-A2ML TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT 
      216.66        47.54       248.65       134.40       162.48        71.21 
TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG 
      124.31        51.62        28.77        54.51        13.81        41.59 
TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB 
      138.81       172.18       127.20        64.08        34.32       201.80 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A199 
       27.35        51.35       109.58        35.44        50.76         9.17 
TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19G 
       77.75        98.40        48.89        12.59        26.37       268.93 
TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P 
      152.35         6.44       131.51        61.05        44.05       162.08 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE 
       50.89        37.25       148.18        79.99        43.82        20.15 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
       16.37        31.27        32.05       247.04        80.32        46.98 
TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 
       33.21         6.77        92.98       174.21        15.72       220.80 
TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW 
       27.85        18.77        38.27        36.26       104.42       216.92 
TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA 
       48.59       228.59        20.91        28.08         7.79        27.72 
TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG 
       48.85       357.37        53.52        40.27        15.45         9.70 
TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ 
       32.75        47.38        23.93       101.26        74.73       133.55 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 
       11.41       148.80        27.09        27.02        77.82        50.14 
TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC 
       66.67        28.73       174.84        34.03        26.73        54.41 
TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
       80.68         0.20        13.51        19.30         9.90         7.23 
TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A26A TCGA-GN-A4U4 
        2.04        15.78        84.72        10.13        32.48        39.35 
TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A8LL TCGA-GN-A9SD 
       10.42        48.89        22.13        50.10        21.37        59.41 
TCGA-HR-A2OG TCGA-HR-A2OH TCGA-LH-A9QB TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 
        0.23        65.88       368.78         7.23        18.05         0.33 
TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1Q 
        0.69       228.16        63.02       121.08         4.01        69.07 
TCGA-W3-AA1R TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8K6 
      111.09        42.08       219.16       105.04        49.05        15.98 
TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-A8ZY 
       98.89        58.98        67.63        11.80        32.58        49.51 
TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YD-A89C TCGA-YD-A9TA 
       12.16        35.01        19.73        22.29         6.90        49.18 
TCGA-Z2-A8RT TCGA-Z2-AA3V 
       27.58        15.98 

  16P LOSS MUTATED 16P LOSS WILD-TYPE 
               2.6                0.2 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
            297.90             369.93 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
            55.590             49.805 
[1] "2.6 - 297.9 (55.6)" "0.2 - 369.9 (49.8)"
[1] "hr=" "1.1"
D69V3, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  16P LOSS MUTATED                   12             3
  16P LOSS WILD-TYPE                 53             2
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  16P LOSS MUTATED                                           8
  16P LOSS WILD-TYPE                                        64
                    vv
clus                 REGIONAL LYMPH NODE
  16P LOSS MUTATED                    43
  16P LOSS WILD-TYPE                 172
D69V4, multiclass
                                           clus
vv                                          16P LOSS MUTATED 16P LOSS WILD-TYPE
  DISTANT METASTASIS                                      12                 53
  PRIMARY TUMOR                                            3                  2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                8                 64
  REGIONAL LYMPH NODE                                     43                172
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  16P LOSS MUTATED             3       2       3        3        5        2
  16P LOSS WILD-TYPE           9       5      25       15       22       22
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  16P LOSS MUTATED           2         8         3        10          3
  16P LOSS WILD-TYPE        12        11         9        27         12
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  16P LOSS MUTATED            5          8        5
  16P LOSS WILD-TYPE         27         52       15
D69V5, multiclass
             clus
vv            16P LOSS MUTATED 16P LOSS WILD-TYPE
  I OR II NOS                3                  9
  STAGE 0                    2                  5
  STAGE I                    3                 25
  STAGE IA                   3                 15
  STAGE IB                   5                 22
  STAGE II                   2                 22
  STAGE IIA                  2                 12
  STAGE IIB                  8                 11
  STAGE IIC                  3                  9
  STAGE III                 10                 27
  STAGE IIIA                 3                 12
  STAGE IIIB                 5                 27
  STAGE IIIC                 8                 52
  STAGE IV                   5                 15
[1] 14  2
[1] TRUE
[1] "dimension of contingency 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       9 13 12 18
  16P LOSS WILD-TYPE    55 59 65 50
D69V6, multiclass
       clus
vv      16P LOSS MUTATED 16P LOSS WILD-TYPE
  T0+T1                9                 55
  T2                  13                 59
  T3                  12                 65
  T4                  18                 50
[1] 4 2
[1] TRUE
[1] "dimension of 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    34  13   6   8
  16P LOSS WILD-TYPE 135  50  32  41
D69V7, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  N0               34                135
  N1               13                 50
  N2                6                 32
  N3                8                 41
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V8, binary
                    cls
clus                   0   1
  16P LOSS MUTATED    57   5
  16P LOSS WILD-TYPE 256  16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED     57    5
  16P LOSS WILD-TYPE  256   16
   clus
vv  16P LOSS MUTATED 16P LOSS WILD-TYPE
  0               57                256
  1                5                 16
[1] 2 2
[1] FALSE
D69V9, binary
                    cls
clus                   0   1
  16P LOSS MUTATED    31  16
  16P LOSS WILD-TYPE 101  72
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED     31   16
  16P LOSS WILD-TYPE  101   72
     clus
vv    16P LOSS MUTATED 16P LOSS WILD-TYPE
  NO                31                101
  YES               16                 72
[1] 2 2
[1] FALSE
D69V10, binary
                    cls
clus                   0   1
  16P LOSS MUTATED     4  63
  16P LOSS WILD-TYPE  40 250
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      4   63
  16P LOSS WILD-TYPE   40  250
     clus
vv    16P LOSS MUTATED 16P LOSS WILD-TYPE
  NO                 4                 40
  YES               63                250
[1] 2 2
[1] FALSE
D69V11, continuous
D69V12, binary
                    cls
clus                   0   1
  16P LOSS MUTATED    29  38
  16P LOSS WILD-TYPE 106 185
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED     29   38
  16P LOSS WILD-TYPE  106  185
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  FEMALE               29                106
  MALE                 38                185
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16P LOSS MUTATED       1                         1    61
  16P LOSS WILD-TYPE     4                         0   283
D69V13, multiclass
                           clus
vv                          16P LOSS MUTATED 16P LOSS WILD-TYPE
  ASIAN                                    1                  4
  BLACK OR AFRICAN AMERICAN                1                  0
  WHITE                                   61                283
[1] 3 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     3  63
  16P LOSS WILD-TYPE   4 281
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      3   63
  16P LOSS WILD-TYPE    4  281
                        clus
vv                       16P LOSS MUTATED 16P LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  4
  NOT HISPANIC OR LATINO               63                281
[1] 2 2
[1] FALSE

Clustering(70) Variable = 16Q LOSS MUTATION ANALYSIS
D70V1, survival
                    sevent
clus2                 0  1
  16Q LOSS MUTATED   31 34
  16Q LOSS WILD-TYPE 90 84
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                65                174 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                34                 84 
$`16Q LOSS MUTATED`
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1QA TCGA-D3-A2JB TCGA-D3-A2JC 
       31.89       110.93       133.25        76.41       168.00        86.30 
TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A3CC TCGA-D3-A8GD TCGA-D3-A8GM 
      171.58        64.83        66.08        40.01        23.61        70.62 
TCGA-D9-A3Z3 TCGA-D9-A6EC TCGA-DA-A1I2 TCGA-DA-A3F8 TCGA-EB-A5SG TCGA-EE-A180 
       16.90        57.90       150.61        14.96        33.24        62.37 
TCGA-EE-A181 TCGA-EE-A20C TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29M TCGA-EE-A29P 
       20.38        75.55        75.22        12.99        47.74        27.16 
TCGA-EE-A29W TCGA-EE-A2GH TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2MJ TCGA-EE-A2MK 
      185.19       189.40       118.32         0.76        63.25        67.50 
TCGA-EE-A2MM TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J4 
      145.45        53.26       122.73        54.51         6.28       111.85 
TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A197 TCGA-ER-A19B TCGA-ER-A19N TCGA-ER-A19W 
      152.81        14.56         1.58        53.29        42.48       146.63 
TCGA-ER-A2ND TCGA-FR-A8YC TCGA-FS-A1Z0 TCGA-FS-A1ZF TCGA-FS-A1ZT TCGA-FS-A1ZU 
        4.70        10.06       195.98        12.92        35.28         4.47 
TCGA-FS-A1ZW TCGA-FW-A3TU TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 
       23.21        55.59        53.29       117.93        17.06        42.48 
TCGA-GN-A4U3 TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O TCGA-W3-AA1R 
      120.53        85.05       297.01         7.23        18.05        79.99 
TCGA-WE-A8K5 TCGA-WE-A8ZQ TCGA-WE-AAA3 TCGA-YG-AA3O TCGA-Z2-AA3S 
       59.64        59.44        16.64        28.21        91.23 

$`16Q LOSS WILD-TYPE`
TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q6 
       60.46        12.99        14.83         8.42        15.72        49.35 
TCGA-D3-A1Q8 TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA 
       19.04        62.60        25.64        45.99        62.86        15.75 
TCGA-D3-A2JD TCGA-D3-A2JE TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JP TCGA-D3-A3C6 
        7.27         9.76       107.61        36.30        43.53        58.06 
TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO 
       46.98       140.98        59.70        16.96        13.87         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R 
       90.21        23.67       173.85       144.46        31.76        62.70 
TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D3-A8GC 
       11.34        42.05        45.70       177.86       124.08        78.21 
TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GP TCGA-D3-A8GR TCGA-D9-A1X3 
      179.97       120.00        69.53       135.12        36.53        10.78 
TCGA-D9-A3Z1 TCGA-D9-A4Z6 TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 
       15.02        18.44        22.85        48.66       106.85        31.96 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 
       82.85        32.42        64.83        58.85        25.12       214.59 
TCGA-EB-A44Q TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y 
        3.91        50.07        45.50         6.64        13.15        24.89 
TCGA-EE-A182 TCGA-EE-A184 TCGA-EE-A20H TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G 
        0.00        67.50       155.90        76.14         0.26        44.28 
TCGA-EE-A29H TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 
       63.12        61.12       346.49       102.38         7.20        77.98 
TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
       26.14       239.11         0.20        68.65        10.62        32.48 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 
       18.35        31.00         0.20        71.31        81.99       103.13 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI 
       15.25         5.75        23.77       209.79        94.19       171.85 
TCGA-EE-A2ML TCGA-EE-A2MP TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AA 
      104.78       227.01        25.08       143.93        23.51       124.31 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB 
       51.62         4.41        67.89        45.90         3.35       201.80 
TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19C TCGA-ER-A19D 
       34.45        47.31         7.82         4.54        39.81        11.47 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19P TCGA-ER-A19Q 
      151.46       150.12        99.06        59.84       120.76        49.71 
TCGA-ER-A19S TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A3ES 
       34.95        47.97        22.36        16.87        10.95       173.29 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7U8 
       55.82        15.48        32.05       174.21       209.23        26.20 
TCGA-FR-A7UA TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZC 
        5.65       171.78        49.74         8.35        27.62       312.07 
TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ 
       32.78        35.90         7.82        36.33        78.61       130.95 
TCGA-FS-A1ZS TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 
      136.27         5.29         3.06        30.90        66.67       173.19 
TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
       13.28        80.68        11.54        19.30         9.90         6.05 
TCGA-GF-A6C8 TCGA-GN-A265 TCGA-GN-A26A TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-GN-A8LK 
        1.91        84.72         7.59        34.49        46.92        43.23 
TCGA-GN-A9SD TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1Q 
       59.41         0.33       174.12         1.97       120.07        44.05 
TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8ZM TCGA-WE-A8ZN 
        8.09       185.13        92.84         1.15        62.99        12.69 
TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 
       19.00        10.95        48.39         1.94        26.60        15.65 

  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
              0.76               0.00 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
            297.01             346.49 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
             57.90              43.38 
[1] "0.8 - 297.0 (57.9)" "0.0 - 346.5 (43.4)"
[1] "hr=" "1"  
D70V2, survival
                    sevent
clus2                  0   1
  16Q LOSS MUTATED    45  55
  16Q LOSS WILD-TYPE 124 125
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
               100                249 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                55                125 
$`16Q LOSS MUTATED`
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1QA TCGA-D3-A2JB TCGA-D3-A2JC 
      112.04       112.57       133.25        90.90       168.00        86.76 
TCGA-D3-A2JF TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A3BZ TCGA-D3-A3CC 
       62.07       171.58        66.48        66.08       130.72        86.93 
TCGA-D3-A51N TCGA-D3-A8GD TCGA-D3-A8GI TCGA-D3-A8GM TCGA-D3-A8GS TCGA-D9-A148 
       22.62        23.61        58.52       107.15       117.17       151.53 
TCGA-D9-A149 TCGA-D9-A3Z3 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HW TCGA-DA-A1I2 
       54.67        22.29        25.18        66.25        36.03       176.55 
TCGA-DA-A1I4 TCGA-DA-A3F8 TCGA-EB-A44R TCGA-EB-A5SG TCGA-EE-A17Z TCGA-EE-A180 
       35.93        15.68        10.36        68.25         8.65        94.98 
TCGA-EE-A181 TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A20I TCGA-EE-A29B TCGA-EE-A29D 
       33.73         4.96       151.27        13.55        85.08        13.97 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 
        2.60        56.84        56.42       195.02        17.92        46.82 
TCGA-EE-A2A5 TCGA-EE-A2GC TCGA-EE-A2GH TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2M5 
       39.29        67.43       208.04       126.81        13.91        21.67 
TCGA-EE-A2MD TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MQ TCGA-EE-A2MU 
       47.28        96.23       158.63       167.90        43.23        53.26 
TCGA-EE-A3AB TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3JA 
      122.73        54.51        13.81       127.20        36.95        53.19 
TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A197 TCGA-ER-A19B TCGA-ER-A19N TCGA-ER-A19T 
      152.81        31.40        13.94        98.40        44.05         8.88 
TCGA-ER-A19W TCGA-ER-A2ND TCGA-FR-A8YC TCGA-FS-A1Z0 TCGA-FS-A1ZB TCGA-FS-A1ZF 
      148.18        23.34        34.82       202.65        48.85        15.45 
TCGA-FS-A1ZP TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A4F2 TCGA-FW-A3I3 
       74.73        53.16        26.56        49.48        50.14         0.20 
TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 
       22.92        55.59       139.89       117.93        64.44        62.79 
TCGA-GN-A26D TCGA-GN-A4U3 TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O 
       39.58       121.91       368.78       297.90         7.23        18.05 
TCGA-W3-AA1R TCGA-WE-A8JZ TCGA-WE-A8K5 TCGA-WE-A8ZQ TCGA-WE-A8ZX TCGA-WE-AAA3 
      111.09        24.03        61.15        59.77        32.58        19.73 
TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-AA3S TCGA-Z2-AA3V 
       37.94        14.43        96.99        15.98 

$`16Q LOSS WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q3 
       17.03        66.48        12.99        14.93        16.57        16.67 
TCGA-D3-A1Q6 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       71.80        28.08        31.59        95.74        43.43       103.10 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JD TCGA-D3-A2JE TCGA-D3-A2JG 
       65.49        23.77       115.53        11.87        27.65       113.52 
TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 
       42.08        12.10        59.57        58.06        46.98        46.32 
TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR 
      166.52        60.23        24.53        13.87         9.34       103.59 
TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J 
       39.75        45.30       174.84        55.73        56.35       145.12 
TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO 
       32.94        63.81        26.89       125.79       135.75       137.92 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GE 
      178.32        18.18       125.19        30.84        79.59        26.43 
TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GQ 
      241.38       170.20        89.13       161.00       152.75        29.06 
TCGA-D3-A8GR TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A4Z6 
      129.63         3.65         7.10        18.12        15.39        18.44 
TCGA-D9-A6E9 TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 
        9.90        22.95        48.89       117.21        20.38       194.83 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
      107.34        61.18        53.92        65.92        23.44        68.09 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5SH 
       28.60        10.49       215.44        13.87        20.35        54.02 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y 
       17.29        52.01         7.04        24.89        29.82        27.22 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H 
       14.70        26.89        68.15       133.81        91.56       168.26 
TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29N 
       63.35        78.97        63.78        72.07        64.64        18.61 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A2A1 
       66.74        14.47        61.28       369.93        25.87       102.90 
TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GI 
       36.82        86.14        59.28       340.14       161.03        48.72 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GR 
      107.38        54.74        79.66        75.48       102.12        42.77 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 
       81.21        44.88        94.82       129.27        28.83        19.76 
TCGA-EE-A2MC TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
       61.51       103.27       268.73       103.20        16.96       204.66 
TCGA-EE-A2ML TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT 
      216.66        47.54       248.65       134.40       162.48        71.21 
TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 
      124.31        51.62        28.77        41.59       138.81       172.18 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH 
       64.08        34.32       201.80        27.35        51.35       109.58 
TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19C TCGA-ER-A19D 
       35.44        50.76         9.17        77.75        48.89        12.59 
TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L 
       13.02        26.37       268.93       152.35         6.44       131.51 
TCGA-ER-A19M TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A1A1 TCGA-ER-A2NC 
       61.05       162.08        50.89        37.25        79.99        43.82 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET 
       20.15        16.37        31.27        32.05       247.04        80.32 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       46.98        33.21         6.77        92.98       174.21        15.72 
TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YD TCGA-FR-A8YE 
      220.80        27.85        18.77        38.27        36.26       104.42 
TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 
      216.92        48.59       228.59        20.91        28.08         7.79 
TCGA-FS-A1ZA TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZH 
       27.72       357.37        53.52        40.27         9.70        32.75 
TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS 
       47.38        23.93       101.26       133.55        11.41       148.80 
TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 
       27.09        27.02        77.82        66.67        28.73       174.84 
TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3TV TCGA-FW-A5DY 
       34.03        26.73        54.41        80.68        13.51        19.30 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A265 TCGA-GN-A266 
        9.90         7.23         2.04        15.78        84.72        10.13 
TCGA-GN-A26A TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK 
       32.48        39.35        10.42        48.89        22.13        50.10 
TCGA-GN-A8LL TCGA-GN-A9SD TCGA-HR-A2OG TCGA-HR-A2OH TCGA-RP-A693 TCGA-RP-A694 
       21.37        59.41         0.23        65.88         0.33         0.69 
TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1Q TCGA-W3-AA1V 
      228.16        63.02       121.08         4.01        69.07        42.08 
TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN 
      219.16       105.04        49.05        15.98        98.89        58.98 
TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 
       67.63        11.80        49.51        12.16        35.01        22.29 
TCGA-YD-A89C TCGA-YD-A9TA TCGA-Z2-A8RT 
        6.90        49.18        27.58 

  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
              0.20               0.23 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
            368.78             369.93 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
             55.13              49.05 
[1] "0.2 - 368.8 (55.1)" "0.2 - 369.9 (49.0)"
[1] "hr=" "1.1"
D70V3, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  16Q LOSS MUTATED                   21             3
  16Q LOSS WILD-TYPE                 44             2
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  16Q LOSS MUTATED                                          16
  16Q LOSS WILD-TYPE                                        56
                    vv
clus                 REGIONAL LYMPH NODE
  16Q LOSS MUTATED                    62
  16Q LOSS WILD-TYPE                 153
D70V4, multiclass
                                           clus
vv                                          16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  DISTANT METASTASIS                                      21                 44
  PRIMARY TUMOR                                            3                  2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               16                 56
  REGIONAL LYMPH NODE                                     62                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                 I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  16Q LOSS MUTATED             3       3       5        7        6        7
  16Q LOSS WILD-TYPE           9       4      23       11       21       17
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  16Q LOSS MUTATED           2         9         6        10          3
  16Q LOSS WILD-TYPE        12        10         6        27         12
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  16Q LOSS MUTATED            9         14        6
  16Q LOSS WILD-TYPE         23         46       14
D70V5, multiclass
             clus
vv            16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  I OR II NOS                3                  9
  STAGE 0                    3                  4
  STAGE I                    5                 23
  STAGE IA                   7                 11
  STAGE IB                   6                 21
  STAGE II                   7                 17
  STAGE IIA                  2                 12
  STAGE IIB                  9                 10
  STAGE IIC                  6                  6
  STAGE III                 10                 27
  STAGE IIIA                 3                 12
  STAGE IIIB                 9                 23
  STAGE IIIC                14                 46
  STAGE IV                   6                 14
[1] 14  2
[1] TRUE
[1] "dimension of contingency 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      17 15 20 26
  16Q LOSS WILD-TYPE    47 57 57 42
D70V6, multiclass
       clus
vv      16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  T0+T1               17                 47
  T2                  15                 57
  T3                  20                 57
  T4                  26                 42
[1] 4 2
[1] TRUE
[1] "dimension of 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    54  16   9  13
  16Q LOSS WILD-TYPE 115  47  29  36
D70V7, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  N0               54                115
  N1               16                 47
  N2                9                 29
  N3               13                 36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V8, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED    86   7
  16Q LOSS WILD-TYPE 227  14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED     86    7
  16Q LOSS WILD-TYPE  227   14
   clus
vv  16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  0               86                227
  1                7                 14
[1] 2 2
[1] FALSE
D70V9, binary
                    cls
clus                  0  1
  16Q LOSS MUTATED   44 26
  16Q LOSS WILD-TYPE 88 62
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED     44   26
  16Q LOSS WILD-TYPE   88   62
     clus
vv    16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  NO                44                 88
  YES               26                 62
[1] 2 2
[1] FALSE
D70V10, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED    10  93
  16Q LOSS WILD-TYPE  34 220
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED     10   93
  16Q LOSS WILD-TYPE   34  220
     clus
vv    16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  NO                10                 34
  YES               93                220
[1] 2 2
[1] FALSE
D70V11, continuous
D70V12, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED    44  59
  16Q LOSS WILD-TYPE  91 164
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED     44   59
  16Q LOSS WILD-TYPE   91  164
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  FEMALE               44                 91
  MALE                 59                164
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16Q LOSS MUTATED       1                         1    97
  16Q LOSS WILD-TYPE     4                         0   247
D70V13, multiclass
                           clus
vv                          16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  ASIAN                                    1                  4
  BLACK OR AFRICAN AMERICAN                1                  0
  WHITE                                   97                247
[1] 3 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     3  99
  16Q LOSS WILD-TYPE   4 245
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      3   99
  16Q LOSS WILD-TYPE    4  245
                        clus
vv                       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  4
  NOT HISPANIC OR LATINO               99                245
[1] 2 2
[1] FALSE

Clustering(71) Variable = 17P LOSS MUTATION ANALYSIS
D71V1, survival
                    sevent
clus2                 0  1
  17P LOSS MUTATED   39 41
  17P LOSS WILD-TYPE 82 77
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                80                159 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                41                 77 
$`17P LOSS MUTATED`
TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1QA TCGA-D3-A2J6 TCGA-D3-A2JB TCGA-D3-A2JD 
       60.46        12.99        76.41        25.64       168.00         7.27 
TCGA-D3-A2JG TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A3ML TCGA-D3-A3MO 
      107.61       171.58        64.83        66.08        13.87         9.34 
TCGA-D3-A51T TCGA-D3-A8GC TCGA-D3-A8GL TCGA-D3-A8GM TCGA-DA-A1HV TCGA-DA-A1HY 
       11.34        78.21        69.53        70.62        48.66       106.85 
TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A3F5 TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A180 
      150.61        82.85       214.59        45.50        13.15        62.37 
TCGA-EE-A184 TCGA-EE-A20C TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H 
       67.50        75.55        76.14         0.26        44.28        63.12 
TCGA-EE-A29M TCGA-EE-A29T TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2GJ TCGA-EE-A2GP 
       47.74       346.49       102.38         7.20        68.65         0.76 
TCGA-EE-A2M6 TCGA-EE-A2MC TCGA-EE-A2MG TCGA-EE-A2MP TCGA-EE-A2MR TCGA-EE-A2MS 
      103.13        23.77        94.19       227.01        25.08       143.93 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3J7 TCGA-EE-A3J8 
       53.26       124.31        51.62        54.51        45.90         3.35 
TCGA-EE-A3JB TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A199 TCGA-ER-A19C TCGA-ER-A19S 
      201.80        14.56        34.45         7.82        39.81        34.95 
TCGA-ER-A2NG TCGA-ER-A3EV TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A8YC TCGA-FS-A1Z4 
       10.95        15.48       174.21       209.23        10.06        27.62 
TCGA-FS-A1ZJ TCGA-FS-A1ZQ TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY 
       36.33       130.95        35.28         4.47        23.21         5.29 
TCGA-FS-A4F9 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A4U3 TCGA-QB-AA9O 
       13.28        84.72        17.06        42.48       120.53        18.05 
TCGA-W3-AA1R TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 
       79.99        92.84         1.15        48.39         1.94        26.60 
TCGA-WE-AAA3 TCGA-YG-AA3O 
       16.64        28.21 

$`17P LOSS WILD-TYPE`
TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 
       14.83         8.42        15.72        31.89       110.93        49.35 
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QB TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA 
      133.25        19.04        62.60        45.99        62.86        15.75 
TCGA-D3-A2JC TCGA-D3-A2JE TCGA-D3-A2JH TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3C7 
       86.30         9.76        36.30        43.53        58.06        46.98 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MR TCGA-D3-A3MU 
      140.98        40.01        59.70        16.96        90.21        23.67 
TCGA-D3-A51E TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A5GL TCGA-D3-A5GN 
      173.85       144.46        31.76        62.70        42.05        45.70 
TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D3-A8GD TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GP 
      177.86       124.08        23.61       179.97       120.00       135.12 
TCGA-D3-A8GR TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6EC 
       36.53        10.78        15.02        16.90        18.44        57.90 
TCGA-D9-A6EG TCGA-DA-A1I1 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 
       22.85        31.96        32.42        64.83        58.85        25.12 
TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A6L9 TCGA-EE-A17Y 
       14.96         3.91        33.24        50.07         6.64        24.89 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A20H TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29P 
       20.38         0.00       155.90        75.22        12.99        27.16 
TCGA-EE-A29Q TCGA-EE-A29W TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE 
       61.12       185.19        77.98        26.14       239.11         0.20 
TCGA-EE-A2GH TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO 
      189.40        10.62        32.48        18.35        31.00       118.32 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MF 
        0.20        71.31        81.99        15.25         5.75       209.79 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MT 
      171.85        63.25        67.50       104.78       145.45        23.51 
TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3JI 
      122.73         4.41         6.28        67.89       111.85       152.81 
TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19G 
        1.58        47.31         4.54        53.29        11.47       151.46 
TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
      150.12        99.06        59.84        42.48       120.76        49.71 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A3ES 
      146.63        47.97        22.36         4.70        16.87       173.29 
TCGA-ER-A3ET TCGA-ER-A3PL TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FS-A1YW TCGA-FS-A1YY 
       55.82        32.05        26.20         5.65       171.78        49.74 
TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF 
      195.98         8.35       312.07        32.78        35.90        12.92 
TCGA-FS-A1ZG TCGA-FS-A1ZM TCGA-FS-A1ZS TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 
        7.82        78.61       136.27         3.06        30.90        66.67 
TCGA-FS-A4F8 TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
      173.19        80.68        55.59        11.54        19.30         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A26A TCGA-GN-A4U4 
        6.05         1.91        53.29       117.93         7.59        34.49 
TCGA-GN-A4U8 TCGA-GN-A8LK TCGA-GN-A9SD TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS 
       46.92        43.23        59.41        85.05       297.01         7.23 
TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1Q TCGA-W3-AA1V 
        0.33       174.12         1.97       120.07        44.05         8.09 
TCGA-W3-AA1W TCGA-WE-A8K5 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ 
      185.13        59.64        62.99        12.69        19.00        59.44 
TCGA-WE-A8ZT TCGA-WE-AAA4 TCGA-Z2-AA3S 
       10.95        15.65        91.23 

  17P LOSS MUTATED 17P LOSS WILD-TYPE 
              0.26               0.00 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
            346.49             312.07 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
            48.065             45.700 
[1] "0.3 - 346.5 (48.1)" "0.0 - 312.1 (45.7)"
[1] "hr=" "1"  
D71V2, survival
                    sevent
clus2                  0   1
  17P LOSS MUTATED    58  64
  17P LOSS WILD-TYPE 111 116
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               122                227 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                64                116 
$`17P LOSS MUTATED`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1QA TCGA-D3-A2J6 TCGA-D3-A2JB 
       17.03        66.48        12.99        90.90        43.43       168.00 
TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A3ML 
       11.87       113.52       171.58        66.48        66.08        13.87 
TCGA-D3-A3MO TCGA-D3-A51N TCGA-D3-A51T TCGA-D3-A5GO TCGA-D3-A8GB TCGA-D3-A8GC 
        9.34        22.62        26.89       137.92        30.84        79.59 
TCGA-D3-A8GI TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D9-A148 TCGA-D9-A1JW 
       58.52        89.13       107.15       161.00       151.53         3.65 
TCGA-D9-A6EA TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I2 TCGA-DA-A1I5 
       25.18        48.89        36.03       117.21       176.55       107.34 
TCGA-DA-A1I8 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-EB-A44R TCGA-EB-A5UL TCGA-EB-A5UN 
       53.92        10.49       215.44        10.36        17.29        52.01 
TCGA-EE-A17X TCGA-EE-A180 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A29C 
       29.82        94.98        68.15         4.96       151.27        78.97 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29S 
       63.78        72.07        64.64         2.60        56.84        61.28 
TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 
      369.93        25.87        17.92       102.90        36.82        39.29 
TCGA-EE-A2GC TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GP TCGA-EE-A2GT TCGA-EE-A2M5 
       67.43        48.72       107.38        13.91        44.88        21.67 
TCGA-EE-A2M6 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2MG TCGA-EE-A2MN TCGA-EE-A2MP 
      129.27        61.51        47.28       103.20        47.54       248.65 
TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AC 
       43.23       134.40       162.48        53.26       124.31        51.62 
TCGA-EE-A3AE TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH 
       54.51        36.95        64.08        34.32       201.80       109.58 
TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A199 TCGA-ER-A19C TCGA-ER-A19S TCGA-ER-A2NG 
       31.40        35.44         9.17        48.89        37.25        31.27 
TCGA-ER-A3EV TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7U9 TCGA-FR-A8YC 
       46.98        92.98       174.21       220.80        18.77        34.82 
TCGA-FS-A1YX TCGA-FS-A1Z4 TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZQ TCGA-FS-A1ZT 
       48.59        28.08        32.75        47.38       133.55        53.16 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F2 TCGA-FS-A4F9 TCGA-FW-A3I3 
       26.56        49.48        27.09        50.14        34.03         0.20 
TCGA-FW-A3R5 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A4U3 
       22.92        84.72        10.13        64.44        62.79       121.91 
TCGA-GN-A4U9 TCGA-HR-A2OG TCGA-QB-AA9O TCGA-W3-AA1R TCGA-W3-AA21 TCGA-WE-A8JZ 
       22.13         0.23        18.05       111.09       105.04        24.03 
TCGA-WE-A8K1 TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 
       49.05        32.58        49.51        12.16        35.01        19.73 
TCGA-YG-AA3O TCGA-Z2-AA3V 
       37.94        15.98 

$`17P LOSS WILD-TYPE`
TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 
       14.93        16.57        16.67       112.04       112.57        71.80 
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QB TCGA-D3-A2J7 TCGA-D3-A2J8 
      133.25        28.08        31.59        95.74       103.10        65.49 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A2JH 
       23.77       115.53        86.76        27.65        62.07        42.08 
TCGA-D3-A2JK TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 
       12.10        59.57       130.72        58.06        46.98        46.32 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MR TCGA-D3-A3MU 
      166.52        86.93        60.23        24.53       103.59        39.75 
TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K 
       45.30       174.84        55.73        56.35       145.12        32.94 
TCGA-D3-A51R TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU 
       63.81       125.79       135.75       178.32        18.18       125.19 
TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GP TCGA-D3-A8GQ 
       23.61        26.43       241.38       170.20       152.75        29.06 
TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A149 TCGA-D9-A1JX TCGA-D9-A1X3 TCGA-D9-A3Z1 
      129.63       117.17        54.67         7.10        18.12        15.39 
TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1I0 
       22.29        18.44         9.90        66.25        22.95        20.38 
TCGA-DA-A1I1 TCGA-DA-A1I4 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
      194.83        35.93        61.18        65.92        23.44        68.09 
TCGA-DA-A3F2 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH 
       28.60        15.68        13.87        20.35        68.25        54.02 
TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 
        7.04        24.89        27.22         8.65        33.73        14.70 
TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A 
       26.89       133.81        91.56       168.26        13.55        63.35 
TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
       85.08        13.97        18.61        56.42        66.74        14.47 
TCGA-EE-A29W TCGA-EE-A2A0 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE 
      195.02        46.82        86.14        59.28       340.14       161.03 
TCGA-EE-A2GH TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO 
      208.04        54.74        79.66        75.48       102.12       126.81 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2ME 
       42.77        81.21        94.82        28.83        19.76       103.27 
TCGA-EE-A2MF TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML 
      268.73        16.96       204.66        96.23       158.63       216.66 
TCGA-EE-A2MM TCGA-EE-A2MT TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG 
      167.90        71.21       122.73        28.77        13.81        41.59 
TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE 
      138.81       172.18       127.20        53.19        27.35        51.35 
TCGA-EE-A3JI TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19D 
      152.81        13.94        50.76        77.75        98.40        12.59 
TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L 
       13.02        26.37       268.93       152.35         6.44       131.51 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19T TCGA-ER-A19W 
       61.05        44.05       162.08        50.89         8.88       148.18 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NH 
       79.99        43.82        23.34        20.15        16.37        32.05 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A69P TCGA-FR-A7U8 
      247.04        80.32        33.21         6.77        15.72        27.85 
TCGA-FR-A7UA TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 
       38.27        36.26       104.42       216.92       228.59       202.65 
TCGA-FS-A1Z3 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD 
       20.91         7.79        27.72        48.85       357.37        53.52 
TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP 
       40.27        15.45         9.70        23.93       101.26        74.73 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 
       11.41       148.80        27.02        77.82        66.67        28.73 
TCGA-FS-A4F8 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV 
      174.84        26.73        54.41        80.68        55.59        13.51 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 
       19.30         9.90         7.23         2.04        15.78       139.89 
TCGA-GN-A264 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 
      117.93        32.48        39.58        39.35        10.42        48.89 
TCGA-GN-A8LK TCGA-GN-A8LL TCGA-GN-A9SD TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X 
       50.10        21.37        59.41        65.88       368.78       297.90 
TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 
        7.23         0.33         0.69       228.16        63.02       121.08 
TCGA-W3-AA1O TCGA-W3-AA1Q TCGA-W3-AA1V TCGA-W3-AA1W TCGA-WE-A8K5 TCGA-WE-A8K6 
        4.01        69.07        42.08       219.16        61.15        15.98 
TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-AAA4 
       98.89        58.98        67.63        59.77        11.80        22.29 
TCGA-YD-A89C TCGA-YD-A9TA TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S 
        6.90        49.18        14.43        27.58        96.99 

  17P LOSS MUTATED 17P LOSS WILD-TYPE 
              0.20               0.33 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
            369.93             368.78 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
             48.97              54.02 
[1] "0.2 - 369.9 (49.0)" "0.3 - 368.8 (54.0)"
[1] "hr=" "1.1"
D71V3, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  17P LOSS MUTATED                   20             1
  17P LOSS WILD-TYPE                 45             4
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  17P LOSS MUTATED                                          18
  17P LOSS WILD-TYPE                                        54
                    vv
clus                 REGIONAL LYMPH NODE
  17P LOSS MUTATED                    87
  17P LOSS WILD-TYPE                 128
D71V4, multiclass
                                           clus
vv                                          17P LOSS MUTATED 17P LOSS WILD-TYPE
  DISTANT METASTASIS                                      20                 45
  PRIMARY TUMOR                                            1                  4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               18                 54
  REGIONAL LYMPH NODE                                     87                128
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  17P LOSS MUTATED             5       3      14       10        9        5
  17P LOSS WILD-TYPE           7       4      14        8       18       19
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  17P LOSS MUTATED           4         7         3        12          7
  17P LOSS WILD-TYPE        10        12         9        25          8
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  17P LOSS MUTATED           11         22        4
  17P LOSS WILD-TYPE         21         38       16
D71V5, multiclass
             clus
vv            17P LOSS MUTATED 17P LOSS WILD-TYPE
  I OR II NOS                5                  7
  STAGE 0                    3                  4
  STAGE I                   14                 14
  STAGE IA                  10                  8
  STAGE IB                   9                 18
  STAGE II                   5                 19
  STAGE IIA                  4                 10
  STAGE IIB                  7                 12
  STAGE IIC                  3                  9
  STAGE III                 12                 25
  STAGE IIIA                 7                  8
  STAGE IIIB                11                 21
  STAGE IIIC                22                 38
  STAGE IV                   4                 16
[1] 14  2
[1] TRUE
[1] "dimension of contingency 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      23 29 25 25
  17P LOSS WILD-TYPE    41 43 52 43
D71V6, multiclass
       clus
vv      17P LOSS MUTATED 17P LOSS WILD-TYPE
  T0+T1               23                 41
  T2                  29                 43
  T3                  25                 52
  T4                  25                 43
[1] 4 2
[1] TRUE
[1] "dimension of 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    60  22  14  18
  17P LOSS WILD-TYPE 109  41  24  31
D71V7, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  N0               60                109
  N1               22                 41
  N2               14                 24
  N3               18                 31
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V8, binary
                    cls
clus                   0   1
  17P LOSS MUTATED   115   5
  17P LOSS WILD-TYPE 198  16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED    115    5
  17P LOSS WILD-TYPE  198   16
   clus
vv  17P LOSS MUTATED 17P LOSS WILD-TYPE
  0              115                198
  1                5                 16
[1] 2 2
[1] FALSE
D71V9, binary
                    cls
clus                  0  1
  17P LOSS MUTATED   55 32
  17P LOSS WILD-TYPE 77 56
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     55   32
  17P LOSS WILD-TYPE   77   56
     clus
vv    17P LOSS MUTATED 17P LOSS WILD-TYPE
  NO                55                 77
  YES               32                 56
[1] 2 2
[1] FALSE
D71V10, binary
                    cls
clus                   0   1
  17P LOSS MUTATED    14 112
  17P LOSS WILD-TYPE  30 201
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     14  112
  17P LOSS WILD-TYPE   30  201
     clus
vv    17P LOSS MUTATED 17P LOSS WILD-TYPE
  NO                14                 30
  YES              112                201
[1] 2 2
[1] FALSE
D71V11, continuous
D71V12, binary
                    cls
clus                   0   1
  17P LOSS MUTATED    39  87
  17P LOSS WILD-TYPE  96 136
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     39   87
  17P LOSS WILD-TYPE   96  136
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  FEMALE               39                 96
  MALE                 87                136
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  17P LOSS MUTATED       1                         1   121
  17P LOSS WILD-TYPE     4                         0   223
D71V13, multiclass
                           clus
vv                          17P LOSS MUTATED 17P LOSS WILD-TYPE
  ASIAN                                    1                  4
  BLACK OR AFRICAN AMERICAN                1                  0
  WHITE                                  121                223
[1] 3 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     1 122
  17P LOSS WILD-TYPE   6 222
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      1  122
  17P LOSS WILD-TYPE    6  222
                        clus
vv                       17P LOSS MUTATED 17P LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO              122                222
[1] 2 2
[1] FALSE

Clustering(72) Variable = 17Q LOSS MUTATION ANALYSIS
D72V1, survival
                    sevent
clus2                  0   1
  17Q LOSS MUTATED    16  23
  17Q LOSS WILD-TYPE 105  95
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                39                200 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                23                 95 
$`17Q LOSS MUTATED`
TCGA-3N-A9WD TCGA-D3-A2J6 TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JN TCGA-D3-A2JO 
       12.99        25.64         7.27       107.61        64.83        66.08 
TCGA-D9-A6EC TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-EE-A180 TCGA-EE-A29C TCGA-EE-A29E 
       57.90       150.61        82.85        62.37        76.14         0.26 
TCGA-EE-A2GP TCGA-EE-A2M6 TCGA-EE-A2MC TCGA-EE-A2MG TCGA-EE-A2MP TCGA-EE-A3AA 
        0.76       103.13        23.77        94.19       227.01       124.31 
TCGA-EE-A3AE TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-ER-A193 TCGA-ER-A19C 
       54.51        45.90         3.35       201.80        14.56        39.81 
TCGA-ER-A19L TCGA-ER-A19S TCGA-FR-A729 TCGA-FR-A8YC TCGA-FS-A1Z4 TCGA-FS-A1ZQ 
       99.06        34.95       209.23        10.06        27.62       130.95 
TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F9 TCGA-GN-A267 TCGA-QB-AA9O 
       35.28        23.21         5.29        13.28        17.06        18.05 
TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-YG-AA3O 
       48.39         1.94        28.21 

$`17Q LOSS WILD-TYPE`
TCGA-3N-A9WC TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 
       60.46        14.83         8.42        15.72        31.89       110.93 
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J7 
       49.35       133.25        19.04        76.41        62.60        45.99 
TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JE TCGA-D3-A2JH 
       62.86        15.75       168.00        86.30         9.76        36.30 
TCGA-D3-A2JL TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CC 
      171.58        43.53        58.06        46.98       140.98        40.01 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU 
       59.70        16.96        13.87         9.34        90.21        23.67 
TCGA-D3-A51E TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL 
      173.85       144.46        31.76        62.70        11.34        42.05 
TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GJ 
       45.70       177.86       124.08        78.21        23.61       179.97 
TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GP TCGA-D3-A8GR TCGA-D9-A1X3 
      120.00        69.53        70.62       135.12        36.53        10.78 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY 
       15.02        16.90        18.44        22.85        48.66       106.85 
TCGA-DA-A1I1 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 
       31.96        32.42        64.83        58.85        25.12       214.59 
TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A6L9 
       14.96         3.91        33.24        50.07        45.50         6.64 
TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A184 TCGA-EE-A20C 
       13.15        24.89        20.38         0.00        67.50        75.55 
TCGA-EE-A20H TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M 
      155.90        75.22        12.99        44.28        63.12        47.74 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A2 
       27.16        61.12       346.49       185.19       102.38         7.20 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ 
       77.98        26.14       239.11         0.20       189.40        68.65 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GR 
       10.62        32.48        18.35        31.00       118.32         0.20 
TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MF TCGA-EE-A2MI 
       71.31        81.99        15.25         5.75       209.79       171.85 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MR TCGA-EE-A2MS 
       63.25        67.50       104.78       145.45        25.08       143.93 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AF 
       23.51        53.26       122.73        51.62         4.41         6.28 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
       67.89       111.85       152.81        34.45         1.58        47.31 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19H 
        7.82         4.54        53.29        11.47       151.46       150.12 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19W TCGA-ER-A1A1 
       59.84        42.48       120.76        49.71       146.63        47.97 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET 
       22.36         4.70        16.87        10.95       173.29        55.82 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A44A TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FS-A1YW 
       15.48        32.05       174.21        26.20         5.65       171.78 
TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE 
       49.74       195.98         8.35       312.07        32.78        35.90 
TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZS TCGA-FS-A1ZU 
       12.92         7.82        36.33        78.61       136.27         4.47 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4FD TCGA-FW-A3TU 
        3.06        30.90        66.67       173.19        80.68        55.59 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 
       11.54        19.30         9.90         6.05         1.91        53.29 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 
      117.93        84.72        42.48         7.59       120.53        34.49 
TCGA-GN-A4U8 TCGA-GN-A8LK TCGA-GN-A9SD TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS 
       46.92        43.23        59.41        85.05       297.01         7.23 
TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1Q TCGA-W3-AA1R 
        0.33       174.12         1.97       120.07        44.05        79.99 
TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8ZM 
        8.09       185.13        92.84         1.15        59.64        62.99 
TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-AAA0 TCGA-WE-AAA3 
       12.69        19.00        59.44        10.95        26.60        16.64 
TCGA-WE-AAA4 TCGA-Z2-AA3S 
       15.65        91.23 

  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
              0.26               0.00 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
            227.01             346.49 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
             39.81              46.95 
[1] "0.3 - 227.0 (39.8)" "0.0 - 346.5 (47.0)"
[1] "hr=" "1.4"
D72V2, survival
                    sevent
clus2                  0   1
  17Q LOSS MUTATED    27  33
  17Q LOSS WILD-TYPE 142 147
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                60                289 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                33                147 
$`17Q LOSS MUTATED`
TCGA-3N-A9WB TCGA-3N-A9WD TCGA-D3-A2J6 TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JN 
       17.03        12.99        43.43        11.87       113.52        66.48 
TCGA-D3-A2JO TCGA-D3-A51N TCGA-D3-A8GI TCGA-D9-A148 TCGA-D9-A6EA TCGA-D9-A6EC 
       66.08        22.62        58.52       151.53        25.18        66.25 
TCGA-DA-A1HW TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-EE-A180 TCGA-EE-A29C 
       36.03       176.55       107.34        53.92        94.98        78.97 
TCGA-EE-A29E TCGA-EE-A29X TCGA-EE-A2A5 TCGA-EE-A2GI TCGA-EE-A2GP TCGA-EE-A2GT 
       63.78        17.92        39.29        48.72        13.91        44.88 
TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2MC TCGA-EE-A2MG TCGA-EE-A2MP TCGA-EE-A2MQ 
       21.67       129.27        61.51       103.20       248.65        43.23 
TCGA-EE-A3AA TCGA-EE-A3AE TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH 
      124.31        54.51        64.08        34.32       201.80       109.58 
TCGA-ER-A193 TCGA-ER-A19C TCGA-ER-A19L TCGA-ER-A19S TCGA-FR-A729 TCGA-FR-A7U9 
       31.40        48.89       131.51        37.25       220.80        18.77 
TCGA-FR-A8YC TCGA-FS-A1Z4 TCGA-FS-A1ZH TCGA-FS-A1ZQ TCGA-FS-A1ZT TCGA-FS-A1ZW 
       34.82        28.08        32.75       133.55        53.16        49.48 
TCGA-FS-A1ZY TCGA-FS-A4F2 TCGA-FS-A4F9 TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-GN-A267 
       27.09        50.14        34.03         0.20        22.92        64.44 
TCGA-QB-AA9O TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-YG-AA3O TCGA-Z2-AA3V 
       18.05        32.58        49.51        12.16        37.94        15.98 

$`17Q LOSS WILD-TYPE`
TCGA-3N-A9WC TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 
       66.48        14.93        16.57        16.67       112.04       112.57 
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB 
       71.80       133.25        28.08        31.59        90.90        95.74 
TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC 
      103.10        65.49        23.77       115.53       168.00        86.76 
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JP 
       27.65        62.07        42.08        12.10       171.58        59.57 
TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC 
      130.72        58.06        46.98        46.32       166.52        86.93 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU 
       60.23        24.53        13.87         9.34       103.59        39.75 
TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K 
       45.30       174.84        55.73        56.35       145.12        32.94 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR 
       63.81        26.89       125.79       135.75       137.92       178.32 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GE 
       18.18       125.19        30.84        79.59        23.61        26.43 
TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GP 
      241.38       170.20        89.13       107.15       161.00       152.75 
TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX 
       29.06       129.63       117.17        54.67         3.65         7.10 
TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EG 
       18.12        15.39        22.29        18.44         9.90        22.95 
TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I4 TCGA-DA-A1I7 
       48.89       117.21        20.38       194.83        35.93        61.18 
TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 
       65.92        23.44        68.09        28.60        10.49       215.44 
TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH 
       15.68        13.87        10.36        20.35        68.25        54.02 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y 
       17.29        52.01         7.04        24.89        29.82        27.22 
TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 
        8.65        33.73        14.70        26.89        68.15         4.96 
TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A 
      133.81       151.27        91.56       168.26        13.55        63.35 
TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M 
       85.08        13.97        72.07        64.64         2.60        56.84 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T 
       18.61        56.42        66.74        14.47        61.28       369.93 
TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 
       25.87       195.02        46.82       102.90        36.82        86.14 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ 
       59.28        67.43       340.14       161.03       208.04       107.38 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GR 
       54.74        79.66        75.48       102.12       126.81        42.77 
TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MD TCGA-EE-A2ME 
       81.21        94.82        28.83        19.76        47.28       103.27 
TCGA-EE-A2MF TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML 
      268.73        16.96       204.66        96.23       158.63       216.66 
TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU 
      167.90        47.54       134.40       162.48        71.21        53.26 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH 
      122.73        51.62        28.77        13.81        41.59       138.81 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE 
      172.18       127.20        36.95        53.19        27.35        51.35 
TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A 
      152.81        35.44        13.94        50.76         9.17        77.75 
TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H 
       98.40        12.59        13.02        26.37       268.93       152.35 
TCGA-ER-A19J TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19T 
        6.44        61.05        44.05       162.08        50.89         8.88 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF 
      148.18        79.99        43.82        23.34        20.15        16.37 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL 
       31.27        32.05       247.04        80.32        46.98        33.21 
TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A7UA 
        6.77        92.98       174.21        15.72        27.85        38.27 
TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
       36.26       104.42       216.92        48.59       228.59       202.65 
TCGA-FS-A1Z3 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD 
       20.91         7.79        27.72        48.85       357.37        53.52 
TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM 
       40.27        15.45         9.70        47.38        23.93       101.26 
TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZZ TCGA-FS-A4F0 
       74.73        11.41       148.80        26.56        27.02        77.82 
TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD 
       66.67        28.73       174.84        26.73        54.41        80.68 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 
       55.59        13.51        19.30         9.90         7.23         2.04 
TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A268 
       15.78       139.89       117.93        84.72        10.13        62.79 
TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 
       32.48        39.58       121.91        39.35        10.42        48.89 
TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A8LL TCGA-GN-A9SD TCGA-HR-A2OG TCGA-HR-A2OH 
       22.13        50.10        21.37        59.41         0.23        65.88 
TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 
      368.78       297.90         7.23         0.33         0.69       228.16 
TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1V 
       63.02       121.08         4.01        69.07       111.09        42.08 
TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8K6 
      219.16       105.04        24.03        49.05        61.15        15.98 
TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-AAA0 
       98.89        58.98        67.63        59.77        11.80        35.01 
TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YD-A89C TCGA-YD-A9TA TCGA-YG-AA3P TCGA-Z2-A8RT 
       19.73        22.29         6.90        49.18        14.43        27.58 
TCGA-Z2-AA3S 
       96.99 

  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
              0.20               0.23 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
            248.65             369.93 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
            48.805             53.190 
[1] "0.2 - 248.7 (48.8)" "0.2 - 369.9 (53.2)"
[1] "hr=" "1.2"
D72V3, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  17Q LOSS MUTATED                   10             2
  17Q LOSS WILD-TYPE                 55             3
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  17Q LOSS MUTATED                                          10
  17Q LOSS WILD-TYPE                                        62
                    vv
clus                 REGIONAL LYMPH NODE
  17Q LOSS MUTATED                    42
  17Q LOSS WILD-TYPE                 173
D72V4, multiclass
                                           clus
vv                                          17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  DISTANT METASTASIS                                      10                 55
  PRIMARY TUMOR                                            2                  3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               10                 62
  REGIONAL LYMPH NODE                                     42                173
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  17Q LOSS MUTATED             3       1       9        5        4        0
  17Q LOSS WILD-TYPE           9       6      19       13       23       24
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  17Q LOSS MUTATED           2         4         1         6          6
  17Q LOSS WILD-TYPE        12        15        11        31          9
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  17Q LOSS MUTATED            5          9        4
  17Q LOSS WILD-TYPE         27         51       16
D72V5, multiclass
             clus
vv            17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  I OR II NOS                3                  9
  STAGE 0                    1                  6
  STAGE I                    9                 19
  STAGE IA                   5                 13
  STAGE IB                   4                 23
  STAGE II                   0                 24
  STAGE IIA                  2                 12
  STAGE IIB                  4                 15
  STAGE IIC                  1                 11
  STAGE III                  6                 31
  STAGE IIIA                 6                  9
  STAGE IIIB                 5                 27
  STAGE IIIC                 9                 51
  STAGE IV                   4                 16
[1] 14  2
[1] TRUE
[1] "dimension of contingency 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      13 15 13 11
  17Q LOSS WILD-TYPE    51 57 64 57
D72V6, multiclass
       clus
vv      17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  T0+T1               13                 51
  T2                  15                 57
  T3                  13                 64
  T4                  11                 57
[1] 4 2
[1] TRUE
[1] "dimension of 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    29  14   5   9
  17Q LOSS WILD-TYPE 140  49  33  40
D72V7, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  N0               29                140
  N1               14                 49
  N2                5                 33
  N3                9                 40
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V8, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED    55   5
  17Q LOSS WILD-TYPE 258  16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     55    5
  17Q LOSS WILD-TYPE  258   16
   clus
vv  17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  0               55                258
  1                5                 16
[1] 2 2
[1] FALSE
D72V9, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED    30  14
  17Q LOSS WILD-TYPE 102  74
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     30   14
  17Q LOSS WILD-TYPE  102   74
     clus
vv    17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  NO                30                102
  YES               14                 74
[1] 2 2
[1] FALSE
D72V10, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED     7  57
  17Q LOSS WILD-TYPE  37 256
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      7   57
  17Q LOSS WILD-TYPE   37  256
     clus
vv    17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  NO                 7                 37
  YES               57                256
[1] 2 2
[1] FALSE
D72V11, continuous
D72V12, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED    21  43
  17Q LOSS WILD-TYPE 114 180
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     21   43
  17Q LOSS WILD-TYPE  114  180
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  FEMALE               21                114
  MALE                 43                180
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  17Q LOSS MUTATED       0                         0    63
  17Q LOSS WILD-TYPE     5                         1   281
D72V13, multiclass
                           clus
vv                          17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  ASIAN                                    0                  5
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   63                281
[1] 3 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     1  63
  17Q LOSS WILD-TYPE   6 281
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      1   63
  17Q LOSS WILD-TYPE    6  281
                        clus
vv                       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO               63                281
[1] 2 2
[1] FALSE

Clustering(73) Variable = 18P LOSS MUTATION ANALYSIS
D73V1, survival
                    sevent
clus2                 0  1
  18P LOSS MUTATED   36 36
  18P LOSS WILD-TYPE 85 82
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                72                167 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                36                 82 
$`18P LOSS MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q6 TCGA-D3-A2J7 TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JL 
        8.42        49.35        45.99        86.30         7.27       171.58 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3MR TCGA-D3-A3MU 
       66.08        43.53        58.06        46.98        90.21        23.67 
TCGA-D3-A51J TCGA-D3-A5GL TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D3-A8GC TCGA-D3-A8GD 
      144.46        42.05       177.86       124.08        78.21        23.61 
TCGA-D3-A8GR TCGA-D9-A1X3 TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1I2 TCGA-DA-A1I7 
       36.53        10.78        22.85        48.66       150.61        32.42 
TCGA-DA-A3F5 TCGA-EB-A5SG TCGA-EB-A5UN TCGA-EE-A20C TCGA-EE-A29D TCGA-EE-A29G 
      214.59        33.24        45.50        75.55        12.99        44.28 
TCGA-EE-A29M TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GP 
       47.74       346.49       185.19       239.11         0.20         0.76 
TCGA-EE-A2GR TCGA-EE-A2MG TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MS TCGA-EE-A2MU 
        0.20        94.19        67.50       145.45       143.93        53.26 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3J3 TCGA-EE-A3J8 
      124.31       122.73         4.41        54.51        67.89         3.35 
TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19H 
      152.81        14.56         7.82        53.29        39.81       150.12 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-FR-A44A TCGA-FR-A7U8 TCGA-FS-A1ZM TCGA-FS-A1ZQ 
       49.71        34.95       174.21        26.20        78.61       130.95 
TCGA-FS-A1ZS TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FW-A3TU TCGA-GN-A268 TCGA-GN-A8LK 
      136.27        23.21         5.29        55.59        42.48        43.23 
TCGA-GN-A9SD TCGA-W3-A825 TCGA-WE-A8K1 TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-YG-AA3O 
       59.41         1.97         1.15        48.39         1.94        28.21 

$`18P LOSS WILD-TYPE`
TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 
       60.46        12.99        14.83        15.72        31.89       110.93 
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J8 
      133.25        19.04        76.41        62.60        25.64        62.86 
TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JE TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JN 
       15.75       168.00         9.76       107.61        36.30        64.83 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO 
      140.98        40.01        59.70        16.96        13.87         9.34 
TCGA-D3-A51E TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A8GJ 
      173.85        31.76        62.70        11.34        45.70       179.97 
TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GP TCGA-D9-A3Z1 TCGA-D9-A3Z3 
      120.00        69.53        70.62       135.12        15.02        16.90 
TCGA-D9-A4Z6 TCGA-D9-A6EC TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I5 TCGA-DA-A1IA 
       18.44        57.90       106.85        31.96        82.85        64.83 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5SH TCGA-EB-A6L9 
       58.85        25.12        14.96         3.91        50.07         6.64 
TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A184 
       13.15        24.89        62.37        20.38         0.00        67.50 
TCGA-EE-A20H TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29P 
      155.90        75.22        76.14         0.26        63.12        27.16 
TCGA-EE-A29Q TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GH 
       61.12       102.38         7.20        77.98        26.14       189.40 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO 
       68.65        10.62        32.48        18.35        31.00       118.32 
TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC 
       71.31        81.99       103.13        15.25         5.75        23.77 
TCGA-EE-A2MF TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MP TCGA-EE-A2MR 
      209.79       171.85        63.25       104.78       227.01        25.08 
TCGA-EE-A2MT TCGA-EE-A3AC TCGA-EE-A3AF TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3JB 
       23.51        51.62         6.28       111.85        45.90       201.80 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19D TCGA-ER-A19G 
       34.45         1.58        47.31         4.54        11.47       151.46 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19W TCGA-ER-A1A1 
       99.06        59.84        42.48       120.76       146.63        47.97 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET 
       22.36         4.70        16.87        10.95       173.29        55.82 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A729 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FS-A1YW 
       15.48        32.05       209.23         5.65        10.06       171.78 
TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD 
       49.74       195.98         8.35        27.62       312.07        32.78 
TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZT TCGA-FS-A1ZU 
       35.90        12.92         7.82        36.33        35.28         4.47 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FD 
        3.06        30.90        66.67       173.19        13.28        80.68 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 
       11.54        19.30         9.90         6.05         1.91        53.29 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 
      117.93        84.72        17.06         7.59       120.53        34.49 
TCGA-GN-A4U8 TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 
       46.92        85.05       297.01         7.23        18.05         0.33 
TCGA-W3-A824 TCGA-W3-A828 TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1V TCGA-W3-AA1W 
      174.12       120.07        44.05        79.99         8.09       185.13 
TCGA-W3-AA21 TCGA-WE-A8K5 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ 
       92.84        59.64        62.99        12.69        19.00        59.44 
TCGA-WE-A8ZT TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-Z2-AA3S 
       10.95        26.60        16.64        15.65        91.23 

  18P LOSS MUTATED 18P LOSS WILD-TYPE 
               0.2                0.0 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
            346.49             312.07 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
            48.525             42.480 
[1] "0.2 - 346.5 (48.5)" "0.0 - 312.1 (42.5)"
[1] "hr=" "1.1"
D73V2, survival
                    sevent
clus2                  0   1
  18P LOSS MUTATED    46  53
  18P LOSS WILD-TYPE 123 127
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                99                250 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                53                127 
$`18P LOSS MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q6 TCGA-D3-A2J7 TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF 
       16.57        71.80       103.10        86.76        11.87        62.07 
TCGA-D3-A2JL TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3MR 
      171.58        66.08        59.57        58.06        46.98       103.59 
TCGA-D3-A3MU TCGA-D3-A51J TCGA-D3-A5GL TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D3-A8GC 
       39.75       145.12       125.79       178.32       125.19        79.59 
TCGA-D3-A8GD TCGA-D3-A8GI TCGA-D3-A8GN TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A1JX 
       23.61        58.52       161.00       129.63       117.17         7.10 
TCGA-D9-A1X3 TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1I2 TCGA-DA-A1I7 TCGA-DA-A1I8 
       18.12        22.95        48.89       176.55        61.18        53.92 
TCGA-DA-A3F5 TCGA-EB-A5SG TCGA-EB-A5UN TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A29A 
      215.44        68.25        52.01       133.81       151.27        63.35 
TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29M TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W 
       13.97        72.07        56.84       369.93        25.87       195.02 
TCGA-EE-A29X TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GP 
       17.92        67.43       340.14       161.03        48.72        13.91 
TCGA-EE-A2GR TCGA-EE-A2MG TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MQ TCGA-EE-A2MS 
       42.77       103.20       158.63       167.90        43.23       162.48 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AG 
       53.26       124.31       122.73        28.77        54.51        41.59 
TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JH TCGA-EE-A3JI 
      138.81       172.18        34.32        53.19       109.58       152.81 
TCGA-ER-A193 TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19E TCGA-ER-A19H 
       31.40         9.17        98.40        48.89        13.02       152.35 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A42K TCGA-FR-A44A TCGA-FR-A69P 
       50.89        37.25         8.88         6.77       174.21        15.72 
TCGA-FR-A7U8 TCGA-FS-A1ZA TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS 
       27.85        27.72       101.26       133.55        11.41       148.80 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FW-A3TU TCGA-GN-A268 TCGA-GN-A4U9 TCGA-GN-A8LK 
       49.48        27.09        55.59        62.79        22.13        50.10 
TCGA-GN-A8LL TCGA-GN-A9SD TCGA-W3-A825 TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8ZY 
       21.37        59.41        63.02        24.03        49.05        49.51 
TCGA-WE-AA9Y TCGA-YG-AA3O TCGA-Z2-A8RT 
       12.16        37.94        27.58 

$`18P LOSS WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
       17.03        66.48        12.99        14.93        16.67       112.04 
TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB 
      112.57       133.25        28.08        31.59        90.90        95.74 
TCGA-D3-A2J6 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JE 
       43.43        65.49        23.77       115.53       168.00        27.65 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JN TCGA-D3-A3BZ TCGA-D3-A3C8 
      113.52        42.08        12.10        66.48       130.72        46.32 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO 
      166.52        86.93        60.23        24.53        13.87         9.34 
TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51K TCGA-D3-A51N 
       45.30       174.84        55.73        56.35        32.94        22.62 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GS TCGA-D3-A8GB 
       63.81        26.89       135.75       137.92        18.18        30.84 
TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GP 
       26.43       241.38       170.20        89.13       107.15       152.75 
TCGA-D3-A8GQ TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       29.06       151.53        54.67         3.65        15.39        22.29 
TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HW TCGA-DA-A1HY 
       18.44         9.90        25.18        66.25        36.03       117.21 
TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1IA TCGA-DA-A1IB 
       20.38       194.83        35.93       107.34        65.92        23.44 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R 
       68.09        28.60        10.49        15.68        13.87        10.36 
TCGA-EB-A5KH TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X 
       20.35        54.02        17.29         7.04        24.89        29.82 
TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
       27.22         8.65        94.98        33.73        14.70        26.89 
TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29B 
       68.15         4.96        91.56       168.26        13.55        85.08 
TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P 
       78.97        63.78        64.64         2.60        18.61        56.42 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
       66.74        14.47        61.28        46.82       102.90        36.82 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK 
       39.29        86.14        59.28       208.04       107.38        54.74 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GS TCGA-EE-A2GT 
       79.66        75.48       102.12       126.81        81.21        44.88 
TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC 
       94.82        21.67       129.27        28.83        19.76        61.51 
TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ 
       47.28       103.27       268.73        16.96       204.66        96.23 
TCGA-EE-A2ML TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A3AC 
      216.66        47.54       248.65       134.40        71.21        51.62 
TCGA-EE-A3AF TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3JB TCGA-EE-A3JD 
       13.81       127.20        36.95        64.08       201.80        27.35 
TCGA-EE-A3JE TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19D 
       51.35        35.44        13.94        50.76        77.75        12.59 
TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
       26.37       268.93         6.44       131.51        61.05        44.05 
TCGA-ER-A19P TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
      162.08       148.18        79.99        43.82        23.34        20.15 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
       16.37        31.27        32.05       247.04        80.32        46.98 
TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A729 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC 
       33.21        92.98       220.80        18.77        38.27        34.82 
TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
       36.26       104.42       216.92        48.59       228.59       202.65 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD 
       20.91        28.08         7.79        48.85       357.37        53.52 
TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK 
       40.27        15.45         9.70        32.75        47.38        23.93 
TCGA-FS-A1ZP TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 
       74.73        53.16        26.56        27.02        77.82        50.14 
TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC 
       66.67        28.73       174.84        34.03        26.73        54.41 
TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
       80.68         0.20        22.92        13.51        19.30         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        7.23         2.04        15.78       139.89       117.93        84.72 
TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A4U4 
       10.13        64.44        32.48        39.58       121.91        39.35 
TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-HR-A2OG TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X 
       10.42        48.89         0.23        65.88       368.78       297.90 
TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A828 
        7.23        18.05         0.33         0.69       228.16       121.08 
TCGA-W3-AA1O TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 
        4.01        69.07       111.09        42.08       219.16       105.04 
TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ 
       61.15        15.98        98.89        58.98        67.63        59.77 
TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YD-A89C 
       11.80        32.58        35.01        19.73        22.29         6.90 
TCGA-YD-A9TA TCGA-YG-AA3P TCGA-Z2-AA3S TCGA-Z2-AA3V 
       49.18        14.43        96.99        15.98 

  18P LOSS MUTATED 18P LOSS WILD-TYPE 
              6.77               0.20 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
            369.93             368.78 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
             58.06              47.33 
[1] "6.8 - 369.9 (58.1)" "0.2 - 368.8 (47.3)"
[1] "hr=" "1.1"
D73V3, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  18P LOSS MUTATED                   18             1
  18P LOSS WILD-TYPE                 47             4
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  18P LOSS MUTATED                                          24
  18P LOSS WILD-TYPE                                        48
                    vv
clus                 REGIONAL LYMPH NODE
  18P LOSS MUTATED                    60
  18P LOSS WILD-TYPE                 155
D73V4, multiclass
                                           clus
vv                                          18P LOSS MUTATED 18P LOSS WILD-TYPE
  DISTANT METASTASIS                                      18                 47
  PRIMARY TUMOR                                            1                  4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               24                 48
  REGIONAL LYMPH NODE                                     60                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                 I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  18P LOSS MUTATED             5       3       7        6       10        7
  18P LOSS WILD-TYPE           7       4      21       12       17       17
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  18P LOSS MUTATED           1         6         2        12          6
  18P LOSS WILD-TYPE        13        13        10        25          9
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  18P LOSS MUTATED            6         19        2
  18P LOSS WILD-TYPE         26         41       18
D73V5, multiclass
             clus
vv            18P LOSS MUTATED 18P LOSS WILD-TYPE
  I OR II NOS                5                  7
  STAGE 0                    3                  4
  STAGE I                    7                 21
  STAGE IA                   6                 12
  STAGE IB                  10                 17
  STAGE II                   7                 17
  STAGE IIA                  1                 13
  STAGE IIB                  6                 13
  STAGE IIC                  2                 10
  STAGE III                 12                 25
  STAGE IIIA                 6                  9
  STAGE IIIB                 6                 26
  STAGE IIIC                19                 41
  STAGE IV                   2                 18
[1] 14  2
[1] TRUE
[1] "dimension of contingency 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      23 21 17 21
  18P LOSS WILD-TYPE    41 51 60 47
D73V6, multiclass
       clus
vv      18P LOSS MUTATED 18P LOSS WILD-TYPE
  T0+T1               23                 41
  T2                  21                 51
  T3                  17                 60
  T4                  21                 47
[1] 4 2
[1] TRUE
[1] "dimension of 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    45  16  13  15
  18P LOSS WILD-TYPE 124  47  25  34
D73V7, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  N0               45                124
  N1               16                 47
  N2               13                 25
  N3               15                 34
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V8, binary
                    cls
clus                   0   1
  18P LOSS MUTATED    93   2
  18P LOSS WILD-TYPE 220  19
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     93    2
  18P LOSS WILD-TYPE  220   19
   clus
vv  18P LOSS MUTATED 18P LOSS WILD-TYPE
  0               93                220
  1                2                 19
[1] 2 2
[1] FALSE
D73V9, binary
                    cls
clus                  0  1
  18P LOSS MUTATED   36 24
  18P LOSS WILD-TYPE 96 64
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     36   24
  18P LOSS WILD-TYPE   96   64
     clus
vv    18P LOSS MUTATED 18P LOSS WILD-TYPE
  NO                36                 96
  YES               24                 64
[1] 2 2
[1] FALSE
D73V10, binary
                    cls
clus                   0   1
  18P LOSS MUTATED    16  86
  18P LOSS WILD-TYPE  28 227
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     16   86
  18P LOSS WILD-TYPE   28  227
     clus
vv    18P LOSS MUTATED 18P LOSS WILD-TYPE
  NO                16                 28
  YES               86                227
[1] 2 2
[1] FALSE
D73V11, continuous
D73V12, binary
                    cls
clus                   0   1
  18P LOSS MUTATED    40  63
  18P LOSS WILD-TYPE  95 160
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     40   63
  18P LOSS WILD-TYPE   95  160
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  FEMALE               40                 95
  MALE                 63                160
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18P LOSS MUTATED       0                         0   101
  18P LOSS WILD-TYPE     5                         1   243
D73V13, multiclass
                           clus
vv                          18P LOSS MUTATED 18P LOSS WILD-TYPE
  ASIAN                                    0                  5
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                  101                243
[1] 3 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     2  99
  18P LOSS WILD-TYPE   5 245
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      2   99
  18P LOSS WILD-TYPE    5  245
                        clus
vv                       18P LOSS MUTATED 18P LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  5
  NOT HISPANIC OR LATINO               99                245
[1] 2 2
[1] FALSE

Clustering(74) Variable = 18Q LOSS MUTATION ANALYSIS
D74V1, survival
                    sevent
clus2                 0  1
  18Q LOSS MUTATED   34 38
  18Q LOSS WILD-TYPE 87 80
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                72                167 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                38                 80 
$`18Q LOSS MUTATED`
TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q6 TCGA-D3-A2J7 TCGA-D3-A2JC TCGA-D3-A2JD 
       14.83         8.42        49.35        45.99        86.30         7.27 
TCGA-D3-A2JL TCGA-D3-A2JO TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3MR TCGA-D3-A3MU 
      171.58        66.08        58.06        59.70        90.21        23.67 
TCGA-D3-A51J TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GR 
      144.46       177.86       124.08        78.21        23.61        36.53 
TCGA-D9-A1X3 TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1I2 TCGA-DA-A1I7 TCGA-DA-A1IA 
       10.78        57.90        48.66       150.61        32.42        64.83 
TCGA-DA-A3F5 TCGA-EB-A5SG TCGA-EB-A5UN TCGA-EE-A20C TCGA-EE-A29D TCGA-EE-A29G 
      214.59        33.24        45.50        75.55        12.99        44.28 
TCGA-EE-A29M TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GP 
       47.74       346.49       185.19       239.11         0.20         0.76 
TCGA-EE-A2GR TCGA-EE-A2MG TCGA-EE-A2MK TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB 
        0.20        94.19        67.50        53.26       124.31       122.73 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3J3 TCGA-EE-A3J8 TCGA-EE-A3JI TCGA-ER-A193 
        4.41        54.51        67.89         3.35       152.81        14.56 
TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19H TCGA-ER-A19S TCGA-ER-A19W 
        7.82        53.29        39.81       150.12        34.95       146.63 
TCGA-ER-A3EV TCGA-FR-A44A TCGA-FR-A7U8 TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS 
       15.48       174.21        26.20        78.61       130.95       136.27 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FW-A3TU TCGA-GN-A268 TCGA-GN-A8LK TCGA-GN-A9SD 
       23.21         5.29        55.59        42.48        43.23        59.41 
TCGA-W3-A825 TCGA-W3-AA1V TCGA-WE-A8K1 TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-YG-AA3O 
        1.97         8.09         1.15        48.39         1.94        28.21 

$`18Q LOSS WILD-TYPE`
TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q7 
       60.46        12.99        15.72        31.89       110.93       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J8 TCGA-D3-A2JA 
       19.04        76.41        62.60        25.64        62.86        15.75 
TCGA-D3-A2JB TCGA-D3-A2JE TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JN TCGA-D3-A2JP 
      168.00         9.76       107.61        36.30        64.83        43.53 
TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO 
       46.98       140.98        40.01        16.96        13.87         9.34 
TCGA-D3-A51E TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN 
      173.85        31.76        62.70        11.34        42.05        45.70 
TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GP TCGA-D9-A3Z1 
      179.97       120.00        69.53        70.62       135.12        15.02 
TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6EG TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I5 
       16.90        18.44        22.85       106.85        31.96        82.85 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5SH TCGA-EB-A6L9 
       58.85        25.12        14.96         3.91        50.07         6.64 
TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A184 
       13.15        24.89        62.37        20.38         0.00        67.50 
TCGA-EE-A20H TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29P 
      155.90        75.22        76.14         0.26        63.12        27.16 
TCGA-EE-A29Q TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GH 
       61.12       102.38         7.20        77.98        26.14       189.40 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO 
       68.65        10.62        32.48        18.35        31.00       118.32 
TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC 
       71.31        81.99       103.13        15.25         5.75        23.77 
TCGA-EE-A2MF TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP 
      209.79       171.85        63.25       104.78       145.45       227.01 
TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AC TCGA-EE-A3AF TCGA-EE-A3J4 
       25.08       143.93        23.51        51.62         6.28       111.85 
TCGA-EE-A3J7 TCGA-EE-A3JB TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A19A 
       45.90       201.80        34.45         1.58        47.31         4.54 
TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P 
       11.47       151.46        99.06        59.84        42.48       120.76 
TCGA-ER-A19Q TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NG 
       49.71        47.97        22.36         4.70        16.87        10.95 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3PL TCGA-FR-A729 TCGA-FR-A7UA TCGA-FR-A8YC 
      173.29        55.82        32.05       209.23         5.65        10.06 
TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZC 
      171.78        49.74       195.98         8.35        27.62       312.07 
TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZT 
       32.78        35.90        12.92         7.82        36.33        35.28 
TCGA-FS-A1ZU TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 
        4.47         3.06        30.90        66.67       173.19        13.28 
TCGA-FS-A4FD TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 
       80.68        11.54        19.30         9.90         6.05         1.91 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A4U3 
       53.29       117.93        84.72        17.06         7.59       120.53 
TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O 
       34.49        46.92        85.05       297.01         7.23        18.05 
TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A828 TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1W 
        0.33       174.12       120.07        44.05        79.99       185.13 
TCGA-W3-AA21 TCGA-WE-A8K5 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ 
       92.84        59.64        62.99        12.69        19.00        59.44 
TCGA-WE-A8ZT TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-Z2-AA3S 
       10.95        26.60        16.64        15.65        91.23 

  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               0.2                0.0 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
            346.49             312.07 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
            49.005             43.530 
[1] "0.2 - 346.5 (49.0)" "0.0 - 312.1 (43.5)"
[1] "hr=" "1"  
D74V2, survival
                    sevent
clus2                  0   1
  18Q LOSS MUTATED    42  51
  18Q LOSS WILD-TYPE 127 129
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                93                256 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                51                129 
$`18Q LOSS MUTATED`
TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q6 TCGA-D3-A1Q9 TCGA-D3-A2J7 TCGA-D3-A2JC 
       14.93        16.57        71.80        31.59       103.10        86.76 
TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JL TCGA-D3-A2JO TCGA-D3-A3C6 TCGA-D3-A3CE 
       11.87        62.07       171.58        66.08        58.06        60.23 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51J TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D3-A8GC 
      103.59        39.75       145.12       178.32       125.19        79.59 
TCGA-D3-A8GD TCGA-D3-A8GI TCGA-D3-A8GN TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A148 
       23.61        58.52       161.00       129.63       117.17       151.53 
TCGA-D9-A1X3 TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1I2 TCGA-DA-A1I7 TCGA-DA-A1I8 
       18.12        66.25        48.89       176.55        61.18        53.92 
TCGA-DA-A1IA TCGA-DA-A3F5 TCGA-EB-A5SG TCGA-EB-A5UN TCGA-EE-A20B TCGA-EE-A20C 
       65.92       215.44        68.25        52.01       133.81       151.27 
TCGA-EE-A29A TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29M TCGA-EE-A29T TCGA-EE-A29V 
       63.35        13.97        72.07        56.84       369.93        25.87 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GI 
      195.02        17.92        67.43       340.14       161.03        48.72 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2MG TCGA-EE-A2MK TCGA-EE-A2MQ TCGA-EE-A2MU 
       13.91        42.77       103.20       158.63        43.23        53.26 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AH TCGA-EE-A3J3 
      124.31       122.73        28.77        54.51       138.81       172.18 
TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A199 
       34.32        53.19       109.58       152.81        31.40         9.17 
TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19H TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W 
       98.40        48.89       152.35        37.25         8.88       148.18 
TCGA-ER-A3EV TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FS-A1ZM TCGA-FS-A1ZQ 
       46.98       174.21        15.72        27.85       101.26       133.55 
TCGA-FS-A1ZS TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FW-A3TU TCGA-GN-A268 TCGA-GN-A4U9 
      148.80        49.48        27.09        55.59        62.79        22.13 
TCGA-GN-A8LK TCGA-GN-A8LL TCGA-GN-A9SD TCGA-W3-A825 TCGA-W3-AA1V TCGA-WE-A8K1 
       50.10        21.37        59.41        63.02        42.08        49.05 
TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-YG-AA3O 
       49.51        12.16        37.94 

$`18Q LOSS WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 
       17.03        66.48        12.99        16.67       112.04       112.57 
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J8 
      133.25        28.08        90.90        95.74        43.43        65.49 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JE TCGA-D3-A2JG TCGA-D3-A2JH 
       23.77       115.53       168.00        27.65       113.52        42.08 
TCGA-D3-A2JK TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3C8 
       12.10        66.48        59.57       130.72        46.98        46.32 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MV 
      166.52        86.93        24.53        13.87         9.34        45.30 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R 
      174.84        55.73        56.35        32.94        22.62        63.81 
TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GS TCGA-D3-A8GB 
       26.89       125.79       135.75       137.92        18.18        30.84 
TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GP 
       26.43       241.38       170.20        89.13       107.15       152.75 
TCGA-D3-A8GQ TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       29.06        54.67         3.65         7.10        15.39        22.29 
TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EG TCGA-DA-A1HW TCGA-DA-A1HY 
       18.44         9.90        25.18        22.95        36.03       117.21 
TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1IB TCGA-DA-A1IC 
       20.38       194.83        35.93       107.34        23.44        68.09 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH 
       28.60        10.49        15.68        13.87        10.36        20.35 
TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y 
       54.02        17.29         7.04        24.89        29.82        27.22 
TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 
        8.65        94.98        33.73        14.70        26.89        68.15 
TCGA-EE-A185 TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29B TCGA-EE-A29C 
        4.96        91.56       168.26        13.55        85.08        78.97 
TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
       63.78        64.64         2.60        18.61        56.42        66.74 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 
       14.47        61.28        46.82       102.90        36.82        39.29 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
       86.14        59.28       208.04       107.38        54.74        79.66 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU 
       75.48       102.12       126.81        81.21        44.88        94.82 
TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD 
       21.67       129.27        28.83        19.76        61.51        47.28 
TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2ML 
      103.27       268.73        16.96       204.66        96.23       216.66 
TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT 
      167.90        47.54       248.65       134.40       162.48        71.21 
TCGA-EE-A3AC TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 
       51.62        13.81        41.59       127.20        36.95        64.08 
TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
      201.80        27.35        51.35        35.44        13.94        50.76 
TCGA-ER-A19A TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19J 
       77.75        12.59        13.02        26.37       268.93         6.44 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A1A1 
      131.51        61.05        44.05       162.08        50.89        79.99 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH 
       43.82        23.34        20.15        16.37        31.27        32.05 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A729 
      247.04        80.32        33.21         6.77        92.98       220.80 
TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW 
       18.77        38.27        34.82        36.26       104.42       216.92 
TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 
       48.59       228.59       202.65        20.91        28.08         7.79 
TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF 
       27.72        48.85       357.37        53.52        40.27        15.45 
TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZR 
        9.70        32.75        47.38        23.93        74.73        11.41 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 
       53.16        26.56        27.02        77.82        50.14        66.67 
TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD 
       28.73       174.84        34.03        26.73        54.41        80.68 
TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
        0.20        22.92        13.51        19.30         9.90         7.23 
TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 
        2.04        15.78       139.89       117.93        84.72        10.13 
TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 
       64.44        32.48        39.58       121.91        39.35        10.42 
TCGA-GN-A4U8 TCGA-HR-A2OG TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS 
       48.89         0.23        65.88       368.78       297.90         7.23 
TCGA-QB-AA9O TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A828 TCGA-W3-AA1O 
       18.05         0.33         0.69       228.16       121.08         4.01 
TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K5 
       69.07       111.09       219.16       105.04        24.03        61.15 
TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT 
       15.98        98.89        58.98        67.63        59.77        11.80 
TCGA-WE-A8ZX TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YD-A89C TCGA-YD-A9TA 
       32.58        35.01        19.73        22.29         6.90        49.18 
TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
       14.43        27.58        96.99        15.98 

  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
              8.88               0.20 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
            369.93             368.78 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
             61.18              46.57 
[1] "8.9 - 369.9 (61.2)" "0.2 - 368.8 (46.6)"
[1] "hr=" "1.1"
D74V3, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  18Q LOSS MUTATED                   20             2
  18Q LOSS WILD-TYPE                 45             3
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  18Q LOSS MUTATED                                          21
  18Q LOSS WILD-TYPE                                        51
                    vv
clus                 REGIONAL LYMPH NODE
  18Q LOSS MUTATED                    55
  18Q LOSS WILD-TYPE                 160
D74V4, multiclass
                                           clus
vv                                          18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  DISTANT METASTASIS                                      20                 45
  PRIMARY TUMOR                                            2                  3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               21                 51
  REGIONAL LYMPH NODE                                     55                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                 I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  18Q LOSS MUTATED             5       3       6        6        8        6
  18Q LOSS WILD-TYPE           7       4      22       12       19       18
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  18Q LOSS MUTATED           1         5         2        12          6
  18Q LOSS WILD-TYPE        13        14        10        25          9
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  18Q LOSS MUTATED            6         17        3
  18Q LOSS WILD-TYPE         26         43       17
D74V5, multiclass
             clus
vv            18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  I OR II NOS                5                  7
  STAGE 0                    3                  4
  STAGE I                    6                 22
  STAGE IA                   6                 12
  STAGE IB                   8                 19
  STAGE II                   6                 18
  STAGE IIA                  1                 13
  STAGE IIB                  5                 14
  STAGE IIC                  2                 10
  STAGE III                 12                 25
  STAGE IIIA                 6                  9
  STAGE IIIB                 6                 26
  STAGE IIIC                17                 43
  STAGE IV                   3                 17
[1] 14  2
[1] TRUE
[1] "dimension of contingency 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      21 18 17 20
  18Q LOSS WILD-TYPE    43 54 60 48
D74V6, multiclass
       clus
vv      18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  T0+T1               21                 43
  T2                  18                 54
  T3                  17                 60
  T4                  20                 48
[1] 4 2
[1] TRUE
[1] "dimension of 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    40  16  12  14
  18Q LOSS WILD-TYPE 129  47  26  35
D74V7, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  N0               40                129
  N1               16                 47
  N2               12                 26
  N3               14                 35
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V8, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED    84   4
  18Q LOSS WILD-TYPE 229  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     84    4
  18Q LOSS WILD-TYPE  229   17
   clus
vv  18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  0               84                229
  1                4                 17
[1] 2 2
[1] FALSE
D74V9, binary
                    cls
clus                  0  1
  18Q LOSS MUTATED   36 20
  18Q LOSS WILD-TYPE 96 68
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     36   20
  18Q LOSS WILD-TYPE   96   68
     clus
vv    18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  NO                36                 96
  YES               20                 68
[1] 2 2
[1] FALSE
D74V10, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED    14  84
  18Q LOSS WILD-TYPE  30 229
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     14   84
  18Q LOSS WILD-TYPE   30  229
     clus
vv    18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  NO                14                 30
  YES               84                229
[1] 2 2
[1] FALSE
D74V11, continuous
D74V12, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED    37  61
  18Q LOSS WILD-TYPE  98 162
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     37   61
  18Q LOSS WILD-TYPE   98  162
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  FEMALE               37                 98
  MALE                 61                162
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18Q LOSS MUTATED       0                         0    97
  18Q LOSS WILD-TYPE     5                         1   247
D74V13, multiclass
                           clus
vv                          18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  ASIAN                                    0                  5
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   97                247
[1] 3 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     2  95
  18Q LOSS WILD-TYPE   5 249
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      2   95
  18Q LOSS WILD-TYPE    5  249
                        clus
vv                       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  5
  NOT HISPANIC OR LATINO               95                249
[1] 2 2
[1] FALSE

Clustering(75) Variable = 19P LOSS MUTATION ANALYSIS
D75V1, survival
                    sevent
clus2                 0  1
  19P LOSS MUTATED   27 22
  19P LOSS WILD-TYPE 94 96
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                49                190 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                22                 96 
$`19P LOSS MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A2JD TCGA-D3-A2JL TCGA-D3-A3CE TCGA-D3-A3MU TCGA-D3-A51T 
        8.42         7.27       171.58        59.70        23.67        11.34 
TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A8GD TCGA-D3-A8GM TCGA-D3-A8GP TCGA-D9-A1X3 
       42.05        45.70        23.61        70.62       135.12        10.78 
TCGA-D9-A3Z3 TCGA-DA-A1HV TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-EE-A17X 
       16.90        48.66        82.85        32.42        64.83        13.15 
TCGA-EE-A20H TCGA-EE-A29D TCGA-EE-A29H TCGA-EE-A2GM TCGA-EE-A2MG TCGA-EE-A2MP 
      155.90        12.99        63.12        18.35        94.19       227.01 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AB TCGA-EE-A3AD TCGA-ER-A19B TCGA-ER-A19C 
      143.93        23.51       122.73         4.41        53.29        39.81 
TCGA-ER-A19Q TCGA-ER-A3EV TCGA-FR-A44A TCGA-FS-A1ZJ TCGA-FS-A1ZQ TCGA-FS-A1ZT 
       49.71        15.48       174.21        36.33       130.95        35.28 
TCGA-FS-A1ZW TCGA-FS-A4FD TCGA-FW-A3TV TCGA-GF-A4EO TCGA-GN-A262 TCGA-GN-A268 
       23.21        80.68        11.54         6.05        53.29        42.48 
TCGA-GN-A26A TCGA-GN-A4U3 TCGA-W3-A825 TCGA-W3-AA1R TCGA-W3-AA1V TCGA-WE-A8K1 
        7.59       120.53         1.97        79.99         8.09         1.15 
TCGA-WE-A8ZM 
       62.99 

$`19P LOSS WILD-TYPE`
TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 
       60.46        12.99        14.83        15.72        31.89       110.93 
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 
       49.35       133.25        19.04        76.41        62.60        25.64 
TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JE 
       45.99        62.86        15.75       168.00        86.30         9.76 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 
      107.61        36.30        64.83        66.08        43.53        58.06 
TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO 
       46.98       140.98        40.01        16.96        13.87         9.34 
TCGA-D3-A3MR TCGA-D3-A51E TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A5GR 
       90.21       173.85       144.46        31.76        62.70       177.86 
TCGA-D3-A5GU TCGA-D3-A8GC TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GR 
      124.08        78.21       179.97       120.00        69.53        36.53 
TCGA-D9-A3Z1 TCGA-D9-A4Z6 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HY TCGA-DA-A1I1 
       15.02        18.44        57.90        22.85       106.85        31.96 
TCGA-DA-A1I2 TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q 
      150.61        58.85        25.12       214.59        14.96         3.91 
TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17Y TCGA-EE-A180 
       33.24        50.07        45.50         6.64        24.89        62.37 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A184 TCGA-EE-A20C TCGA-EE-A29B TCGA-EE-A29C 
       20.38         0.00        67.50        75.55        75.22        76.14 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T 
        0.26        44.28        47.74        27.16        61.12       346.49 
TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD 
      185.19       102.38         7.20        77.98        26.14       239.11 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN 
        0.20       189.40        68.65        10.62        32.48        31.00 
TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 
      118.32         0.76         0.20        71.31        81.99       103.13 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MI TCGA-EE-A2MJ 
       15.25         5.75        23.77       209.79       171.85        63.25 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MR TCGA-EE-A2MU TCGA-EE-A3AA 
       67.50       104.78       145.45        25.08        53.26       124.31 
TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 
       51.62        54.51         6.28        67.89       111.85        45.90 
TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
        3.35       201.80       152.81        14.56        34.45         1.58 
TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19H 
       47.31         7.82         4.54        11.47       151.46       150.12 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19S TCGA-ER-A19W 
       99.06        59.84        42.48       120.76        34.95       146.63 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A3ES 
       47.97        22.36         4.70        16.87        10.95       173.29 
TCGA-ER-A3ET TCGA-ER-A3PL TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FR-A8YC 
       55.82        32.05       209.23        26.20         5.65        10.06 
TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZC 
      171.78        49.74       195.98         8.35        27.62       312.07 
TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZM TCGA-FS-A1ZS 
       32.78        35.90        12.92         7.82        78.61       136.27 
TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 
        4.47         5.29         3.06        30.90        66.67       173.19 
TCGA-FS-A4F9 TCGA-FW-A3TU TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GN-A264 
       13.28        55.59        19.30         9.90         1.91       117.93 
TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-GN-A8LK TCGA-GN-A9SD 
       84.72        17.06        34.49        46.92        43.23        59.41 
TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 TCGA-W3-A824 
       85.05       297.01         7.23        18.05         0.33       174.12 
TCGA-W3-A828 TCGA-W3-AA1Q TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K5 TCGA-WE-A8ZN 
      120.07        44.05       185.13        92.84        59.64        12.69 
TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 
       19.00        59.44        10.95        48.39         1.94        26.60 
TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-Z2-AA3S 
       16.64        15.65        28.21        91.23 

  19P LOSS MUTATED 19P LOSS WILD-TYPE 
              1.15               0.00 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
            227.01             346.49 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
            42.050             47.145 
[1] "1.1 - 227.0 (42.0)" "0.0 - 346.5 (47.1)"
[1] "hr=" "1"  
D75V2, survival
                    sevent
clus2                  0   1
  19P LOSS MUTATED    36  38
  19P LOSS WILD-TYPE 133 142
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                74                275 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                38                142 
$`19P LOSS MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q9 TCGA-D3-A2JD TCGA-D3-A2JL TCGA-D3-A3CE TCGA-D3-A3MU 
       16.57        31.59        11.87       171.58        60.23        39.75 
TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A8GD TCGA-D3-A8GM TCGA-D3-A8GN 
       26.89       125.79       135.75        23.61       107.15       161.00 
TCGA-D3-A8GP TCGA-D3-A8GS TCGA-D9-A148 TCGA-D9-A1X3 TCGA-D9-A3Z3 TCGA-D9-A6EA 
      152.75       117.17       151.53        18.12        22.29        25.18 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
       48.89        36.03        20.38       107.34        61.18        53.92 
TCGA-DA-A1IA TCGA-EB-A44R TCGA-EB-A5UL TCGA-EE-A17X TCGA-EE-A20H TCGA-EE-A20I 
       65.92        10.36        17.29        29.82       168.26        13.55 
TCGA-EE-A29D TCGA-EE-A29H TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2GM TCGA-EE-A2MG 
       13.97        64.64        17.92        46.82        75.48       103.20 
TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3J5 
      248.65       162.48        71.21       122.73        28.77        36.95 
TCGA-EE-A3JA TCGA-EE-A3JD TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19Q TCGA-ER-A19T 
       53.19        27.35        98.40        48.89        50.89         8.88 
TCGA-ER-A2NH TCGA-ER-A3EV TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1ZH TCGA-FS-A1ZJ 
       32.05        46.98       174.21        15.72        32.75        47.38 
TCGA-FS-A1ZQ TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A4FB TCGA-FS-A4FD TCGA-FW-A3TV 
      133.55        53.16        49.48        26.73        80.68        13.51 
TCGA-GF-A4EO TCGA-GN-A262 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U7 
        7.23       139.89        62.79        32.48       121.91        10.42 
TCGA-W3-A825 TCGA-W3-AA1R TCGA-W3-AA1V TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8ZM 
       63.02       111.09        42.08        24.03        49.05        98.89 
TCGA-YD-A9TA TCGA-YG-AA3P 
       49.18        14.43 

$`19P LOSS WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
       17.03        66.48        12.99        14.93        16.67       112.04 
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB 
      112.57        71.80       133.25        28.08        90.90        95.74 
TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB 
       43.43       103.10        65.49        23.77       115.53       168.00 
TCGA-D3-A2JC TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK 
       86.76        27.65        62.07       113.52        42.08        12.10 
TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 
       66.48        66.08        59.57       130.72        58.06        46.98 
TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO 
       46.32       166.52        86.93        24.53        13.87         9.34 
TCGA-D3-A3MR TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J 
      103.59        45.30       174.84        55.73        56.35       145.12 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       32.94        22.62        63.81       137.92       178.32        18.18 
TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GE TCGA-D3-A8GI TCGA-D3-A8GJ 
      125.19        30.84        79.59        26.43        58.52       241.38 
TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D9-A149 TCGA-D9-A1JW 
      170.20        89.13        29.06       129.63        54.67         3.65 
TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-D9-A6EG 
        7.10        15.39        18.44         9.90        66.25        22.95 
TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1IB TCGA-DA-A1IC 
      117.21       194.83       176.55        35.93        23.44        68.09 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH 
       28.60        10.49       215.44        15.68        13.87        20.35 
TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17Y 
       68.25        54.02        52.01         7.04        24.89        27.22 
TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 
        8.65        94.98        33.73        14.70        26.89        68.15 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29A TCGA-EE-A29B 
        4.96       133.81       151.27        91.56        63.35        85.08 
TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N 
       78.97        63.78        72.07         2.60        56.84        18.61 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V 
       56.42        66.74        14.47        61.28       369.93        25.87 
TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
      195.02       102.90        36.82        39.29        86.14        59.28 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       67.43       340.14       161.03       208.04        48.72       107.38 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR 
       54.74        79.66       102.12       126.81        13.91        42.77 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 
       81.21        44.88        94.82        21.67       129.27        28.83 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MH 
       19.76        61.51        47.28       103.27       268.73        16.96 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN 
      204.66        96.23       158.63       216.66       167.90        47.54 
TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AE 
       43.23       134.40        53.26       124.31        51.62        54.51 
TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 
       13.81        41.59       138.81       172.18       127.20        64.08 
TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 
       34.32       201.80        51.35       109.58       152.81        31.40 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19D 
       35.44        13.94        50.76         9.17        77.75        12.59 
TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L 
       13.02        26.37       268.93       152.35         6.44       131.51 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 
       61.05        44.05       162.08        37.25       148.18        79.99 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES 
       43.82        23.34        20.15        16.37        31.27       247.04 
TCGA-ER-A3ET TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A729 TCGA-FR-A7U8 
       80.32        33.21         6.77        92.98       220.80        27.85 
TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW 
       18.77        38.27        34.82        36.26       104.42       216.92 
TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 
       48.59       228.59       202.65        20.91        28.08         7.79 
TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF 
       27.72        48.85       357.37        53.52        40.27        15.45 
TCGA-FS-A1ZG TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZS 
        9.70        23.93       101.26        74.73        11.41       148.80 
TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 
       26.56        27.09        27.02        77.82        50.14        66.67 
TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A3I3 TCGA-FW-A3R5 
       28.73       174.84        34.03        54.41         0.20        22.92 
TCGA-FW-A3TU TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A264 
       55.59        19.30         9.90         2.04        15.78       117.93 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A26D TCGA-GN-A4U4 TCGA-GN-A4U8 
       84.72        10.13        64.44        39.58        39.35        48.89 
TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A8LL TCGA-GN-A9SD TCGA-HR-A2OG TCGA-HR-A2OH 
       22.13        50.10        21.37        59.41         0.23        65.88 
TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 TCGA-RP-A694 
      368.78       297.90         7.23        18.05         0.33         0.69 
TCGA-W3-A824 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1Q TCGA-W3-AA1W TCGA-W3-AA21 
      228.16       121.08         4.01        69.07       219.16       105.04 
TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT 
       61.15        15.98        58.98        67.63        59.77        11.80 
TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 
       32.58        49.51        12.16        35.01        19.73        22.29 
TCGA-YD-A89C TCGA-YG-AA3O TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
        6.90        37.94        27.58        96.99        15.98 

  19P LOSS MUTATED 19P LOSS WILD-TYPE 
              7.23               0.20 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
            248.65             369.93 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
             48.97              53.26 
[1] "7.2 - 248.7 (49.0)" "0.2 - 369.9 (53.3)"
[1] "hr=" "1.1"
D75V3, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  19P LOSS MUTATED                   14             2
  19P LOSS WILD-TYPE                 51             3
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  19P LOSS MUTATED                                          12
  19P LOSS WILD-TYPE                                        60
                    vv
clus                 REGIONAL LYMPH NODE
  19P LOSS MUTATED                    47
  19P LOSS WILD-TYPE                 168
D75V4, multiclass
                                           clus
vv                                          19P LOSS MUTATED 19P LOSS WILD-TYPE
  DISTANT METASTASIS                                      14                 51
  PRIMARY TUMOR                                            2                  3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               12                 60
  REGIONAL LYMPH NODE                                     47                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                 I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  19P LOSS MUTATED             4       0       7        2        4        5
  19P LOSS WILD-TYPE           8       7      21       16       23       19
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  19P LOSS MUTATED           1         3         1        12          2
  19P LOSS WILD-TYPE        13        16        11        25         13
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  19P LOSS MUTATED           10         13        5
  19P LOSS WILD-TYPE         22         47       15
D75V5, multiclass
             clus
vv            19P LOSS MUTATED 19P LOSS WILD-TYPE
  I OR II NOS                4                  8
  STAGE 0                    0                  7
  STAGE I                    7                 21
  STAGE IA                   2                 16
  STAGE IB                   4                 23
  STAGE II                   5                 19
  STAGE IIA                  1                 13
  STAGE IIB                  3                 16
  STAGE IIC                  1                 11
  STAGE III                 12                 25
  STAGE IIIA                 2                 13
  STAGE IIIB                10                 22
  STAGE IIIC                13                 47
  STAGE IV                   5                 15
[1] 14  2
[1] TRUE
[1] "dimension of contingency 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      14 17 14 16
  19P LOSS WILD-TYPE    50 55 63 52
D75V6, multiclass
       clus
vv      19P LOSS MUTATED 19P LOSS WILD-TYPE
  T0+T1               14                 50
  T2                  17                 55
  T3                  14                 63
  T4                  16                 52
[1] 4 2
[1] TRUE
[1] "dimension of 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    31  17  11  13
  19P LOSS WILD-TYPE 138  46  27  36
D75V7, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  N0               31                138
  N1               17                 46
  N2               11                 27
  N3               13                 36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V8, binary
                    cls
clus                   0   1
  19P LOSS MUTATED    65   6
  19P LOSS WILD-TYPE 248  15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED     65    6
  19P LOSS WILD-TYPE  248   15
   clus
vv  19P LOSS MUTATED 19P LOSS WILD-TYPE
  0               65                248
  1                6                 15
[1] 2 2
[1] FALSE
D75V9, binary
                    cls
clus                   0   1
  19P LOSS MUTATED    29  15
  19P LOSS WILD-TYPE 103  73
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED     29   15
  19P LOSS WILD-TYPE  103   73
     clus
vv    19P LOSS MUTATED 19P LOSS WILD-TYPE
  NO                29                103
  YES               15                 73
[1] 2 2
[1] FALSE
D75V10, binary
                    cls
clus                   0   1
  19P LOSS MUTATED     9  66
  19P LOSS WILD-TYPE  35 247
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      9   66
  19P LOSS WILD-TYPE   35  247
     clus
vv    19P LOSS MUTATED 19P LOSS WILD-TYPE
  NO                 9                 35
  YES               66                247
[1] 2 2
[1] FALSE
D75V11, continuous
D75V12, binary
                    cls
clus                   0   1
  19P LOSS MUTATED    33  42
  19P LOSS WILD-TYPE 102 181
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED     33   42
  19P LOSS WILD-TYPE  102  181
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  FEMALE               33                102
  MALE                 42                181
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  19P LOSS MUTATED       1                         0    72
  19P LOSS WILD-TYPE     4                         1   272
D75V13, multiclass
                           clus
vv                          19P LOSS MUTATED 19P LOSS WILD-TYPE
  ASIAN                                    1                  4
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   72                272
[1] 3 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     1  72
  19P LOSS WILD-TYPE   6 272
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      1   72
  19P LOSS WILD-TYPE    6  272
                        clus
vv                       19P LOSS MUTATED 19P LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO               72                272
[1] 2 2
[1] FALSE

Clustering(76) Variable = 19Q LOSS MUTATION ANALYSIS
D76V1, survival
                    sevent
clus2                 0  1
  19Q LOSS MUTATED   27 19
  19Q LOSS WILD-TYPE 94 99
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                46                193 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                19                 99 
$`19Q LOSS MUTATED`
TCGA-D3-A2JD TCGA-D3-A2JL TCGA-D3-A3MU TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN 
        7.27       171.58        23.67        11.34        42.05        45.70 
TCGA-D3-A8GM TCGA-D3-A8GP TCGA-D9-A1X3 TCGA-D9-A3Z3 TCGA-DA-A1HV TCGA-DA-A1I5 
       70.62       135.12        10.78        16.90        48.66        82.85 
TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-EE-A17X TCGA-EE-A20H TCGA-EE-A29D TCGA-EE-A29H 
       32.42        64.83        13.15       155.90        12.99        63.12 
TCGA-EE-A29M TCGA-EE-A2GO TCGA-EE-A2MG TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MS 
       47.74       118.32        94.19       145.45       227.01       143.93 
TCGA-EE-A2MT TCGA-EE-A3AB TCGA-EE-A3AD TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A3EV 
       23.51       122.73         4.41        53.29        39.81        15.48 
TCGA-FR-A44A TCGA-FS-A1ZJ TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A4FD TCGA-FW-A3TV 
      174.21        36.33        35.28        23.21        80.68        11.54 
TCGA-GF-A4EO TCGA-GN-A262 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-W3-A825 
        6.05        53.29        42.48         7.59       120.53         1.97 
TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8ZM 
       92.84         1.15        59.64        62.99 

$`19Q LOSS WILD-TYPE`
TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
       60.46        12.99        14.83         8.42        15.72        31.89 
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB 
      110.93        49.35       133.25        19.04        76.41        62.60 
TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC 
       25.64        45.99        62.86        15.75       168.00        86.30 
TCGA-D3-A2JE TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP 
        9.76       107.61        36.30        64.83        66.08        43.53 
TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF 
       58.06        46.98       140.98        40.01        59.70        16.96 
TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A51E TCGA-D3-A51J TCGA-D3-A51K 
       13.87         9.34        90.21       173.85       144.46        31.76 
TCGA-D3-A51R TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GJ 
       62.70       177.86       124.08        78.21        23.61       179.97 
TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GR TCGA-D9-A3Z1 TCGA-D9-A4Z6 TCGA-D9-A6EC 
      120.00        69.53        36.53        15.02        18.44        57.90 
TCGA-D9-A6EG TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1IC TCGA-DA-A3F2 
       22.85       106.85        31.96       150.61        58.85        25.12 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN 
      214.59        14.96         3.91        33.24        50.07        45.50 
TCGA-EB-A6L9 TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A184 
        6.64        24.89        62.37        20.38         0.00        67.50 
TCGA-EE-A20C TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29P 
       75.55        75.22        76.14         0.26        44.28        27.16 
TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 
       61.12       346.49       185.19       102.38         7.20        77.98 
TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK 
       26.14       239.11         0.20       189.40        68.65        10.62 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
       32.48        18.35        31.00         0.76         0.20        71.31 
TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MF 
       81.99       103.13        15.25         5.75        23.77       209.79 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MR TCGA-EE-A2MU 
      171.85        63.25        67.50       104.78        25.08        53.26 
TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 
      124.31        51.62        54.51         6.28        67.89       111.85 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 
       45.90         3.35       201.80       152.81        14.56        34.45 
TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19D TCGA-ER-A19G 
        1.58        47.31         7.82         4.54        11.47       151.46 
TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
      150.12        99.06        59.84        42.48       120.76        49.71 
TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
       34.95       146.63        47.97        22.36         4.70        16.87 
TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3PL TCGA-FR-A729 TCGA-FR-A7U8 
       10.95       173.29        55.82        32.05       209.23        26.20 
TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
        5.65        10.06       171.78        49.74       195.98         8.35 
TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG 
       27.62       312.07        32.78        35.90        12.92         7.82 
TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A1ZZ 
       78.61       130.95       136.27         4.47         5.29         3.06 
TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FW-A3TU TCGA-FW-A5DY 
       30.90        66.67       173.19        13.28        55.59        19.30 
TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A4U4 
        9.90         1.91       117.93        84.72        17.06        34.49 
TCGA-GN-A4U8 TCGA-GN-A8LK TCGA-GN-A9SD TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS 
       46.92        43.23        59.41        85.05       297.01         7.23 
TCGA-QB-AA9O TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A828 TCGA-W3-AA1Q TCGA-W3-AA1R 
       18.05         0.33       174.12       120.07        44.05        79.99 
TCGA-W3-AA1V TCGA-W3-AA1W TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT 
        8.09       185.13        12.69        19.00        59.44        10.95 
TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O 
       48.39         1.94        26.60        16.64        15.65        28.21 
TCGA-Z2-AA3S 
       91.23 

  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
              1.15               0.00 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
            227.01             346.49 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
             46.72              45.99 
[1] "1.1 - 227.0 (46.7)" "0.0 - 346.5 (46.0)"
[1] "hr=" "1.2"
D76V2, survival
                    sevent
clus2                  0   1
  19Q LOSS MUTATED    34  35
  19Q LOSS WILD-TYPE 135 145
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                69                280 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                35                145 
$`19Q LOSS MUTATED`
TCGA-D3-A1Q9 TCGA-D3-A2JD TCGA-D3-A2JL TCGA-D3-A3MU TCGA-D3-A51T TCGA-D3-A5GL 
       31.59        11.87       171.58        39.75        26.89       125.79 
TCGA-D3-A5GN TCGA-D3-A8GM TCGA-D3-A8GP TCGA-D3-A8GS TCGA-D9-A148 TCGA-D9-A1X3 
      135.75       107.15       152.75       117.17       151.53        18.12 
TCGA-D9-A3Z3 TCGA-D9-A6EA TCGA-DA-A1HV TCGA-DA-A1I0 TCGA-DA-A1I5 TCGA-DA-A1I7 
       22.29        25.18        48.89        20.38       107.34        61.18 
TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-EB-A44R TCGA-EE-A17X TCGA-EE-A20H TCGA-EE-A20I 
       53.92        65.92        10.36        29.82       168.26        13.55 
TCGA-EE-A29D TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29S TCGA-EE-A29X TCGA-EE-A2GO 
       13.97        64.64        56.84        61.28        17.92       126.81 
TCGA-EE-A2MG TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AB 
      103.20       167.90       248.65       162.48        71.21       122.73 
TCGA-EE-A3AD TCGA-EE-A3AG TCGA-EE-A3JA TCGA-EE-A3JD TCGA-ER-A19B TCGA-ER-A19C 
       28.77        41.59        53.19        27.35        98.40        48.89 
TCGA-ER-A19T TCGA-ER-A2NH TCGA-ER-A3EV TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1ZH 
        8.88        32.05        46.98       174.21        15.72        32.75 
TCGA-FS-A1ZJ TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A4F2 TCGA-FS-A4FB TCGA-FS-A4FD 
       47.38        53.16        49.48        50.14        26.73        80.68 
TCGA-FW-A3TV TCGA-GF-A4EO TCGA-GN-A262 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
       13.51         7.23       139.89        62.79        32.48        39.58 
TCGA-GN-A4U3 TCGA-GN-A4U7 TCGA-W3-A825 TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8K5 
      121.91        10.42        63.02       105.04        49.05        61.15 
TCGA-WE-A8ZM TCGA-YD-A9TA TCGA-YG-AA3P 
       98.89        49.18        14.43 

$`19Q LOSS WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q3 
       17.03        66.48        12.99        14.93        16.57        16.67 
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA 
      112.04       112.57        71.80       133.25        28.08        90.90 
TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA 
       95.74        43.43       103.10        65.49        23.77       115.53 
TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH 
      168.00        86.76        27.65        62.07       113.52        42.08 
TCGA-D3-A2JK TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 
       12.10        66.48        66.08        59.57       130.72        58.06 
TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF 
       46.98        46.32       166.52        86.93        60.23        24.53 
TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F 
       13.87         9.34       103.59        45.30       174.84        55.73 
TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A5GO 
       56.35       145.12        32.94        22.62        63.81       137.92 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GD 
      178.32        18.18       125.19        30.84        79.59        23.61 
TCGA-D3-A8GE TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GN 
       26.43        58.52       241.38       170.20        89.13       161.00 
TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 
       29.06       129.63        54.67         3.65         7.10        15.39 
TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HW TCGA-DA-A1HY 
       18.44         9.90        66.25        22.95        36.03       117.21 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
      194.83       176.55        35.93        23.44        68.09        28.60 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5SG 
       10.49       215.44        15.68        13.87        20.35        68.25 
TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17Y 
       54.02        17.29        52.01         7.04        24.89        27.22 
TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 
        8.65        94.98        33.73        14.70        26.89        68.15 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29A TCGA-EE-A29B 
        4.96       133.81       151.27        91.56        63.35        85.08 
TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P 
       78.97        63.78        72.07         2.60        18.61        56.42 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A2A0 
       66.74        14.47       369.93        25.87       195.02        46.82 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC 
      102.90        36.82        39.29        86.14        59.28        67.43 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
      340.14       161.03       208.04        48.72       107.38        54.74 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
       79.66        75.48       102.12        13.91        42.77        81.21 
TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 
       44.88        94.82        21.67       129.27        28.83        19.76 
TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MH TCGA-EE-A2MI 
       61.51        47.28       103.27       268.73        16.96       204.66 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MR 
       96.23       158.63       216.66        47.54        43.23       134.40 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AH 
       53.26       124.31        51.62        54.51        13.81       138.81 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB 
      172.18       127.20        36.95        64.08        34.32       201.80 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
       51.35       109.58       152.81        31.40        35.44        13.94 
TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F 
       50.76         9.17        77.75        12.59        13.02        26.37 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
      268.93       152.35         6.44       131.51        61.05        44.05 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
      162.08        50.89        37.25       148.18        79.99        43.82 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET 
       23.34        20.15        16.37        31.27       247.04        80.32 
TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 
       33.21         6.77        92.98       220.80        27.85        18.77 
TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YX 
       38.27        34.82        36.26       104.42       216.92        48.59 
TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA 
      228.59       202.65        20.91        28.08         7.79        27.72 
TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG 
       48.85       357.37        53.52        40.27        15.45         9.70 
TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS 
       23.93       101.26        74.73       133.55        11.41       148.80 
TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 
       26.56        27.09        27.02        77.82        66.67        28.73 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU 
      174.84        34.03        54.41         0.20        22.92        55.59 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A264 TCGA-GN-A265 
       19.30         9.90         2.04        15.78       117.93        84.72 
TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK 
       10.13        64.44        39.35        48.89        22.13        50.10 
TCGA-GN-A8LL TCGA-GN-A9SD TCGA-HR-A2OG TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X 
       21.37        59.41         0.23        65.88       368.78       297.90 
TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A828 
        7.23        18.05         0.33         0.69       228.16       121.08 
TCGA-W3-AA1O TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1V TCGA-W3-AA1W TCGA-WE-A8JZ 
        4.01        69.07       111.09        42.08       219.16        24.03 
TCGA-WE-A8K6 TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX 
       15.98        58.98        67.63        59.77        11.80        32.58 
TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YD-A89C 
       49.51        12.16        35.01        19.73        22.29         6.90 
TCGA-YG-AA3O TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
       37.94        27.58        96.99        15.98 

  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
              7.23               0.20 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
            248.65             369.93 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
             50.14              51.12 
[1] "7.2 - 248.7 (50.1)" "0.2 - 369.9 (51.1)"
[1] "hr=" "1"  
D76V3, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  19Q LOSS MUTATED                   12             2
  19Q LOSS WILD-TYPE                 53             3
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  19Q LOSS MUTATED                                          14
  19Q LOSS WILD-TYPE                                        58
                    vv
clus                 REGIONAL LYMPH NODE
  19Q LOSS MUTATED                    42
  19Q LOSS WILD-TYPE                 173
D76V4, multiclass
                                           clus
vv                                          19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  DISTANT METASTASIS                                      12                 53
  PRIMARY TUMOR                                            2                  3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               14                 58
  REGIONAL LYMPH NODE                                     42                173
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  19Q LOSS MUTATED             2       0       9        2        5        4
  19Q LOSS WILD-TYPE          10       7      19       16       22       20
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  19Q LOSS MUTATED           1         3         2        10          2
  19Q LOSS WILD-TYPE        13        16        10        27         13
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  19Q LOSS MUTATED            8         11        6
  19Q LOSS WILD-TYPE         24         49       14
D76V5, multiclass
             clus
vv            19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  I OR II NOS                2                 10
  STAGE 0                    0                  7
  STAGE I                    9                 19
  STAGE IA                   2                 16
  STAGE IB                   5                 22
  STAGE II                   4                 20
  STAGE IIA                  1                 13
  STAGE IIB                  3                 16
  STAGE IIC                  2                 10
  STAGE III                 10                 27
  STAGE IIIA                 2                 13
  STAGE IIIB                 8                 24
  STAGE IIIC                11                 49
  STAGE IV                   6                 14
[1] 14  2
[1] TRUE
[1] "dimension of contingency 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      12 21 13 14
  19Q LOSS WILD-TYPE    52 51 64 54
D76V6, multiclass
       clus
vv      19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  T0+T1               12                 52
  T2                  21                 51
  T3                  13                 64
  T4                  14                 54
[1] 4 2
[1] TRUE
[1] "dimension of 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    31  12  12  12
  19Q LOSS WILD-TYPE 138  51  26  37
D76V7, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  N0               31                138
  N1               12                 51
  N2               12                 26
  N3               12                 37
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V8, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED    58   7
  19Q LOSS WILD-TYPE 255  14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED     58    7
  19Q LOSS WILD-TYPE  255   14
   clus
vv  19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  0               58                255
  1                7                 14
[1] 2 2
[1] FALSE
D76V9, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED    28  14
  19Q LOSS WILD-TYPE 104  74
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED     28   14
  19Q LOSS WILD-TYPE  104   74
     clus
vv    19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  NO                28                104
  YES               14                 74
[1] 2 2
[1] FALSE
D76V10, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED     8  62
  19Q LOSS WILD-TYPE  36 251
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      8   62
  19Q LOSS WILD-TYPE   36  251
     clus
vv    19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  NO                 8                 36
  YES               62                251
[1] 2 2
[1] FALSE
D76V11, continuous
D76V12, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED    30  40
  19Q LOSS WILD-TYPE 105 183
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED     30   40
  19Q LOSS WILD-TYPE  105  183
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  FEMALE               30                105
  MALE                 40                183
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  19Q LOSS MUTATED       1                         0    68
  19Q LOSS WILD-TYPE     4                         1   276
D76V13, multiclass
                           clus
vv                          19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  ASIAN                                    1                  4
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   68                276
[1] 3 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     1  68
  19Q LOSS WILD-TYPE   6 276
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      1   68
  19Q LOSS WILD-TYPE    6  276
                        clus
vv                       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO               68                276
[1] 2 2
[1] FALSE

Clustering(77) Variable = 20P LOSS MUTATION ANALYSIS
D77V1, survival
                    sevent
clus2                  0   1
  20P LOSS MUTATED    10   8
  20P LOSS WILD-TYPE 111 110
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                18                221 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 8                110 
$`20P LOSS MUTATED`
TCGA-D3-A2JC TCGA-D3-A3CF TCGA-D3-A8GK TCGA-DA-A1HV TCGA-DA-A1I1 TCGA-EE-A29E 
       86.30        16.96       120.00        48.66        31.96         0.26 
TCGA-EE-A29G TCGA-ER-A19C TCGA-ER-A19H TCGA-ER-A19W TCGA-ER-A2NG TCGA-ER-A3PL 
       44.28        39.81       150.12       146.63        10.95        32.05 
TCGA-FS-A1ZE TCGA-FS-A4F4 TCGA-GN-A4U3 TCGA-W3-AA1W TCGA-WE-A8K5 TCGA-YG-AA3O 
       35.90        66.67       120.53       185.13        59.64        28.21 

$`20P LOSS WILD-TYPE`
TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
       60.46        12.99        14.83         8.42        15.72        31.89 
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB 
      110.93        49.35       133.25        19.04        76.41        62.60 
TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JD 
       25.64        45.99        62.86        15.75       168.00         7.27 
TCGA-D3-A2JE TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
        9.76       107.61        36.30       171.58        64.83        66.08 
TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE 
       43.53        58.06        46.98       140.98        40.01        59.70 
TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51J 
       13.87         9.34        90.21        23.67       173.85       144.46 
TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR 
       31.76        62.70        11.34        42.05        45.70       177.86 
TCGA-D3-A5GU TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GJ TCGA-D3-A8GL TCGA-D3-A8GM 
      124.08        78.21        23.61       179.97        69.53        70.62 
TCGA-D3-A8GP TCGA-D3-A8GR TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 
      135.12        36.53        10.78        15.02        16.90        18.44 
TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HY TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 
       57.90        22.85       106.85       150.61        82.85        32.42 
TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q 
       64.83        58.85        25.12       214.59        14.96         3.91 
TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y 
       33.24        50.07        45.50         6.64        13.15        24.89 
TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A184 TCGA-EE-A20C TCGA-EE-A20H 
       62.37        20.38         0.00        67.50        75.55       155.90 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P 
       75.22        76.14        12.99        63.12        47.74        27.16 
TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 
       61.12       346.49       185.19       102.38         7.20        77.98 
TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK 
       26.14       239.11         0.20       189.40        68.65        10.62 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR 
       32.48        18.35        31.00       118.32         0.76         0.20 
TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC 
       71.31        81.99       103.13        15.25         5.75        23.77 
TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML 
      209.79        94.19       171.85        63.25        67.50       104.78 
TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU 
      145.45       227.01        25.08       143.93        23.51        53.26 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
      124.31       122.73        51.62         4.41        54.51         6.28 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JI 
       67.89       111.85        45.90         3.35       201.80       152.81 
TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A 
       14.56        34.45         1.58        47.31         7.82         4.54 
TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
       53.29        11.47       151.46        99.06        59.84        42.48 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
      120.76        49.71        34.95        47.97        22.36         4.70 
TCGA-ER-A2NE TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-FR-A44A TCGA-FR-A729 
       16.87       173.29        55.82        15.48       174.21       209.23 
TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 
       26.20         5.65        10.06       171.78        49.74       195.98 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZG 
        8.35        27.62       312.07        32.78        12.92         7.82 
TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU 
       36.33        78.61       130.95       136.27        35.28         4.47 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F8 TCGA-FS-A4F9 
       23.21         5.29         3.06        30.90       173.19        13.28 
TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
       80.68        55.59        11.54        19.30         9.90         6.05 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 
        1.91        53.29       117.93        84.72        17.06        42.48 
TCGA-GN-A26A TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-GN-A8LK TCGA-GN-A9SD TCGA-LH-A9QB 
        7.59        34.49        46.92        43.23        59.41        85.05 
TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A825 
      297.01         7.23        18.05         0.33       174.12         1.97 
TCGA-W3-A828 TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1V TCGA-W3-AA21 TCGA-WE-A8K1 
      120.07        44.05        79.99         8.09        92.84         1.15 
TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZY 
       62.99        12.69        19.00        59.44        10.95        48.39 
TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-Z2-AA3S 
        1.94        26.60        16.64        15.65        91.23 

  20P LOSS MUTATED 20P LOSS WILD-TYPE 
              0.26               0.00 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
            185.13             346.49 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
             46.47              45.99 
[1] "0.3 - 185.1 (46.5)" "0.0 - 346.5 (46.0)"
[1] "hr=" "1.2"
D77V2, survival
                    sevent
clus2                  0   1
  20P LOSS MUTATED    12  12
  20P LOSS WILD-TYPE 157 168
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                24                325 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                12                168 
$`20P LOSS MUTATED`
TCGA-3N-A9WB TCGA-D3-A2JC TCGA-D3-A3CF TCGA-D3-A5GO TCGA-D3-A8GK TCGA-DA-A1HV 
       17.03        86.76        24.53       137.92       170.20        48.89 
TCGA-DA-A1I1 TCGA-EE-A29E TCGA-EE-A29G TCGA-ER-A19C TCGA-ER-A19E TCGA-ER-A19H 
      194.83        63.78        72.07        48.89        13.02       152.35 
TCGA-ER-A19W TCGA-ER-A2NG TCGA-ER-A3PL TCGA-FS-A1ZE TCGA-FS-A1ZR TCGA-FS-A4F4 
      148.18        31.27        33.21        40.27        11.41        66.67 
TCGA-GN-A4U3 TCGA-GN-A4U7 TCGA-W3-AA1W TCGA-WE-A8K5 TCGA-YG-AA3O TCGA-YG-AA3P 
      121.91        10.42       219.16        61.15        37.94        14.43 

$`20P LOSS WILD-TYPE`
TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
       66.48        12.99        14.93        16.57        16.67       112.04 
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA 
      112.57        71.80       133.25        28.08        31.59        90.90 
TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA 
       95.74        43.43       103.10        65.49        23.77       115.53 
TCGA-D3-A2JB TCGA-D3-A2JD TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH 
      168.00        11.87        27.65        62.07       113.52        42.08 
TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ 
       12.10       171.58        66.48        66.08        59.57       130.72 
TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE 
       58.06        46.98        46.32       166.52        86.93        60.23 
TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E 
       13.87         9.34       103.59        39.75        45.30       174.84 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R 
       55.73        56.35       145.12        32.94        22.62        63.81 
TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU 
       26.89       125.79       135.75       178.32        18.18       125.19 
TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GI TCGA-D3-A8GJ 
       30.84        79.59        23.61        26.43        58.52       241.38 
TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR 
       89.13       107.15       161.00       152.75        29.06       129.63 
TCGA-D3-A8GS TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A1X3 
      117.17       151.53        54.67         3.65         7.10        18.12 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC 
       15.39        22.29        18.44         9.90        25.18        66.25 
TCGA-D9-A6EG TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 
       22.95        36.03       117.21        20.38       176.55        35.93 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
      107.34        61.18        53.92        65.92        23.44        68.09 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R 
       28.60        10.49       215.44        15.68        13.87        10.36 
TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV 
       20.35        68.25        54.02        17.29        52.01         7.04 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 
       24.89        29.82        27.22         8.65        94.98        33.73 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C 
       14.70        26.89        68.15         4.96       133.81       151.27 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C 
       91.56       168.26        13.55        63.35        85.08        78.97 
TCGA-EE-A29D TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P 
       13.97        64.64         2.60        56.84        18.61        56.42 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W 
       66.74        14.47        61.28       369.93        25.87       195.02 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
       17.92        46.82       102.90        36.82        39.29        86.14 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
       59.28        67.43       340.14       161.03       208.04        48.72 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO 
      107.38        54.74        79.66        75.48       102.12       126.81 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 
       13.91        42.77        81.21        44.88        94.82        21.67 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME 
      129.27        28.83        19.76        61.51        47.28       103.27 
TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK 
      268.73       103.20        16.96       204.66        96.23       158.63 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR 
      216.66       167.90        47.54       248.65        43.23       134.40 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC 
      162.48        71.21        53.26       124.31       122.73        51.62 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 
       28.77        54.51        13.81        41.59       138.81       172.18 
TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB 
      127.20        36.95        64.08        34.32        53.19       201.80 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 
       27.35        51.35       109.58       152.81        31.40        35.44 
TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19D 
       13.94        50.76         9.17        77.75        98.40        12.59 
TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
       26.37       268.93         6.44       131.51        61.05        44.05 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A1A1 TCGA-ER-A2NC 
      162.08        50.89        37.25         8.88        79.99        43.82 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET 
       23.34        20.15        16.37        32.05       247.04        80.32 
TCGA-ER-A3EV TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 
       46.98         6.77        92.98       174.21        15.72       220.80 
TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE 
       27.85        18.77        38.27        34.82        36.26       104.42 
TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 
      216.92        48.59       228.59       202.65        20.91        28.08 
TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZF 
        7.79        27.72        48.85       357.37        53.52        15.45 
TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP 
        9.70        32.75        47.38        23.93       101.26        74.73 
TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY 
      133.55       148.80        53.16        26.56        49.48        27.09 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 
       27.02        77.82        50.14        28.73       174.84        34.03 
TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU 
       26.73        54.41        80.68         0.20        22.92        55.59 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 
       13.51        19.30         9.90         7.23         2.04        15.78 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
      139.89       117.93        84.72        10.13        64.44        62.79 
TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK 
       32.48        39.58        39.35        48.89        22.13        50.10 
TCGA-GN-A8LL TCGA-GN-A9SD TCGA-HR-A2OG TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X 
       21.37        59.41         0.23        65.88       368.78       297.90 
TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 
        7.23        18.05         0.33         0.69       228.16        63.02 
TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1V TCGA-W3-AA21 
      121.08         4.01        69.07       111.09        42.08       105.04 
TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO 
       24.03        49.05        15.98        98.89        58.98        67.63 
TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 
       59.77        11.80        32.58        49.51        12.16        35.01 
TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YD-A89C TCGA-YD-A9TA TCGA-Z2-A8RT TCGA-Z2-AA3S 
       19.73        22.29         6.90        49.18        27.58        96.99 
TCGA-Z2-AA3V 
       15.98 

  20P LOSS MUTATED 20P LOSS WILD-TYPE 
             10.42               0.20 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
            219.16             369.93 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
             55.02              50.89 
[1] "10.4 - 219.2 (55.0)" "0.2 - 369.9 (50.9)" 
[1] "hr=" "1.1"
D77V3, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  20P LOSS MUTATED                    8             0
  20P LOSS WILD-TYPE                 57             5
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  20P LOSS MUTATED                                           8
  20P LOSS WILD-TYPE                                        64
                    vv
clus                 REGIONAL LYMPH NODE
  20P LOSS MUTATED                     9
  20P LOSS WILD-TYPE                 206
D77V4, multiclass
                                           clus
vv                                          20P LOSS MUTATED 20P LOSS WILD-TYPE
  DISTANT METASTASIS                                       8                 57
  PRIMARY TUMOR                                            0                  5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                8                 64
  REGIONAL LYMPH NODE                                      9                206
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  20P LOSS MUTATED             0       0       1        1        1        4
  20P LOSS WILD-TYPE          12       7      27       17       26       20
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  20P LOSS MUTATED           1         1         1         2          1
  20P LOSS WILD-TYPE        13        18        11        35         14
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  20P LOSS MUTATED            2          4        3
  20P LOSS WILD-TYPE         30         56       17
D77V5, multiclass
             clus
vv            20P LOSS MUTATED 20P LOSS WILD-TYPE
  I OR II NOS                0                 12
  STAGE 0                    0                  7
  STAGE I                    1                 27
  STAGE IA                   1                 17
  STAGE IB                   1                 26
  STAGE II                   4                 20
  STAGE IIA                  1                 13
  STAGE IIB                  1                 18
  STAGE IIC                  1                 11
  STAGE III                  2                 35
  STAGE IIIA                 1                 14
  STAGE IIIB                 2                 30
  STAGE IIIC                 4                 56
  STAGE IV                   3                 17
[1] 14  2
[1] TRUE
[1] "dimension of contingency 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       4  5  7  5
  20P LOSS WILD-TYPE    60 67 70 63
D77V6, multiclass
       clus
vv      20P LOSS MUTATED 20P LOSS WILD-TYPE
  T0+T1                4                 60
  T2                   5                 67
  T3                   7                 70
  T4                   5                 63
[1] 4 2
[1] TRUE
[1] "dimension of 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    10   2   3   5
  20P LOSS WILD-TYPE 159  61  35  44
D77V7, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  N0               10                159
  N1                2                 61
  N2                3                 35
  N3                5                 44
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V8, binary
                    cls
clus                   0   1
  20P LOSS MUTATED    20   3
  20P LOSS WILD-TYPE 293  18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED     20    3
  20P LOSS WILD-TYPE  293   18
   clus
vv  20P LOSS MUTATED 20P LOSS WILD-TYPE
  0               20                293
  1                3                 18
[1] 2 2
[1] FALSE
D77V9, binary
                    cls
clus                   0   1
  20P LOSS MUTATED    12   5
  20P LOSS WILD-TYPE 120  83
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED     12    5
  20P LOSS WILD-TYPE  120   83
     clus
vv    20P LOSS MUTATED 20P LOSS WILD-TYPE
  NO                12                120
  YES                5                 83
[1] 2 2
[1] FALSE
D77V10, binary
                    cls
clus                   0   1
  20P LOSS MUTATED     3  22
  20P LOSS WILD-TYPE  41 291
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      3   22
  20P LOSS WILD-TYPE   41  291
     clus
vv    20P LOSS MUTATED 20P LOSS WILD-TYPE
  NO                 3                 41
  YES               22                291
[1] 2 2
[1] FALSE
D77V11, continuous
D77V12, binary
                    cls
clus                   0   1
  20P LOSS MUTATED     8  17
  20P LOSS WILD-TYPE 127 206
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      8   17
  20P LOSS WILD-TYPE  127  206
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  FEMALE                8                127
  MALE                 17                206
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  20P LOSS MUTATED       0                         0    23
  20P LOSS WILD-TYPE     5                         1   321
D77V13, multiclass
                           clus
vv                          20P LOSS MUTATED 20P LOSS WILD-TYPE
  ASIAN                                    0                  5
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   23                321
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V14, binary
                    cls
clus                   0   1
  20P LOSS MUTATED     2  22
  20P LOSS WILD-TYPE   5 322
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      2   22
  20P LOSS WILD-TYPE    5  322
                        clus
vv                       20P LOSS MUTATED 20P LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  5
  NOT HISPANIC OR LATINO               22                322
[1] 2 2
[1] FALSE

Clustering(78) Variable = 20Q LOSS MUTATION ANALYSIS
D78V1, survival
                    sevent
clus2                  0   1
  20Q LOSS MUTATED     3   3
  20Q LOSS WILD-TYPE 118 115
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 6                233 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 3                115 
$`20Q LOSS MUTATED`
TCGA-DA-A1I1 TCGA-EE-A29G TCGA-ER-A19C TCGA-FS-A1ZE TCGA-GN-A4U3 TCGA-WE-A8K5 
       31.96        44.28        39.81        35.90       120.53        59.64 

$`20Q LOSS WILD-TYPE`
TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
       60.46        12.99        14.83         8.42        15.72        31.89 
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB 
      110.93        49.35       133.25        19.04        76.41        62.60 
TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC 
       25.64        45.99        62.86        15.75       168.00        86.30 
TCGA-D3-A2JD TCGA-D3-A2JE TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN 
        7.27         9.76       107.61        36.30       171.58        64.83 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CC 
       66.08        43.53        58.06        46.98       140.98        40.01 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU 
       59.70        16.96        13.87         9.34        90.21        23.67 
TCGA-D3-A51E TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL 
      173.85       144.46        31.76        62.70        11.34        42.05 
TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GJ 
       45.70       177.86       124.08        78.21        23.61       179.97 
TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GP TCGA-D3-A8GR TCGA-D9-A1X3 
      120.00        69.53        70.62       135.12        36.53        10.78 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV 
       15.02        16.90        18.44        57.90        22.85        48.66 
TCGA-DA-A1HY TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC 
      106.85       150.61        82.85        32.42        64.83        58.85 
TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5SG TCGA-EB-A5SH 
       25.12       214.59        14.96         3.91        33.24        50.07 
TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A181 
       45.50         6.64        13.15        24.89        62.37        20.38 
TCGA-EE-A182 TCGA-EE-A184 TCGA-EE-A20C TCGA-EE-A20H TCGA-EE-A29B TCGA-EE-A29C 
        0.00        67.50        75.55       155.90        75.22        76.14 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29Q 
       12.99         0.26        63.12        47.74        27.16        61.12 
TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB 
      346.49       185.19       102.38         7.20        77.98        26.14 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
      239.11         0.20       189.40        68.65        10.62        32.48 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
       18.35        31.00       118.32         0.76         0.20        71.31 
TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MF 
       81.99       103.13        15.25         5.75        23.77       209.79 
TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM 
       94.19       171.85        63.25        67.50       104.78       145.45 
TCGA-EE-A2MP TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA 
      227.01        25.08       143.93        23.51        53.26       124.31 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J3 
      122.73        51.62         4.41        54.51         6.28        67.89 
TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JI TCGA-ER-A193 
      111.85        45.90         3.35       201.80       152.81        14.56 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B 
       34.45         1.58        47.31         7.82         4.54        53.29 
TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
       11.47       151.46       150.12        99.06        59.84        42.48 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
      120.76        49.71        34.95       146.63        47.97        22.36 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
        4.70        16.87        10.95       173.29        55.82        15.48 
TCGA-ER-A3PL TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FR-A8YC 
       32.05       174.21       209.23        26.20         5.65        10.06 
TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZC 
      171.78        49.74       195.98         8.35        27.62       312.07 
TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ 
       32.78        12.92         7.82        36.33        78.61       130.95 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ 
      136.27        35.28         4.47        23.21         5.29         3.06 
TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TU 
       30.90        66.67       173.19        13.28        80.68        55.59 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 
       11.54        19.30         9.90         6.05         1.91        53.29 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U4 
      117.93        84.72        17.06        42.48         7.59        34.49 
TCGA-GN-A4U8 TCGA-GN-A8LK TCGA-GN-A9SD TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS 
       46.92        43.23        59.41        85.05       297.01         7.23 
TCGA-QB-AA9O TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1Q 
       18.05         0.33       174.12         1.97       120.07        44.05 
TCGA-W3-AA1R TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8ZM 
       79.99         8.09       185.13        92.84         1.15        62.99 
TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AA9Y 
       12.69        19.00        59.44        10.95        48.39         1.94 
TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-Z2-AA3S 
       26.60        16.64        15.65        28.21        91.23 

  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
             31.96               0.00 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
            120.53             346.49 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
            42.045             46.920 
[1] "32.0 - 120.5 (42.0)" "0.0 - 346.5 (46.9)" 
[1] "hr=" "1.2"
D78V2, survival
                    sevent
clus2                  0   1
  20Q LOSS MUTATED     4   4
  20Q LOSS WILD-TYPE 165 176
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 8                341 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 4                176 
$`20Q LOSS MUTATED`
TCGA-DA-A1I1 TCGA-EE-A29G TCGA-ER-A19C TCGA-FS-A1ZE TCGA-GN-A4U3 TCGA-GN-A4U7 
      194.83        72.07        48.89        40.27       121.91        10.42 
TCGA-WE-A8K5 TCGA-YG-AA3P 
       61.15        14.43 

$`20Q LOSS WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q3 
       17.03        66.48        12.99        14.93        16.57        16.67 
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 
      112.04       112.57        71.80       133.25        28.08        31.59 
TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 
       90.90        95.74        43.43       103.10        65.49        23.77 
TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JE TCGA-D3-A2JF 
      115.53       168.00        86.76        11.87        27.65        62.07 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
      113.52        42.08        12.10       171.58        66.48        66.08 
TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB 
       59.57       130.72        58.06        46.98        46.32       166.52 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR 
       86.93        60.23        24.53        13.87         9.34       103.59 
TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J 
       39.75        45.30       174.84        55.73        56.35       145.12 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN 
       32.94        22.62        63.81        26.89       125.79       135.75 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GC 
      137.92       178.32        18.18       125.19        30.84        79.59 
TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL 
       23.61        26.43        58.52       241.38       170.20        89.13 
TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS 
      107.15       161.00       152.75        29.06       129.63       117.17 
TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A1X3 TCGA-D9-A3Z1 
      151.53        54.67         3.65         7.10        18.12        15.39 
TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG 
       22.29        18.44         9.90        25.18        66.25        22.95 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 
       48.89        36.03       117.21        20.38       176.55        35.93 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
      107.34        61.18        53.92        65.92        23.44        68.09 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R 
       28.60        10.49       215.44        15.68        13.87        10.36 
TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV 
       20.35        68.25        54.02        17.29        52.01         7.04 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 
       24.89        29.82        27.22         8.65        94.98        33.73 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C 
       14.70        26.89        68.15         4.96       133.81       151.27 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C 
       91.56       168.26        13.55        63.35        85.08        78.97 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N 
       13.97        63.78        64.64         2.60        56.84        18.61 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V 
       56.42        66.74        14.47        61.28       369.93        25.87 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 
      195.02        17.92        46.82       102.90        36.82        39.29 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
       86.14        59.28        67.43       340.14       161.03       208.04 
TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN 
       48.72       107.38        54.74        79.66        75.48       102.12 
TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU 
      126.81        13.91        42.77        81.21        44.88        94.82 
TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD 
       21.67       129.27        28.83        19.76        61.51        47.28 
TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ 
      103.27       268.73       103.20        16.96       204.66        96.23 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ 
      158.63       216.66       167.90        47.54       248.65        43.23 
TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB 
      134.40       162.48        71.21        53.26       124.31       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH 
       51.62        28.77        54.51        13.81        41.59       138.81 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA 
      172.18       127.20        36.95        64.08        34.32        53.19 
TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 
      201.80        27.35        51.35       109.58       152.81        31.40 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B 
       35.44        13.94        50.76         9.17        77.75        98.40 
TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J 
       12.59        13.02        26.37       268.93       152.35         6.44 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S 
      131.51        61.05        44.05       162.08        50.89        37.25 
TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
        8.88       148.18        79.99        43.82        23.34        20.15 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
       16.37        31.27        32.05       247.04        80.32        46.98 
TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 
       33.21         6.77        92.98       174.21        15.72       220.80 
TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE 
       27.85        18.77        38.27        34.82        36.26       104.42 
TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 
      216.92        48.59       228.59       202.65        20.91        28.08 
TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZF 
        7.79        27.72        48.85       357.37        53.52        15.45 
TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP 
        9.70        32.75        47.38        23.93       101.26        74.73 
TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW 
      133.55        11.41       148.80        53.16        26.56        49.48 
TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 
       27.09        27.02        77.82        50.14        66.67        28.73 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 
      174.84        34.03        26.73        54.41        80.68         0.20 
TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
       22.92        55.59        13.51        19.30         9.90         7.23 
TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 
        2.04        15.78       139.89       117.93        84.72        10.13 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U4 TCGA-GN-A4U8 
       64.44        62.79        32.48        39.58        39.35        48.89 
TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A8LL TCGA-GN-A9SD TCGA-HR-A2OG TCGA-HR-A2OH 
       22.13        50.10        21.37        59.41         0.23        65.88 
TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 TCGA-RP-A694 
      368.78       297.90         7.23        18.05         0.33         0.69 
TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1Q TCGA-W3-AA1R 
      228.16        63.02       121.08         4.01        69.07       111.09 
TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K6 
       42.08       219.16       105.04        24.03        49.05        15.98 
TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX 
       98.89        58.98        67.63        59.77        11.80        32.58 
TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YD-A89C 
       49.51        12.16        35.01        19.73        22.29         6.90 
TCGA-YD-A9TA TCGA-YG-AA3O TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
       49.18        37.94        27.58        96.99        15.98 

  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
             10.42               0.20 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
            194.83             369.93 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
             55.02              50.89 
[1] "10.4 - 194.8 (55.0)" "0.2 - 369.9 (50.9)" 
[1] "hr=" "1"  
D78V3, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  20Q LOSS MUTATED                    4             0
  20Q LOSS WILD-TYPE                 61             5
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  20Q LOSS MUTATED                                           3
  20Q LOSS WILD-TYPE                                        69
                    vv
clus                 REGIONAL LYMPH NODE
  20Q LOSS MUTATED                     2
  20Q LOSS WILD-TYPE                 213
D78V4, multiclass
                                           clus
vv                                          20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  DISTANT METASTASIS                                       4                 61
  PRIMARY TUMOR                                            0                  5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                3                 69
  REGIONAL LYMPH NODE                                      2                213
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  20Q LOSS MUTATED             0       0       1        0        0        0
  20Q LOSS WILD-TYPE          12       7      27       18       27       24
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  20Q LOSS MUTATED           0         1         1         1          1
  20Q LOSS WILD-TYPE        14        18        11        36         14
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  20Q LOSS MUTATED            0          2        2
  20Q LOSS WILD-TYPE         32         58       18
D78V5, multiclass
             clus
vv            20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  I OR II NOS                0                 12
  STAGE 0                    0                  7
  STAGE I                    1                 27
  STAGE IA                   0                 18
  STAGE IB                   0                 27
  STAGE II                   0                 24
  STAGE IIA                  0                 14
  STAGE IIB                  1                 18
  STAGE IIC                  1                 11
  STAGE III                  1                 36
  STAGE IIIA                 1                 14
  STAGE IIIB                 0                 32
  STAGE IIIC                 2                 58
  STAGE IV                   2                 18
[1] 14  2
[1] TRUE
[1] "dimension of contingency 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       1  3  1  3
  20Q LOSS WILD-TYPE    63 69 76 65
D78V6, multiclass
       clus
vv      20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  T0+T1                1                 63
  T2                   3                 69
  T3                   1                 76
  T4                   3                 65
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  20Q LOSS MUTATED     2   1   1   3
  20Q LOSS WILD-TYPE 167  62  37  46
D78V7, multiclass
    clus
vv   20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  N0                2                167
  N1                1                 62
  N2                1                 37
  N3                3                 46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V8, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     7   2
  20Q LOSS WILD-TYPE 306  19
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      7    2
  20Q LOSS WILD-TYPE  306   19
   clus
vv  20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  0                7                306
  1                2                 19
[1] 2 2
[1] FALSE
D78V9, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     6   1
  20Q LOSS WILD-TYPE 126  87
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      6    1
  20Q LOSS WILD-TYPE  126   87
     clus
vv    20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  NO                 6                126
  YES                1                 87
[1] 2 2
[1] FALSE
D78V10, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     1   8
  20Q LOSS WILD-TYPE  43 305
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      1    8
  20Q LOSS WILD-TYPE   43  305
     clus
vv    20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  NO                 1                 43
  YES                8                305
[1] 2 2
[1] FALSE
D78V11, continuous
D78V12, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     2   7
  20Q LOSS WILD-TYPE 133 216
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      2    7
  20Q LOSS WILD-TYPE  133  216
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  FEMALE                2                133
  MALE                  7                216
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  20Q LOSS MUTATED       0                         0     8
  20Q LOSS WILD-TYPE     5                         1   336
D78V13, multiclass
                           clus
vv                          20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  ASIAN                                    0                  5
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                    8                336
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V14, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     1   8
  20Q LOSS WILD-TYPE   6 336
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      1    8
  20Q LOSS WILD-TYPE    6  336
                        clus
vv                       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO                8                336
[1] 2 2
[1] FALSE

Clustering(79) Variable = 21Q LOSS MUTATION ANALYSIS
D79V1, survival
                    sevent
clus2                  0   1
  21Q LOSS MUTATED    23  18
  21Q LOSS WILD-TYPE  98 100
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                41                198 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                18                100 
$`21Q LOSS MUTATED`
TCGA-3N-A9WD TCGA-D3-A1Q5 TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JH TCGA-D3-A2JL 
       12.99       110.93       168.00        86.30        36.30       171.58 
TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A51T TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A181 
       64.83        66.08        11.34        24.89        62.37        20.38 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A2 TCGA-EE-A2A6 
       44.28        63.12       346.49       185.19         7.20        77.98 
TCGA-EE-A2GB TCGA-EE-A2GO TCGA-EE-A2M6 TCGA-EE-A2MK TCGA-EE-A2MS TCGA-ER-A197 
       26.14       118.32       103.13        67.50       143.93         1.58 
TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZM TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW 
       35.90         7.82        78.61        35.28         4.47        23.21 
TCGA-FW-A5DY TCGA-GN-A262 TCGA-GN-A268 TCGA-GN-A4U3 TCGA-GN-A9SD TCGA-OD-A75X 
       19.30        53.29        42.48       120.53        59.41       297.01 
TCGA-QB-AA9O TCGA-W3-AA1R TCGA-WE-A8ZQ TCGA-WE-A8ZY TCGA-YG-AA3O 
       18.05        79.99        59.44        48.39        28.21 

$`21Q LOSS WILD-TYPE`
TCGA-3N-A9WC TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q6 
       60.46        14.83         8.42        15.72        31.89        49.35 
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
      133.25        19.04        76.41        62.60        25.64        45.99 
TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JD TCGA-D3-A2JE TCGA-D3-A2JG TCGA-D3-A2JP 
       62.86        15.75         7.27         9.76       107.61        43.53 
TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF 
       58.06        46.98       140.98        40.01        59.70        16.96 
TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51J 
       13.87         9.34        90.21        23.67       173.85       144.46 
TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GU 
       31.76        62.70        42.05        45.70       177.86       124.08 
TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM 
       78.21        23.61       179.97       120.00        69.53        70.62 
TCGA-D3-A8GP TCGA-D3-A8GR TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 
      135.12        36.53        10.78        15.02        16.90        18.44 
TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 
       57.90        22.85        48.66       106.85        31.96       150.61 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 
       82.85        32.42        64.83        58.85        25.12       214.59 
TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A6L9 
       14.96         3.91        33.24        50.07        45.50         6.64 
TCGA-EE-A17X TCGA-EE-A182 TCGA-EE-A184 TCGA-EE-A20C TCGA-EE-A20H TCGA-EE-A29B 
       13.15         0.00        67.50        75.55       155.90        75.22 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29Q 
       76.14        12.99         0.26        47.74        27.16        61.12 
TCGA-EE-A2A1 TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK 
      102.38       239.11         0.20       189.40        68.65        10.62 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
       32.48        18.35        31.00         0.76         0.20        71.31 
TCGA-EE-A2GU TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MG 
       81.99        15.25         5.75        23.77       209.79        94.19 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MR 
      171.85        63.25       104.78       145.45       227.01        25.08 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
       23.51        53.26       124.31       122.73        51.62         4.41 
TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 
       54.51         6.28        67.89       111.85        45.90         3.35 
TCGA-EE-A3JB TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A199 
      201.80       152.81        14.56        34.45        47.31         7.82 
TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19H 
        4.54        53.29        39.81        11.47       151.46       150.12 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S 
       99.06        59.84        42.48       120.76        49.71        34.95 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NG 
      146.63        47.97        22.36         4.70        16.87        10.95 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A44A TCGA-FR-A729 
      173.29        55.82        15.48        32.05       174.21       209.23 
TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 
       26.20         5.65        10.06       171.78        49.74       195.98 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZJ 
        8.35        27.62       312.07        32.78        12.92        36.33 
TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 
      130.95       136.27         5.29         3.06        30.90        66.67 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV TCGA-GF-A3OT 
      173.19        13.28        80.68        55.59        11.54         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A26A 
        6.05         1.91       117.93        84.72        17.06         7.59 
TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-GN-A8LK TCGA-LH-A9QB TCGA-QB-A6FS TCGA-RP-A693 
       34.49        46.92        43.23        85.05         7.23         0.33 
TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1Q TCGA-W3-AA1V TCGA-W3-AA1W 
      174.12         1.97       120.07        44.05         8.09       185.13 
TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO 
       92.84         1.15        59.64        62.99        12.69        19.00 
TCGA-WE-A8ZT TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-Z2-AA3S 
       10.95         1.94        26.60        16.64        15.65        91.23 

  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
              1.58               0.00 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
            346.49             312.07 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
             59.41              45.60 
[1] "1.6 - 346.5 (59.4)" "0.0 - 312.1 (45.6)"
[1] "hr=" "1.4"
D79V2, survival
                    sevent
clus2                  0   1
  21Q LOSS MUTATED    33  34
  21Q LOSS WILD-TYPE 136 146
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                67                282 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                34                146 
$`21Q LOSS MUTATED`
TCGA-3N-A9WD TCGA-D3-A1Q5 TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JH TCGA-D3-A2JL 
       12.99       112.57       168.00        86.76        42.08       171.58 
TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A3C8 TCGA-D3-A51T TCGA-D3-A5GS TCGA-D3-A8GN 
       66.48        66.08        46.32        26.89        18.18       161.00 
TCGA-D9-A1JX TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-DA-A1I0 TCGA-EB-A44R TCGA-EE-A17Y 
        7.10         9.90        25.18        20.38        10.36        27.22 
TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A20B TCGA-EE-A20I TCGA-EE-A29G TCGA-EE-A29H 
       94.98        33.73       133.81        13.55        72.07        64.64 
TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A2 TCGA-EE-A2A6 
      369.93        25.87       195.02        17.92        36.82        86.14 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GI TCGA-EE-A2GO TCGA-EE-A2M5 TCGA-EE-A2M6 
       59.28        67.43        48.72       126.81        21.67       129.27 
TCGA-EE-A2MK TCGA-EE-A2MN TCGA-EE-A2MS TCGA-EE-A3AH TCGA-EE-A3J5 TCGA-EE-A3JA 
      158.63        47.54       162.48       138.81        36.95        53.19 
TCGA-ER-A197 TCGA-ER-A19E TCGA-FS-A1ZA TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZM 
       13.94        13.02        27.72        40.27         9.70       101.26 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FW-A5DY TCGA-GN-A262 TCGA-GN-A266 
       53.16        26.56        49.48        19.30       139.89        10.13 
TCGA-GN-A268 TCGA-GN-A4U3 TCGA-GN-A4U9 TCGA-GN-A9SD TCGA-OD-A75X TCGA-QB-AA9O 
       62.79       121.91        22.13        59.41       297.90        18.05 
TCGA-RP-A694 TCGA-W3-AA1O TCGA-W3-AA1R TCGA-WE-A8ZQ TCGA-WE-A8ZY TCGA-YD-A89C 
        0.69         4.01       111.09        59.77        49.51         6.90 
TCGA-YG-AA3O 
       37.94 

$`21Q LOSS WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
       17.03        66.48        14.93        16.57        16.67       112.04 
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB 
       71.80       133.25        28.08        31.59        90.90        95.74 
TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JD 
       43.43       103.10        65.49        23.77       115.53        11.87 
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JK TCGA-D3-A2JP TCGA-D3-A3BZ 
       27.65        62.07       113.52        12.10        59.57       130.72 
TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF 
       58.06        46.98       166.52        86.93        60.23        24.53 
TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E 
       13.87         9.34       103.59        39.75        45.30       174.84 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R 
       55.73        56.35       145.12        32.94        22.62        63.81 
TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D3-A8GB 
      125.79       135.75       137.92       178.32       125.19        30.84 
TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GK 
       79.59        23.61        26.43        58.52       241.38       170.20 
TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS 
       89.13       107.15       152.75        29.06       129.63       117.17 
TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 
      151.53        54.67         3.65        18.12        15.39        22.29 
TCGA-D9-A4Z6 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY 
       18.44        66.25        22.95        48.89        36.03       117.21 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
      194.83       176.55        35.93       107.34        61.18        53.92 
TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 
       65.92        23.44        68.09        28.60        10.49       215.44 
TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL 
       15.68        13.87        20.35        68.25        54.02        17.29 
TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A182 
       52.01         7.04        24.89        29.82         8.65        14.70 
TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H 
       26.89        68.15         4.96       151.27        91.56       168.26 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29L 
       63.35        85.08        78.97        13.97        63.78         2.60 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
       56.84        18.61        56.42        66.74        14.47        61.28 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
       46.82       102.90        39.29       340.14       161.03       208.04 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP 
      107.38        54.74        79.66        75.48       102.12        13.91 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M7 TCGA-EE-A2M8 
       42.77        81.21        44.88        94.82        28.83        19.76 
TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH 
       61.51        47.28       103.27       268.73       103.20        16.96 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MQ 
      204.66        96.23       216.66       167.90       248.65        43.23 
TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC 
      134.40        71.21        53.26       124.31       122.73        51.62 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3J4 
       28.77        54.51        13.81        41.59       172.18       127.20 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH 
       64.08        34.32       201.80        27.35        51.35       109.58 
TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A 
      152.81        31.40        35.44        50.76         9.17        77.75 
TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H 
       98.40        48.89        12.59        26.37       268.93       152.35 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
        6.44       131.51        61.05        44.05       162.08        50.89 
TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
       37.25         8.88       148.18        79.99        43.82        23.34 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET 
       20.15        16.37        31.27        32.05       247.04        80.32 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       46.98        33.21         6.77        92.98       174.21        15.72 
TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD 
      220.80        27.85        18.77        38.27        34.82        36.26 
TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
      104.42       216.92        48.59       228.59       202.65        20.91 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZF 
       28.08         7.79        48.85       357.37        53.52        15.45 
TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR 
       32.75        47.38        23.93        74.73       133.55        11.41 
TCGA-FS-A1ZS TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 
      148.80        27.09        27.02        77.82        50.14        66.67 
TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD 
       28.73       174.84        34.03        26.73        54.41        80.68 
TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-GF-A3OT TCGA-GF-A4EO 
        0.20        22.92        55.59        13.51         9.90         7.23 
TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A26A 
        2.04        15.78       117.93        84.72        64.44        32.48 
TCGA-GN-A26D TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A8LK TCGA-GN-A8LL 
       39.58        39.35        10.42        48.89        50.10        21.37 
TCGA-HR-A2OG TCGA-HR-A2OH TCGA-LH-A9QB TCGA-QB-A6FS TCGA-RP-A693 TCGA-W3-A824 
        0.23        65.88       368.78         7.23         0.33       228.16 
TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1Q TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 
       63.02       121.08        69.07        42.08       219.16       105.04 
TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN 
       24.03        49.05        61.15        15.98        98.89        58.98 
TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 
       67.63        11.80        32.58        12.16        35.01        19.73 
TCGA-WE-AAA4 TCGA-YD-A9TA TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
       22.29        49.18        14.43        27.58        96.99        15.98 

  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
              0.69               0.20 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
            369.93             368.78 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
            48.720             51.815 
[1] "0.7 - 369.9 (48.7)" "0.2 - 368.8 (51.8)"
[1] "hr=" "1"  
D79V3, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  21Q LOSS MUTATED                   11             2
  21Q LOSS WILD-TYPE                 54             3
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  21Q LOSS MUTATED                                          15
  21Q LOSS WILD-TYPE                                        57
                    vv
clus                 REGIONAL LYMPH NODE
  21Q LOSS MUTATED                    39
  21Q LOSS WILD-TYPE                 176
D79V4, multiclass
                                           clus
vv                                          21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  DISTANT METASTASIS                                      11                 54
  PRIMARY TUMOR                                            2                  3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               15                 57
  REGIONAL LYMPH NODE                                     39                176
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  21Q LOSS MUTATED             3       3       3        5        4        6
  21Q LOSS WILD-TYPE           9       4      25       13       23       18
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  21Q LOSS MUTATED           2         2         2        10          3
  21Q LOSS WILD-TYPE        12        17        10        27         12
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  21Q LOSS MUTATED            6          9        4
  21Q LOSS WILD-TYPE         26         51       16
D79V5, multiclass
             clus
vv            21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  I OR II NOS                3                  9
  STAGE 0                    3                  4
  STAGE I                    3                 25
  STAGE IA                   5                 13
  STAGE IB                   4                 23
  STAGE II                   6                 18
  STAGE IIA                  2                 12
  STAGE IIB                  2                 17
  STAGE IIC                  2                 10
  STAGE III                 10                 27
  STAGE IIIA                 3                 12
  STAGE IIIB                 6                 26
  STAGE IIIC                 9                 51
  STAGE IV                   4                 16
[1] 14  2
[1] TRUE
[1] "dimension of contingency 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 11 14 14
  21Q LOSS WILD-TYPE    54 61 63 54
D79V6, multiclass
       clus
vv      21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  T0+T1               10                 54
  T2                  11                 61
  T3                  14                 63
  T4                  14                 54
[1] 4 2
[1] TRUE
[1] "dimension of 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    30  15   7   6
  21Q LOSS WILD-TYPE 139  48  31  43
D79V7, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  N0               30                139
  N1               15                 48
  N2                7                 31
  N3                6                 43
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V8, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED    60   4
  21Q LOSS WILD-TYPE 253  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     60    4
  21Q LOSS WILD-TYPE  253   17
   clus
vv  21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  0               60                253
  1                4                 17
[1] 2 2
[1] FALSE
D79V9, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED    28  16
  21Q LOSS WILD-TYPE 104  72
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     28   16
  21Q LOSS WILD-TYPE  104   72
     clus
vv    21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  NO                28                104
  YES               16                 72
[1] 2 2
[1] FALSE
D79V10, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED     7  61
  21Q LOSS WILD-TYPE  37 252
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      7   61
  21Q LOSS WILD-TYPE   37  252
     clus
vv    21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  NO                 7                 37
  YES               61                252
[1] 2 2
[1] FALSE
D79V11, continuous
D79V12, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED    27  41
  21Q LOSS WILD-TYPE 108 182
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     27   41
  21Q LOSS WILD-TYPE  108  182
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  FEMALE               27                108
  MALE                 41                182
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  21Q LOSS MUTATED       2                         1    63
  21Q LOSS WILD-TYPE     3                         0   281
D79V13, multiclass
                           clus
vv                          21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  ASIAN                                    2                  3
  BLACK OR AFRICAN AMERICAN                1                  0
  WHITE                                   63                281
[1] 3 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     1  66
  21Q LOSS WILD-TYPE   6 278
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      1   66
  21Q LOSS WILD-TYPE    6  278
                        clus
vv                       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO               66                278
[1] 2 2
[1] FALSE

Clustering(80) Variable = 22Q LOSS MUTATION ANALYSIS
D80V1, survival
                    sevent
clus2                  0   1
  22Q LOSS MUTATED     8  16
  22Q LOSS WILD-TYPE 113 102
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                24                215 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                16                102 
$`22Q LOSS MUTATED`
TCGA-D3-A1Q3 TCGA-D3-A1Q8 TCGA-D3-A2JB TCGA-D3-A2JL TCGA-DA-A1I2 TCGA-EE-A184 
       15.72        19.04       168.00       171.58       150.61        67.50 
TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A2A6 TCGA-EE-A2GP TCGA-EE-A2MG TCGA-EE-A2MM 
       76.14         0.26        77.98         0.76        94.19       145.45 
TCGA-ER-A19D TCGA-ER-A19H TCGA-ER-A19P TCGA-FS-A1YW TCGA-FS-A1ZJ TCGA-FS-A1ZY 
       11.47       150.12       120.76       171.78        36.33         5.29 
TCGA-FS-A4F0 TCGA-GF-A4EO TCGA-GN-A4U3 TCGA-RP-A693 TCGA-W3-A825 TCGA-WE-A8ZQ 
       30.90         6.05       120.53         0.33         1.97        59.44 

$`22Q LOSS WILD-TYPE`
TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 
       60.46        12.99        14.83         8.42        31.89       110.93 
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       49.35       133.25        76.41        62.60        25.64        45.99 
TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JE TCGA-D3-A2JG 
       62.86        15.75        86.30         7.27         9.76       107.61 
TCGA-D3-A2JH TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3C7 
       36.30        64.83        66.08        43.53        58.06        46.98 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO 
      140.98        40.01        59.70        16.96        13.87         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R 
       90.21        23.67       173.85       144.46        31.76        62.70 
TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D3-A8GC 
       11.34        42.05        45.70       177.86       124.08        78.21 
TCGA-D3-A8GD TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GP 
       23.61       179.97       120.00        69.53        70.62       135.12 
TCGA-D3-A8GR TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6EC 
       36.53        10.78        15.02        16.90        18.44        57.90 
TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I5 TCGA-DA-A1I7 
       22.85        48.66       106.85        31.96        82.85        32.42 
TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q 
       64.83        58.85        25.12       214.59        14.96         3.91 
TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y 
       33.24        50.07        45.50         6.64        13.15        24.89 
TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A20C TCGA-EE-A20H TCGA-EE-A29B 
       62.37        20.38         0.00        75.55       155.90        75.22 
TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29Q 
       12.99        44.28        63.12        47.74        27.16        61.12 
TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2GB TCGA-EE-A2GD 
      346.49       185.19       102.38         7.20        26.14       239.11 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
        0.20       189.40        68.65        10.62        32.48        18.35 
TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 
       31.00       118.32         0.20        71.31        81.99       103.13 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MI TCGA-EE-A2MJ 
       15.25         5.75        23.77       209.79       171.85        63.25 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MP TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT 
       67.50       104.78       227.01        25.08       143.93        23.51 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
       53.26       124.31       122.73        51.62         4.41        54.51 
TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB 
        6.28        67.89       111.85        45.90         3.35       201.80 
TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 
      152.81        14.56        34.45         1.58        47.31         7.82 
TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19G TCGA-ER-A19L TCGA-ER-A19M 
        4.54        53.29        39.81       151.46        99.06        59.84 
TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
       42.48        49.71        34.95       146.63        47.97        22.36 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
        4.70        16.87        10.95       173.29        55.82        15.48 
TCGA-ER-A3PL TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FR-A8YC 
       32.05       174.21       209.23        26.20         5.65        10.06 
TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD 
       49.74       195.98         8.35        27.62       312.07        32.78 
TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS 
       35.90        12.92         7.82        78.61       130.95       136.27 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZZ TCGA-FS-A4F4 TCGA-FS-A4F8 
       35.28         4.47        23.21         3.06        66.67       173.19 
TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
       13.28        80.68        55.59        11.54        19.30         9.90 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 
        1.91        53.29       117.93        84.72        17.06        42.48 
TCGA-GN-A26A TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-GN-A8LK TCGA-GN-A9SD TCGA-LH-A9QB 
        7.59        34.49        46.92        43.23        59.41        85.05 
TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O TCGA-W3-A824 TCGA-W3-A828 TCGA-W3-AA1Q 
      297.01         7.23        18.05       174.12       120.07        44.05 
TCGA-W3-AA1R TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8K5 
       79.99         8.09       185.13        92.84         1.15        59.64 
TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AA9Y 
       62.99        12.69        19.00        10.95        48.39         1.94 
TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-Z2-AA3S 
       26.60        16.64        15.65        28.21        91.23 

  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
              0.26               0.00 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
            171.78             346.49 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
             63.47              45.90 
[1] "0.3 - 171.8 (63.5)" "0.0 - 346.5 (45.9)"
[1] "hr=" "1.3"
D80V2, survival
                    sevent
clus2                  0   1
  22Q LOSS MUTATED    12  25
  22Q LOSS WILD-TYPE 157 155
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                37                312 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                25                155 
$`22Q LOSS MUTATED`
TCGA-D3-A1Q3 TCGA-D3-A1Q8 TCGA-D3-A2JB TCGA-D3-A2JF TCGA-D3-A2JL TCGA-D3-A5GO 
       16.67        28.08       168.00        62.07       171.58       137.92 
TCGA-D3-A8GB TCGA-D3-A8GN TCGA-D9-A149 TCGA-DA-A1I2 TCGA-EB-A44R TCGA-EE-A184 
       30.84       161.00        54.67       176.55        10.36        68.15 
TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A2A6 TCGA-EE-A2GP TCGA-EE-A2MG TCGA-EE-A2MM 
       78.97        63.78        86.14        13.91       103.20       167.90 
TCGA-EE-A3JA TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19H TCGA-ER-A19P TCGA-ER-A19T 
       53.19        12.59        13.02       152.35       162.08         8.88 
TCGA-FR-A8YD TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1ZJ TCGA-FS-A1ZY TCGA-FS-A4F0 
       36.26       216.92        48.59        47.38        27.09        77.82 
TCGA-GF-A4EO TCGA-GN-A266 TCGA-GN-A4U3 TCGA-GN-A4U9 TCGA-RP-A693 TCGA-W3-A825 
        7.23        10.13       121.91        22.13         0.33        63.02 
TCGA-WE-A8ZQ 
       59.77 

$`22Q LOSS WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q4 
       17.03        66.48        12.99        14.93        16.57       112.04 
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB 
      112.57        71.80       133.25        31.59        90.90        95.74 
TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JC 
       43.43       103.10        65.49        23.77       115.53        86.76 
TCGA-D3-A2JD TCGA-D3-A2JE TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JN 
       11.87        27.65       113.52        42.08        12.10        66.48 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 
       66.08        59.57       130.72        58.06        46.98        46.32 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO 
      166.52        86.93        60.23        24.53        13.87         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
      103.59        39.75        45.30       174.84        55.73        56.35 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL 
      145.12        32.94        22.62        63.81        26.89       125.79 
TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GC TCGA-D3-A8GD 
      135.75       178.32        18.18       125.19        79.59        23.61 
TCGA-D3-A8GE TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM 
       26.43        58.52       241.38       170.20        89.13       107.15 
TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A148 TCGA-D9-A1JW 
      152.75        29.06       129.63       117.17       151.53         3.65 
TCGA-D9-A1JX TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 
        7.10        18.12        15.39        22.29        18.44         9.90 
TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY 
       25.18        66.25        22.95        48.89        36.03       117.21 
TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
       20.38       194.83        35.93       107.34        61.18        53.92 
TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 
       65.92        23.44        68.09        28.60        10.49       215.44 
TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL 
       15.68        13.87        20.35        68.25        54.02        17.29 
TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
       52.01         7.04        24.89        29.82        27.22         8.65 
TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B 
       94.98        33.73        14.70        26.89         4.96       133.81 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
      151.27        91.56       168.26        13.55        63.35        85.08 
TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N 
       13.97        72.07        64.64         2.60        56.84        18.61 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V 
       56.42        66.74        14.47        61.28       369.93        25.87 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 
      195.02        17.92        46.82       102.90        36.82        39.29 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
       59.28        67.43       340.14       161.03       208.04        48.72 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO 
      107.38        54.74        79.66        75.48       102.12       126.81 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 
       42.77        81.21        44.88        94.82        21.67       129.27 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF 
       28.83        19.76        61.51        47.28       103.27       268.73 
TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MN 
       16.96       204.66        96.23       158.63       216.66        47.54 
TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU 
      248.65        43.23       134.40       162.48        71.21        53.26 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
      124.31       122.73        51.62        28.77        54.51        13.81 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 
       41.59       138.81       172.18       127.20        36.95        64.08 
TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI 
       34.32       201.80        27.35        51.35       109.58       152.81 
TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A 
       31.40        35.44        13.94        50.76         9.17        77.75 
TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19J TCGA-ER-A19L 
       98.40        48.89        26.37       268.93         6.44       131.51 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 
       61.05        44.05        50.89        37.25       148.18        79.99 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH 
       43.82        23.34        20.15        16.37        31.27        32.05 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN 
      247.04        80.32        46.98        33.21         6.77        92.98 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA 
      174.21        15.72       220.80        27.85        18.77        38.27 
TCGA-FR-A8YC TCGA-FR-A8YE TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 
       34.82       104.42       228.59       202.65        20.91        28.08 
TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE 
        7.79        27.72        48.85       357.37        53.52        40.27 
TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP 
       15.45         9.70        32.75        23.93       101.26        74.73 
TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW 
      133.55        11.41       148.80        53.16        26.56        49.48 
TCGA-FS-A1ZZ TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 
       27.02        50.14        66.67        28.73       174.84        34.03 
TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU 
       26.73        54.41        80.68         0.20        22.92        55.59 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 
       13.51        19.30         9.90         2.04        15.78       139.89 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
      117.93        84.72        64.44        62.79        32.48        39.58 
TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A8LK TCGA-GN-A8LL TCGA-GN-A9SD 
       39.35        10.42        48.89        50.10        21.37        59.41 
TCGA-HR-A2OG TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O 
        0.23        65.88       368.78       297.90         7.23        18.05 
TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1Q TCGA-W3-AA1R 
        0.69       228.16       121.08         4.01        69.07       111.09 
TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K5 
       42.08       219.16       105.04        24.03        49.05        61.15 
TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-A8ZX 
       15.98        98.89        58.98        67.63        11.80        32.58 
TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YD-A89C 
       49.51        12.16        35.01        19.73        22.29         6.90 
TCGA-YD-A9TA TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
       49.18        37.94        14.43        27.58        96.99        15.98 

  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
              0.33               0.20 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
            216.92             369.93 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
             59.77              50.12 
[1] "0.3 - 216.9 (59.8)" "0.2 - 369.9 (50.1)"
[1] "hr=" "1.3"
D80V3, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  22Q LOSS MUTATED                    9             1
  22Q LOSS WILD-TYPE                 56             4
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  22Q LOSS MUTATED                                           7
  22Q LOSS WILD-TYPE                                        65
                    vv
clus                 REGIONAL LYMPH NODE
  22Q LOSS MUTATED                    21
  22Q LOSS WILD-TYPE                 194
D80V4, multiclass
                                           clus
vv                                          22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  DISTANT METASTASIS                                       9                 56
  PRIMARY TUMOR                                            1                  4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                7                 65
  REGIONAL LYMPH NODE                                     21                194
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  22Q LOSS MUTATED             3       1       4        2        6        2
  22Q LOSS WILD-TYPE           9       6      24       16       21       22
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  22Q LOSS MUTATED           1         2         2         1          0
  22Q LOSS WILD-TYPE        13        17        10        36         15
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  22Q LOSS MUTATED            4          3        3
  22Q LOSS WILD-TYPE         28         57       17
D80V5, multiclass
             clus
vv            22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  I OR II NOS                3                  9
  STAGE 0                    1                  6
  STAGE I                    4                 24
  STAGE IA                   2                 16
  STAGE IB                   6                 21
  STAGE II                   2                 22
  STAGE IIA                  1                 13
  STAGE IIB                  2                 17
  STAGE IIC                  2                 10
  STAGE III                  1                 36
  STAGE IIIA                 0                 15
  STAGE IIIB                 4                 28
  STAGE IIIC                 3                 57
  STAGE IV                   3                 17
[1] 14  2
[1] TRUE
[1] "dimension of contingency 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 11  6  7
  22Q LOSS WILD-TYPE    59 61 71 61
D80V6, multiclass
       clus
vv      22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  T0+T1                5                 59
  T2                  11                 61
  T3                   6                 71
  T4                   7                 61
[1] 4 2
[1] TRUE
[1] "dimension of 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    25   5   2   4
  22Q LOSS WILD-TYPE 144  58  36  45
D80V7, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  N0               25                144
  N1                5                 58
  N2                2                 36
  N3                4                 45
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V8, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED    34   3
  22Q LOSS WILD-TYPE 279  18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     34    3
  22Q LOSS WILD-TYPE  279   18
   clus
vv  22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  0               34                279
  1                3                 18
[1] 2 2
[1] FALSE
D80V9, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED    17   6
  22Q LOSS WILD-TYPE 115  82
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     17    6
  22Q LOSS WILD-TYPE  115   82
     clus
vv    22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  NO                17                115
  YES                6                 82
[1] 2 2
[1] FALSE
D80V10, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED     5  33
  22Q LOSS WILD-TYPE  39 280
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      5   33
  22Q LOSS WILD-TYPE   39  280
     clus
vv    22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  NO                 5                 39
  YES               33                280
[1] 2 2
[1] FALSE
D80V11, continuous
D80V12, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED    15  23
  22Q LOSS WILD-TYPE 120 200
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     15   23
  22Q LOSS WILD-TYPE  120  200
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  FEMALE               15                120
  MALE                 23                200
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  22Q LOSS MUTATED       1                         1    35
  22Q LOSS WILD-TYPE     4                         0   309
D80V13, multiclass
                           clus
vv                          22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  ASIAN                                    1                  4
  BLACK OR AFRICAN AMERICAN                1                  0
  WHITE                                   35                309
[1] 3 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     1  37
  22Q LOSS WILD-TYPE   6 307
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      1   37
  22Q LOSS WILD-TYPE    6  307
                        clus
vv                       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO               37                307
[1] 2 2
[1] FALSE

Clustering(81) Variable = XP LOSS MUTATION ANALYSIS
D81V1, survival
                   sevent
clus2                0  1
  XP LOSS MUTATED   28 40
  XP LOSS WILD-TYPE 93 78
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               68               171 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               40                78 
$`XP LOSS MUTATED`
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q8 TCGA-D3-A2J6 TCGA-D3-A2JC TCGA-D3-A2JG 
       31.89       110.93        19.04        25.64        86.30       107.61 
TCGA-D3-A2JL TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CC TCGA-D3-A51T TCGA-D3-A5GL 
      171.58        58.06        46.98        40.01        11.34        42.05 
TCGA-D3-A8GC TCGA-D3-A8GR TCGA-D9-A1X3 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-DA-A1I5 
       78.21        36.53        10.78        16.90        18.44        82.85 
TCGA-EE-A17Y TCGA-EE-A20C TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29H TCGA-EE-A29Q 
       24.89        75.55        76.14        12.99        63.12        61.12 
TCGA-EE-A2A2 TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2MF TCGA-EE-A2MK TCGA-EE-A2MM 
        7.20         0.20        71.31       209.79        67.50       145.45 
TCGA-EE-A2MS TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3J8 TCGA-ER-A193 TCGA-ER-A19G 
      143.93         4.41         6.28         3.35        14.56       151.46 
TCGA-ER-A19L TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A3ET TCGA-FR-A7U8 TCGA-FS-A1YW 
       99.06         4.70        16.87        55.82        26.20       171.78 
TCGA-FS-A1YY TCGA-FS-A1ZC TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZQ 
       49.74       312.07        12.92         7.82        36.33       130.95 
TCGA-FS-A1ZS TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F9 TCGA-FW-A3TU 
      136.27         3.06        30.90        66.67        13.28        55.59 
TCGA-FW-A3TV TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A268 TCGA-GN-A8LK TCGA-LH-A9QB 
       11.54         1.91        53.29        42.48        43.23        85.05 
TCGA-OD-A75X TCGA-W3-AA1R TCGA-W3-AA1V TCGA-WE-A8ZM TCGA-WE-A8ZT TCGA-WE-A8ZY 
      297.01        79.99         8.09        62.99        10.95        48.39 
TCGA-WE-AA9Y TCGA-Z2-AA3S 
        1.94        91.23 

$`XP LOSS WILD-TYPE`
TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q6 
       60.46        12.99        14.83         8.42        15.72        49.35 
TCGA-D3-A1Q7 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA 
      133.25        76.41        62.60        45.99        62.86        15.75 
TCGA-D3-A2JB TCGA-D3-A2JD TCGA-D3-A2JE TCGA-D3-A2JH TCGA-D3-A2JN TCGA-D3-A2JO 
      168.00         7.27         9.76        36.30        64.83        66.08 
TCGA-D3-A2JP TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO 
       43.53       140.98        59.70        16.96        13.87         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R 
       90.21        23.67       173.85       144.46        31.76        62.70 
TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D3-A8GD TCGA-D3-A8GJ TCGA-D3-A8GK 
       45.70       177.86       124.08        23.61       179.97       120.00 
TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GP TCGA-D9-A3Z1 TCGA-D9-A6EC TCGA-D9-A6EG 
       69.53        70.62       135.12        15.02        57.90        22.85 
TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I7 TCGA-DA-A1IA 
       48.66       106.85        31.96       150.61        32.42        64.83 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5SG 
       58.85        25.12       214.59        14.96         3.91        33.24 
TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A180 TCGA-EE-A181 
       50.07        45.50         6.64        13.15        62.37        20.38 
TCGA-EE-A182 TCGA-EE-A184 TCGA-EE-A20H TCGA-EE-A29B TCGA-EE-A29E TCGA-EE-A29G 
        0.00        67.50       155.90        75.22         0.26        44.28 
TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A6 
       47.74        27.16       346.49       185.19       102.38        77.98 
TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK 
       26.14       239.11         0.20       189.40        68.65        10.62 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GU 
       32.48        18.35        31.00       118.32         0.76        81.99 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MG TCGA-EE-A2MI 
      103.13        15.25         5.75        23.77        94.19       171.85 
TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MP TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A2MU 
       63.25       104.78       227.01        25.08        23.51        53.26 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3J3 TCGA-EE-A3J4 
      124.31       122.73        51.62        54.51        67.89       111.85 
TCGA-EE-A3J7 TCGA-EE-A3JB TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
       45.90       201.80       152.81        34.45         1.58        47.31 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19H 
        7.82         4.54        53.29        39.81        11.47       150.12 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W 
       59.84        42.48       120.76        49.71        34.95       146.63 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3EV TCGA-ER-A3PL 
       47.97        22.36        10.95       173.29        15.48        32.05 
TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FS-A1Z0 TCGA-FS-A1Z3 
      174.21       209.23         5.65        10.06       195.98         8.35 
TCGA-FS-A1Z4 TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZM TCGA-FS-A1ZT TCGA-FS-A1ZU 
       27.62        32.78        35.90        78.61        35.28         4.47 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F8 TCGA-FS-A4FD TCGA-FW-A5DY TCGA-GF-A3OT 
       23.21         5.29       173.19        80.68        19.30         9.90 
TCGA-GF-A4EO TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A4U3 
        6.05       117.93        84.72        17.06         7.59       120.53 
TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-GN-A9SD TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 
       34.49        46.92        59.41         7.23        18.05         0.33 
TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1Q TCGA-W3-AA1W TCGA-W3-AA21 
      174.12         1.97       120.07        44.05       185.13        92.84 
TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-AAA0 
        1.15        59.64        12.69        19.00        59.44        26.60 
TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O 
       16.64        15.65        28.21 

  XP LOSS MUTATED XP LOSS WILD-TYPE 
              0.2               0.0 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
           312.07            346.49 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
           45.105            45.990 
[1] "0.2 - 312.1 (45.1)" "0.0 - 346.5 (46.0)"
[1] "hr=" "1.4"
D81V2, survival
                   sevent
clus2                 0   1
  XP LOSS MUTATED    41  52
  XP LOSS WILD-TYPE 128 128
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               93               256 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               52               128 
$`XP LOSS MUTATED`
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q8 TCGA-D3-A2J6 TCGA-D3-A2JC TCGA-D3-A2JG 
      112.04       112.57        28.08        43.43        86.76       113.52 
TCGA-D3-A2JL TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CC TCGA-D3-A51N TCGA-D3-A51T 
      171.58        58.06        46.98        86.93        22.62        26.89 
TCGA-D3-A5GL TCGA-D3-A5GO TCGA-D3-A8GC TCGA-D3-A8GR TCGA-D9-A148 TCGA-D9-A1X3 
      125.79       137.92        79.59       129.63       151.53        18.12 
TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-DA-A1HW TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-EE-A17Y 
       22.29        18.44        36.03       107.34        53.92        27.22 
TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29C TCGA-EE-A29D 
        4.96       151.27        91.56        13.55        78.97        13.97 
TCGA-EE-A29H TCGA-EE-A29Q TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A2 TCGA-EE-A2GC 
       64.64        66.74        25.87        17.92        36.82        67.43 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2MF TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MS 
       42.77        81.21       268.73       158.63       167.90       162.48 
TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J8 TCGA-EE-A3JH TCGA-ER-A193 
       28.77        13.81       138.81        34.32       109.58        31.40 
TCGA-ER-A19E TCGA-ER-A19G TCGA-ER-A19L TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF 
       13.02       268.93       131.51        23.34        20.15        16.37 
TCGA-ER-A2NH TCGA-ER-A3ET TCGA-FR-A7U8 TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1ZC 
       32.05        80.32        27.85       216.92       228.59       357.37 
TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZQ TCGA-FS-A1ZR 
       15.45         9.70        32.75        47.38       133.55        11.41 
TCGA-FS-A1ZS TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F9 TCGA-FS-A4FB 
      148.80        27.02        77.82        66.67        34.03        26.73 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A268 
       55.59        13.51         2.04        15.78       139.89        62.79 
TCGA-GN-A8LK TCGA-GN-A8LL TCGA-LH-A9QB TCGA-OD-A75X TCGA-W3-AA1R TCGA-W3-AA1V 
       50.10        21.37       368.78       297.90       111.09        42.08 
TCGA-WE-A8JZ TCGA-WE-A8ZM TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-YD-A9TA 
       24.03        98.89        11.80        49.51        12.16        49.18 
TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S 
       14.43        27.58        96.99 

$`XP LOSS WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q3 
       17.03        66.48        12.99        14.93        16.57        16.67 
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J7 
       71.80       133.25        31.59        90.90        95.74       103.10 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JD TCGA-D3-A2JE 
       65.49        23.77       115.53       168.00        11.87        27.65 
TCGA-D3-A2JF TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP 
       62.07        42.08        12.10        66.48        66.08        59.57 
TCGA-D3-A3BZ TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML 
      130.72        46.32       166.52        60.23        24.53        13.87 
TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F 
        9.34       103.59        39.75        45.30       174.84        55.73 
TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A5GR 
       56.35       145.12        32.94        63.81       135.75       178.32 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GI 
       18.18       125.19        30.84        23.61        26.43        58.52 
TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GP 
      241.38       170.20        89.13       107.15       161.00       152.75 
TCGA-D3-A8GQ TCGA-D3-A8GS TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 
       29.06       117.17        54.67         3.65         7.10        15.39 
TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY 
        9.90        25.18        66.25        22.95        48.89       117.21 
TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I7 TCGA-DA-A1IA 
       20.38       194.83       176.55        35.93        61.18        65.92 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 
       23.44        68.09        28.60        10.49       215.44        15.68 
TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL 
       13.87        10.36        20.35        68.25        54.02        17.29 
TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A180 
       52.01         7.04        24.89        29.82         8.65        94.98 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A20B TCGA-EE-A20H 
       33.73        14.70        26.89        68.15       133.81       168.26 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29L TCGA-EE-A29M 
       63.35        85.08        63.78        72.07         2.60        56.84 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29W 
       18.61        56.42        14.47        61.28       369.93       195.02 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD 
       46.82       102.90        39.29        86.14        59.28       340.14 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
      161.03       208.04        48.72       107.38        54.74        79.66 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GT TCGA-EE-A2GU 
       75.48       102.12       126.81        13.91        44.88        94.82 
TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD 
       21.67       129.27        28.83        19.76        61.51        47.28 
TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2ML 
      103.27       103.20        16.96       204.66        96.23       216.66 
TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A2MU 
       47.54       248.65        43.23       134.40        71.21        53.26 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3AG TCGA-EE-A3J3 
      124.31       122.73        51.62        54.51        41.59       172.18 
TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JD 
      127.20        36.95        64.08        53.19       201.80        27.35 
TCGA-EE-A3JE TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 
       51.35       152.81        35.44        13.94        50.76         9.17 
TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19H 
       77.75        98.40        48.89        12.59        26.37       152.35 
TCGA-ER-A19J TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S 
        6.44        61.05        44.05       162.08        50.89        37.25 
TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NG TCGA-ER-A3ES 
        8.88       148.18        79.99        43.82        31.27       247.04 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       46.98        33.21         6.77        92.98       174.21        15.72 
TCGA-FR-A729 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE 
      220.80        18.77        38.27        34.82        36.26       104.42 
TCGA-FS-A1YX TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA 
       48.59       202.65        20.91        28.08         7.79        27.72 
TCGA-FS-A1ZB TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP 
       48.85        53.52        40.27        23.93       101.26        74.73 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F2 TCGA-FS-A4F5 
       53.16        26.56        49.48        27.09        50.14        28.73 
TCGA-FS-A4F8 TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A5DY 
      174.84        54.41        80.68         0.20        22.92        19.30 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 
        9.90         7.23       117.93        84.72        10.13        64.44 
TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 
       32.48        39.58       121.91        39.35        10.42        48.89 
TCGA-GN-A4U9 TCGA-GN-A9SD TCGA-HR-A2OG TCGA-HR-A2OH TCGA-QB-A6FS TCGA-QB-AA9O 
       22.13        59.41         0.23        65.88         7.23        18.05 
TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O 
        0.33         0.69       228.16        63.02       121.08         4.01 
TCGA-W3-AA1Q TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8K6 
       69.07       219.16       105.04        49.05        61.15        15.98 
TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZX TCGA-WE-AAA0 TCGA-WE-AAA3 
       58.98        67.63        59.77        32.58        35.01        19.73 
TCGA-WE-AAA4 TCGA-YD-A89C TCGA-YG-AA3O TCGA-Z2-AA3V 
       22.29         6.90        37.94        15.98 

  XP LOSS MUTATED XP LOSS WILD-TYPE 
             2.04              0.20 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
           368.78            369.93 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
           49.510            51.485 
[1] "2.0 - 368.8 (49.5)" "0.2 - 369.9 (51.5)"
[1] "hr=" "1"  
D81V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  XP LOSS MUTATED                   22             1
  XP LOSS WILD-TYPE                 43             4
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  XP LOSS MUTATED                                          17
  XP LOSS WILD-TYPE                                        55
                   vv
clus                REGIONAL LYMPH NODE
  XP LOSS MUTATED                    56
  XP LOSS WILD-TYPE                 159
D81V4, multiclass
                                           clus
vv                                          XP LOSS MUTATED XP LOSS WILD-TYPE
  DISTANT METASTASIS                                     22                43
  PRIMARY TUMOR                                           1                 4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE              17                55
  REGIONAL LYMPH NODE                                    56               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                I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  XP LOSS MUTATED             5       3       5        2        9        8
  XP LOSS WILD-TYPE           7       4      23       16       18       16
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  XP LOSS MUTATED           2        10         3         6          3
  XP LOSS WILD-TYPE        12         9         9        31         12
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  XP LOSS MUTATED            6         17        7
  XP LOSS WILD-TYPE         26         43       13
D81V5, multiclass
             clus
vv            XP LOSS MUTATED XP LOSS WILD-TYPE
  I OR II NOS               5                 7
  STAGE 0                   3                 4
  STAGE I                   5                23
  STAGE IA                  2                16
  STAGE IB                  9                18
  STAGE II                  8                16
  STAGE IIA                 2                12
  STAGE IIB                10                 9
  STAGE IIC                 3                 9
  STAGE III                 6                31
  STAGE IIIA                3                12
  STAGE IIIB                6                26
  STAGE IIIC               17                43
  STAGE IV                  7                13
[1] 14  2
[1] TRUE
[1] "dimension of contingency 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      15 15 23 20
  XP LOSS WILD-TYPE    49 57 54 48
D81V6, multiclass
       clus
vv      XP LOSS MUTATED XP LOSS WILD-TYPE
  T0+T1              15                49
  T2                 15                57
  T3                 23                54
  T4                 20                48
[1] 4 2
[1] TRUE
[1] "dimension of 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    47  18   5  13
  XP LOSS WILD-TYPE 122  45  33  36
D81V7, multiclass
    clus
vv   XP LOSS MUTATED XP LOSS WILD-TYPE
  N0              47               122
  N1              18                45
  N2               5                33
  N3              13                36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D81V8, binary
                   cls
clus                  0   1
  XP LOSS MUTATED    79   8
  XP LOSS WILD-TYPE 234  13
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED     79    8
  XP LOSS WILD-TYPE  234   13
   clus
vv  XP LOSS MUTATED XP LOSS WILD-TYPE
  0              79               234
  1               8                13
[1] 2 2
[1] FALSE
D81V9, binary
                   cls
clus                  0   1
  XP LOSS MUTATED    31  26
  XP LOSS WILD-TYPE 101  62
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED     31   26
  XP LOSS WILD-TYPE  101   62
     clus
vv    XP LOSS MUTATED XP LOSS WILD-TYPE
  NO               31               101
  YES              26                62
[1] 2 2
[1] FALSE
D81V10, binary
                   cls
clus                  0   1
  XP LOSS MUTATED     9  87
  XP LOSS WILD-TYPE  35 226
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED      9   87
  XP LOSS WILD-TYPE   35  226
     clus
vv    XP LOSS MUTATED XP LOSS WILD-TYPE
  NO                9                35
  YES              87               226
[1] 2 2
[1] FALSE
D81V11, continuous
D81V12, binary
                   cls
clus                  0   1
  XP LOSS MUTATED    46  50
  XP LOSS WILD-TYPE  89 173
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED     46   50
  XP LOSS WILD-TYPE   89  173
        clus
vv       XP LOSS MUTATED XP LOSS WILD-TYPE
  FEMALE              46                89
  MALE                50               173
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  XP LOSS MUTATED       1                         0    93
  XP LOSS WILD-TYPE     4                         1   251
D81V13, multiclass
                           clus
vv                          XP LOSS MUTATED XP LOSS WILD-TYPE
  ASIAN                                   1                 4
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  93               251
[1] 3 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     2  91
  XP LOSS WILD-TYPE   5 253
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED      2   91
  XP LOSS WILD-TYPE    5  253
                        clus
vv                       XP LOSS MUTATED XP LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                 5
  NOT HISPANIC OR LATINO              91               253
[1] 2 2
[1] FALSE

Clustering(82) Variable = XQ LOSS MUTATION ANALYSIS
D82V1, survival
                   sevent
clus2                0  1
  XQ LOSS MUTATED   28 36
  XQ LOSS WILD-TYPE 93 82
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               64               175 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               36                82 
$`XQ LOSS MUTATED`
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q8 TCGA-D3-A2J6 TCGA-D3-A2JC TCGA-D3-A2JL 
       31.89       110.93        19.04        25.64        86.30       171.58 
TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A8GC TCGA-D3-A8GR 
       58.06        46.98        11.34        42.05        78.21        36.53 
TCGA-D9-A1X3 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-DA-A1I5 TCGA-EE-A17Y TCGA-EE-A20C 
       10.78        16.90        18.44        82.85        24.89        75.55 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29H TCGA-EE-A29Q TCGA-EE-A2A2 TCGA-EE-A2GR 
       76.14        12.99        63.12        61.12         7.20         0.20 
TCGA-EE-A2GS TCGA-EE-A2MF TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MS TCGA-EE-A3AD 
       71.31       209.79        67.50       145.45       143.93         4.41 
TCGA-EE-A3AF TCGA-EE-A3J8 TCGA-ER-A193 TCGA-ER-A19G TCGA-ER-A19L TCGA-ER-A2NE 
        6.28         3.35        14.56       151.46        99.06        16.87 
TCGA-ER-A2NG TCGA-ER-A3ET TCGA-FR-A7U8 TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1ZC 
       10.95        55.82        26.20       171.78        49.74       312.07 
TCGA-FS-A1ZF TCGA-FS-A1ZJ TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZZ TCGA-FS-A4F0 
       12.92        36.33       130.95       136.27         3.06        30.90 
TCGA-FS-A4F4 TCGA-FS-A4F9 TCGA-FW-A3TU TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A4U3 
       66.67        13.28        55.59         1.91        53.29       120.53 
TCGA-GN-A8LK TCGA-LH-A9QB TCGA-OD-A75X TCGA-W3-AA1R TCGA-W3-AA1V TCGA-W3-AA1W 
       43.23        85.05       297.01        79.99         8.09       185.13 
TCGA-WE-A8ZM TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-Z2-AA3S 
       62.99        48.39         1.94        91.23 

$`XQ LOSS WILD-TYPE`
TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q6 
       60.46        12.99        14.83         8.42        15.72        49.35 
TCGA-D3-A1Q7 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA 
      133.25        76.41        62.60        45.99        62.86        15.75 
TCGA-D3-A2JB TCGA-D3-A2JD TCGA-D3-A2JE TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JN 
      168.00         7.27         9.76       107.61        36.30        64.83 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF 
       66.08        43.53       140.98        40.01        59.70        16.96 
TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51J 
       13.87         9.34        90.21        23.67       173.85       144.46 
TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D3-A8GD 
       31.76        62.70        45.70       177.86       124.08        23.61 
TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GP TCGA-D9-A3Z1 
      179.97       120.00        69.53        70.62       135.12        15.02 
TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 
       57.90        22.85        48.66       106.85        31.96       150.61 
TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 
       32.42        64.83        58.85        25.12       214.59        14.96 
TCGA-EB-A44Q TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X 
        3.91        33.24        50.07        45.50         6.64        13.15 
TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A184 TCGA-EE-A20H TCGA-EE-A29B 
       62.37        20.38         0.00        67.50       155.90        75.22 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29T TCGA-EE-A29W 
        0.26        44.28        47.74        27.16       346.49       185.19 
TCGA-EE-A2A1 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
      102.38        77.98        26.14       239.11         0.20       189.40 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO 
       68.65        10.62        32.48        18.35        31.00       118.32 
TCGA-EE-A2GP TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC 
        0.76        81.99       103.13        15.25         5.75        23.77 
TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MP TCGA-EE-A2MR 
       94.19       171.85        63.25       104.78       227.01        25.08 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AE 
       23.51        53.26       124.31       122.73        51.62        54.51 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3JB TCGA-EE-A3JI TCGA-ER-A195 
       67.89       111.85        45.90       201.80       152.81        34.45 
TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C 
        1.58        47.31         7.82         4.54        53.29        39.81 
TCGA-ER-A19D TCGA-ER-A19H TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
       11.47       150.12        59.84        42.48       120.76        49.71 
TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A3ES 
       34.95       146.63        47.97        22.36         4.70       173.29 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7UA TCGA-FR-A8YC 
       15.48        32.05       174.21       209.23         5.65        10.06 
TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG 
      195.98         8.35        27.62        32.78        35.90         7.82 
TCGA-FS-A1ZM TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F8 
       78.61        35.28         4.47        23.21         5.29       173.19 
TCGA-FS-A4FD TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GN-A264 
       80.68        11.54        19.30         9.90         6.05       117.93 
TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U4 TCGA-GN-A4U8 
       84.72        17.06        42.48         7.59        34.49        46.92 
TCGA-GN-A9SD TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A825 
       59.41         7.23        18.05         0.33       174.12         1.97 
TCGA-W3-A828 TCGA-W3-AA1Q TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8ZN 
      120.07        44.05        92.84         1.15        59.64        12.69 
TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 
       19.00        59.44        10.95        26.60        16.64        15.65 
TCGA-YG-AA3O 
       28.21 

  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
              0.2               0.0 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
           312.07            346.49 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
           51.515            45.500 
[1] "0.2 - 312.1 (51.5)" "0.0 - 346.5 (45.5)"
[1] "hr=" "1.1"
D82V2, survival
                   sevent
clus2                 0   1
  XQ LOSS MUTATED    39  49
  XQ LOSS WILD-TYPE 130 131
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               88               261 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               49               131 
$`XQ LOSS MUTATED`
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q8 TCGA-D3-A2J6 TCGA-D3-A2JC TCGA-D3-A2JL 
      112.04       112.57        28.08        43.43        86.76       171.58 
TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A51N TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GO 
       58.06        46.98        22.62        26.89       125.79       137.92 
TCGA-D3-A8GC TCGA-D3-A8GR TCGA-D9-A148 TCGA-D9-A1X3 TCGA-D9-A3Z3 TCGA-D9-A4Z6 
       79.59       129.63       151.53        18.12        22.29        18.44 
TCGA-DA-A1HW TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-EE-A17Y TCGA-EE-A185 TCGA-EE-A20C 
       36.03       107.34        53.92        27.22         4.96       151.27 
TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29H TCGA-EE-A29Q 
       91.56        13.55        78.97        13.97        64.64        66.74 
TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A2 TCGA-EE-A2GC TCGA-EE-A2GR TCGA-EE-A2GS 
       25.87        17.92        36.82        67.43        42.77        81.21 
TCGA-EE-A2MF TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MS TCGA-EE-A3AD TCGA-EE-A3AF 
      268.73       158.63       167.90       162.48        28.77        13.81 
TCGA-EE-A3AH TCGA-EE-A3J8 TCGA-ER-A193 TCGA-ER-A19E TCGA-ER-A19G TCGA-ER-A19L 
      138.81        34.32        31.40        13.02       268.93       131.51 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ET TCGA-FR-A7U8 
       20.15        16.37        31.27        32.05        80.32        27.85 
TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1ZA TCGA-FS-A1ZC TCGA-FS-A1ZF TCGA-FS-A1ZH 
      216.92       228.59        27.72       357.37        15.45        32.75 
TCGA-FS-A1ZJ TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZZ TCGA-FS-A4F0 
       47.38       133.55        11.41       148.80        27.02        77.82 
TCGA-FS-A4F4 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FW-A3TU TCGA-GF-A6C8 TCGA-GN-A262 
       66.67        34.03        26.73        55.59         2.04       139.89 
TCGA-GN-A4U3 TCGA-GN-A8LK TCGA-GN-A8LL TCGA-LH-A9QB TCGA-OD-A75X TCGA-W3-AA1R 
      121.91        50.10        21.37       368.78       297.90       111.09 
TCGA-W3-AA1V TCGA-W3-AA1W TCGA-WE-A8JZ TCGA-WE-A8ZM TCGA-WE-A8ZY TCGA-WE-AA9Y 
       42.08       219.16        24.03        98.89        49.51        12.16 
TCGA-YD-A9TA TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S 
       49.18        14.43        27.58        96.99 

$`XQ LOSS WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q3 
       17.03        66.48        12.99        14.93        16.57        16.67 
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J7 
       71.80       133.25        31.59        90.90        95.74       103.10 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JD TCGA-D3-A2JE 
       65.49        23.77       115.53       168.00        11.87        27.65 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JN TCGA-D3-A2JO 
       62.07       113.52        42.08        12.10        66.48        66.08 
TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE 
       59.57       130.72        46.32       166.52        86.93        60.23 
TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV 
       24.53        13.87         9.34       103.59        39.75        45.30 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R 
      174.84        55.73        56.35       145.12        32.94        63.81 
TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GD 
      135.75       178.32        18.18       125.19        30.84        23.61 
TCGA-D3-A8GE TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM 
       26.43        58.52       241.38       170.20        89.13       107.15 
TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GS TCGA-D9-A149 TCGA-D9-A1JW 
      161.00       152.75        29.06       117.17        54.67         3.65 
TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG 
        7.10        15.39         9.90        25.18        66.25        22.95 
TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 
       48.89       117.21        20.38       194.83       176.55        35.93 
TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
       61.18        65.92        23.44        68.09        28.60        10.49 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG 
      215.44        15.68        13.87        10.36        20.35        68.25 
TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X 
       54.02        17.29        52.01         7.04        24.89        29.82 
TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 
        8.65        94.98        33.73        14.70        26.89        68.15 
TCGA-EE-A20B TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29E TCGA-EE-A29G 
      133.81       168.26        63.35        85.08        63.78        72.07 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A29S 
        2.60        56.84        18.61        56.42        14.47        61.28 
TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-EE-A2A6 
      369.93       195.02        46.82       102.90        39.29        86.14 
TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       59.28       340.14       161.03       208.04        48.72       107.38 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP 
       54.74        79.66        75.48       102.12       126.81        13.91 
TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 
       44.88        94.82        21.67       129.27        28.83        19.76 
TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
       61.51        47.28       103.27       103.20        16.96       204.66 
TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR 
       96.23       216.66        47.54       248.65        43.23       134.40 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AE 
       71.21        53.26       124.31       122.73        51.62        54.51 
TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3JA 
       41.59       172.18       127.20        36.95        64.08        53.19 
TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 
      201.80        27.35        51.35       109.58       152.81        35.44 
TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C 
       13.94        50.76         9.17        77.75        98.40        48.89 
TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19M TCGA-ER-A19N 
       12.59        26.37       152.35         6.44        61.05        44.05 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 
      162.08        50.89        37.25         8.88       148.18        79.99 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A3ES TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K 
       43.82        23.34       247.04        46.98        33.21         6.77 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U9 TCGA-FR-A7UA 
       92.98       174.21        15.72       220.80        18.77        38.27 
TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YX TCGA-FS-A1Z0 TCGA-FS-A1Z3 
       34.82        36.26       104.42        48.59       202.65        20.91 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZB TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG 
       28.08         7.79        48.85        53.52        40.27         9.70 
TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW 
       23.93       101.26        74.73        53.16        26.56        49.48 
TCGA-FS-A1ZY TCGA-FS-A4F2 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4FC TCGA-FS-A4FD 
       27.09        50.14        28.73       174.84        54.41        80.68 
TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
        0.20        22.92        13.51        19.30         9.90         7.23 
TCGA-GF-A6C9 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
       15.78       117.93        84.72        10.13        64.44        62.79 
TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A4U9 
       32.48        39.58        39.35        10.42        48.89        22.13 
TCGA-GN-A9SD TCGA-HR-A2OG TCGA-HR-A2OH TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 
       59.41         0.23        65.88         7.23        18.05         0.33 
TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1Q 
        0.69       228.16        63.02       121.08         4.01        69.07 
TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZN TCGA-WE-A8ZO 
      105.04        49.05        61.15        15.98        58.98        67.63 
TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 
       59.77        11.80        32.58        35.01        19.73        22.29 
TCGA-YD-A89C TCGA-YG-AA3O TCGA-Z2-AA3V 
        6.90        37.94        15.98 

  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
             2.04              0.20 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
           368.78            369.93 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
           49.805            51.350 
[1] "2.0 - 368.8 (49.8)" "0.2 - 369.9 (51.4)"
[1] "hr=" "1.1"
D82V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  XQ LOSS MUTATED                   23             1
  XQ LOSS WILD-TYPE                 42             4
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  XQ LOSS MUTATED                                          16
  XQ LOSS WILD-TYPE                                        56
                   vv
clus                REGIONAL LYMPH NODE
  XQ LOSS MUTATED                    52
  XQ LOSS WILD-TYPE                 163
D82V4, multiclass
                                           clus
vv                                          XQ LOSS MUTATED XQ LOSS WILD-TYPE
  DISTANT METASTASIS                                     23                42
  PRIMARY TUMOR                                           1                 4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE              16                56
  REGIONAL LYMPH NODE                                    52               163
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  XQ LOSS MUTATED             6       3       5        2        8        9
  XQ LOSS WILD-TYPE           6       4      23       16       19       15
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  XQ LOSS MUTATED           2         9         2         6          2
  XQ LOSS WILD-TYPE        12        10        10        31         13
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  XQ LOSS MUTATED            6         16        6
  XQ LOSS WILD-TYPE         26         44       14
D82V5, multiclass
             clus
vv            XQ LOSS MUTATED XQ LOSS WILD-TYPE
  I OR II NOS               6                 6
  STAGE 0                   3                 4
  STAGE I                   5                23
  STAGE IA                  2                16
  STAGE IB                  8                19
  STAGE II                  9                15
  STAGE IIA                 2                12
  STAGE IIB                 9                10
  STAGE IIC                 2                10
  STAGE III                 6                31
  STAGE IIIA                2                13
  STAGE IIIB                6                26
  STAGE IIIC               16                44
  STAGE IV                  6                14
[1] 14  2
[1] TRUE
[1] "dimension of contingency 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      13 14 24 18
  XQ LOSS WILD-TYPE    51 58 53 50
D82V6, multiclass
       clus
vv      XQ LOSS MUTATED XQ LOSS WILD-TYPE
  T0+T1              13                51
  T2                 14                58
  T3                 24                53
  T4                 18                50
[1] 4 2
[1] TRUE
[1] "dimension of 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    46  17   4  13
  XQ LOSS WILD-TYPE 123  46  34  36
D82V7, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  N0              46               123
  N1              17                46
  N2               4                34
  N3              13                36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D82V8, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED    77   7
  XQ LOSS WILD-TYPE 236  14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     77    7
  XQ LOSS WILD-TYPE  236   14
   clus
vv  XQ LOSS MUTATED XQ LOSS WILD-TYPE
  0              77               236
  1               7                14
[1] 2 2
[1] FALSE
D82V9, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED    30  25
  XQ LOSS WILD-TYPE 102  63
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     30   25
  XQ LOSS WILD-TYPE  102   63
     clus
vv    XQ LOSS MUTATED XQ LOSS WILD-TYPE
  NO               30               102
  YES              25                63
[1] 2 2
[1] FALSE
D82V10, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED     8  84
  XQ LOSS WILD-TYPE  36 229
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      8   84
  XQ LOSS WILD-TYPE   36  229
     clus
vv    XQ LOSS MUTATED XQ LOSS WILD-TYPE
  NO                8                36
  YES              84               229
[1] 2 2
[1] FALSE
D82V11, continuous
D82V12, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED    42  50
  XQ LOSS WILD-TYPE  93 173
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     42   50
  XQ LOSS WILD-TYPE   93  173
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  FEMALE              42                93
  MALE                50               173
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  XQ LOSS MUTATED       1                         0    89
  XQ LOSS WILD-TYPE     4                         1   255
D82V13, multiclass
                           clus
vv                          XQ LOSS MUTATED XQ LOSS WILD-TYPE
  ASIAN                                   1                 4
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  89               255
[1] 3 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     2  87
  XQ LOSS WILD-TYPE   5 257
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      2   87
  XQ LOSS WILD-TYPE    5  257
                        clus
vv                       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                 5
  NOT HISPANIC OR LATINO              87               257
[1] 2 2
[1] FALSE
