[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/19775519/SKCM-TM.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/SKCM-TM/19784515/transformed.cor.cli.txt"

nPatients in clinical file=368, in cluster file=366, common to both=366
[1]  82 366
[1] "1P GAIN MUTATION ANALYSIS"
[1] 3
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               87               279 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               87               279 
[1] "1Q GAIN MUTATION ANALYSIS"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              171               195 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              171               195 
[1] "2P GAIN MUTATION ANALYSIS"
[1] 3
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               67               299 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               67               299 
[1] "2Q GAIN MUTATION ANALYSIS"
[1] 3
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               65               301 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               65               301 
[1] "3P GAIN MUTATION ANALYSIS"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               63               303 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               63               303 
[1] "3Q GAIN MUTATION ANALYSIS"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               72               294 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               72               294 
[1] "4P GAIN MUTATION ANALYSIS"
[1] 3
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               56               310 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               56               310 
[1] "4Q GAIN MUTATION ANALYSIS"
[1] 3
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               47               319 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               47               319 
[1] "5P GAIN MUTATION ANALYSIS"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               76               290 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               76               290 
[1] "5Q GAIN MUTATION ANALYSIS"
[1] 3
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               52               314 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               52               314 
[1] "6P GAIN MUTATION ANALYSIS"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
              144               222 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
              144               222 
[1] "6Q GAIN MUTATION ANALYSIS"
[1] 3
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               48               318 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               48               318 
[1] "7P GAIN MUTATION ANALYSIS"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              203               163 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              203               163 
[1] "7Q GAIN MUTATION ANALYSIS"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              200               166 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              200               166 
[1] "8P GAIN MUTATION ANALYSIS"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
              121               245 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
              121               245 
[1] "8Q GAIN MUTATION ANALYSIS"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              169               197 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              169               197 
[1] "9P GAIN MUTATION ANALYSIS"
[1] 3
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               16               350 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               16               350 
[1] "9Q GAIN MUTATION ANALYSIS"
[1] 3
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               21               345 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               21               345 
[1] "10P GAIN MUTATION ANALYSIS"
[1] 3
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                12                354 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                12                354 
[1] "10Q GAIN MUTATION ANALYSIS"
[1] 3
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 3                363 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 3                363 
[1] "11P GAIN MUTATION ANALYSIS"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                35                331 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                35                331 
[1] "11Q GAIN MUTATION ANALYSIS"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                29                337 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                29                337 
[1] "12P GAIN MUTATION ANALYSIS"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                65                301 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                65                301 
[1] "12Q GAIN MUTATION ANALYSIS"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                39                327 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                39                327 
[1] "13Q GAIN MUTATION ANALYSIS"
[1] 3
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                94                272 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                94                272 
[1] "14Q GAIN MUTATION ANALYSIS"
[1] 3
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                41                325 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                41                325 
[1] "15Q GAIN MUTATION ANALYSIS"
[1] 3
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                85                281 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                85                281 
[1] "16P GAIN MUTATION ANALYSIS"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                58                308 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                58                308 
[1] "16Q GAIN MUTATION ANALYSIS"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                44                322 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                44                322 
[1] "17P GAIN MUTATION ANALYSIS"
[1] 3
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                37                329 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                37                329 
[1] "17Q GAIN MUTATION ANALYSIS"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                65                301 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                65                301 
[1] "18P GAIN MUTATION ANALYSIS"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                55                311 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                55                311 
[1] "18Q GAIN MUTATION ANALYSIS"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                44                322 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                44                322 
[1] "19P GAIN MUTATION ANALYSIS"
[1] 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                57                309 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                57                309 
[1] "19Q GAIN MUTATION ANALYSIS"
[1] 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                56                310 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                56                310 
[1] "20P GAIN MUTATION ANALYSIS"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               147                219 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               147                219 
[1] "20Q GAIN MUTATION ANALYSIS"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               179                187 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               179                187 
[1] "21Q GAIN MUTATION ANALYSIS"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                67                299 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                67                299 
[1] "22Q GAIN MUTATION ANALYSIS"
[1] 3
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
               126                240 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
               126                240 
[1] "XP GAIN MUTATION ANALYSIS"
[1] 3
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               41               325 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               41               325 
[1] "XQ GAIN MUTATION ANALYSIS"
[1] 3
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               43               323 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               43               323 
[1] "1P LOSS MUTATION ANALYSIS"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               53               313 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               53               313 
[1] "1Q LOSS MUTATION ANALYSIS"
[1] 3
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               28               338 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               28               338 
[1] "2P LOSS MUTATION ANALYSIS"
[1] 3
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               51               315 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               51               315 
[1] "2Q LOSS MUTATION ANALYSIS"
[1] 3
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               52               314 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               52               314 
[1] "3P LOSS MUTATION ANALYSIS"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               61               305 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               61               305 
[1] "3Q LOSS MUTATION ANALYSIS"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               53               313 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               53               313 
[1] "4P LOSS MUTATION ANALYSIS"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               80               286 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               80               286 
[1] "4Q LOSS MUTATION ANALYSIS"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               85               281 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               85               281 
[1] "5P LOSS MUTATION ANALYSIS"
[1] 3
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               79               287 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               79               287 
[1] "5Q LOSS MUTATION ANALYSIS"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               99               267 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               99               267 
[1] "6P LOSS MUTATION ANALYSIS"
[1] 3
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               68               298 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               68               298 
[1] "6Q LOSS MUTATION ANALYSIS"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
              172               194 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
              172               194 
[1] "7P LOSS MUTATION ANALYSIS"
[1] 3
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               18               348 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               18               348 
[1] "7Q LOSS MUTATION ANALYSIS"
[1] 3
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               17               349 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               17               349 
[1] "8P LOSS MUTATION ANALYSIS"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               67               299 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               67               299 
[1] "8Q LOSS MUTATION ANALYSIS"
[1] 3
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               27               339 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               27               339 
[1] "9P LOSS MUTATION ANALYSIS"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              236               130 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              236               130 
[1] "9Q LOSS MUTATION ANALYSIS"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
              185               181 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
              185               181 
[1] "10P LOSS MUTATION ANALYSIS"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
               204                162 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
               204                162 
[1] "10Q LOSS MUTATION ANALYSIS"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
               224                142 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
               224                142 
[1] "11P LOSS MUTATION ANALYSIS"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
               126                240 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
               126                240 
[1] "11Q LOSS MUTATION ANALYSIS"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
               148                218 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
               148                218 
[1] "12P LOSS MUTATION ANALYSIS"
[1] 3
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                59                307 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                59                307 
[1] "12Q LOSS MUTATION ANALYSIS"
[1] 3
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                67                299 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                67                299 
[1] "13Q LOSS MUTATION ANALYSIS"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                80                286 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                80                286 
[1] "14Q LOSS MUTATION ANALYSIS"
[1] 3
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               112                254 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               112                254 
[1] "15Q LOSS MUTATION ANALYSIS"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                52                314 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                52                314 
[1] "16P LOSS MUTATION ANALYSIS"
[1] 3
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                68                298 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                68                298 
[1] "16Q LOSS MUTATION ANALYSIS"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
               106                260 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
               106                260 
[1] "17P LOSS MUTATION ANALYSIS"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               127                239 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               127                239 
[1] "17Q LOSS MUTATION ANALYSIS"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                64                302 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                64                302 
[1] "18P LOSS MUTATION ANALYSIS"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
               104                262 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
               104                262 
[1] "18Q LOSS MUTATION ANALYSIS"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               100                266 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               100                266 
[1] "19P LOSS MUTATION ANALYSIS"
[1] 3
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                77                289 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                77                289 
[1] "19Q LOSS MUTATION ANALYSIS"
[1] 3
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                73                293 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                73                293 
[1] "20P LOSS MUTATION ANALYSIS"
[1] 3
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                26                340 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                26                340 
[1] "20Q LOSS MUTATION ANALYSIS"
[1] 3
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 9                357 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 9                357 
[1] "21Q LOSS MUTATION ANALYSIS"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                70                296 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                70                296 
[1] "22Q LOSS MUTATION ANALYSIS"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                39                327 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                39                327 
[1] "XP LOSS MUTATION ANALYSIS"
[1] 3
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               97               269 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               97               269 
[1] "XQ LOSS MUTATION ANALYSIS"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               93               273 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               93               273 
[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] "PATHOLOGIC_STAGE"                    
 [7] "PATHOLOGY_T_STAGE"                   
 [8] "PATHOLOGY_N_STAGE"                   
 [9] "PATHOLOGY_M_STAGE"                   
[10] "MELANOMA_ULCERATION"                 
[11] "MELANOMA_PRIMARY_KNOWN"              
[12] "BRESLOW_THICKNESS"                   
[13] "GENDER"                              
[14] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"
[15] "RADIATION_THERAPY"                   
[16] "RACE"                                
[17] "ETHNICITY"                           

Input Data has 17 rows and 366 columns.

[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=188,	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=210,	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=287,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 6:'PATHOLOGIC_STAGE':	nDistinctValues=14,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY_T_STAGE':	nDistinctValues=15,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY_N_STAGE':	nDistinctValues=10,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY_M_STAGE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'MELANOMA_ULCERATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'MELANOMA_PRIMARY_KNOWN':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'BRESLOW_THICKNESS':	nDistinctValues=109,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 13:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'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 15:'RADIATION_THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "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 366 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"         "PATHOLOGIC_STAGE"       "PATHOLOGY_T_STAGE"     
 [4] "PATHOLOGY_N_STAGE"      "PATHOLOGY_M_STAGE"      "MELANOMA_ULCERATION"   
 [7] "MELANOMA_PRIMARY_KNOWN" "BRESLOW_THICKNESS"      "GENDER"                
[10] "RADIATION_THERAPY"      "RACE"                   "ETHNICITY"             
YEARS_TO_BIRTH, nv=68, binary=FALSE, numeric=TRUE
PATHOLOGIC_STAGE, 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 73 78 70 
[1] "table(vv)"
vv
T0+T1    T2    T3    T4 
   64    73    78    70 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
T0 T1 T2 T3 T4 
23 41 73 78 70 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


T0+T1    T2    T3    T4 
   64    73    78    70 
PATHOLOGY_N_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2  N3 
177  65  39  45 
[1] "table(vv)"
vv
 N0  N1  N2  N3 
177  65  39  45 
$ClinVariableName
[1] "PATHOLOGY_N_STAGE"

$Table
vv
 N0  N1  N2  N3 
177  65  39  45 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 N0  N1  N2  N3 
177  65  39  45 
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=109, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
RADIATION_THERAPY, 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 28
  1P GAIN WILD-TYPE 95 95
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               55               190 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               28                95 
$`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-DA-A95Y TCGA-DA-A95Z TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A181 
       69.21        14.14        12.30        24.89        62.37        20.38 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A2 
       12.99         0.26        44.28       346.49       185.19        30.02 
TCGA-EE-A2GM TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2M6 TCGA-EE-A2MJ TCGA-EE-A2MM 
       18.35         0.76        71.31       103.13        63.25       145.45 
TCGA-EE-A2MR TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3J7 TCGA-ER-A199 TCGA-ER-A19G 
       25.08        53.26       122.73        45.90         7.82       151.46 
TCGA-ER-A3ET TCGA-ER-A3PL TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7UA TCGA-FS-A1Z0 
       68.52        32.05       174.21       209.23         5.65       195.98 
TCGA-FS-A1ZQ TCGA-FS-A1ZU TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A8LK 
      130.95         4.47        17.06         7.59       120.53        43.23 
TCGA-W3-A828 TCGA-W3-AA1Q TCGA-W3-AA1W TCGA-WE-A8K1 TCGA-WE-A8ZY TCGA-WE-AAA0 
      120.07        44.05       185.13         1.15        48.39        31.99 
TCGA-YG-AA3O 
       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        76.34       138.67 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC 
       53.65       150.61        95.51        45.07        64.83        58.85 
TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A95V TCGA-DA-A95X TCGA-EB-A44Q TCGA-EB-A5SG 
       30.44       225.11        72.10        52.90         3.91        33.24 
TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A182 TCGA-EE-A184 
       50.07        52.41        18.21        13.15         0.00        67.50 
TCGA-EE-A20C TCGA-EE-A20H TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29H TCGA-EE-A29M 
       75.55       155.90        75.22        76.14        63.12        47.74 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A2A1 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD 
       27.16        61.12       115.43        77.98        26.14       239.11 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN 
       12.95       201.60        68.65        10.62        32.48        31.00 
TCGA-EE-A2GO TCGA-EE-A2GR TCGA-EE-A2GU TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC 
      118.32         0.20        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        89.26       104.78       227.01 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
      143.93        23.51       124.31        64.04         4.41        54.51 
TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH 
        6.28        67.89       111.85         3.35       201.80        19.86 
TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A19A 
      152.81        14.56        34.45         1.58        47.31         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        47.18       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-ER-A42L TCGA-FR-A7U8 TCGA-FR-A8YC TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z3 
       74.47        26.20        10.06       171.78        49.74         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        42.08        12.92         7.82 
TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A1ZY 
       36.33        78.61       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-A4EO TCGA-GF-A6C8 
       55.59        11.54        19.30         9.90         6.05         1.91 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A268 TCGA-GN-A4U4 TCGA-GN-A4U8 
       53.29       117.93        96.92        42.48        34.49        46.92 
TCGA-GN-A9SD TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A690 
       59.41        85.05       297.01         7.23        18.05         0.20 
TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-AA1R TCGA-W3-AA1V TCGA-W3-AA21 
        0.33       174.12         1.97        79.99         8.09        92.84 
TCGA-WE-A8K5 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT 
       59.64        65.42        12.69        21.90        62.89        10.95 
TCGA-WE-AA9Y TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-Z2-AA3S 
        1.94        18.31        18.35        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 
           45.900            47.245 
[1] "0.3 - 346.5 (45.9)" "0.0 - 312.1 (47.2)"
[1] "hr=" "1.1"
D1V2, survival
                   sevent
clus2                 0   1
  1P GAIN MUTATED    39  46
  1P GAIN WILD-TYPE 131 141
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               85               272 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               46               141 
$`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-DA-A95Y TCGA-DA-A95Z TCGA-EB-A5UL TCGA-EE-A17Y 
       77.56        20.38        14.14        13.02        29.29        27.22 
TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A29D TCGA-EE-A29E 
       94.98        33.73        26.89       133.81        13.97        63.78 
TCGA-EE-A29G TCGA-EE-A29L TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A2 
       72.07         2.60       369.93       195.02        17.92        59.64 
TCGA-EE-A2GI TCGA-EE-A2GM TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2M6 TCGA-EE-A2MD 
       48.72        75.48        13.91        81.21       129.27        47.28 
TCGA-EE-A2MJ TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MU 
       96.23       167.90        47.54        43.23       134.40        53.26 
TCGA-EE-A3AB TCGA-EE-A3AG TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-ER-A199 TCGA-ER-A19F 
      122.73        41.59        64.08        53.19         9.17        26.37 
TCGA-ER-A19G TCGA-ER-A3ET TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A 
      268.93        93.01        33.21        12.95        92.98       174.21 
TCGA-FR-A729 TCGA-FR-A7UA TCGA-FS-A1YX TCGA-FS-A1Z0 TCGA-FS-A1ZH TCGA-FS-A1ZQ 
      220.80        38.27        48.59       202.65        32.75       133.55 
TCGA-FS-A1ZU TCGA-FS-A4F5 TCGA-GF-A6C9 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A26A 
       26.56        28.73        15.78        10.13        64.44        32.48 
TCGA-GN-A4U3 TCGA-GN-A8LK TCGA-HR-A2OG TCGA-HR-A2OH TCGA-W3-A828 TCGA-W3-AA1O 
      121.91        50.10         0.23        65.88       121.08         4.01 
TCGA-W3-AA1Q TCGA-W3-AA1W TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8ZY TCGA-WE-AAA0 
       69.07       219.16        24.03        49.05        49.51        40.41 
TCGA-YG-AA3O 
       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-D3-A8GV TCGA-D9-A148 
      152.75        29.06       129.63       117.17       167.70       151.53 
TCGA-D9-A149 TCGA-D9-A1JX TCGA-D9-A1X3 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6EG 
       54.67         7.10        18.12        22.29        18.44        22.95 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 
       76.57        36.03       144.89       207.48       176.55        35.93 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
      120.00        73.84        53.92        65.92        40.60        68.09 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-DA-A95V TCGA-DA-A95W 
       33.93        10.49       225.96        15.68        72.10        25.15 
TCGA-DA-A95X TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH 
       61.81        13.87        10.36        20.35        68.25        54.02 
TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A182 
       58.92         7.04        36.46        29.82         8.65        14.70 
TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I 
       68.15         4.96       151.27        91.56       168.26        13.55 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N 
       63.35        85.08        78.97        64.64        56.84        18.61 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A2A0 
       56.42        66.74        14.47        61.28        25.87        46.82 
TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD 
      115.96        39.29        86.14        59.28        67.43       340.14 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN 
      173.79       220.24       107.38        54.74        79.66       102.12 
TCGA-EE-A2GO TCGA-EE-A2GR TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M7 
      126.81        42.77        44.88        94.82        21.67        28.83 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH 
       19.76        61.51       103.27       268.73       103.20        16.96 
TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MT 
      204.66       180.39       216.66       248.65       162.48        71.21 
TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AH 
      124.31        64.04        28.77        54.51        13.81       138.81 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JD 
      172.18       127.20        36.95        34.32       201.80        27.35 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
       51.35       134.33       152.81        31.40        35.44        13.94 
TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E 
       50.76        77.75        98.40        48.89        12.59        13.02 
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        49.48         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-A42L TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A8YC 
       46.98       149.03        15.72        27.85        18.77        34.82 
TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1Z4 
       36.26       104.42       216.92       228.59        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        46.45 
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-A1ZT TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ 
       11.41       148.80        53.16        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-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-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-A26D TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 
       96.92        62.79        48.00        39.35        10.42        48.89 
TCGA-GN-A4U9 TCGA-GN-A8LL TCGA-GN-A9SD TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS 
       22.13        21.37        59.41       368.78       297.90         7.23 
TCGA-QB-AA9O TCGA-RP-A690 TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 
       18.05         0.20         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        17.95       101.33 
TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-AA9Y 
       58.98        70.52        63.22        11.80        35.80        12.16 
TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YD-A89C TCGA-YD-A9TA TCGA-YG-AA3P TCGA-Z2-A8RT 
       21.40        24.99         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             53.34 
[1] "0.2 - 369.9 (50.1)" "0.2 - 368.8 (53.3)"
[1] "hr=" "1"  
D1V3, continuous
                   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          10       4      22       13       20       17
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  1P GAIN MUTATED           1         2         3        11          9
  1P GAIN WILD-TYPE        13        17        12        29          6
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  1P GAIN MUTATED            6         10        4
  1P GAIN WILD-TYPE         27         45       17
D1V4, multiclass
             clus
vv            1P GAIN MUTATED 1P GAIN WILD-TYPE
  I OR II NOS               3                10
  STAGE 0                   3                 4
  STAGE I                   7                22
  STAGE IA                  5                13
  STAGE IB                  8                20
  STAGE II                  8                17
  STAGE IIA                 1                13
  STAGE IIB                 2                17
  STAGE IIC                 3                12
  STAGE III                11                29
  STAGE IIIA                9                 6
  STAGE IIIB                6                27
  STAGE IIIC               10                45
  STAGE IV                  4                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 19
  1P GAIN WILD-TYPE    50 58 56 51
D1V5, multiclass
       clus
vv      1P GAIN MUTATED 1P GAIN WILD-TYPE
  T0+T1              14                50
  T2                 15                58
  T3                 22                56
  T4                 19                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
  1P GAIN MUTATED    44  19   9   8
  1P GAIN WILD-TYPE 133  46  30  37
D1V6, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  N0              44               133
  N1              19                46
  N2               9                30
  N3               8                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"
D1V7, binary
                   cls
clus                  0   1
  1P GAIN MUTATED    78   4
  1P GAIN WILD-TYPE 240  18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     78    4
  1P GAIN WILD-TYPE  240   18
   clus
vv  1P GAIN MUTATED 1P GAIN WILD-TYPE
  0              78               240
  1               4                18
[1] 2 2
[1] FALSE
D1V8, binary
                   cls
clus                 0  1
  1P GAIN MUTATED   37 21
  1P GAIN WILD-TYPE 97 69
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     37   21
  1P GAIN WILD-TYPE   97   69
     clus
vv    1P GAIN MUTATED 1P GAIN WILD-TYPE
  NO               37                97
  YES              21                69
[1] 2 2
[1] FALSE
D1V9, binary
                   cls
clus                  0   1
  1P GAIN MUTATED    10  77
  1P GAIN WILD-TYPE  37 242
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     10   77
  1P GAIN WILD-TYPE   37  242
     clus
vv    1P GAIN MUTATED 1P GAIN WILD-TYPE
  NO               10                37
  YES              77               242
[1] 2 2
[1] FALSE
D1V10, continuous
D1V11, binary
                   cls
clus                  0   1
  1P GAIN MUTATED    29  58
  1P GAIN WILD-TYPE 108 171
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     29   58
  1P GAIN WILD-TYPE  108  171
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  FEMALE              29               108
  MALE                58               171
[1] 2 2
[1] FALSE
D1V12, binary
                   cls
clus                  0   1
  1P GAIN MUTATED    71  16
  1P GAIN WILD-TYPE 246  31
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     71   16
  1P GAIN WILD-TYPE  246   31
     clus
vv    1P GAIN MUTATED 1P GAIN WILD-TYPE
  NO               71               246
  YES              16                31
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  1P GAIN MUTATED       1                         0    82
  1P GAIN WILD-TYPE     4                         1   270
D1V13, multiclass
                           clus
vv                          1P GAIN MUTATED 1P GAIN WILD-TYPE
  ASIAN                                   1                 4
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  82               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"
D1V14, binary
                   cls
clus                  0   1
  1P GAIN MUTATED     2  81
  1P GAIN WILD-TYPE   5 270
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      2   81
  1P GAIN WILD-TYPE    5  270
                        clus
vv                       1P GAIN MUTATED 1P GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 5
  NOT HISPANIC OR LATINO              81               270
[1] 2 2
[1] FALSE

Clustering(2) Variable = 1Q GAIN MUTATION ANALYSIS
D2V1, survival
                   sevent
clus2                0  1
  1Q GAIN MUTATED   58 61
  1Q GAIN WILD-TYPE 64 62
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              119               126 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               61                62 
$`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        69.21        22.85        53.65        95.51        64.83 
TCGA-DA-A1IC TCGA-DA-A3F5 TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A5SH TCGA-EB-A5UN 
       58.85       225.11        14.14        12.30        50.07        52.41 
TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A184 TCGA-EE-A29B TCGA-EE-A29D 
       24.89        62.37        20.38        67.50        75.22        12.99 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29M TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 
        0.26        44.28        47.74       346.49       185.19       115.43 
TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GM 
       30.02        77.98       239.11        12.95       201.60        18.35 
TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M7 TCGA-EE-A2MJ 
       31.00       118.32        71.31        81.99        15.25        63.25 
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        64.04 
TCGA-EE-A3AD TCGA-EE-A3J7 TCGA-EE-A3JH TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19D 
        4.41        45.90        19.86         1.58         7.82        11.47 
TCGA-ER-A19G TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A2ND TCGA-ER-A3ET TCGA-ER-A3PL 
      151.46       120.76        49.71         4.70        68.52        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-A1ZC TCGA-FS-A1ZF TCGA-FS-A1ZQ TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZY 
      312.07        12.92       130.95        35.28         4.47         5.29 
TCGA-FS-A1ZZ TCGA-FS-A4FD TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 
        3.06        80.68        17.06         7.59       120.53        34.49 
TCGA-GN-A4U8 TCGA-GN-A8LK TCGA-GN-A9SD TCGA-LH-A9QB TCGA-QB-A6FS TCGA-W3-A825 
       46.92        43.23        59.41        85.05         7.23         1.97 
TCGA-W3-A828 TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 
      120.07        44.05        79.99       185.13        92.84         1.15 
TCGA-WE-A8ZO TCGA-WE-A8ZY TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-YG-AA3O 
       21.90        48.39        31.99        18.35        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        76.34       138.67       150.61        45.07 
TCGA-DA-A3F2 TCGA-DA-A95V TCGA-DA-A95X TCGA-EB-A44Q TCGA-EB-A5SG TCGA-EB-A6L9 
       30.44        72.10        52.90         3.91        33.24        18.21 
TCGA-EE-A17X TCGA-EE-A182 TCGA-EE-A20C TCGA-EE-A20H TCGA-EE-A29C TCGA-EE-A29H 
       13.15         0.00        75.55       155.90        76.14        63.12 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A2GB TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
       27.16        61.12        26.14        68.65        10.62        32.48 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2M6 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MF 
        0.76         0.20       103.13         5.75        23.77       209.79 
TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP 
       94.19       171.85        89.26       104.78       145.45       227.01 
TCGA-EE-A3AA TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J8 
      124.31        54.51         6.28        67.89       111.85         3.35 
TCGA-EE-A3JB TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A19A 
      201.80       152.81        14.56        34.45        47.31         4.54 
TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
       53.29        39.81       150.12        99.06        59.84        42.48 
TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NG 
       47.18       146.63        47.97        22.36        16.87        10.95 
TCGA-ER-A3ES TCGA-ER-A3EV TCGA-ER-A42L TCGA-FR-A7U8 TCGA-FS-A1YW TCGA-FS-A1YY 
      173.29        15.48        74.47        26.20       171.78        49.74 
TCGA-FS-A1Z4 TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM 
       27.62        32.78        42.08         7.82        36.33        78.61 
TCGA-FS-A1ZS TCGA-FS-A1ZW TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 
      136.27        23.21        30.90        66.67       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-A264 TCGA-GN-A265 TCGA-GN-A268 TCGA-OD-A75X TCGA-QB-AA9O 
       53.29       117.93        96.92        42.48       297.01        18.05 
TCGA-RP-A690 TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-AA1V TCGA-WE-A8K5 TCGA-WE-A8ZM 
        0.20         0.33       174.12         8.09        59.64        65.42 
TCGA-WE-A8ZN TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-AA9Y TCGA-WE-AAA3 TCGA-Z2-AA3S 
       12.69        62.89        10.95         1.94        18.31        91.23 

  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
             0.26              0.00 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
           346.49            297.01 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
           46.920            47.245 
[1] "0.3 - 346.5 (46.9)" "0.0 - 297.0 (47.2)"
[1] "hr=" "1"  
D2V2, survival
                   sevent
clus2                0  1
  1Q GAIN MUTATED   76 91
  1Q GAIN WILD-TYPE 94 96
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              167               190 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               91                96 
$`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        77.56        22.95 
TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1IA TCGA-DA-A1IC 
       20.38       207.48        35.93       120.00        65.92        68.09 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44R TCGA-EB-A5SH 
       10.49       225.96        14.14        13.02        10.36        54.02 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 
       29.29        58.92        27.22         8.65        94.98        33.73 
TCGA-EE-A184 TCGA-EE-A20B TCGA-EE-A20I TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29E 
       68.15       133.81        13.55        85.08        13.97        63.78 
TCGA-EE-A29G TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T 
       72.07         2.60        56.84        14.47        61.28       369.93 
TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GD TCGA-EE-A2GE 
      195.02       115.96        59.64        86.14       340.14       173.79 
TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GS 
      220.24        48.72        75.48       102.12       126.81        81.21 
TCGA-EE-A2GU TCGA-EE-A2M7 TCGA-EE-A2MD TCGA-EE-A2MJ TCGA-EE-A2MN TCGA-EE-A2MQ 
       94.82        28.83        47.28        96.23        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        64.04 
TCGA-EE-A3AD TCGA-EE-A3AG TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-EE-A3JH TCGA-ER-A197 
       28.77        41.59        64.08        53.19       134.33        13.94 
TCGA-ER-A199 TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19P TCGA-ER-A19Q 
        9.17        12.59        26.37       268.93       162.08        50.89 
TCGA-ER-A2ND TCGA-ER-A2NF TCGA-ER-A2NH TCGA-ER-A3ET TCGA-ER-A3PL TCGA-ER-A42K 
       23.34        16.37        32.05        93.01        33.21        12.95 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FS-A1YX 
       92.98       174.21       220.80        38.27        34.82        48.59 
TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1ZA TCGA-FS-A1ZC TCGA-FS-A1ZF TCGA-FS-A1ZH 
      202.65        20.91        27.72       357.37        15.45        32.75 
TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZY 
       23.93        74.73       133.55        53.16        26.56        27.09 
TCGA-FS-A1ZZ TCGA-FS-A4F5 TCGA-FS-A4FD TCGA-GF-A6C9 TCGA-GN-A266 TCGA-GN-A267 
       27.02        28.73        80.68        15.78        10.13        64.44 
TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 
       32.48        48.00       121.91        39.35        10.42        48.89 
TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A9SD TCGA-HR-A2OG TCGA-HR-A2OH TCGA-LH-A9QB 
       22.13        50.10        59.41         0.23        65.88       368.78 
TCGA-QB-A6FS TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1Q TCGA-W3-AA1R 
        7.23        63.02       121.08         4.01        69.07       111.09 
TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8ZO TCGA-WE-A8ZX 
      219.16       105.04        24.03        49.05        70.52        35.80 
TCGA-WE-A8ZY TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-YD-A9TA TCGA-YG-AA3O 
       49.51        40.41        24.99        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-D3-A8GV TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JX TCGA-D9-A1X3 
      117.17       167.70       151.53        54.67         7.10        18.12 
TCGA-D9-A4Z6 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I2 TCGA-DA-A1I7 
       18.44        76.57        36.03       144.89       176.55        73.84 
TCGA-DA-A1I8 TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-DA-A3F8 TCGA-DA-A95V TCGA-DA-A95W 
       53.92        40.60        33.93        15.68        72.10        25.15 
TCGA-DA-A95X TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5VV TCGA-EB-A6L9 
       61.81        13.87        20.35        68.25         7.04        36.46 
TCGA-EE-A17X TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A20F 
       29.82        14.70        26.89         4.96       151.27        91.56 
TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29H TCGA-EE-A29N TCGA-EE-A29P 
      168.26        63.35        78.97        64.64        18.61        56.42 
TCGA-EE-A29Q TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A5 TCGA-EE-A2GB 
       66.74        25.87        17.92        46.82        39.29        59.28 
TCGA-EE-A2GC TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GP TCGA-EE-A2GR 
       67.43       107.38        54.74        79.66        13.91        42.77 
TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2ME 
       44.88        21.67       129.27        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       180.39       216.66 
TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A3AA TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AH 
      167.90       248.65       124.31        54.51        13.81       138.81 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JD 
      172.18       127.20        36.95        34.32       201.80        27.35 
TCGA-EE-A3JE TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A19A 
       51.35       152.81        31.40        35.44        50.76        77.75 
TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19E TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L 
       98.40        48.89        13.02       152.35         6.44       131.51 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 
       61.05        44.05        49.48         8.88       148.18        79.99 
TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3EV TCGA-ER-A42L 
       43.82        20.15        31.27       247.04        46.98       149.03 
TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW 
       15.72        27.85        18.77        36.26       104.42       216.92 
TCGA-FS-A1YY TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZB TCGA-FS-A1ZD TCGA-FS-A1ZE 
      228.59        28.08         7.79        48.85        53.52        46.45 
TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZW 
        9.70        47.38       101.26        11.41       148.80        49.48 
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-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-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        9.90         7.23         2.04       139.89       117.93        96.92 
TCGA-GN-A268 TCGA-GN-A8LL TCGA-OD-A75X TCGA-QB-AA9O TCGA-RP-A690 TCGA-RP-A693 
       62.79        21.37       297.90        18.05         0.20         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        17.95       101.33 
TCGA-WE-A8ZN TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-AA9Y TCGA-WE-AAA3 TCGA-YD-A89C 
       58.98        63.22        11.80        12.16        21.40         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 
           53.190            51.055 
[1] "0.2 - 369.9 (53.2)" "0.2 - 297.9 (51.1)"
[1] "hr=" "1"  
D2V3, continuous
                   vv
clus                I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  1Q GAIN MUTATED             4       3      10        9       16       16
  1Q GAIN WILD-TYPE           9       4      19        9       12        9
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  1Q GAIN MUTATED           6         8         7        20         12
  1Q GAIN WILD-TYPE         8        11         8        20          3
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  1Q GAIN MUTATED           17         22        8
  1Q GAIN WILD-TYPE         16         33       13
D2V4, multiclass
             clus
vv            1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  I OR II NOS               4                 9
  STAGE 0                   3                 4
  STAGE I                  10                19
  STAGE IA                  9                 9
  STAGE IB                 16                12
  STAGE II                 16                 9
  STAGE IIA                 6                 8
  STAGE IIB                 8                11
  STAGE IIC                 7                 8
  STAGE III                20                20
  STAGE IIIA               12                 3
  STAGE IIIB               17                16
  STAGE IIIC               22                33
  STAGE IV                  8                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 31
  1Q GAIN WILD-TYPE    34 38 35 39
D2V5, multiclass
       clus
vv      1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  T0+T1              30                34
  T2                 35                38
  T3                 43                35
  T4                 31                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
  1Q GAIN MUTATED   85 29 23 18
  1Q GAIN WILD-TYPE 92 36 16 27
D2V6, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  N0              85                92
  N1              29                36
  N2              23                16
  N3              18                27
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V7, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED   153   8
  1Q GAIN WILD-TYPE 165  14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED    153    8
  1Q GAIN WILD-TYPE  165   14
   clus
vv  1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  0             153               165
  1               8                14
[1] 2 2
[1] FALSE
D2V8, binary
                   cls
clus                 0  1
  1Q GAIN MUTATED   69 41
  1Q GAIN WILD-TYPE 65 49
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     69   41
  1Q GAIN WILD-TYPE   65   49
     clus
vv    1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  NO               69                65
  YES              41                49
[1] 2 2
[1] FALSE
D2V9, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED    19 152
  1Q GAIN WILD-TYPE  28 167
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     19  152
  1Q GAIN WILD-TYPE   28  167
     clus
vv    1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  NO               19                28
  YES             152               167
[1] 2 2
[1] FALSE
D2V10, continuous
D2V11, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED    61 110
  1Q GAIN WILD-TYPE  76 119
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     61  110
  1Q GAIN WILD-TYPE   76  119
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  FEMALE              61                76
  MALE               110               119
[1] 2 2
[1] FALSE
D2V12, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED   146  25
  1Q GAIN WILD-TYPE 171  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED    146   25
  1Q GAIN WILD-TYPE  171   22
     clus
vv    1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  NO              146               171
  YES              25                22
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  1Q GAIN MUTATED       2                         0   164
  1Q GAIN WILD-TYPE     3                         1   188
D2V13, multiclass
                           clus
vv                          1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  ASIAN                                   2                 3
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                 164               188
[1] 3 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     5 162
  1Q GAIN WILD-TYPE   2 189
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      5  162
  1Q GAIN WILD-TYPE    2  189
                        clus
vv                       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   5                 2
  NOT HISPANIC OR LATINO             162               189
[1] 2 2
[1] FALSE

Clustering(3) Variable = 2P GAIN MUTATION ANALYSIS
D3V1, survival
                   sevent
clus2                 0   1
  2P GAIN MUTATED    21  23
  2P GAIN WILD-TYPE 101 100
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               44               201 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               23               100 
$`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-EB-A5SH TCGA-EE-A20H TCGA-EE-A29D TCGA-EE-A29M 
      138.67       225.11        50.07       155.90        12.99        47.74 
TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2GM TCGA-EE-A2GN 
       61.12       346.49       185.19       115.43        18.35        31.00 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MR TCGA-EE-A2MU TCGA-EE-A3AE TCGA-EE-A3JB 
      103.13        15.25        25.08        53.26        54.51       201.80 
TCGA-EE-A3JI TCGA-ER-A197 TCGA-ER-A19B TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19N 
      152.81         1.58        53.29       151.46       150.12        42.48 
TCGA-ER-A2NC TCGA-ER-A42L TCGA-FS-A1ZD TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-QB-AA9O 
       22.36        74.47        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        69.21        22.85        76.34 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC 
       53.65       150.61        95.51        45.07        64.83        58.85 
TCGA-DA-A3F2 TCGA-DA-A95V TCGA-DA-A95X TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q 
       30.44        72.10        52.90        14.14        12.30         3.91 
TCGA-EB-A5SG TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A180 
       33.24        52.41        18.21        13.15        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-A29H TCGA-EE-A29P TCGA-EE-A2A2 TCGA-EE-A2A6 
        0.26        44.28        63.12        27.16        30.02        77.98 
TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK 
       26.14       239.11        12.95       201.60        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-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-A2MS TCGA-EE-A2MT 
       89.26       104.78       145.45       227.01       143.93        23.51 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3J3 
      124.31       122.73        64.04         4.41         6.28        67.89 
TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 
      111.85        45.90         3.35        19.86        14.56        34.45 
TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19L 
       47.31         7.82         4.54        39.81        11.47        99.06 
TCGA-ER-A19M TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 
       59.84       120.76        49.71        47.18       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        68.52        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-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZS TCGA-FS-A1ZT 
       42.08        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-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        96.92 
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-A690 
       43.23        59.41        85.05       297.01         7.23         0.20 
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        65.42        12.69 
TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 
       21.90        62.89        10.95         1.94        31.99        18.31 
TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-Z2-AA3S 
       18.35        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 
           51.665            45.900 
[1] "1.6 - 346.5 (51.7)" "0.0 - 312.1 (45.9)"
[1] "hr=" "1.1"
D3V2, survival
                   sevent
clus2                 0   1
  2P GAIN MUTATED    32  33
  2P GAIN WILD-TYPE 138 154
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               65               292 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               33               154 
$`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 
      144.89        53.92       225.96        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       115.96        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-ER-A42L TCGA-FR-A3YN TCGA-FS-A1ZD TCGA-FS-A1ZK 
       44.05        43.82       149.03        92.98        53.52        23.93 
TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FW-A3I3 TCGA-QB-AA9O TCGA-W3-A825 TCGA-W3-AA1O 
      101.26       133.55         0.20        18.05        63.02         4.01 
TCGA-WE-A8JZ TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-YD-A89C TCGA-YD-A9TA 
       24.03        35.80        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-D3-A8GV TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX 
      129.63       117.17       167.70        54.67         3.65         7.10 
TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6EA TCGA-D9-A6EC 
       18.12        15.39        22.29        18.44        25.18        77.56 
TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 
       22.95        76.57        36.03        20.38       207.48       176.55 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
       35.93       120.00        73.84        65.92        40.60        68.09 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A95V TCGA-DA-A95W TCGA-DA-A95X TCGA-DA-A95Y 
       33.93        10.49        72.10        25.15        61.81        14.14 
TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5UL 
       13.02        13.87        10.36        20.35        68.25        29.29 
TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
       58.92         7.04        36.46        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        59.64        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       173.79       220.24        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       180.39       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        64.04 
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       134.33 
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        49.48         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        93.01 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 
       46.98        33.21        12.95       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        46.45        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 
       96.92        10.13        64.44        62.79        32.48        48.00 
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-A690 TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A828 
        7.23         0.20         0.33         0.69       228.16       121.08 
TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 
       69.07       111.09        42.08       219.16       105.04        49.05 
TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ 
       61.15        17.95       101.33        58.98        70.52        63.22 
TCGA-WE-A8ZT TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O 
       11.80        12.16        40.41        21.40        24.99        37.94 
TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
       14.43        27.58        96.99        15.98 

  2P GAIN MUTATED 2P GAIN WILD-TYPE 
              0.2               0.2 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
           369.93            368.78 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
            56.84             49.79 
[1] "0.2 - 369.9 (56.8)" "0.2 - 368.8 (49.8)"
[1] "hr=" "1.1"
D3V3, continuous
                   vv
clus                I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  2P GAIN MUTATED             3       2       6        4        5        5
  2P GAIN WILD-TYPE          10       5      23       14       23       20
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  2P GAIN MUTATED           3         1         3         8          4
  2P GAIN WILD-TYPE        11        18        12        32         11
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  2P GAIN MUTATED            6          9        1
  2P GAIN WILD-TYPE         27         46       20
D3V4, multiclass
             clus
vv            2P GAIN MUTATED 2P GAIN WILD-TYPE
  I OR II NOS               3                10
  STAGE 0                   2                 5
  STAGE I                   6                23
  STAGE IA                  4                14
  STAGE IB                  5                23
  STAGE II                  5                20
  STAGE IIA                 3                11
  STAGE IIB                 1                18
  STAGE IIC                 3                12
  STAGE III                 8                32
  STAGE IIIA                4                11
  STAGE IIIB                6                27
  STAGE IIIC                9                46
  STAGE IV                  1                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
  2P GAIN MUTATED      10 17 12 12
  2P GAIN WILD-TYPE    54 56 66 58
D3V5, multiclass
       clus
vv      2P GAIN MUTATED 2P GAIN WILD-TYPE
  T0+T1              10                54
  T2                 17                56
  T3                 12                66
  T4                 12                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
  2P GAIN MUTATED    35  13   7   7
  2P GAIN WILD-TYPE 142  52  32  38
D3V6, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  N0              35               142
  N1              13                52
  N2               7                32
  N3               7                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"
D3V7, binary
                   cls
clus                  0   1
  2P GAIN MUTATED    63   2
  2P GAIN WILD-TYPE 255  20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     63    2
  2P GAIN WILD-TYPE  255   20
   clus
vv  2P GAIN MUTATED 2P GAIN WILD-TYPE
  0              63               255
  1               2                20
[1] 2 2
[1] FALSE
D3V8, binary
                   cls
clus                  0   1
  2P GAIN MUTATED    22  17
  2P GAIN WILD-TYPE 112  73
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     22   17
  2P GAIN WILD-TYPE  112   73
     clus
vv    2P GAIN MUTATED 2P GAIN WILD-TYPE
  NO               22               112
  YES              17                73
[1] 2 2
[1] FALSE
D3V9, binary
                   cls
clus                  0   1
  2P GAIN MUTATED     8  59
  2P GAIN WILD-TYPE  39 260
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      8   59
  2P GAIN WILD-TYPE   39  260
     clus
vv    2P GAIN MUTATED 2P GAIN WILD-TYPE
  NO                8                39
  YES              59               260
[1] 2 2
[1] FALSE
D3V10, continuous
D3V11, binary
                   cls
clus                  0   1
  2P GAIN MUTATED    24  43
  2P GAIN WILD-TYPE 113 186
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     24   43
  2P GAIN WILD-TYPE  113  186
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  FEMALE              24               113
  MALE                43               186
[1] 2 2
[1] FALSE
D3V12, binary
                   cls
clus                  0   1
  2P GAIN MUTATED    56  10
  2P GAIN WILD-TYPE 261  37
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     56   10
  2P GAIN WILD-TYPE  261   37
     clus
vv    2P GAIN MUTATED 2P GAIN WILD-TYPE
  NO               56               261
  YES              10                37
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  2P GAIN MUTATED       0                         0    66
  2P GAIN WILD-TYPE     5                         1   286
D3V13, multiclass
                           clus
vv                          2P GAIN MUTATED 2P GAIN WILD-TYPE
  ASIAN                                   0                 5
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  66               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"
D3V14, binary
                   cls
clus                  0   1
  2P GAIN MUTATED     0  65
  2P GAIN WILD-TYPE   7 286
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      0   65
  2P GAIN WILD-TYPE    7  286
                        clus
vv                       2P GAIN MUTATED 2P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 7
  NOT HISPANIC OR LATINO              65               286
[1] 2 2
[1] FALSE

Clustering(4) Variable = 2Q GAIN MUTATION ANALYSIS
D4V1, survival
                   sevent
clus2                 0   1
  2Q GAIN MUTATED    22  19
  2Q GAIN WILD-TYPE 100 104
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               41               204 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               19               104 
$`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-EB-A5SH TCGA-EE-A20H TCGA-EE-A29M 
       78.21       138.67       225.11        50.07       155.90        47.74 
TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2GM TCGA-EE-A2GN 
       61.12       346.49       185.19       115.43        18.35        31.00 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MR TCGA-EE-A2MU TCGA-EE-A3AE TCGA-EE-A3JB 
      103.13        15.25        25.08        53.26        54.51       201.80 
TCGA-EE-A3JI TCGA-ER-A19B TCGA-ER-A19G TCGA-ER-A19N TCGA-ER-A2NC TCGA-ER-A42L 
      152.81        53.29       151.46        42.48        22.36        74.47 
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        69.21        22.85        76.34        53.65 
TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 
      150.61        95.51        45.07        64.83        58.85        30.44 
TCGA-DA-A95V TCGA-DA-A95X TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5SG 
       72.10        52.90        14.14        12.30         3.91        33.24 
TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A181 
       52.41        18.21        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-A29P TCGA-EE-A2A2 TCGA-EE-A2A6 
        0.26        44.28        63.12        27.16        30.02        77.98 
TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK 
       26.14       239.11        12.95       201.60        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-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-A2MS TCGA-EE-A2MT 
       89.26       104.78       145.45       227.01       143.93        23.51 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3J3 
      124.31       122.73        64.04         4.41         6.28        67.89 
TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 
      111.85        45.90         3.35        19.86        14.56        34.45 
TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19C TCGA-ER-A19D 
        1.58        47.31         7.82         4.54        39.81        11.47 
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        47.18 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A3ES 
      146.63        47.97         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 
       68.52        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-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZJ 
       27.62       312.07        42.08        12.92         7.82        36.33 
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-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
       53.29       117.93        96.92        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-RP-A690 TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A828 TCGA-W3-AA1Q 
        7.23         0.20         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 
       65.42        12.69        21.90        62.89        10.95        48.39 
TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-Z2-AA3S 
        1.94        31.99        18.31        18.35        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 
           53.290            45.485 
[1] "2.0 - 346.5 (53.3)" "0.0 - 312.1 (45.5)"
[1] "hr=" "1.3"
D4V2, survival
                   sevent
clus2                 0   1
  2Q GAIN MUTATED    33  29
  2Q GAIN WILD-TYPE 137 158
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               62               295 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               29               158 
$`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 
      144.89        53.92       225.96        15.68        54.02        29.29 
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       115.96        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-ER-A42L TCGA-FR-A3YN TCGA-FS-A1ZD TCGA-FS-A1ZM TCGA-FS-A4F5 TCGA-FW-A3I3 
      149.03        92.98        53.52       101.26        28.73         0.20 
TCGA-GN-A9SD TCGA-QB-AA9O TCGA-W3-A825 TCGA-W3-AA1O TCGA-WE-A8JZ TCGA-WE-A8ZX 
       59.41        18.05        63.02         4.01        24.03        35.80 
TCGA-YD-A89C TCGA-YD-A9TA 
        6.90        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-D3-A8GV TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX 
      117.17       167.70       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-A6EC 
       18.12        15.39        22.29        18.44        25.18        77.56 
TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 
       22.95        76.57        36.03        20.38       207.48       176.55 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
       35.93       120.00        73.84        65.92        40.60        68.09 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A95V TCGA-DA-A95W TCGA-DA-A95X TCGA-DA-A95Y 
       33.93        10.49        72.10        25.15        61.81        14.14 
TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5UN 
       13.02        13.87        10.36        20.35        68.25        58.92 
TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 
        7.04        36.46        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        59.64        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       173.79       220.24        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       180.39       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        64.04 
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       134.33 
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        49.48         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        93.01        46.98        33.21        12.95       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 
       46.45        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        96.92        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        48.00       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-A690 TCGA-RP-A693 TCGA-RP-A694 
      368.78       297.90         7.23         0.20         0.33         0.69 
TCGA-W3-A824 TCGA-W3-A828 TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1V TCGA-W3-AA1W 
      228.16       121.08        69.07       111.09        42.08       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        17.95       101.33        58.98 
TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 
       70.52        63.22        11.80        49.51        12.16        40.41 
TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S 
       21.40        24.99        37.94        14.43        27.58        96.99 
TCGA-Z2-AA3V 
       15.98 

  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
              0.2               0.2 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
           369.93            368.78 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
            57.68             49.51 
[1] "0.2 - 369.9 (57.7)" "0.2 - 368.8 (49.5)"
[1] "hr=" "1.2"
D4V3, continuous
                   vv
clus                I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  2Q GAIN MUTATED             3       2       6        5        6        4
  2Q GAIN WILD-TYPE          10       5      23       13       22       21
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  2Q GAIN MUTATED           2         1         3        10          4
  2Q GAIN WILD-TYPE        12        18        12        30         11
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  2Q GAIN MUTATED            5          8        1
  2Q GAIN WILD-TYPE         28         47       20
D4V4, multiclass
             clus
vv            2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  I OR II NOS               3                10
  STAGE 0                   2                 5
  STAGE I                   6                23
  STAGE IA                  5                13
  STAGE IB                  6                22
  STAGE II                  4                21
  STAGE IIA                 2                12
  STAGE IIB                 1                18
  STAGE IIC                 3                12
  STAGE III                10                30
  STAGE IIIA                4                11
  STAGE IIIB                5                28
  STAGE IIIC                8                47
  STAGE IV                  1                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
  2Q GAIN MUTATED      12 18 10 10
  2Q GAIN WILD-TYPE    52 55 68 60
D4V5, multiclass
       clus
vv      2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  T0+T1              12                52
  T2                 18                55
  T3                 10                68
  T4                 10                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
  2Q GAIN MUTATED    34  12   8   6
  2Q GAIN WILD-TYPE 143  53  31  39
D4V6, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  N0              34               143
  N1              12                53
  N2               8                31
  N3               6                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"
D4V7, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED    62   1
  2Q GAIN WILD-TYPE 256  21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     62    1
  2Q GAIN WILD-TYPE  256   21
   clus
vv  2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  0              62               256
  1               1                21
[1] 2 2
[1] FALSE
D4V8, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED    22  15
  2Q GAIN WILD-TYPE 112  75
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     22   15
  2Q GAIN WILD-TYPE  112   75
     clus
vv    2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  NO               22               112
  YES              15                75
[1] 2 2
[1] FALSE
D4V9, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED     9  56
  2Q GAIN WILD-TYPE  38 263
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      9   56
  2Q GAIN WILD-TYPE   38  263
     clus
vv    2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  NO                9                38
  YES              56               263
[1] 2 2
[1] FALSE
D4V10, continuous
D4V11, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED    26  39
  2Q GAIN WILD-TYPE 111 190
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     26   39
  2Q GAIN WILD-TYPE  111  190
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  FEMALE              26               111
  MALE                39               190
[1] 2 2
[1] FALSE
D4V12, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED    55   9
  2Q GAIN WILD-TYPE 262  38
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     55    9
  2Q GAIN WILD-TYPE  262   38
     clus
vv    2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  NO               55               262
  YES               9                38
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  2Q GAIN MUTATED       0                         0    64
  2Q GAIN WILD-TYPE     5                         1   288
D4V13, multiclass
                           clus
vv                          2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  ASIAN                                   0                 5
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  64               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"
D4V14, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED     0  63
  2Q GAIN WILD-TYPE   7 288
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      0   63
  2Q GAIN WILD-TYPE    7  288
                        clus
vv                       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 7
  NOT HISPANIC OR LATINO              63               288
[1] 2 2
[1] FALSE

Clustering(5) Variable = 3P GAIN MUTATION ANALYSIS
D5V1, survival
                   sevent
clus2                 0   1
  3P GAIN MUTATED    22  13
  3P GAIN WILD-TYPE 100 110
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               35               210 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               13               110 
$`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-EB-A5SG TCGA-EB-A5SH 
       23.61        70.62        64.83       225.11        33.24        50.07 
TCGA-EE-A180 TCGA-EE-A184 TCGA-EE-A20H TCGA-EE-A29M TCGA-EE-A29T TCGA-EE-A29W 
       62.37        67.50       155.90        47.74       346.49       185.19 
TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2MP TCGA-EE-A2MU TCGA-EE-A3AE TCGA-EE-A3JH 
       31.00         0.76       227.01        53.26        54.51        19.86 
TCGA-EE-A3JI TCGA-ER-A19G TCGA-ER-A3ET TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A7UA 
      152.81       151.46        68.52        32.05        74.47         5.65 
TCGA-FS-A1Z0 TCGA-W3-AA1W TCGA-WE-A8K1 TCGA-WE-A8ZY TCGA-WE-AAA3 
      195.98       185.13         1.15        48.39        18.31 

$`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        69.21        22.85        76.34       138.67        53.65 
TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A95V 
      150.61        95.51        45.07        58.85        30.44        72.10 
TCGA-DA-A95X TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5UN TCGA-EB-A6L9 
       52.90        14.14        12.30         3.91        52.41        18.21 
TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A20C TCGA-EE-A29B 
       13.15        24.89        20.38         0.00        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-A29Q TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD 
       61.12       115.43        30.02        77.98        26.14       239.11 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
       12.95       201.60        68.65        10.62        32.48        18.35 
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-A2MJ 
        5.75        23.77       209.79        94.19       171.85        63.25 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT 
       89.26       104.78       145.45        25.08       143.93        23.51 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3J3 
      124.31       122.73        64.04         4.41         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-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-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        47.18       146.63        47.97        22.36         4.70 
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        42.08        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        96.92        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-A690 TCGA-RP-A693 
       85.05       297.01         7.23        18.05         0.20         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-A8K5 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ 
       92.84        59.64        65.42        12.69        21.90        62.89 
TCGA-WE-A8ZT TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-Z2-AA3S 
       10.95         1.94        31.99        18.35        28.21        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 
           62.860            44.165 
[1] "0.8 - 346.5 (62.9)" "0.0 - 312.1 (44.2)"
[1] "hr=" "2.2"
D5V2, survival
                   sevent
clus2                 0   1
  3P GAIN MUTATED    35  26
  3P GAIN WILD-TYPE 135 161
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               61               296 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               26               161 
$`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       225.96        15.68        68.25 
TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EE-A180 TCGA-EE-A184 TCGA-EE-A20B TCGA-EE-A20H 
       54.02        29.29        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       134.33       152.81       268.93        93.01 
TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A7UA TCGA-FR-A8YD TCGA-FS-A1Z0 TCGA-FS-A1ZK 
       33.21       149.03        38.27        36.26       202.65        23.93 
TCGA-FS-A4F2 TCGA-GF-A6C9 TCGA-GN-A266 TCGA-GN-A8LL TCGA-HR-A2OG TCGA-HR-A2OH 
       50.14        15.78        10.13        21.37         0.23        65.88 
TCGA-W3-AA1W TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K6 TCGA-WE-A8ZY TCGA-WE-AAA3 
      219.16        24.03        49.05        17.95        49.51        21.40 
TCGA-Z2-AA3V 
       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-D3-A8GV 
      170.20        89.13       152.75       129.63       117.17       167.70 
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        77.56        22.95 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 
       76.57        36.03       144.89        20.38       207.48       176.55 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IB TCGA-DA-A1IC 
       35.93       120.00        73.84        53.92        40.60        68.09 
TCGA-DA-A3F2 TCGA-DA-A95V TCGA-DA-A95W TCGA-DA-A95X TCGA-DA-A95Y TCGA-DA-A95Z 
       33.93        72.10        25.15        61.81        14.14        13.02 
TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 
       13.87        10.36        20.35        58.92         7.04        36.46 
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 
      115.96        59.64        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       173.79       220.24       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       180.39 
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        64.04        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        49.48         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        12.95        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        46.45        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        96.92        64.44        62.79        32.48        48.00 
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-A690 
       59.41       368.78       297.90         7.23        18.05         0.20 
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-AA21 TCGA-WE-A8K5 TCGA-WE-A8ZM 
       69.07       111.09        42.08       105.04        61.15       101.33 
TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-AA9Y 
       58.98        70.52        63.22        11.80        35.80        12.16 
TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-YD-A89C TCGA-YD-A9TA TCGA-YG-AA3O TCGA-YG-AA3P 
       40.41        24.99         6.90        49.18        37.94        14.43 
TCGA-Z2-A8RT TCGA-Z2-AA3S 
       27.58        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 
            54.51             50.43 
[1] "0.2 - 369.9 (54.5)" "0.2 - 368.8 (50.4)"
[1] "hr=" "1.5"
D5V3, continuous
                   vv
clus                I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  3P GAIN MUTATED             4       1       6        7        6        5
  3P GAIN WILD-TYPE           9       6      23       11       22       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        11        34         14
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  3P GAIN MUTATED            9          5        1
  3P GAIN WILD-TYPE         24         50       20
D5V4, multiclass
             clus
vv            3P GAIN MUTATED 3P GAIN WILD-TYPE
  I OR II NOS               4                 9
  STAGE 0                   1                 6
  STAGE I                   6                23
  STAGE IA                  7                11
  STAGE IB                  6                22
  STAGE II                  5                20
  STAGE IIA                 2                12
  STAGE IIB                 1                18
  STAGE IIC                 4                11
  STAGE III                 6                34
  STAGE IIIA                1                14
  STAGE IIIB                9                24
  STAGE IIIC                5                50
  STAGE IV                  1                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
  3P GAIN MUTATED      12 16 11 13
  3P GAIN WILD-TYPE    52 57 67 57
D5V5, multiclass
       clus
vv      3P GAIN MUTATED 3P GAIN WILD-TYPE
  T0+T1              12                52
  T2                 16                57
  T3                 11                67
  T4                 13                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
  3P GAIN MUTATED    38  10   5   3
  3P GAIN WILD-TYPE 139  55  34  42
D5V6, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  N0              38               139
  N1              10                55
  N2               5                34
  N3               3                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"
D5V7, binary
                   cls
clus                  0   1
  3P GAIN MUTATED    58   1
  3P GAIN WILD-TYPE 260  21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     58    1
  3P GAIN WILD-TYPE  260   21
   clus
vv  3P GAIN MUTATED 3P GAIN WILD-TYPE
  0              58               260
  1               1                21
[1] 2 2
[1] FALSE
D5V8, binary
                   cls
clus                  0   1
  3P GAIN MUTATED    23  17
  3P GAIN WILD-TYPE 111  73
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     23   17
  3P GAIN WILD-TYPE  111   73
     clus
vv    3P GAIN MUTATED 3P GAIN WILD-TYPE
  NO               23               111
  YES              17                73
[1] 2 2
[1] FALSE
D5V9, binary
                   cls
clus                  0   1
  3P GAIN MUTATED     5  58
  3P GAIN WILD-TYPE  42 261
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      5   58
  3P GAIN WILD-TYPE   42  261
     clus
vv    3P GAIN MUTATED 3P GAIN WILD-TYPE
  NO                5                42
  YES              58               261
[1] 2 2
[1] FALSE
D5V10, continuous
D5V11, binary
                   cls
clus                  0   1
  3P GAIN MUTATED    27  36
  3P GAIN WILD-TYPE 110 193
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     27   36
  3P GAIN WILD-TYPE  110  193
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  FEMALE              27               110
  MALE                36               193
[1] 2 2
[1] FALSE
D5V12, binary
                   cls
clus                  0   1
  3P GAIN MUTATED    52  11
  3P GAIN WILD-TYPE 265  36
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     52   11
  3P GAIN WILD-TYPE  265   36
     clus
vv    3P GAIN MUTATED 3P GAIN WILD-TYPE
  NO               52               265
  YES              11                36
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3P GAIN MUTATED       0                         0    60
  3P GAIN WILD-TYPE     5                         1   292
D5V13, multiclass
                           clus
vv                          3P GAIN MUTATED 3P GAIN WILD-TYPE
  ASIAN                                   0                 5
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  60               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"
D5V14, binary
                   cls
clus                  0   1
  3P GAIN MUTATED     0  60
  3P GAIN WILD-TYPE   7 291
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      0   60
  3P GAIN WILD-TYPE    7  291
                        clus
vv                       3P GAIN MUTATED 3P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 7
  NOT HISPANIC OR LATINO              60               291
[1] 2 2
[1] FALSE

Clustering(6) Variable = 3Q GAIN MUTATION ANALYSIS
D6V1, survival
                   sevent
clus2                 0   1
  3Q GAIN MUTATED    26  18
  3Q GAIN WILD-TYPE  96 105
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               44               201 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               18               105 
$`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        69.21        64.83 
TCGA-DA-A3F5 TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A182 TCGA-EE-A184 TCGA-EE-A20H 
      225.11        33.24        62.37         0.00        67.50       155.90 
TCGA-EE-A29M TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2M6 
       47.74       346.49       185.19        31.00         0.76       103.13 
TCGA-EE-A2ML TCGA-EE-A2MP TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AE TCGA-EE-A3J7 
      104.78       227.01        53.26       124.31        54.51        45.90 
TCGA-EE-A3JH TCGA-ER-A19G TCGA-ER-A19M TCGA-ER-A2ND TCGA-ER-A3ET TCGA-ER-A3PL 
       19.86       151.46        59.84         4.70        68.52        32.05 
TCGA-ER-A42L TCGA-FR-A7UA TCGA-FS-A1Z0 TCGA-GN-A26A TCGA-W3-AA1W TCGA-WE-A8K1 
       74.47         5.65       195.98         7.59       185.13         1.15 
TCGA-WE-A8ZY TCGA-WE-AAA3 
       48.39        18.31 

$`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 
       76.34       138.67        53.65       150.61        95.51        45.07 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A95V TCGA-DA-A95X TCGA-DA-A95Y TCGA-DA-A95Z 
       58.85        30.44        72.10        52.90        14.14        12.30 
TCGA-EB-A44Q TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y 
        3.91        50.07        52.41        18.21        13.15        24.89 
TCGA-EE-A181 TCGA-EE-A20C TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
       20.38        75.55        75.22        76.14        12.99         0.26 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A2A1 TCGA-EE-A2A2 
       44.28        63.12        27.16        61.12       115.43        30.02 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ 
       77.98        26.14       239.11        12.95       201.60        68.65 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GO TCGA-EE-A2GR TCGA-EE-A2GS 
       10.62        32.48        18.35       118.32         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-A2MM TCGA-EE-A2MR TCGA-EE-A2MS 
      171.85        63.25        89.26       145.45        25.08       143.93 
TCGA-EE-A2MT TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3J3 
       23.51       122.73        64.04         4.41         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-A19H TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
       11.47       150.12        99.06        42.48       120.76        49.71 
TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NG 
       47.18       146.63        47.97        22.36        16.87        10.95 
TCGA-ER-A3ES TCGA-ER-A3EV TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A8YC 
      173.29        15.48       174.21       209.23        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-A1ZQ 
       42.08        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-A4U3 TCGA-GN-A4U4 
      117.93        96.92        17.06        42.48       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-A690 TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 
       18.05         0.20         0.33       174.12         1.97       120.07 
TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1V TCGA-W3-AA21 TCGA-WE-A8K5 TCGA-WE-A8ZM 
       44.05        79.99         8.09        92.84        59.64        65.42 
TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-AA9Y TCGA-WE-AAA0 
       12.69        21.90        62.89        10.95         1.94        31.99 
TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-Z2-AA3S 
       18.35        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 
           63.845            43.530 
[1] "0.0 - 346.5 (63.8)" "0.2 - 312.1 (43.5)"
[1] "hr=" "1.8"
D6V2, survival
                   sevent
clus2                 0   1
  3Q GAIN MUTATED    40  30
  3Q GAIN WILD-TYPE 130 157
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               70               287 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               30               157 
$`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        77.56        65.92        10.49 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A5SG TCGA-EB-A5UL TCGA-EE-A180 TCGA-EE-A182 
      225.96        15.68        68.25        29.29        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       134.33       268.93        61.05 
TCGA-ER-A2ND TCGA-ER-A3ET TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A7UA TCGA-FR-A8YD 
       23.34        93.01        33.21       149.03        38.27        36.26 
TCGA-FS-A1Z0 TCGA-FS-A1ZK TCGA-FS-A4F2 TCGA-GF-A6C9 TCGA-GN-A266 TCGA-GN-A26A 
      202.65        23.93        50.14        15.78        10.13        32.48 
TCGA-HR-A2OG TCGA-HR-A2OH TCGA-W3-AA1O TCGA-W3-AA1W TCGA-WE-A8JZ TCGA-WE-A8K1 
        0.23        65.88         4.01       219.16        24.03        49.05 
TCGA-WE-A8K6 TCGA-WE-A8ZY TCGA-WE-AAA3 TCGA-Z2-AA3V 
       17.95        49.51        21.40        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-D3-A8GV TCGA-D9-A148 TCGA-D9-A149 
      152.75       129.63       117.17       167.70       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-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY 
        9.90        25.18        22.95        76.57        36.03       144.89 
TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 
       20.38       207.48       176.55        35.93       120.00        73.84 
TCGA-DA-A1I8 TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A95V TCGA-DA-A95W 
       53.92        40.60        68.09        33.93        72.10        25.15 
TCGA-DA-A95X TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH 
       61.81        14.14        13.02        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        58.92         7.04        36.46        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       115.96        59.64        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       173.79       220.24 
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       180.39       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        64.04        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        49.48         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        12.95        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        46.45        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        96.92 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 
       64.44        62.79        48.00       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-A690 TCGA-RP-A693 TCGA-RP-A694 
      297.90         7.23        18.05         0.20         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-AA21 TCGA-WE-A8K5 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ 
      105.04        61.15       101.33        58.98        70.52        63.22 
TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-YD-A89C 
       11.80        35.80        12.16        40.41        24.99         6.90 
TCGA-YD-A9TA TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S 
       49.18        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 
            61.56             49.48 
[1] "0.2 - 369.9 (61.6)" "0.2 - 368.8 (49.5)"
[1] "hr=" "1.6"
D6V3, continuous
                   vv
clus                I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  3Q GAIN MUTATED             5       1       8        7        7        6
  3Q GAIN WILD-TYPE           8       6      21       11       21       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        13        32         11
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  3Q GAIN MUTATED            9          6        1
  3Q GAIN WILD-TYPE         24         49       20
D6V4, multiclass
             clus
vv            3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  I OR II NOS               5                 8
  STAGE 0                   1                 6
  STAGE I                   8                21
  STAGE IA                  7                11
  STAGE IB                  7                21
  STAGE II                  6                19
  STAGE IIA                 2                12
  STAGE IIB                 1                18
  STAGE IIC                 2                13
  STAGE III                 8                32
  STAGE IIIA                4                11
  STAGE IIIB                9                24
  STAGE IIIC                6                49
  STAGE IV                  1                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
  3Q GAIN MUTATED      17 18 14 10
  3Q GAIN WILD-TYPE    47 55 64 60
D6V5, multiclass
       clus
vv      3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  T0+T1              17                47
  T2                 18                55
  T3                 14                64
  T4                 10                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
  3Q GAIN MUTATED    41  15   7   3
  3Q GAIN WILD-TYPE 136  50  32  42
D6V6, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  N0              41               136
  N1              15                50
  N2               7                32
  N3               3                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"
D6V7, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED    67   1
  3Q GAIN WILD-TYPE 251  21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     67    1
  3Q GAIN WILD-TYPE  251   21
   clus
vv  3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  0              67               251
  1               1                21
[1] 2 2
[1] FALSE
D6V8, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED    29  15
  3Q GAIN WILD-TYPE 105  75
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     29   15
  3Q GAIN WILD-TYPE  105   75
     clus
vv    3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  NO               29               105
  YES              15                75
[1] 2 2
[1] FALSE
D6V9, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED     8  64
  3Q GAIN WILD-TYPE  39 255
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      8   64
  3Q GAIN WILD-TYPE   39  255
     clus
vv    3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  NO                8                39
  YES              64               255
[1] 2 2
[1] FALSE
D6V10, continuous
D6V11, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED    29  43
  3Q GAIN WILD-TYPE 108 186
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     29   43
  3Q GAIN WILD-TYPE  108  186
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  FEMALE              29               108
  MALE                43               186
[1] 2 2
[1] FALSE
D6V12, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED    61  11
  3Q GAIN WILD-TYPE 256  36
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     61   11
  3Q GAIN WILD-TYPE  256   36
     clus
vv    3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  NO               61               256
  YES              11                36
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3Q GAIN MUTATED       0                         0    69
  3Q GAIN WILD-TYPE     5                         1   283
D6V13, multiclass
                           clus
vv                          3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  ASIAN                                   0                 5
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  69               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"
D6V14, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED     0  69
  3Q GAIN WILD-TYPE   7 282
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      0   69
  3Q GAIN WILD-TYPE    7  282
                        clus
vv                       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 7
  NOT HISPANIC OR LATINO              69               282
[1] 2 2
[1] FALSE

Clustering(7) Variable = 4P GAIN MUTATION ANALYSIS
D7V1, survival
                   sevent
clus2                 0   1
  4P GAIN MUTATED    21  20
  4P GAIN WILD-TYPE 101 103
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               41               204 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               20               103 
$`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        76.34        53.65       225.11 
TCGA-DA-A95V TCGA-EB-A5SH TCGA-EB-A6L9 TCGA-EE-A184 TCGA-EE-A29G TCGA-EE-A29P 
       72.10        50.07        18.21        67.50        44.28        27.16 
TCGA-EE-A2GB TCGA-EE-A2GP TCGA-EE-A2MJ TCGA-EE-A2MP TCGA-EE-A3AA TCGA-EE-A3J3 
       26.14         0.76        63.25       227.01       124.31        67.89 
TCGA-EE-A3J7 TCGA-EE-A3JB TCGA-ER-A19H TCGA-ER-A3ET TCGA-ER-A3PL TCGA-FR-A8YC 
       45.90       201.80       150.12        68.52        32.05        10.06 
TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZU TCGA-GF-A4EO TCGA-GN-A264 
       36.33        78.61       130.95         4.47         6.05       117.93 
TCGA-GN-A268 TCGA-GN-A8LK TCGA-QB-AA9O TCGA-WE-A8ZN TCGA-WE-A8ZQ 
       42.48        43.23        18.05        12.69        62.89 

$`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 
       69.21        22.85       138.67       150.61        95.51        45.07 
TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A95X TCGA-DA-A95Y TCGA-DA-A95Z 
       64.83        58.85        30.44        52.90        14.14        12.30 
TCGA-EB-A44Q TCGA-EB-A5SG TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A180 
        3.91        33.24        52.41        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-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-A2GD TCGA-EE-A2GE 
      185.19       115.43        30.02        77.98       239.11        12.95 
TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN 
      201.60        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        89.26 
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-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J4 
      122.73        64.04         4.41        54.51         6.28       111.85 
TCGA-EE-A3J8 TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
        3.35        19.86       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-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
      151.46        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 
       47.18       146.63        47.97        22.36         4.70        16.87 
TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3EV TCGA-ER-A42L TCGA-FR-A44A TCGA-FR-A729 
       10.95       173.29        15.48        74.47       174.21       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-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG 
       27.62       312.07        32.78        42.08        12.92         7.82 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 
      136.27        35.28        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-A265 TCGA-GN-A267 
       19.30         9.90         1.91        53.29        96.92        17.06 
TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-GN-A9SD TCGA-LH-A9QB 
        7.59       120.53        34.49        46.92        59.41        85.05 
TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A825 
      297.01         7.23         0.20         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-A8ZO TCGA-WE-A8ZT TCGA-WE-A8ZY 
        1.15        59.64        65.42        21.90        10.95        48.39 
TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-Z2-AA3S 
        1.94        31.99        18.31        18.35        28.21        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 
           53.650            46.455 
[1] "0.8 - 227.0 (53.6)" "0.0 - 346.5 (46.5)"
[1] "hr=" "1.1"
D7V2, survival
                   sevent
clus2                 0   1
  4P GAIN MUTATED    26  28
  4P GAIN WILD-TYPE 144 159
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               54               303 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               28               159 
$`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-DA-A95V TCGA-EB-A5SH 
       76.57       207.48        40.60       225.96        72.10        54.02 
TCGA-EB-A6L9 TCGA-EE-A184 TCGA-EE-A20F TCGA-EE-A29G TCGA-EE-A29P TCGA-EE-A2GB 
       36.46        68.15        91.56        72.07        56.42        59.28 
TCGA-EE-A2GI TCGA-EE-A2GP TCGA-EE-A2MJ TCGA-EE-A2MP TCGA-EE-A3AA TCGA-EE-A3J3 
       48.72        13.91        96.23       248.65       124.31       172.18 
TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-ER-A19H TCGA-ER-A3ET TCGA-ER-A3PL 
       64.08        53.19       201.80       152.35        93.01        33.21 
TCGA-FR-A3YN TCGA-FR-A8YC TCGA-FS-A1YX TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM 
       92.98        34.82        48.59        47.38        23.93       101.26 
TCGA-FS-A1ZQ TCGA-FS-A1ZU TCGA-FS-A4F2 TCGA-FS-A4F5 TCGA-GF-A4EO TCGA-GN-A264 
      133.55        26.56        50.14        28.73         7.23       117.93 
TCGA-GN-A268 TCGA-GN-A26D TCGA-GN-A8LK TCGA-QB-AA9O TCGA-WE-A8ZN TCGA-WE-A8ZQ 
       62.79        48.00        50.10        18.05        58.98        63.22 

$`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-D3-A8GV TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX 
      129.63       167.70       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        77.56 
TCGA-D9-A6EG TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 
       22.95        36.03       144.89        20.38       176.55        35.93 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 
      120.00        73.84        53.92        65.92        68.09        33.93 
TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-DA-A95W TCGA-DA-A95X TCGA-DA-A95Y TCGA-DA-A95Z 
       10.49        15.68        25.15        61.81        14.14        13.02 
TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5UL TCGA-EB-A5UN 
       13.87        10.36        20.35        68.25        29.29        58.92 
TCGA-EB-A5VV TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 
        7.04        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-A20H 
       14.70        26.89         4.96       133.81       151.27       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-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29R 
       64.64         2.60        56.84        18.61        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-A2A6 TCGA-EE-A2GC TCGA-EE-A2GD 
      115.96        59.64        39.29        86.14        67.43       340.14 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
      173.79       220.24       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-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-A2MK 
      103.27       268.73       103.20        16.96       204.66       180.39 
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-A2MU TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
       71.21        53.26       122.73        64.04        28.77        54.51 
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-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 
       27.35        51.35       134.33       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-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-A19T 
       61.05        44.05       162.08        50.89        49.48         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-A3EV TCGA-ER-A42K TCGA-ER-A42L 
       31.27        32.05       247.04        46.98        12.95       149.03 
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 
       46.45        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        96.92        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-A690 TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 
        7.23         0.20         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        17.95       101.33 
TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 
       70.52        11.80        35.80        49.51        12.16        40.41 
TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YD-A89C TCGA-YD-A9TA TCGA-YG-AA3O TCGA-YG-AA3P 
       21.40        24.99         6.90        49.18        37.94        14.43 
TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
       27.58        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 
            59.13             49.48 
[1] "7.2 - 248.7 (59.1)" "0.2 - 369.9 (49.5)"
[1] "hr=" "1.1"
D7V3, continuous
                   vv
clus                I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  4P GAIN MUTATED             2       0       7        1        8        1
  4P GAIN WILD-TYPE          11       7      22       17       20       24
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  4P GAIN MUTATED           2         3         6         9          3
  4P GAIN WILD-TYPE        12        16         9        31         12
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  4P GAIN MUTATED            4          6        1
  4P GAIN WILD-TYPE         29         49       20
D7V4, multiclass
             clus
vv            4P GAIN MUTATED 4P GAIN WILD-TYPE
  I OR II NOS               2                11
  STAGE 0                   0                 7
  STAGE I                   7                22
  STAGE IA                  1                17
  STAGE IB                  8                20
  STAGE II                  1                24
  STAGE IIA                 2                12
  STAGE IIB                 3                16
  STAGE IIC                 6                 9
  STAGE III                 9                31
  STAGE IIIA                3                12
  STAGE IIIB                4                29
  STAGE IIIC                6                49
  STAGE IV                  1                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
  4P GAIN MUTATED      12 16  7 14
  4P GAIN WILD-TYPE    52 57 71 56
D7V5, multiclass
       clus
vv      4P GAIN MUTATED 4P GAIN WILD-TYPE
  T0+T1              12                52
  T2                 16                57
  T3                  7                71
  T4                 14                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 GAIN MUTATED    31   7   8   5
  4P GAIN WILD-TYPE 146  58  31  40
D7V6, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  N0              31               146
  N1               7                58
  N2               8                31
  N3               5                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"
D7V7, binary
                   cls
clus                  0   1
  4P GAIN MUTATED    50   1
  4P GAIN WILD-TYPE 268  21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED     50    1
  4P GAIN WILD-TYPE  268   21
   clus
vv  4P GAIN MUTATED 4P GAIN WILD-TYPE
  0              50               268
  1               1                21
[1] 2 2
[1] FALSE
D7V8, binary
                   cls
clus                  0   1
  4P GAIN MUTATED    20  15
  4P GAIN WILD-TYPE 114  75
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED     20   15
  4P GAIN WILD-TYPE  114   75
     clus
vv    4P GAIN MUTATED 4P GAIN WILD-TYPE
  NO               20               114
  YES              15                75
[1] 2 2
[1] FALSE
D7V9, binary
                   cls
clus                  0   1
  4P GAIN MUTATED     7  49
  4P GAIN WILD-TYPE  40 270
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      7   49
  4P GAIN WILD-TYPE   40  270
     clus
vv    4P GAIN MUTATED 4P GAIN WILD-TYPE
  NO                7                40
  YES              49               270
[1] 2 2
[1] FALSE
D7V10, continuous
D7V11, binary
                   cls
clus                  0   1
  4P GAIN MUTATED    22  34
  4P GAIN WILD-TYPE 115 195
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED     22   34
  4P GAIN WILD-TYPE  115  195
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  FEMALE              22               115
  MALE                34               195
[1] 2 2
[1] FALSE
D7V12, binary
                   cls
clus                  0   1
  4P GAIN MUTATED    50   6
  4P GAIN WILD-TYPE 267  41
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED     50    6
  4P GAIN WILD-TYPE  267   41
     clus
vv    4P GAIN MUTATED 4P GAIN WILD-TYPE
  NO               50               267
  YES               6                41
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  4P GAIN MUTATED       1                         0    53
  4P GAIN WILD-TYPE     4                         1   299
D7V13, multiclass
                           clus
vv                          4P GAIN MUTATED 4P GAIN WILD-TYPE
  ASIAN                                   1                 4
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  53               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"
D7V14, binary
                   cls
clus                  0   1
  4P GAIN MUTATED     1  55
  4P GAIN WILD-TYPE   6 296
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      1   55
  4P GAIN WILD-TYPE    6  296
                        clus
vv                       4P GAIN MUTATED 4P GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 6
  NOT HISPANIC OR LATINO              55               296
[1] 2 2
[1] FALSE

Clustering(8) Variable = 4Q GAIN MUTATION ANALYSIS
D8V1, survival
                   sevent
clus2                 0   1
  4Q GAIN MUTATED    17  18
  4Q GAIN WILD-TYPE 105 105
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               35               210 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               18               105 
$`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 
       76.34        53.65       225.11        50.07        18.21        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        62.89 

$`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        69.21        22.85       138.67 
TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 
      150.61        95.51        45.07        64.83        58.85        30.44 
TCGA-DA-A95V TCGA-DA-A95X TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5SG 
       72.10        52.90        14.14        12.30         3.91        33.24 
TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 
       52.41        13.15        24.89        62.37        20.38         0.00 
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-A29Q TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A2 
       47.74        61.12       346.49       185.19       115.43        30.02 
TCGA-EE-A2A6 TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK 
       77.98       239.11        12.95       201.60        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-A2MC TCGA-EE-A2MF 
       81.99       103.13        15.25         5.75        23.77       209.79 
TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MS 
       94.19       171.85        89.26       104.78       145.45       143.93 
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        64.04        54.51 
TCGA-EE-A3AF TCGA-EE-A3J4 TCGA-EE-A3J8 TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 
        6.28       111.85         3.35        19.86       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-A19C TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
       39.81        11.47       151.46        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        47.18       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        68.52        15.48 
TCGA-ER-A42L TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FS-A1YW 
       74.47       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 
       42.08        12.92         7.82        36.33       136.27        35.28 
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-A6C8 TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A4U3 
        1.91        53.29        96.92        17.06         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-QB-AA9O TCGA-RP-A690 TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 
       18.05         0.20         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        65.42        12.69        21.90        10.95        48.39 
TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-Z2-AA3S 
        1.94        31.99        18.31        18.35        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 
            53.65             46.95 
[1] "0.8 - 227.0 (53.6)" "0.0 - 346.5 (47.0)"
[1] "hr=" "1"  
D8V2, survival
                   sevent
clus2                 0   1
  4Q GAIN MUTATED    21  24
  4Q GAIN WILD-TYPE 149 163
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               45               312 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               24               163 
$`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        76.57       207.48        40.60 
TCGA-DA-A3F5 TCGA-EB-A5SH TCGA-EB-A6L9 TCGA-EE-A184 TCGA-EE-A20F TCGA-EE-A29D 
      225.96        54.02        36.46        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 
       48.00        59.41        63.22 

$`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-D3-A8GV TCGA-D9-A148 
      107.15       161.00        29.06       129.63       167.70       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-A6EC TCGA-D9-A6EG TCGA-DA-A1HW TCGA-DA-A1HY 
       18.44         9.90        77.56        22.95        36.03       144.89 
TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
       20.38       176.55        35.93       120.00        73.84        53.92 
TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-DA-A95V 
       65.92        68.09        33.93        10.49        15.68        72.10 
TCGA-DA-A95W TCGA-DA-A95X TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A44R 
       25.15        61.81        14.14        13.02        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        29.29        58.92         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       115.96        59.64        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       173.79       220.24        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       180.39       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        64.04        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       134.33 
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        49.48         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-ER-A42L TCGA-FR-A44A TCGA-FR-A69P 
       93.01        46.98        12.95       149.03       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-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 
      216.92       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        46.45        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-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-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC 
       50.14        66.67       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-A265 TCGA-GN-A266 
        9.90         2.04        15.78       139.89        96.92        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-HR-A2OG TCGA-HR-A2OH TCGA-LH-A9QB 
       22.13        50.10        21.37         0.23        65.88       368.78 
TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A690 TCGA-RP-A693 TCGA-RP-A694 
      297.90         7.23        18.05         0.20         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-A8ZT TCGA-WE-A8ZX 
       17.95       101.33        58.98        70.52        11.80        35.80 
TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YD-A89C 
       49.51        12.16        40.41        21.40        24.99         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 

  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 
           60.230            49.495 
[1] "7.2 - 248.7 (60.2)" "0.2 - 369.9 (49.5)"
[1] "hr=" "1.1"
D8V3, continuous
                   vv
clus                I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  4Q GAIN MUTATED             2       0       7        1        7        0
  4Q GAIN WILD-TYPE          11       7      22       17       21       25
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  4Q GAIN MUTATED           1         2         3         8          2
  4Q GAIN WILD-TYPE        13        17        12        32         13
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  4Q GAIN MUTATED            4          6        1
  4Q GAIN WILD-TYPE         29         49       20
D8V4, multiclass
             clus
vv            4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  I OR II NOS               2                11
  STAGE 0                   0                 7
  STAGE I                   7                22
  STAGE IA                  1                17
  STAGE IB                  7                21
  STAGE II                  0                25
  STAGE IIA                 1                13
  STAGE IIB                 2                17
  STAGE IIC                 3                12
  STAGE III                 8                32
  STAGE IIIA                2                13
  STAGE IIIB                4                29
  STAGE IIIC                6                49
  STAGE IV                  1                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
  4Q GAIN MUTATED      10 15  7  9
  4Q GAIN WILD-TYPE    54 58 71 61
D8V5, multiclass
       clus
vv      4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  T0+T1              10                54
  T2                 15                58
  T3                  7                71
  T4                  9                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
  4Q GAIN MUTATED    26   7   7   4
  4Q GAIN WILD-TYPE 151  58  32  41
D8V6, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  N0              26               151
  N1               7                58
  N2               7                32
  N3               4                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"
D8V7, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED    43   1
  4Q GAIN WILD-TYPE 275  21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED     43    1
  4Q GAIN WILD-TYPE  275   21
   clus
vv  4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  0              43               275
  1               1                21
[1] 2 2
[1] FALSE
D8V8, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED    18  12
  4Q GAIN WILD-TYPE 116  78
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED     18   12
  4Q GAIN WILD-TYPE  116   78
     clus
vv    4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  NO               18               116
  YES              12                78
[1] 2 2
[1] FALSE
D8V9, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     5  42
  4Q GAIN WILD-TYPE  42 277
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      5   42
  4Q GAIN WILD-TYPE   42  277
     clus
vv    4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  NO                5                42
  YES              42               277
[1] 2 2
[1] FALSE
D8V10, continuous
D8V11, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED    18  29
  4Q GAIN WILD-TYPE 119 200
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED     18   29
  4Q GAIN WILD-TYPE  119  200
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  FEMALE              18               119
  MALE                29               200
[1] 2 2
[1] FALSE
D8V12, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED    41   6
  4Q GAIN WILD-TYPE 276  41
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED     41    6
  4Q GAIN WILD-TYPE  276   41
     clus
vv    4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  NO               41               276
  YES               6                41
[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   307
D8V13, multiclass
                           clus
vv                          4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  ASIAN                                   1                 4
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  45               307
[1] 3 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   6 305
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      1   46
  4Q GAIN WILD-TYPE    6  305
                        clus
vv                       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 6
  NOT HISPANIC OR LATINO              46               305
[1] 2 2
[1] FALSE

Clustering(9) Variable = 5P GAIN MUTATION ANALYSIS
D9V1, survival
                   sevent
clus2                 0   1
  5P GAIN MUTATED    24  22
  5P GAIN WILD-TYPE  98 101
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               46               199 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               22               101 
$`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        69.21 
TCGA-DA-A95V TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A20H TCGA-EE-A29T TCGA-EE-A29W 
       72.10        62.37        20.38       155.90       346.49       185.19 
TCGA-EE-A2GM TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A3AA 
       18.35       103.13        15.25       227.01       143.93       124.31 
TCGA-EE-A3AB TCGA-EE-A3AE TCGA-EE-A3J3 TCGA-EE-A3JI TCGA-ER-A19B TCGA-ER-A19C 
      122.73        54.51        67.89       152.81        53.29        39.81 
TCGA-ER-A19G TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A2ND TCGA-ER-A3PL 
      151.46        59.84        42.48       120.76         4.70        32.05 
TCGA-FR-A44A TCGA-FR-A8YC TCGA-FS-A1ZE TCGA-FS-A1ZQ TCGA-FW-A3TU TCGA-GF-A4EO 
      174.21        10.06        42.08       130.95        55.59         6.05 
TCGA-GN-A265 TCGA-QB-AA9O TCGA-W3-AA1V TCGA-WE-A8ZQ 
       96.92        18.05         8.09        62.89 

$`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        76.34 
TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA 
      138.67        53.65       150.61        95.51        45.07        64.83 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A95X TCGA-DA-A95Y TCGA-DA-A95Z 
       58.85        30.44       225.11        52.90        14.14        12.30 
TCGA-EB-A44Q TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X 
        3.91        33.24        50.07        52.41        18.21        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-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-A2GB TCGA-EE-A2GD 
       61.12       115.43        30.02        77.98        26.14       239.11 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN 
       12.95       201.60        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-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        89.26 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AC 
      104.78       145.45        25.08        23.51        53.26        64.04 
TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB 
        4.41         6.28       111.85        45.90         3.35       201.80 
TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 
       19.86        14.56        34.45         1.58        47.31         7.82 
TCGA-ER-A19A TCGA-ER-A19D TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19Q TCGA-ER-A19S 
        4.54        11.47       150.12        99.06        49.71        47.18 
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-ER-A42L TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7UA 
       68.52        15.48        74.47       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-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZS 
       32.78        12.92         7.82        36.33        78.61       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-A3TV TCGA-FW-A5DY 
       66.67       173.19        13.28        80.68        11.54        19.30 
TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 
        9.90         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-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-A690 TCGA-RP-A693 TCGA-W3-A824 
       85.05       297.01         7.23         0.20         0.33       174.12 
TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1W TCGA-W3-AA21 
        1.97       120.07        44.05        79.99       185.13        92.84 
TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT 
        1.15        59.64        65.42        12.69        21.90        10.95 
TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O 
       48.39         1.94        31.99        18.31        18.35        28.21 
TCGA-Z2-AA3S 
       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 
            63.86             44.05 
[1] "4.7 - 346.5 (63.9)" "0.0 - 312.1 (44.0)"
[1] "hr=" "1.5"
D9V2, survival
                   sevent
clus2                 0   1
  5P GAIN MUTATED    38  35
  5P GAIN WILD-TYPE 132 152
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               73               284 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               35               152 
$`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-DA-A95V TCGA-EB-A44R 
        3.65         9.90        25.18        77.56        72.10        10.36 
TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A20B TCGA-EE-A20H TCGA-EE-A29T TCGA-EE-A29W 
       94.98        33.73       133.81       168.26       369.93       195.02 
TCGA-EE-A2A0 TCGA-EE-A2GM TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MP TCGA-EE-A2MS 
       46.82        75.48       129.27        28.83       248.65       162.48 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AE TCGA-EE-A3J3 TCGA-EE-A3JA TCGA-EE-A3JI 
      124.31       122.73        54.51       172.18        53.19       152.81 
TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19G TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P 
       98.40        48.89       268.93        61.05        44.05       162.08 
TCGA-ER-A19T TCGA-ER-A2ND TCGA-ER-A3PL TCGA-FR-A44A TCGA-FR-A7U9 TCGA-FR-A8YC 
        8.88        23.34        33.21       174.21        18.77        34.82 
TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YX TCGA-FS-A1ZE TCGA-FS-A1ZK TCGA-FS-A1ZQ 
       36.26       104.42        48.59        46.45        23.93       133.55 
TCGA-FS-A4F5 TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-GF-A4EO TCGA-GN-A265 TCGA-GN-A4U9 
       28.73         0.20        55.59         7.23        96.92        22.13 
TCGA-QB-AA9O TCGA-W3-AA1O TCGA-W3-AA1V TCGA-WE-A8JZ TCGA-WE-A8ZQ TCGA-YG-AA3P 
       18.05         4.01        42.08        24.03        63.22        14.43 
TCGA-Z2-A8RT 
       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-D3-A8GV TCGA-D9-A149 TCGA-D9-A1JX TCGA-D9-A1X3 TCGA-D9-A3Z1 
      117.17       167.70        54.67         7.10        18.12        15.39 
TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY 
       22.29        18.44        22.95        76.57        36.03       144.89 
TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 
       20.38       207.48       176.55        35.93       120.00        73.84 
TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
       53.92        65.92        40.60        68.09        33.93        10.49 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-DA-A95W TCGA-DA-A95X TCGA-DA-A95Y TCGA-DA-A95Z 
      225.96        15.68        25.15        61.81        14.14        13.02 
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        29.29        58.92 
TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A182 
        7.04        36.46        29.82        27.22         8.65        14.70 
TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I 
       26.89        68.15         4.96       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-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A2 
       14.47        61.28        25.87        17.92       115.96        59.64 
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       173.79 
TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN 
      220.24        48.72       107.38        54.74        79.66       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-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF 
       21.67        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       180.39       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-A3AC TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J4 
       64.04        28.77        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-A3JE 
       36.95        64.08        34.32       201.80        27.35        51.35 
TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 
      134.33        31.40        35.44        13.94        50.76         9.17 
TCGA-ER-A19A TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19H TCGA-ER-A19J 
       77.75        12.59        13.02        26.37       152.35         6.44 
TCGA-ER-A19L TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
      131.51        50.89        49.48       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        93.01 
TCGA-ER-A3EV TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A69P TCGA-FR-A729 
       46.98        12.95       149.03        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        48.00       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-A690 TCGA-RP-A693 
       65.88       368.78       297.90         7.23         0.20         0.33 
TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1Q TCGA-W3-AA1R 
        0.69       228.16        63.02       121.08        69.07       111.09 
TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZM 
      219.16       105.04        49.05        61.15        17.95       101.33 
TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AA9Y 
       58.98        70.52        11.80        35.80        49.51        12.16 
TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YD-A89C TCGA-YD-A9TA TCGA-YG-AA3O 
       40.41        21.40        24.99         6.90        49.18        37.94 
TCGA-Z2-AA3S TCGA-Z2-AA3V 
       96.99        15.98 

  5P GAIN MUTATED 5P GAIN WILD-TYPE 
              0.2               0.2 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
           369.93            368.78 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
           55.590            50.825 
[1] "0.2 - 369.9 (55.6)" "0.2 - 368.8 (50.8)"
[1] "hr=" "1.2"
D9V3, continuous
                   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           9       5      22       13       22       18
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  5P GAIN MUTATED           2         4         5         6          3
  5P GAIN WILD-TYPE        12        15        10        34         12
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  5P GAIN MUTATED            3          8        5
  5P GAIN WILD-TYPE         30         47       16
D9V4, multiclass
             clus
vv            5P GAIN MUTATED 5P GAIN WILD-TYPE
  I OR II NOS               4                 9
  STAGE 0                   2                 5
  STAGE I                   7                22
  STAGE IA                  5                13
  STAGE IB                  6                22
  STAGE II                  7                18
  STAGE IIA                 2                12
  STAGE IIB                 4                15
  STAGE IIC                 5                10
  STAGE III                 6                34
  STAGE IIIA                3                12
  STAGE IIIB                3                30
  STAGE IIIC                8                47
  STAGE IV                  5                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
  5P GAIN MUTATED      18 13 17 13
  5P GAIN WILD-TYPE    46 60 61 57
D9V5, multiclass
       clus
vv      5P GAIN MUTATED 5P GAIN WILD-TYPE
  T0+T1              18                46
  T2                 13                60
  T3                 17                61
  T4                 13                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
  5P GAIN MUTATED    46   7   7  10
  5P GAIN WILD-TYPE 131  58  32  35
D9V6, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  N0              46               131
  N1               7                58
  N2               7                32
  N3              10                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"
D9V7, binary
                   cls
clus                  0   1
  5P GAIN MUTATED    66   6
  5P GAIN WILD-TYPE 252  16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     66    6
  5P GAIN WILD-TYPE  252   16
   clus
vv  5P GAIN MUTATED 5P GAIN WILD-TYPE
  0              66               252
  1               6                16
[1] 2 2
[1] FALSE
D9V8, binary
                   cls
clus                  0   1
  5P GAIN MUTATED    31  13
  5P GAIN WILD-TYPE 103  77
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     31   13
  5P GAIN WILD-TYPE  103   77
     clus
vv    5P GAIN MUTATED 5P GAIN WILD-TYPE
  NO               31               103
  YES              13                77
[1] 2 2
[1] FALSE
D9V9, binary
                   cls
clus                  0   1
  5P GAIN MUTATED    11  65
  5P GAIN WILD-TYPE  36 254
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     11   65
  5P GAIN WILD-TYPE   36  254
     clus
vv    5P GAIN MUTATED 5P GAIN WILD-TYPE
  NO               11                36
  YES              65               254
[1] 2 2
[1] FALSE
D9V10, continuous
D9V11, binary
                   cls
clus                  0   1
  5P GAIN MUTATED    29  47
  5P GAIN WILD-TYPE 108 182
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     29   47
  5P GAIN WILD-TYPE  108  182
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  FEMALE              29               108
  MALE                47               182
[1] 2 2
[1] FALSE
D9V12, binary
                   cls
clus                  0   1
  5P GAIN MUTATED    64  11
  5P GAIN WILD-TYPE 253  36
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     64   11
  5P GAIN WILD-TYPE  253   36
     clus
vv    5P GAIN MUTATED 5P GAIN WILD-TYPE
  NO               64               253
  YES              11                36
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  5P GAIN MUTATED       1                         0    72
  5P GAIN WILD-TYPE     4                         1   280
D9V13, multiclass
                           clus
vv                          5P GAIN MUTATED 5P GAIN WILD-TYPE
  ASIAN                                   1                 4
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  72               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"
D9V14, binary
                   cls
clus                  0   1
  5P GAIN MUTATED     2  73
  5P GAIN WILD-TYPE   5 278
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      2   73
  5P GAIN WILD-TYPE    5  278
                        clus
vv                       5P GAIN MUTATED 5P GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 5
  NOT HISPANIC OR LATINO              73               278
[1] 2 2
[1] FALSE

Clustering(10) Variable = 5Q GAIN MUTATION ANALYSIS
D10V1, survival
                   sevent
clus2                 0   1
  5Q GAIN MUTATED    18  14
  5Q GAIN WILD-TYPE 104 109
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               32               213 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               14               109 
$`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-DA-A95V TCGA-DA-A95Z TCGA-EE-A180 
      177.86       124.08        70.62        72.10        12.30        62.37 
TCGA-EE-A181 TCGA-EE-A29W TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A3AA TCGA-EE-A3AE 
       20.38       185.19       227.01       143.93       124.31        54.51 
TCGA-EE-A3J3 TCGA-EE-A3JI TCGA-ER-A19C TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A2ND 
       67.89       152.81        39.81        42.48       120.76         4.70 
TCGA-ER-A3PL TCGA-FR-A8YC TCGA-FS-A1ZD TCGA-FW-A3TU TCGA-GF-A4EO TCGA-GN-A265 
       32.05        10.06        32.78        55.59         6.05        96.92 
TCGA-QB-AA9O TCGA-WE-A8ZQ 
       18.05        62.89 

$`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 
       69.21        22.85        76.34       138.67        53.65       150.61 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 
       95.51        45.07        64.83        58.85        30.44       225.11 
TCGA-DA-A95X TCGA-DA-A95Y TCGA-EB-A44Q TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN 
       52.90        14.14         3.91        33.24        50.07        52.41 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A182 TCGA-EE-A184 TCGA-EE-A20C 
       18.21        13.15        24.89         0.00        67.50        75.55 
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-A29M TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A2A1 
       63.12        47.74        27.16        61.12       346.49       115.43 
TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
       30.02        77.98        26.14       239.11        12.95       201.60 
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-A2MR TCGA-EE-A2MT TCGA-EE-A2MU 
       89.26       104.78       145.45        25.08        23.51        53.26 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3J4 TCGA-EE-A3J7 
      122.73        64.04         4.41         6.28       111.85        45.90 
TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
        3.35       201.80        19.86        14.56        34.45         1.58 
TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19G 
       47.31         7.82         4.54        53.29        11.47       151.46 
TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W 
      150.12        99.06        59.84        49.71        47.18       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        68.52 
TCGA-ER-A3EV TCGA-ER-A42L TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7UA 
       15.48        74.47       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-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ 
       42.08        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-A3TV 
       30.90        66.67       173.19        13.28        80.68        11.54 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A267 
       19.30         9.90         1.91        53.29       117.93        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-RP-A690 TCGA-RP-A693 
       59.41        85.05       297.01         7.23         0.20         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        65.42        12.69 
TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 
       21.90        10.95        48.39         1.94        31.99        18.31 
TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-Z2-AA3S 
       18.35        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 
           58.025            46.920 
[1] "4.7 - 227.0 (58.0)" "0.0 - 346.5 (46.9)"
[1] "hr=" "1.3"
D10V2, survival
                   sevent
clus2                 0   1
  5Q GAIN MUTATED    29  22
  5Q GAIN WILD-TYPE 141 165
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               51               306 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               22               165 
$`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-DA-A95V TCGA-DA-A95Z TCGA-EB-A44R 
      151.53         3.65         9.90        72.10        13.02        10.36 
TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A20B TCGA-EE-A29W TCGA-EE-A2MP TCGA-EE-A2MS 
       94.98        33.73       133.81       195.02       248.65       162.48 
TCGA-EE-A3AA TCGA-EE-A3AE TCGA-EE-A3J3 TCGA-EE-A3JA TCGA-EE-A3JI TCGA-ER-A19C 
      124.31        54.51       172.18        53.19       152.81        48.89 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19T TCGA-ER-A2ND TCGA-ER-A3PL TCGA-FR-A7U9 
       44.05       162.08         8.88        23.34        33.21        18.77 
TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1ZD TCGA-FS-A1ZK TCGA-FS-A4F5 
       34.82        36.26       104.42        53.52        23.93        28.73 
TCGA-FW-A3TU TCGA-GF-A4EO TCGA-GN-A265 TCGA-GN-A4U9 TCGA-QB-AA9O TCGA-WE-A8JZ 
       55.59         7.23        96.92        22.13        18.05        24.03 
TCGA-WE-A8ZQ TCGA-YG-AA3P TCGA-Z2-A8RT 
       63.22        14.43        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-D3-A8GV TCGA-D9-A149 TCGA-D9-A1JX TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 
      167.70        54.67         7.10        18.12        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        77.56        22.95        76.57        36.03 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
      144.89        20.38       207.48       176.55        35.93       120.00 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
       73.84        53.92        65.92        40.60        68.09        33.93 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-DA-A95W TCGA-DA-A95X TCGA-DA-A95Y 
       10.49       225.96        15.68        25.15        61.81        14.14 
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        29.29        58.92 
TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A182 
        7.04        36.46        29.82        27.22         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-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-A29T TCGA-EE-A29V TCGA-EE-A29X 
       66.74        14.47        61.28       369.93        25.87        17.92 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
       46.82       115.96        59.64        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       173.79       220.24        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-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-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML 
      103.20        16.96       204.66        96.23       180.39       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-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH 
      122.73        64.04        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       134.33        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-A19Q 
      268.93       152.35         6.44       131.51        61.05        50.89 
TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NF 
       49.48       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        93.01        46.98        12.95 
TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 
      149.03        92.98       174.21        15.72       220.80        27.85 
TCGA-FR-A7UA TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
       38.27       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        46.45 
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-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-A4F8 
       27.09        27.02        77.82        50.14        66.67       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-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-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
      117.93        10.13        64.44        62.79        32.48        48.00 
TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A8LK TCGA-GN-A8LL 
      121.91        39.35        10.42        48.89        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-RP-A690 TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 
        0.20         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        17.95       101.33        58.98        70.52 
TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 
       11.80        35.80        49.51        12.16        40.41        21.40 
TCGA-WE-AAA4 TCGA-YD-A89C TCGA-YD-A9TA TCGA-YG-AA3O TCGA-Z2-AA3S TCGA-Z2-AA3V 
       24.99         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             53.21 
[1] "3.6 - 248.7 (48.9)" "0.2 - 369.9 (53.2)"
[1] "hr=" "1.1"
D10V3, continuous
                   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          12       6      26       14       24       21
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  5Q GAIN MUTATED           3         4         3         4          2
  5Q GAIN WILD-TYPE        11        15        12        36         13
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  5Q GAIN MUTATED            3          6        4
  5Q GAIN WILD-TYPE         30         49       17
D10V4, multiclass
             clus
vv            5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  I OR II NOS               1                12
  STAGE 0                   1                 6
  STAGE I                   3                26
  STAGE IA                  4                14
  STAGE IB                  4                24
  STAGE II                  4                21
  STAGE IIA                 3                11
  STAGE IIB                 4                15
  STAGE IIC                 3                12
  STAGE III                 4                36
  STAGE IIIA                2                13
  STAGE IIIB                3                30
  STAGE IIIC                6                49
  STAGE IV                  4                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  8
  5Q GAIN WILD-TYPE    51 63 67 62
D10V5, multiclass
       clus
vv      5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  T0+T1              13                51
  T2                 10                63
  T3                 11                67
  T4                  8                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
  5Q GAIN MUTATED    28   5   5   8
  5Q GAIN WILD-TYPE 149  60  34  37
D10V6, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  N0              28               149
  N1               5                60
  N2               5                34
  N3               8                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"
D10V7, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED    43   5
  5Q GAIN WILD-TYPE 275  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     43    5
  5Q GAIN WILD-TYPE  275   17
   clus
vv  5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  0              43               275
  1               5                17
[1] 2 2
[1] FALSE
D10V8, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED    20  12
  5Q GAIN WILD-TYPE 114  78
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     20   12
  5Q GAIN WILD-TYPE  114   78
     clus
vv    5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  NO               20               114
  YES              12                78
[1] 2 2
[1] FALSE
D10V9, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED     8  44
  5Q GAIN WILD-TYPE  39 275
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      8   44
  5Q GAIN WILD-TYPE   39  275
     clus
vv    5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  NO                8                39
  YES              44               275
[1] 2 2
[1] FALSE
D10V10, continuous
D10V11, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED    18  34
  5Q GAIN WILD-TYPE 119 195
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     18   34
  5Q GAIN WILD-TYPE  119  195
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  FEMALE              18               119
  MALE                34               195
[1] 2 2
[1] FALSE
D10V12, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED    45   7
  5Q GAIN WILD-TYPE 272  40
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     45    7
  5Q GAIN WILD-TYPE  272   40
     clus
vv    5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  NO               45               272
  YES               7                40
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  5Q GAIN MUTATED       1                         0    48
  5Q GAIN WILD-TYPE     4                         1   304
D10V13, multiclass
                           clus
vv                          5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  ASIAN                                   1                 4
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  48               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"
D10V14, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED     3  48
  5Q GAIN WILD-TYPE   4 303
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      3   48
  5Q GAIN WILD-TYPE    4  303
                        clus
vv                       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                 4
  NOT HISPANIC OR LATINO              48               303
[1] 2 2
[1] FALSE

Clustering(11) Variable = 6P GAIN MUTATION ANALYSIS
D11V1, survival
                   sevent
clus2                0  1
  6P GAIN MUTATED   42 57
  6P GAIN WILD-TYPE 80 66
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               99               146 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               57                66 
$`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        76.34       150.61 
TCGA-DA-A1IA TCGA-DA-A95V TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A5SG TCGA-EB-A5SH 
       64.83        72.10        14.14        12.30        33.24        50.07 
TCGA-EE-A181 TCGA-EE-A184 TCGA-EE-A20H TCGA-EE-A29B TCGA-EE-A29P TCGA-EE-A2GB 
       20.38        67.50       155.90        75.22        27.16        26.14 
TCGA-EE-A2GD TCGA-EE-A2GH TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
      239.11       201.60        31.00         0.76         0.20        71.31 
TCGA-EE-A2GU TCGA-EE-A2MF TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MP 
       81.99       209.79       171.85        89.26       145.45       227.01 
TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3J3 
      143.93        53.26       124.31         4.41         6.28        67.89 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JI TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19C 
       45.90         3.35       152.81         1.58         7.82        39.81 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A2NC 
       59.84        42.48       120.76        49.71        47.18        22.36 
TCGA-ER-A3ES TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1ZC 
      173.29        15.48        32.05       195.98         8.35       312.07 
TCGA-FS-A1ZE TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A1ZZ 
       42.08        36.33        78.61         4.47         5.29         3.06 
TCGA-FS-A4F8 TCGA-FS-A4FD TCGA-GF-A4EO TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A26A 
      173.19        80.68         6.05       117.93        17.06         7.59 
TCGA-GN-A8LK TCGA-GN-A9SD TCGA-LH-A9QB TCGA-QB-AA9O TCGA-RP-A690 TCGA-W3-AA1Q 
       43.23        59.41        85.05        18.05         0.20        44.05 
TCGA-W3-AA1R TCGA-W3-AA1V TCGA-W3-AA21 TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT 
       79.99         8.09        92.84        21.90        62.89        10.95 
TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O 
       18.31        18.35        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        69.21 
TCGA-D9-A6EG TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IC 
       22.85       138.67        53.65        95.51        45.07        58.85 
TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A95X TCGA-EB-A44Q TCGA-EB-A5UN TCGA-EB-A6L9 
       30.44       225.11        52.90         3.91        52.41        18.21 
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       115.43        30.02        77.98        12.95 
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        64.04        54.51       111.85 
TCGA-EE-A3JB TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A19A 
      201.80        19.86        14.56        34.45        47.31         4.54 
TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19W 
       53.29        11.47       151.46       150.12        99.06       146.63 
TCGA-ER-A1A1 TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A3ET TCGA-ER-A42L 
       47.97         4.70        16.87        10.95        68.52        74.47 
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-A1Z4 TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZQ 
       49.74        27.62        32.78        12.92         7.82       130.95 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F9 
      136.27        35.28        23.21        30.90        66.67        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-A265 TCGA-GN-A268 TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-OD-A75X 
       96.92        42.48       120.53        34.49        46.92       297.01 
TCGA-QB-A6FS TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1W 
        7.23         0.33       174.12         1.97       120.07       185.13 
TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZY TCGA-WE-AA9Y 
        1.15        59.64        65.42        12.69        48.39         1.94 
TCGA-WE-AAA0 TCGA-Z2-AA3S 
       31.99        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             46.95 
[1] "0.2 - 312.1 (49.7)" "0.0 - 346.5 (47.0)"
[1] "hr=" "1.2"
D11V2, survival
                   sevent
clus2                 0   1
  6P GAIN MUTATED    56  84
  6P GAIN WILD-TYPE 114 103
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
              140               217 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               84               103 
$`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-DA-A95V 
       76.57        20.38       176.55        65.92        10.49        72.10 
TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A17Z 
       14.14        13.02        20.35        68.25        54.02         8.65 
TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20H 
       33.73        26.89        68.15         4.96       133.81       168.26 
TCGA-EE-A29B TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A2A5 TCGA-EE-A2GB 
       85.08        56.42        14.47        61.28        39.29        59.28 
TCGA-EE-A2GD TCGA-EE-A2GH TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
      340.14       220.24       102.12        13.91        42.77        81.21 
TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MI TCGA-EE-A2MK 
       44.88        94.82       103.27       268.73       204.66       180.39 
TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A2MU 
      167.90        47.54       248.65        43.23       162.48        53.26 
TCGA-EE-A3AA TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3J5 
      124.31        28.77        13.81        41.59       172.18        36.95 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JI TCGA-ER-A197 TCGA-ER-A199 
       64.08        34.32        53.19       152.81        13.94         9.17 
TCGA-ER-A19C TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P 
       48.89        13.02        26.37        61.05        44.05       162.08 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A2NC TCGA-ER-A2NF TCGA-ER-A3ES TCGA-ER-A3EV 
       50.89        49.48        43.82        16.37       247.04        46.98 
TCGA-ER-A3PL TCGA-FR-A8YD TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1ZC TCGA-FS-A1ZE 
       33.21        36.26       202.65        20.91       357.37        46.45 
TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZU TCGA-FS-A1ZY 
       47.38        23.93       101.26        74.73        26.56        27.09 
TCGA-FS-A1ZZ TCGA-FS-A4F2 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4FD TCGA-FW-A3I3 
       27.02        50.14        28.73       174.84        80.68         0.20 
TCGA-GF-A4EO TCGA-GF-A6C9 TCGA-GN-A264 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A26A 
        7.23        15.78       117.93        10.13        64.44        32.48 
TCGA-GN-A26D TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A8LL TCGA-GN-A9SD TCGA-LH-A9QB 
       48.00        22.13        50.10        21.37        59.41       368.78 
TCGA-QB-AA9O TCGA-RP-A690 TCGA-RP-A694 TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1V 
       18.05         0.20         0.69        69.07       111.09        42.08 
TCGA-W3-AA21 TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-AAA3 
      105.04        70.52        63.22        11.80        35.80        21.40 
TCGA-WE-AAA4 TCGA-YG-AA3O 
       24.99        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-D3-A8GV TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6EA TCGA-D9-A6EC 
      167.70         7.10        15.39        22.29        25.18        77.56 
TCGA-D9-A6EG TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I4 TCGA-DA-A1I5 
       22.95        36.03       144.89       207.48        35.93       120.00 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 
       73.84        53.92        40.60        68.09        33.93       225.96 
TCGA-DA-A3F8 TCGA-DA-A95W TCGA-DA-A95X TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5UL 
       15.68        25.15        61.81        13.87        10.36        29.29 
TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A180 
       58.92         7.04        36.46        29.82        27.22        94.98 
TCGA-EE-A182 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29C 
       14.70       151.27        91.56        13.55        63.35        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-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X 
       18.61        66.74       369.93        25.87       195.02        17.92 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GC TCGA-EE-A2GE 
       46.82       115.96        59.64        86.14        67.43       173.79 
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-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-A2MG TCGA-EE-A2MH TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MR TCGA-EE-A2MT 
      103.20        16.96        96.23       216.66       134.40        71.21 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3JB 
      122.73        64.04        54.51       138.81       127.20       201.80 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A198 
       27.35        51.35       134.33        31.40        35.44        50.76 
TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J 
       77.75        98.40        12.59       268.93       152.35         6.44 
TCGA-ER-A19L TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2ND TCGA-ER-A2NE 
      131.51         8.88       148.18        79.99        23.34        20.15 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ET TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A3YN 
       31.27        32.05        93.01        12.95       149.03        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-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z4 
       34.82       104.42       216.92        48.59       228.59        28.08 
TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZG 
        7.79        27.72        48.85        53.52        15.45         9.70 
TCGA-FS-A1ZH TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZW 
       32.75       133.55        11.41       148.80        53.16        49.48 
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-A265 TCGA-GN-A268 TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 
       96.92        62.79       121.91        39.35        10.42        48.89 
TCGA-HR-A2OG TCGA-HR-A2OH TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A693 TCGA-W3-A824 
        0.23        65.88       297.90         7.23         0.33       228.16 
TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1W TCGA-WE-A8JZ TCGA-WE-A8K1 
       63.02       121.08         4.01       219.16        24.03        49.05 
TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZY TCGA-WE-AA9Y 
       61.15        17.95       101.33        58.98        49.51        12.16 
TCGA-WE-AAA0 TCGA-YD-A89C TCGA-YD-A9TA TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S 
       40.41         6.90        49.18        14.43        27.58        96.99 
TCGA-Z2-AA3V 
       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             53.92 
[1] "0.2 - 368.8 (50.1)" "0.2 - 369.9 (53.9)"
[1] "hr=" "1.2"
D11V3, continuous
                   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          11       5      15       13       13       14
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  6P GAIN MUTATED           5         6        11        14          6
  6P GAIN WILD-TYPE         9        13         4        26          9
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  6P GAIN MUTATED           11         17        7
  6P GAIN WILD-TYPE         22         38       14
D11V4, multiclass
             clus
vv            6P GAIN MUTATED 6P GAIN WILD-TYPE
  I OR II NOS               2                11
  STAGE 0                   2                 5
  STAGE I                  14                15
  STAGE IA                  5                13
  STAGE IB                 15                13
  STAGE II                 11                14
  STAGE IIA                 5                 9
  STAGE IIB                 6                13
  STAGE IIC                11                 4
  STAGE III                14                26
  STAGE IIIA                6                 9
  STAGE IIIB               11                22
  STAGE IIIC               17                38
  STAGE IV                  7                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 35
  6P GAIN WILD-TYPE    42 39 54 35
D11V5, multiclass
       clus
vv      6P GAIN MUTATED 6P GAIN WILD-TYPE
  T0+T1              22                42
  T2                 34                39
  T3                 24                54
  T4                 35                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    76  22  13  15
  6P GAIN WILD-TYPE 101  43  26  30
D11V6, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  N0              76               101
  N1              22                43
  N2              13                26
  N3              15                30
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V7, binary
                   cls
clus                  0   1
  6P GAIN MUTATED   120   8
  6P GAIN WILD-TYPE 198  14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED    120    8
  6P GAIN WILD-TYPE  198   14
   clus
vv  6P GAIN MUTATED 6P GAIN WILD-TYPE
  0             120               198
  1               8                14
[1] 2 2
[1] FALSE
D11V8, binary
                   cls
clus                 0  1
  6P GAIN MUTATED   50 36
  6P GAIN WILD-TYPE 84 54
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     50   36
  6P GAIN WILD-TYPE   84   54
     clus
vv    6P GAIN MUTATED 6P GAIN WILD-TYPE
  NO               50                84
  YES              36                54
[1] 2 2
[1] FALSE
D11V9, binary
                   cls
clus                  0   1
  6P GAIN MUTATED    21 123
  6P GAIN WILD-TYPE  26 196
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     21  123
  6P GAIN WILD-TYPE   26  196
     clus
vv    6P GAIN MUTATED 6P GAIN WILD-TYPE
  NO               21                26
  YES             123               196
[1] 2 2
[1] FALSE
D11V10, continuous
D11V11, binary
                   cls
clus                  0   1
  6P GAIN MUTATED    59  85
  6P GAIN WILD-TYPE  78 144
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     59   85
  6P GAIN WILD-TYPE   78  144
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  FEMALE              59                78
  MALE                85               144
[1] 2 2
[1] FALSE
D11V12, binary
                   cls
clus                  0   1
  6P GAIN MUTATED   126  16
  6P GAIN WILD-TYPE 191  31
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED    126   16
  6P GAIN WILD-TYPE  191   31
     clus
vv    6P GAIN MUTATED 6P GAIN WILD-TYPE
  NO              126               191
  YES              16                31
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  6P GAIN MUTATED       1                         0   140
  6P GAIN WILD-TYPE     4                         1   212
D11V13, multiclass
                           clus
vv                          6P GAIN MUTATED 6P GAIN WILD-TYPE
  ASIAN                                   1                 4
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                 140               212
[1] 3 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     2 142
  6P GAIN WILD-TYPE   5 209
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      2  142
  6P GAIN WILD-TYPE    5  209
                        clus
vv                       6P GAIN MUTATED 6P GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 5
  NOT HISPANIC OR LATINO             142               209
[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 112 102
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               31               214 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               21               102 
$`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        89.26       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        47.18        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        69.21        22.85 
TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 
       76.34       138.67        53.65       150.61        95.51        45.07 
TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A95V TCGA-DA-A95X 
       64.83        58.85        30.44       225.11        72.10        52.90 
TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5SG TCGA-EB-A5UN TCGA-EB-A6L9 
       14.14        12.30         3.91        33.24        52.41        18.21 
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-A20C TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H 
       75.55        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       115.43 
TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
       30.02        77.98        26.14       239.11        12.95       201.60 
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-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 
        0.76         0.20        81.99       103.13        15.25         5.75 
TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MM 
       23.77       209.79        94.19        63.25       104.78       145.45 
TCGA-EE-A2MP TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC 
      227.01        25.08        23.51       124.31       122.73        64.04 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3JB 
        4.41        54.51         6.28       111.85        45.90       201.80 
TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A 
       19.86        14.56        34.45        47.31         7.82         4.54 
TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19N 
       53.29        11.47       151.46       150.12        99.06        42.48 
TCGA-ER-A19P TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NG 
      120.76       146.63        47.97         4.70        16.87        10.95 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A44A TCGA-FR-A729 
      173.29        68.52        32.05        74.47       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-A1ZE TCGA-FS-A1ZF 
        8.35        27.62       312.07        32.78        42.08        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-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        96.92        17.06 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-LH-A9QB 
       42.48         7.59       120.53        34.49        46.92        85.05 
TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A825 
      297.01         7.23         0.20         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        65.42 
TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 
       12.69        21.90        62.89        48.39         1.94        31.99 
TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-Z2-AA3S 
       18.31        18.35        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 
           50.070            46.455 
[1] "1.6 - 173.8 (50.1)" "0.0 - 346.5 (46.5)"
[1] "hr=" "1.4"
D12V2, survival
                   sevent
clus2                 0   1
  6Q GAIN MUTATED    18  30
  6Q GAIN WILD-TYPE 152 157
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               48               309 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               30               157 
$`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       180.39 
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        49.48        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        35.80 

$`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-D3-A8GV TCGA-D9-A148 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 
      117.17       167.70       151.53         3.65         7.10        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        77.56        22.95        76.57 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
       36.03       144.89       207.48       176.55        35.93       120.00 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
       73.84        53.92        65.92        40.60        68.09        33.93 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-DA-A95V TCGA-DA-A95W TCGA-DA-A95X 
       10.49       225.96        15.68        72.10        25.15        61.81 
TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG 
       14.14        13.02        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 
       29.29        58.92         7.04        36.46        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       115.96        59.64 
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       173.79 
TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
      220.24        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        64.04 
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       134.33        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        93.01        33.21 
TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 
       12.95       149.03        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        46.45 
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-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-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F9 
       27.09        27.02        77.82        66.67        28.73        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-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U3 
       96.92        64.44        62.79        32.48        48.00       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-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 
       65.88       368.78       297.90         7.23         0.20         0.33 
TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1R 
        0.69       228.16        63.02       121.08         4.01       111.09 
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        17.95       101.33 
TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 
       58.98        70.52        63.22        49.51        12.16        40.41 
TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YD-A89C TCGA-YD-A9TA TCGA-YG-AA3O TCGA-YG-AA3P 
       21.40        24.99         6.90        49.18        37.94        14.43 
TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
       27.58        96.99        15.98 

  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
              0.2               0.2 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
           204.66            369.93 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
            50.12             53.92 
[1] "0.2 - 204.7 (50.1)" "0.2 - 369.9 (53.9)"
[1] "hr=" "1.3"
D12V3, continuous
                   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          12       7      22       16       20       21
                   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        12        35         13
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  6Q GAIN MUTATED            3          2        3
  6Q GAIN WILD-TYPE         30         53       18
D12V4, multiclass
             clus
vv            6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  I OR II NOS               1                12
  STAGE 0                   0                 7
  STAGE I                   7                22
  STAGE IA                  2                16
  STAGE IB                  8                20
  STAGE II                  4                21
  STAGE IIA                 1                13
  STAGE IIB                 2                17
  STAGE IIC                 3                12
  STAGE III                 5                35
  STAGE IIIA                2                13
  STAGE IIIB                3                30
  STAGE IIIC                2                53
  STAGE IV                  3                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
  6Q GAIN MUTATED       5 13  7 15
  6Q GAIN WILD-TYPE    59 60 71 55
D12V5, multiclass
       clus
vv      6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  T0+T1               5                59
  T2                 13                60
  T3                  7                71
  T4                 15                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
  6Q GAIN MUTATED    30   9   1   2
  6Q GAIN WILD-TYPE 147  56  38  43
D12V6, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  N0              30               147
  N1               9                56
  N2               1                38
  N3               2                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"
D12V7, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED    40   3
  6Q GAIN WILD-TYPE 278  19
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED     40    3
  6Q GAIN WILD-TYPE  278   19
   clus
vv  6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  0              40               278
  1               3                19
[1] 2 2
[1] FALSE
D12V8, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED    23  10
  6Q GAIN WILD-TYPE 111  80
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED     23   10
  6Q GAIN WILD-TYPE  111   80
     clus
vv    6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  NO               23               111
  YES              10                80
[1] 2 2
[1] FALSE
D12V9, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED     7  41
  6Q GAIN WILD-TYPE  40 278
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      7   41
  6Q GAIN WILD-TYPE   40  278
     clus
vv    6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  NO                7                40
  YES              41               278
[1] 2 2
[1] FALSE
D12V10, continuous
D12V11, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED    17  31
  6Q GAIN WILD-TYPE 120 198
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED     17   31
  6Q GAIN WILD-TYPE  120  198
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  FEMALE              17               120
  MALE                31               198
[1] 2 2
[1] FALSE
D12V12, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED    41   6
  6Q GAIN WILD-TYPE 276  41
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED     41    6
  6Q GAIN WILD-TYPE  276   41
     clus
vv    6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  NO               41               276
  YES               6                41
[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   304
D12V13, multiclass
                           clus
vv                          6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  ASIAN                                   0                 5
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  48               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"
D12V14, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED     0  48
  6Q GAIN WILD-TYPE   7 303
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      0   48
  6Q GAIN WILD-TYPE    7  303
                        clus
vv                       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 7
  NOT HISPANIC OR LATINO              48               303
[1] 2 2
[1] FALSE

Clustering(13) Variable = 7P GAIN MUTATION ANALYSIS
D13V1, survival
                   sevent
clus2                0  1
  7P GAIN MUTATED   71 62
  7P GAIN WILD-TYPE 51 61
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              133               112 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               62                61 
$`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        69.21        22.85        76.34 
TCGA-DA-A1HY TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC 
      138.67       150.61        95.51        45.07        64.83        58.85 
TCGA-DA-A3F5 TCGA-DA-A95V TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5UN TCGA-EB-A6L9 
      225.11        72.10        12.30         3.91        52.41        18.21 
TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A20H TCGA-EE-A29C TCGA-EE-A29D 
       24.89        62.37        20.38       155.90        76.14        12.99 
TCGA-EE-A29E TCGA-EE-A29P TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A6 TCGA-EE-A2GB 
        0.26        27.16       346.49       185.19        77.98        26.14 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN 
       12.95       201.60        68.65        32.48        18.35        31.00 
TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MJ TCGA-EE-A2MK 
      118.32         0.76       103.13        15.25        63.25        89.26 
TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AA 
      145.45       227.01        25.08       143.93        53.26       124.31 
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-ER-A197 TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19G 
      201.80         1.58         7.82        53.29        39.81       151.46 
TCGA-ER-A19H TCGA-ER-A19P TCGA-ER-A19S TCGA-ER-A2ND TCGA-ER-A3EV TCGA-ER-A3PL 
      150.12       120.76        47.18         4.70        15.48        32.05 
TCGA-ER-A42L TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FS-A1Z3 
       74.47       174.21       209.23         5.65        10.06         8.35 
TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZG TCGA-FS-A1ZM TCGA-FS-A1ZQ 
       27.62       312.07        32.78         7.82        78.61       130.95 
TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F8 TCGA-FW-A5DY TCGA-GF-A4EO TCGA-GN-A264 
        5.29         3.06       173.19        19.30         6.05       117.93 
TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U8 TCGA-GN-A8LK 
       96.92        17.06        42.48         7.59        46.92        43.23 
TCGA-GN-A9SD TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A690 TCGA-W3-AA1R TCGA-W3-AA1W 
       59.41         7.23        18.05         0.20        79.99       185.13 
TCGA-W3-AA21 TCGA-WE-A8K5 TCGA-WE-A8ZM TCGA-WE-A8ZQ TCGA-WE-AA9Y TCGA-WE-AAA3 
       92.84        59.64        65.42        62.89         1.94        18.31 
TCGA-YG-AA3O 
       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-A95X TCGA-DA-A95Y TCGA-EB-A5SG TCGA-EB-A5SH 
       53.65        30.44        52.90        14.14        33.24        50.07 
TCGA-EE-A17X TCGA-EE-A182 TCGA-EE-A184 TCGA-EE-A20C TCGA-EE-A29B TCGA-EE-A29G 
       13.15         0.00        67.50        75.55        75.22        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       115.43        30.02       239.11 
TCGA-EE-A2GK TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M8 TCGA-EE-A2MC 
       10.62         0.20        71.31        81.99         5.75        23.77 
TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2ML TCGA-EE-A2MT TCGA-EE-A3AB 
      209.79        94.19       171.85       104.78        23.51       122.73 
TCGA-EE-A3AC TCGA-EE-A3J8 TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 
       64.04         3.35        19.86       152.81        14.56        34.45 
TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19D TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
       47.31         4.54        11.47        99.06        59.84        42.48 
TCGA-ER-A19Q TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NG 
       49.71       146.63        47.97        22.36        16.87        10.95 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-FR-A7U8 TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 
      173.29        68.52        26.20       171.78        49.74       195.98 
TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZJ TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU 
       42.08        12.92        36.33       136.27        35.28         4.47 
TCGA-FS-A1ZW TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TU 
       23.21        30.90        66.67        13.28        80.68        55.59 
TCGA-FW-A3TV TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A4U3 TCGA-GN-A4U4 
       11.54         9.90         1.91        53.29       120.53        34.49 
TCGA-LH-A9QB TCGA-OD-A75X TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 
       85.05       297.01         0.33       174.12         1.97       120.07 
TCGA-W3-AA1Q TCGA-W3-AA1V TCGA-WE-A8K1 TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT 
       44.05         8.09         1.15        12.69        21.90        10.95 
TCGA-WE-A8ZY TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-Z2-AA3S 
       48.39        31.99        18.35        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 
           52.410            44.165 
[1] "0.2 - 346.5 (52.4)" "0.0 - 297.0 (44.2)"
[1] "hr=" "1.3"
D13V2, survival
                   sevent
clus2                 0   1
  7P GAIN MUTATED    98 100
  7P GAIN WILD-TYPE  72  87
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              198               159 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              100                87 
$`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-D3-A8GV TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JX TCGA-D9-A3Z3 
      117.17       167.70       151.53        54.67         7.10        22.29 
TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW 
        9.90        25.18        77.56        22.95        76.57        36.03 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 
      144.89        20.38       176.55        35.93       120.00        73.84 
TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F5 TCGA-DA-A95V TCGA-DA-A95W 
       53.92        65.92        68.09       225.96        72.10        25.15 
TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A6L9 
       13.02        13.87        20.35        29.29        58.92        36.46 
TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A20B TCGA-EE-A20H TCGA-EE-A29A 
       27.22        94.98        33.73       133.81       168.26        63.35 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29T 
       78.97        13.97        63.78        18.61        56.42       369.93 
TCGA-EE-A29W TCGA-EE-A2A0 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH 
      195.02        46.82        86.14        59.28       173.79       220.24 
TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO 
       48.72       107.38        79.66        75.48       102.12       126.81 
TCGA-EE-A2GP TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MH TCGA-EE-A2MJ TCGA-EE-A2MK 
       13.91       129.27        28.83        16.96        96.23       180.39 
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-A2MU TCGA-EE-A3AA TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG 
       53.26       124.31        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-A3JB 
      138.81       172.18       127.20        36.95        64.08       201.80 
TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19E TCGA-ER-A19G 
       13.94         9.17        98.40        48.89        13.02       268.93 
TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19P TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A2ND 
      152.35         6.44       162.08        49.48         8.88        23.34 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A 
       46.98        33.21        12.95       149.03        92.98       174.21 
TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD 
       15.72       220.80        18.77        38.27        34.82        36.26 
TCGA-FR-A8YE TCGA-FS-A1YX TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZC 
      104.42        48.59        20.91        28.08         7.79       357.37 
TCGA-FS-A1ZD TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZR 
       53.52         9.70        32.75       101.26       133.55        11.41 
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        96.92        10.13 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U7 TCGA-GN-A4U8 
       64.44        62.79        32.48        48.00        10.42        48.89 
TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A9SD TCGA-HR-A2OG TCGA-HR-A2OH TCGA-QB-A6FS 
       22.13        50.10        59.41         0.23        65.88         7.23 
TCGA-QB-AA9O TCGA-RP-A690 TCGA-W3-AA1O TCGA-W3-AA1R TCGA-W3-AA1W TCGA-W3-AA21 
       18.05         0.20         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        17.95       101.33        63.22        35.80 
TCGA-WE-AA9Y TCGA-WE-AAA3 TCGA-YD-A89C TCGA-YD-A9TA TCGA-YG-AA3O TCGA-YG-AA3P 
       12.16        21.40         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       207.48        40.60        33.93 
TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-DA-A95X TCGA-DA-A95Y TCGA-EB-A44R TCGA-EB-A5SG 
       10.49        15.68        61.81        14.14        10.36        68.25 
TCGA-EB-A5SH TCGA-EB-A5VV TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A182 TCGA-EE-A183 
       54.02         7.04        29.82         8.65        14.70        26.89 
TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29B 
       68.15         4.96       151.27        91.56        13.55        85.08 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29Q TCGA-EE-A29R 
       72.07        64.64         2.60        56.84        66.74        14.47 
TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 
       61.28        25.87        17.92       115.96        59.64        39.29 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GK TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT 
       67.43       340.14        54.74        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-A2MI TCGA-EE-A2ML TCGA-EE-A2MT TCGA-EE-A3AB 
      268.73       103.20       204.66       216.66        71.21       122.73 
TCGA-EE-A3AC TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH 
       64.04        34.32        53.19        27.35        51.35       134.33 
TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19D 
      152.81        31.40        35.44        50.76        77.75        12.59 
TCGA-ER-A19F TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A19W 
       26.37       131.51        61.05        44.05        50.89       148.18 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH 
       79.99        43.82        20.15        16.37        31.27        32.05 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-FR-A7U8 TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 
      247.04        93.01        27.85       216.92       228.59       202.65 
TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZJ TCGA-FS-A1ZK 
       27.72        48.85        46.45        15.45        47.38        23.93 
TCGA-FS-A1ZP TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A4F0 
       74.73       148.80        53.16        26.56        49.48        77.82 
TCGA-FS-A4F4 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3R5 
       66.67        34.03        26.73        54.41        80.68        22.92 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A4U3 
       55.59        13.51         9.90         2.04       139.89       121.91 
TCGA-GN-A4U4 TCGA-GN-A8LL TCGA-LH-A9QB TCGA-OD-A75X TCGA-RP-A693 TCGA-RP-A694 
       39.35        21.37       368.78       297.90         0.33         0.69 
TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1Q TCGA-W3-AA1V TCGA-WE-A8K1 
      228.16        63.02       121.08        69.07        42.08        49.05 
TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AAA0 TCGA-WE-AAA4 
       58.98        70.52        11.80        49.51        40.41        24.99 
TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
       27.58        96.99        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 
            51.70             53.16 
[1] "0.2 - 369.9 (51.7)" "0.3 - 368.8 (53.2)"
[1] "hr=" "1.1"
D13V3, continuous
                   vv
clus                I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  7P GAIN MUTATED            11       1      18        9        9       13
  7P GAIN WILD-TYPE           2       6      11        9       19       12
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  7P GAIN MUTATED           8         6        10        26         11
  7P GAIN WILD-TYPE         6        13         5        14          4
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  7P GAIN MUTATED           21         29       13
  7P GAIN WILD-TYPE         12         26        8
D13V4, multiclass
             clus
vv            7P GAIN MUTATED 7P GAIN WILD-TYPE
  I OR II NOS              11                 2
  STAGE 0                   1                 6
  STAGE I                  18                11
  STAGE IA                  9                 9
  STAGE IB                  9                19
  STAGE II                 13                12
  STAGE IIA                 8                 6
  STAGE IIB                 6                13
  STAGE IIC                10                 5
  STAGE III                26                14
  STAGE IIIA               11                 4
  STAGE IIIB               21                12
  STAGE IIIC               29                26
  STAGE IV                 13                 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 42 40
  7P GAIN WILD-TYPE    24 37 36 30
D13V5, multiclass
       clus
vv      7P GAIN MUTATED 7P GAIN WILD-TYPE
  T0+T1              40                24
  T2                 36                37
  T3                 42                36
  T4                 40                30
[1] 4 2
[1] TRUE
[1] "dimension of 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   92 42 20 28
  7P GAIN WILD-TYPE 85 23 19 17
D13V6, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  N0              92                85
  N1              42                23
  N2              20                19
  N3              28                17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V7, binary
                   cls
clus                  0   1
  7P GAIN MUTATED   173  14
  7P GAIN WILD-TYPE 145   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED    173   14
  7P GAIN WILD-TYPE  145    8
   clus
vv  7P GAIN MUTATED 7P GAIN WILD-TYPE
  0             173               145
  1              14                 8
[1] 2 2
[1] FALSE
D13V8, binary
                   cls
clus                 0  1
  7P GAIN MUTATED   76 46
  7P GAIN WILD-TYPE 58 44
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     76   46
  7P GAIN WILD-TYPE   58   44
     clus
vv    7P GAIN MUTATED 7P GAIN WILD-TYPE
  NO               76                58
  YES              46                44
[1] 2 2
[1] FALSE
D13V9, binary
                   cls
clus                  0   1
  7P GAIN MUTATED    31 172
  7P GAIN WILD-TYPE  16 147
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     31  172
  7P GAIN WILD-TYPE   16  147
     clus
vv    7P GAIN MUTATED 7P GAIN WILD-TYPE
  NO               31                16
  YES             172               147
[1] 2 2
[1] FALSE
D13V10, continuous
D13V11, binary
                   cls
clus                  0   1
  7P GAIN MUTATED    82 121
  7P GAIN WILD-TYPE  55 108
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     82  121
  7P GAIN WILD-TYPE   55  108
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  FEMALE              82                55
  MALE               121               108
[1] 2 2
[1] FALSE
D13V12, binary
                   cls
clus                  0   1
  7P GAIN MUTATED   176  25
  7P GAIN WILD-TYPE 141  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED    176   25
  7P GAIN WILD-TYPE  141   22
     clus
vv    7P GAIN MUTATED 7P GAIN WILD-TYPE
  NO              176               141
  YES              25                22
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  7P GAIN MUTATED       4                         0   193
  7P GAIN WILD-TYPE     1                         1   159
D13V13, multiclass
                           clus
vv                          7P GAIN MUTATED 7P GAIN WILD-TYPE
  ASIAN                                   4                 1
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                 193               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"
D13V14, binary
                   cls
clus                  0   1
  7P GAIN MUTATED     5 192
  7P GAIN WILD-TYPE   2 159
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      5  192
  7P GAIN WILD-TYPE    2  159
                        clus
vv                       7P GAIN MUTATED 7P GAIN WILD-TYPE
  HISPANIC OR LATINO                   5                 2
  NOT HISPANIC OR LATINO             192               159
[1] 2 2
[1] FALSE

Clustering(14) Variable = 7Q GAIN MUTATION ANALYSIS
D14V1, survival
                   sevent
clus2                0  1
  7Q GAIN MUTATED   69 61
  7Q GAIN WILD-TYPE 53 62
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              130               115 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               61                62 
$`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        69.21        22.85        76.34       138.67 
TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F5 
      150.61        95.51        45.07        64.83        58.85       225.11 
TCGA-DA-A95V TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5UN TCGA-EB-A6L9 
       72.10        14.14        12.30         3.91        52.41        18.21 
TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A20H TCGA-EE-A29C TCGA-EE-A29E 
       24.89        62.37        20.38       155.90        76.14         0.26 
TCGA-EE-A29P TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE 
       27.16       346.49       185.19        77.98        26.14        12.95 
TCGA-EE-A2GH TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2M6 
      201.60        32.48        18.35       118.32         0.76       103.13 
TCGA-EE-A2M7 TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MR 
       15.25        63.25        89.26       145.45       227.01        25.08 
TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J3 
      143.93        53.26       124.31        54.51         6.28        67.89 
TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3JB TCGA-ER-A193 TCGA-ER-A197 TCGA-ER-A199 
      111.85        45.90       201.80        14.56         1.58         7.82 
TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19P TCGA-ER-A19S 
       53.29        39.81       151.46       150.12       120.76        47.18 
TCGA-ER-A2ND TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A44A TCGA-FR-A729 
        4.70        15.48        32.05        74.47       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-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZY 
       12.92         7.82        78.61       130.95       136.27         5.29 
TCGA-FS-A1ZZ TCGA-FS-A4F8 TCGA-FW-A5DY TCGA-GF-A4EO TCGA-GN-A264 TCGA-GN-A265 
        3.06       173.19        19.30         6.05       117.93        96.92 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A8LK TCGA-GN-A9SD TCGA-LH-A9QB 
       17.06        42.48         7.59        43.23        59.41        85.05 
TCGA-QB-A6FS TCGA-QB-AA9O TCGA-W3-AA1R TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K5 
        7.23        18.05        79.99       185.13        92.84        59.64 
TCGA-WE-A8ZQ TCGA-WE-AA9Y TCGA-WE-AAA3 TCGA-YG-AA3O 
       62.89         1.94        18.31        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-DA-A95X TCGA-EB-A5SG TCGA-EB-A5SH 
       18.44        53.65        30.44        52.90        33.24        50.07 
TCGA-EE-A17X TCGA-EE-A182 TCGA-EE-A184 TCGA-EE-A20C TCGA-EE-A29B TCGA-EE-A29D 
       13.15         0.00        67.50        75.55        75.22        12.99 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29Q TCGA-EE-A2A1 TCGA-EE-A2A2 
       44.28        63.12        47.74        61.12       115.43        30.02 
TCGA-EE-A2GD TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GN TCGA-EE-A2GR TCGA-EE-A2GS 
      239.11        68.65        10.62        31.00         0.20        71.31 
TCGA-EE-A2GU TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI 
       81.99         5.75        23.77       209.79        94.19       171.85 
TCGA-EE-A2ML TCGA-EE-A2MT TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3J8 
      104.78        23.51       122.73        64.04         4.41         3.35 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19D 
       19.86       152.81        34.45        47.31         4.54        11.47 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A19W TCGA-ER-A1A1 
       99.06        59.84        42.48        49.71       146.63        47.97 
TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-FR-A7U8 
       22.36        16.87        10.95       173.29        68.52        26.20 
TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1ZE TCGA-FS-A1ZJ TCGA-FS-A1ZT 
      171.78        49.74       195.98        42.08        36.33        35.28 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F9 TCGA-FS-A4FD 
        4.47        23.21        30.90        66.67        13.28        80.68 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A4U3 
       55.59        11.54         9.90         1.91        53.29       120.53 
TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-OD-A75X TCGA-RP-A690 TCGA-RP-A693 TCGA-W3-A824 
       34.49        46.92       297.01         0.20         0.33       174.12 
TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1Q TCGA-W3-AA1V TCGA-WE-A8K1 TCGA-WE-A8ZM 
        1.97       120.07        44.05         8.09         1.15        65.42 
TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AAA0 TCGA-WE-AAA4 
       12.69        21.90        10.95        48.39        31.99        18.35 
TCGA-Z2-AA3S 
       91.23 

  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
             0.26              0.00 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
           346.49            297.01 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
           52.835            44.280 
[1] "0.3 - 346.5 (52.8)" "0.0 - 297.0 (44.3)"
[1] "hr=" "1.4"
D14V2, survival
                   sevent
clus2                0  1
  7Q GAIN MUTATED   96 99
  7Q GAIN WILD-TYPE 74 88
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              195               162 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               99                88 
$`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-D3-A8GV TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JX TCGA-D9-A3Z3 TCGA-D9-A6E9 
      167.70       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        77.56        22.95        76.57        36.03       144.89 
TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
       20.38       176.55        35.93       120.00        73.84        53.92 
TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-DA-A95V TCGA-DA-A95W 
       65.92        68.09       225.96        15.68        72.10        25.15 
TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A6L9 
       14.14        13.02        13.87        29.29        58.92        36.46 
TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20H 
       27.22        94.98        33.73        26.89       133.81       168.26 
TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29T 
       63.35        78.97        63.78        18.61        56.42       369.93 
TCGA-EE-A29W TCGA-EE-A2A0 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH 
      195.02        46.82        86.14        59.28       173.79       220.24 
TCGA-EE-A2GI TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2M6 
       48.72        79.66        75.48       126.81        13.91       129.27 
TCGA-EE-A2M7 TCGA-EE-A2MH TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MP 
       28.83        16.96        96.23       180.39       167.90       248.65 
TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AE 
       43.23       134.40       162.48        53.26       124.31        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-EE-A3JD TCGA-ER-A193 TCGA-ER-A197 TCGA-ER-A199 
       64.08       201.80        27.35        31.40        13.94         9.17 
TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19E TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J 
       98.40        48.89        13.02       268.93       152.35         6.44 
TCGA-ER-A19P TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A2ND TCGA-ER-A3EV TCGA-ER-A3PL 
      162.08        49.48         8.88        23.34        46.98        33.21 
TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 
       12.95       149.03        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        96.92        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        48.00        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        17.95        63.22        35.80        12.16        21.40 
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       207.48        40.60 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A95X TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG 
       33.93        10.49        61.81        10.36        20.35        68.25 
TCGA-EB-A5SH TCGA-EB-A5VV TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A182 TCGA-EE-A184 
       54.02         7.04        29.82         8.65        14.70        68.15 
TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29B TCGA-EE-A29D 
        4.96       151.27        91.56        13.55        85.08        13.97 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29Q TCGA-EE-A29R 
       72.07        64.64         2.60        56.84        66.74        14.47 
TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 
       61.28        25.87        17.92       115.96        59.64        39.29 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GN TCGA-EE-A2GR 
       67.43       340.14       107.38        54.74       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-A2MI TCGA-EE-A2ML 
       47.28       103.27       268.73       103.20       204.66       216.66 
TCGA-EE-A2MN TCGA-EE-A2MT TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3J8 
       47.54        71.21       122.73        64.04        28.77        34.32 
TCGA-EE-A3JA TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A198 
       53.19        51.35       134.33       152.81        35.44        50.76 
TCGA-ER-A19A TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
       77.75        12.59        26.37       131.51        61.05        44.05 
TCGA-ER-A19Q TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NF 
       50.89       148.18        79.99        43.82        20.15        16.37 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-FR-A7U8 TCGA-FS-A1YW 
       31.27        32.05       247.04        93.01        27.85       216.92 
TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZE TCGA-FS-A1ZJ 
      228.59       202.65        27.72        48.85        46.45        47.38 
TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A4F0 
       23.93        74.73        53.16        26.56        49.48        77.82 
TCGA-FS-A4F4 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3R5 
       66.67        34.03        26.73        54.41        80.68        22.92 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A4U3 
       55.59        13.51         9.90         2.04       139.89       121.91 
TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-GN-A8LL TCGA-OD-A75X TCGA-RP-A690 TCGA-RP-A693 
       39.35        48.89        21.37       297.90         0.20         0.33 
TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1Q TCGA-W3-AA1V 
        0.69       228.16        63.02       121.08        69.07        42.08 
TCGA-WE-A8K1 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-A8ZY 
       49.05       101.33        58.98        70.52        11.80        49.51 
TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-YD-A9TA TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
       40.41        24.99        49.18        27.58        96.99        15.98 

  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              0.2               0.2 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
           369.93            340.14 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
           53.260            52.255 
[1] "0.2 - 369.9 (53.3)" "0.2 - 340.1 (52.3)"
[1] "hr=" "1.1"
D14V3, continuous
                   vv
clus                I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  7Q GAIN MUTATED            11       2      18        8        9       13
  7Q GAIN WILD-TYPE           2       5      11       10       19       12
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  7Q GAIN MUTATED           6         7        12        25         11
  7Q GAIN WILD-TYPE         8        12         3        15          4
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  7Q GAIN MUTATED           22         28       12
  7Q GAIN WILD-TYPE         11         27        9
D14V4, multiclass
             clus
vv            7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  I OR II NOS              11                 2
  STAGE 0                   2                 5
  STAGE I                  18                11
  STAGE IA                  8                10
  STAGE IB                  9                19
  STAGE II                 13                12
  STAGE IIA                 6                 8
  STAGE IIB                 7                12
  STAGE IIC                12                 3
  STAGE III                25                15
  STAGE IIIA               11                 4
  STAGE IIIB               22                11
  STAGE IIIC               28                27
  STAGE IV                 12                 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 42 42
  7Q GAIN WILD-TYPE    28 37 36 28
D14V5, multiclass
       clus
vv      7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  T0+T1              36                28
  T2                 36                37
  T3                 42                36
  T4                 42                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   95 38 23 27
  7Q GAIN WILD-TYPE 82 27 16 18
D14V6, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  N0              95                82
  N1              38                27
  N2              23                16
  N3              27                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"
D14V7, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED   173  13
  7Q GAIN WILD-TYPE 145   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED    173   13
  7Q GAIN WILD-TYPE  145    9
   clus
vv  7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  0             173               145
  1              13                 9
[1] 2 2
[1] FALSE
D14V8, binary
                   cls
clus                 0  1
  7Q GAIN MUTATED   76 46
  7Q GAIN WILD-TYPE 58 44
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     76   46
  7Q GAIN WILD-TYPE   58   44
     clus
vv    7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  NO               76                58
  YES              46                44
[1] 2 2
[1] FALSE
D14V9, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED    29 171
  7Q GAIN WILD-TYPE  18 148
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     29  171
  7Q GAIN WILD-TYPE   18  148
     clus
vv    7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  NO               29                18
  YES             171               148
[1] 2 2
[1] FALSE
D14V10, continuous
D14V11, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED    83 117
  7Q GAIN WILD-TYPE  54 112
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     83  117
  7Q GAIN WILD-TYPE   54  112
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  FEMALE              83                54
  MALE               117               112
[1] 2 2
[1] FALSE
D14V12, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED   176  23
  7Q GAIN WILD-TYPE 141  24
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED    176   23
  7Q GAIN WILD-TYPE  141   24
     clus
vv    7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  NO              176               141
  YES              23                24
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  7Q GAIN MUTATED       3                         0   191
  7Q GAIN WILD-TYPE     2                         1   161
D14V13, multiclass
                           clus
vv                          7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  ASIAN                                   3                 2
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                 191               161
[1] 3 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     5 189
  7Q GAIN WILD-TYPE   2 162
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      5  189
  7Q GAIN WILD-TYPE    2  162
                        clus
vv                       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   5                 2
  NOT HISPANIC OR LATINO             189               162
[1] 2 2
[1] FALSE

Clustering(15) Variable = 8P GAIN MUTATION ANALYSIS
D15V1, survival
                   sevent
clus2                0  1
  8P GAIN MUTATED   43 38
  8P GAIN WILD-TYPE 79 85
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               81               164 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               38                85 
$`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        69.21        22.85       138.67 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A3F5 TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5SH 
       53.65       150.61       225.11        12.30         3.91        50.07 
TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A2GD TCGA-EE-A2GE 
       24.89        20.38        12.99        44.28       239.11        12.95 
TCGA-EE-A2GH TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP 
      201.60        32.48        18.35        31.00       118.32         0.76 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MR TCGA-EE-A3AB TCGA-EE-A3AD 
      103.13        15.25         5.75        25.08       122.73         4.41 
TCGA-EE-A3AE TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-ER-A19C TCGA-ER-A19G TCGA-ER-A19H 
       54.51       111.85        45.90        39.81       151.46       150.12 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A2NC TCGA-ER-A42L TCGA-FR-A44A 
       99.06        59.84        42.48        22.36        74.47       174.21 
TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FS-A1YW TCGA-FS-A1Z4 TCGA-FS-A1ZD 
      209.23        26.20         5.65       171.78        27.62        32.78 
TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZY TCGA-FS-A4F4 TCGA-FS-A4FD TCGA-FW-A3TV 
       78.61       130.95         5.29        66.67        80.68        11.54 
TCGA-GF-A3OT TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A9SD TCGA-RP-A693 
        9.90        17.06         7.59       120.53        59.41         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        65.42        12.69 
TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-YG-AA3O 
       62.89        10.95        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 
       76.34        95.51        45.07        64.83        58.85        30.44 
TCGA-DA-A95V TCGA-DA-A95X TCGA-DA-A95Y TCGA-EB-A5SG TCGA-EB-A5UN TCGA-EB-A6L9 
       72.10        52.90        14.14        33.24        52.41        18.21 
TCGA-EE-A17X TCGA-EE-A180 TCGA-EE-A182 TCGA-EE-A184 TCGA-EE-A20C TCGA-EE-A20H 
       13.15        62.37         0.00        67.50        75.55       155.90 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P 
       75.22        76.14         0.26        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       115.43        30.02        77.98 
TCGA-EE-A2GB TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU 
       26.14        68.65        10.62         0.20        71.31        81.99 
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        89.26 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU 
      104.78       145.45       227.01       143.93        23.51        53.26 
TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J8 TCGA-EE-A3JB 
      124.31        64.04         6.28        67.89         3.35       201.80 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
       19.86       152.81        14.56        34.45         1.58        47.31 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19P TCGA-ER-A19Q 
        7.82         4.54        53.29        11.47       120.76        49.71 
TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NG 
       47.18       146.63        47.97         4.70        16.87        10.95 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A8YC TCGA-FS-A1YY 
      173.29        68.52        15.48        32.05        10.06        49.74 
TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1ZC TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG 
      195.98         8.35       312.07        42.08        12.92         7.82 
TCGA-FS-A1ZJ TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZZ 
       36.33       136.27        35.28         4.47        23.21         3.06 
TCGA-FS-A4F0 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FW-A3TU TCGA-FW-A5DY TCGA-GF-A4EO 
       30.90       173.19        13.28        55.59        19.30         6.05 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A268 TCGA-GN-A4U4 
        1.91        53.29       117.93        96.92        42.48        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-A690 TCGA-W3-A828 TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1W TCGA-WE-A8K1 
        0.20       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-AAA3 
       59.64        21.90        48.39         1.94        31.99        18.31 
TCGA-WE-AAA4 TCGA-Z2-AA3S 
       18.35        91.23 

  8P GAIN MUTATED 8P GAIN WILD-TYPE 
             0.33              0.00 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
           239.11            346.49 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
            49.35             47.08 
[1] "0.3 - 239.1 (49.4)" "0.0 - 346.5 (47.1)"
[1] "hr=" "1.1"
D15V2, survival
                   sevent
clus2                 0   1
  8P GAIN MUTATED    57  60
  8P GAIN WILD-TYPE 113 127
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
              117               240 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               60               127 
$`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        77.56        22.95        36.03 
TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A3F5 TCGA-DA-A95W 
      144.89       207.48       176.55        35.93       225.96        25.15 
TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SH TCGA-EE-A17Y 
       13.02        13.87        10.36        20.35        54.02        27.22 
TCGA-EE-A181 TCGA-EE-A20B TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29R TCGA-EE-A2GD 
       33.73       133.81        13.97        72.07        14.47       340.14 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO 
      173.79       220.24        79.66        75.48       102.12       126.81 
TCGA-EE-A2GP TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MH TCGA-EE-A2MR 
       13.91       129.27        28.83        19.76        16.96       134.40 
TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 
      122.73        28.77        54.51       127.20        36.95        64.08 
TCGA-EE-A3JA TCGA-ER-A19C TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L 
       53.19        48.89       268.93       152.35         6.44       131.51 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A2NC TCGA-ER-A2NF TCGA-ER-A42L TCGA-FR-A44A 
       61.05        44.05        43.82        16.37       149.03       174.21 
TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YD TCGA-FS-A1YW 
      220.80        27.85        18.77        38.27        36.26       216.92 
TCGA-FS-A1YX TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZD TCGA-FS-A1ZK TCGA-FS-A1ZM 
       48.59        28.08         7.79        53.52        23.93       101.26 
TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZY TCGA-FS-A4F2 TCGA-FS-A4F4 
       74.73       133.55        11.41        27.09        50.14        66.67 
TCGA-FS-A4F5 TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TV TCGA-GF-A3OT TCGA-GN-A266 
       28.73        80.68         0.20        13.51         9.90        10.13 
TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A8LL TCGA-GN-A9SD 
       64.44        32.48        48.00       121.91        21.37        59.41 
TCGA-HR-A2OH TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-AA1V 
       65.88         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        17.95       101.33        58.98        63.22        11.80 
TCGA-WE-A8ZX TCGA-YG-AA3O TCGA-Z2-AA3V 
       35.80        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-D3-A8GV TCGA-D9-A148 TCGA-D9-A149 
       29.06       129.63       117.17       167.70       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-DA-A1HV TCGA-DA-A1I0 TCGA-DA-A1I5 TCGA-DA-A1I7 
        9.90        25.18        76.57        20.38       120.00        73.84 
TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
       53.92        65.92        40.60        68.09        33.93        10.49 
TCGA-DA-A3F8 TCGA-DA-A95V TCGA-DA-A95X TCGA-DA-A95Y TCGA-EB-A5SG TCGA-EB-A5UL 
       15.68        72.10        61.81        14.14        68.25        29.29 
TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A180 
       58.92         7.04        36.46        29.82         8.65        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-A29C TCGA-EE-A29E 
      168.26        13.55        63.35        85.08        78.97        63.78 
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 
      115.96        59.64        39.29        86.14        59.28        67.43 
TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT 
       48.72       107.38        54.74        42.77        81.21        44.88 
TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF 
       94.82        21.67        61.51        47.28       103.27       268.73 
TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM 
      103.20       204.66        96.23       180.39       216.66       167.90 
TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU 
       47.54       248.65        43.23       162.48        71.21        53.26 
TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 
      124.31        64.04        13.81        41.59       138.81       172.18 
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       134.33       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-A19P TCGA-ER-A19Q 
       98.40        12.59        13.02        26.37       162.08        50.89 
TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2ND TCGA-ER-A2NE 
       49.48         8.88       148.18        79.99        23.34        20.15 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL 
       31.27        32.05       247.04        93.01        46.98        33.21 
TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A69P TCGA-FR-A8YC TCGA-FR-A8YE TCGA-FS-A1YY 
       12.95        92.98        15.72        34.82       104.42       228.59 
TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZE 
      202.65        20.91        27.72        48.85       357.37        46.45 
TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZS TCGA-FS-A1ZT 
       15.45         9.70        32.75        47.38       148.80        53.16 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F8 TCGA-FS-A4F9 
       26.56        49.48        27.02        77.82       174.84        34.03 
TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A5DY TCGA-GF-A4EO 
       26.73        54.41        22.92        55.59        19.30         7.23 
TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A268 
        2.04        15.78       139.89       117.93        96.92        62.79 
TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-HR-A2OG 
       39.35        10.42        48.89        22.13        50.10         0.23 
TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A690 TCGA-W3-A828 
      368.78       297.90         7.23        18.05         0.20       121.08 
TCGA-W3-AA1O TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1W TCGA-WE-A8JZ TCGA-WE-A8K1 
        4.01        69.07       111.09       219.16        24.03        49.05 
TCGA-WE-A8K5 TCGA-WE-A8ZO TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 
       61.15        70.52        49.51        12.16        40.41        21.40 
TCGA-WE-AAA4 TCGA-YD-A89C TCGA-YD-A9TA TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S 
       24.99         6.90        49.18        14.43        27.58        96.99 

  8P GAIN MUTATED 8P GAIN WILD-TYPE 
              0.2               0.2 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
           340.14            369.93 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
           54.020            50.825 
[1] "0.2 - 340.1 (54.0)" "0.2 - 369.9 (50.8)"
[1] "hr=" "1"  
D15V3, continuous
                   vv
clus                I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  8P GAIN MUTATED             3       1      12        6        7       13
  8P GAIN WILD-TYPE          10       6      17       12       21       12
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  8P GAIN MUTATED           5         3         6        20          7
  8P GAIN WILD-TYPE         9        16         9        20          8
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  8P GAIN MUTATED           11         13        7
  8P GAIN WILD-TYPE         22         42       14
D15V4, multiclass
             clus
vv            8P GAIN MUTATED 8P GAIN WILD-TYPE
  I OR II NOS               3                10
  STAGE 0                   1                 6
  STAGE I                  12                17
  STAGE IA                  6                12
  STAGE IB                  7                21
  STAGE II                 13                12
  STAGE IIA                 5                 9
  STAGE IIB                 3                16
  STAGE IIC                 6                 9
  STAGE III                20                20
  STAGE IIIA                7                 8
  STAGE IIIB               11                22
  STAGE IIIC               13                42
  STAGE IV                  7                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 28 22
  8P GAIN WILD-TYPE    39 49 50 48
D15V5, multiclass
       clus
vv      8P GAIN MUTATED 8P GAIN WILD-TYPE
  T0+T1              25                39
  T2                 24                49
  T3                 28                50
  T4                 22                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
  8P GAIN MUTATED    56  29  14   9
  8P GAIN WILD-TYPE 121  36  25  36
D15V6, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  N0              56               121
  N1              29                36
  N2              14                25
  N3               9                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"
D15V7, binary
                   cls
clus                  0   1
  8P GAIN MUTATED   108   7
  8P GAIN WILD-TYPE 210  15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED    108    7
  8P GAIN WILD-TYPE  210   15
   clus
vv  8P GAIN MUTATED 8P GAIN WILD-TYPE
  0             108               210
  1               7                15
[1] 2 2
[1] FALSE
D15V8, binary
                   cls
clus                 0  1
  8P GAIN MUTATED   41 33
  8P GAIN WILD-TYPE 93 57
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     41   33
  8P GAIN WILD-TYPE   93   57
     clus
vv    8P GAIN MUTATED 8P GAIN WILD-TYPE
  NO               41                93
  YES              33                57
[1] 2 2
[1] FALSE
D15V9, binary
                   cls
clus                  0   1
  8P GAIN MUTATED    18 103
  8P GAIN WILD-TYPE  29 216
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     18  103
  8P GAIN WILD-TYPE   29  216
     clus
vv    8P GAIN MUTATED 8P GAIN WILD-TYPE
  NO               18                29
  YES             103               216
[1] 2 2
[1] FALSE
D15V10, continuous
D15V11, binary
                   cls
clus                  0   1
  8P GAIN MUTATED    41  80
  8P GAIN WILD-TYPE  96 149
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     41   80
  8P GAIN WILD-TYPE   96  149
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  FEMALE              41                96
  MALE                80               149
[1] 2 2
[1] FALSE
D15V12, binary
                   cls
clus                  0   1
  8P GAIN MUTATED   105  15
  8P GAIN WILD-TYPE 212  32
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED    105   15
  8P GAIN WILD-TYPE  212   32
     clus
vv    8P GAIN MUTATED 8P GAIN WILD-TYPE
  NO              105               212
  YES              15                32
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  8P GAIN MUTATED       4                         0   113
  8P GAIN WILD-TYPE     1                         1   239
D15V13, multiclass
                           clus
vv                          8P GAIN MUTATED 8P GAIN WILD-TYPE
  ASIAN                                   4                 1
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                 113               239
[1] 3 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     2 115
  8P GAIN WILD-TYPE   5 236
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      2  115
  8P GAIN WILD-TYPE    5  236
                        clus
vv                       8P GAIN MUTATED 8P GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 5
  NOT HISPANIC OR LATINO             115               236
[1] 2 2
[1] FALSE

Clustering(16) Variable = 8Q GAIN MUTATION ANALYSIS
D16V1, survival
                   sevent
clus2                0  1
  8Q GAIN MUTATED   65 57
  8Q GAIN WILD-TYPE 57 66
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              122               123 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               57                66 
$`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 
       69.21        22.85       138.67        53.65       150.61       225.11 
TCGA-DA-A95V TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A6L9 
       72.10        12.30         3.91        33.24        50.07        18.21 
TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29T 
       24.89        20.38        76.14         0.26        44.28       346.49 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN 
      239.11        12.95       201.60        32.48        18.35        31.00 
TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 
      118.32         0.76        71.31       103.13        15.25         5.75 
TCGA-EE-A2MR TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3J3 
       25.08       124.31       122.73         4.41        54.51        67.89 
TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-ER-A197 TCGA-ER-A19C TCGA-ER-A19G TCGA-ER-A19H 
      111.85        45.90         1.58        39.81       151.46       150.12 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A2NC 
       99.06        59.84        42.48        49.71        47.18        22.36 
TCGA-ER-A2ND TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A42L TCGA-FR-A44A TCGA-FR-A729 
        4.70        68.52        15.48        74.47       174.21       209.23 
TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z4 
       26.20         5.65       171.78        49.74       195.98        27.62 
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-A1ZY TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4FD TCGA-FW-A3TV TCGA-GF-A3OT 
        5.29        66.67       173.19        80.68        11.54         9.90 
TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A9SD TCGA-OD-A75X 
       96.92        17.06         7.59       120.53        59.41       297.01 
TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-AA1V 
        7.23        18.05         0.33       174.12         1.97         8.09 
TCGA-W3-AA21 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-AAA3 
       92.84        65.42        12.69        62.89        10.95        18.31 
TCGA-YG-AA3O TCGA-Z2-AA3S 
       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        76.34        95.51        45.07 
TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A95X TCGA-DA-A95Y TCGA-EB-A5UN 
       64.83        58.85        30.44        52.90        14.14        52.41 
TCGA-EE-A17X TCGA-EE-A180 TCGA-EE-A182 TCGA-EE-A184 TCGA-EE-A20C TCGA-EE-A20H 
       13.15        62.37         0.00        67.50        75.55       155.90 
TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29Q 
       75.22        12.99        63.12        47.74        27.16        61.12 
TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GJ 
      185.19       115.43        30.02        77.98        26.14        68.65 
TCGA-EE-A2GK TCGA-EE-A2GR TCGA-EE-A2GU TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MG 
       10.62         0.20        81.99        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        89.26       104.78       145.45       227.01 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AC TCGA-EE-A3AF TCGA-EE-A3J8 
      143.93        23.51        53.26        64.04         6.28         3.35 
TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A198 
      201.80        19.86       152.81        14.56        34.45        47.31 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19P TCGA-ER-A19W 
        7.82         4.54        53.29        11.47       120.76       146.63 
TCGA-ER-A1A1 TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3PL TCGA-FR-A8YC 
       47.97        16.87        10.95       173.29        32.05        10.06 
TCGA-FS-A1Z3 TCGA-FS-A1ZC TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZJ 
        8.35       312.07        42.08        12.92         7.82        36.33 
TCGA-FS-A1ZW TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F9 TCGA-FW-A3TU TCGA-FW-A5DY 
       23.21         3.06        30.90        13.28        55.59        19.30 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A268 TCGA-GN-A4U4 
        6.05         1.91        53.29       117.93        42.48        34.49 
TCGA-GN-A4U8 TCGA-GN-A8LK TCGA-LH-A9QB TCGA-RP-A690 TCGA-W3-A828 TCGA-W3-AA1Q 
       46.92        43.23        85.05         0.20       120.07        44.05 
TCGA-W3-AA1R TCGA-W3-AA1W TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8ZO TCGA-WE-A8ZY 
       79.99       185.13         1.15        59.64        21.90        48.39 
TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 
        1.94        31.99        18.35 

  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
             0.26              0.00 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
           346.49            312.07 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
            49.53             46.92 
[1] "0.3 - 346.5 (49.5)" "0.0 - 312.1 (46.9)"
[1] "hr=" "1.3"
D16V2, survival
                   sevent
clus2                 0   1
  8Q GAIN MUTATED    81  84
  8Q GAIN WILD-TYPE  89 103
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              165               192 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               84               103 
$`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        77.56        22.95        36.03       144.89        20.38 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A95V 
      207.48       176.55        35.93        10.49       225.96        72.10 
TCGA-DA-A95W TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH 
       25.15        13.02        13.87        10.36        68.25        54.02 
TCGA-EB-A6L9 TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A20B TCGA-EE-A29C 
       36.46        27.22         8.65        33.73       133.81        78.97 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29R TCGA-EE-A29T TCGA-EE-A2A5 TCGA-EE-A2GD 
       63.78        72.07        14.47       369.93        39.29       340.14 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO 
      173.79       220.24        79.66        75.48       102.12       126.81 
TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MH 
       13.91        81.21       129.27        28.83        19.76        16.96 
TCGA-EE-A2MN TCGA-EE-A2MR TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE 
       47.54       134.40       124.31       122.73        28.77        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-ER-A197 TCGA-ER-A19C TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L 
       13.94        48.89       268.93       152.35         6.44       131.51 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A2NC 
       61.05        44.05        50.89        49.48         8.88        43.82 
TCGA-ER-A2ND TCGA-ER-A2NF TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A42L TCGA-FR-A44A 
       23.34        16.37        93.01        46.98       149.03       174.21 
TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YD TCGA-FS-A1YW 
      220.80        27.85        18.77        38.27        36.26       216.92 
TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZD 
       48.59       228.59       202.65        28.08         7.79        53.52 
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-A1ZY TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 
       53.16        26.56        27.09        50.14        66.67        28.73 
TCGA-FS-A4F8 TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TV TCGA-GF-A3OT TCGA-GN-A265 
      174.84        80.68         0.20        13.51         9.90        96.92 
TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A8LL 
       10.13        64.44        32.48        48.00       121.91        21.37 
TCGA-GN-A9SD TCGA-HR-A2OH TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 
       59.41        65.88       297.90         7.23        18.05         0.33 
TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-AA1V TCGA-W3-AA21 TCGA-WE-A8K6 
        0.69       228.16        63.02        42.08       105.04        17.95 
TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-AAA3 
      101.33        58.98        63.22        11.80        35.80        21.40 
TCGA-YG-AA3O TCGA-Z2-AA3S TCGA-Z2-AA3V 
       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-D3-A8GV TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JX TCGA-D9-A1X3 TCGA-D9-A3Z1 
      167.70       151.53        54.67         7.10        18.12        15.39 
TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-DA-A1HV TCGA-DA-A1I5 
       22.29        18.44         9.90        25.18        76.57       120.00 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
       73.84        53.92        65.92        40.60        68.09        33.93 
TCGA-DA-A3F8 TCGA-DA-A95X TCGA-DA-A95Y TCGA-EB-A5KH TCGA-EB-A5UL TCGA-EB-A5UN 
       15.68        61.81        14.14        20.35        29.29        58.92 
TCGA-EB-A5VV TCGA-EE-A17X TCGA-EE-A180 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 
        7.04        29.82        94.98        14.70        26.89        68.15 
TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A 
        4.96       151.27        91.56       168.26        13.55        63.35 
TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N 
       85.08        13.97        64.64         2.60        56.84        18.61 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X 
       56.42        66.74        61.28        25.87       195.02        17.92 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC 
       46.82       115.96        59.64        86.14        59.28        67.43 
TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GR TCGA-EE-A2GT TCGA-EE-A2GU 
       48.72       107.38        54.74        42.77        44.88        94.82 
TCGA-EE-A2M5 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG 
       21.67        61.51        47.28       103.27       268.73       103.20 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP 
      204.66        96.23       180.39       216.66       167.90       248.65 
TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AC TCGA-EE-A3AF 
       43.23       162.48        71.21        53.26        64.04        13.81 
TCGA-EE-A3AH TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH 
      138.81        34.32       201.80        27.35        51.35       134.33 
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-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19P TCGA-ER-A19W 
       98.40        12.59        13.02        26.37       162.08       148.18 
TCGA-ER-A1A1 TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3PL 
       79.99        20.15        31.27        32.05       247.04        33.21 
TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A69P TCGA-FR-A8YC TCGA-FR-A8YE TCGA-FS-A1Z3 
       12.95        92.98        15.72        34.82       104.42        20.91 
TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG 
       27.72        48.85       357.37        46.45        15.45         9.70 
TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZW TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F9 
       32.75        47.38        49.48        27.02        77.82        34.03 
TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A5DY TCGA-GF-A4EO 
       26.73        54.41        22.92        55.59        19.30         7.23 
TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A268 TCGA-GN-A4U4 
        2.04        15.78       139.89       117.93        62.79        39.35 
TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-HR-A2OG TCGA-LH-A9QB 
       10.42        48.89        22.13        50.10         0.23       368.78 
TCGA-RP-A690 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1W 
        0.20       121.08         4.01        69.07       111.09       219.16 
TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8ZO TCGA-WE-A8ZY TCGA-WE-AA9Y 
       24.03        49.05        61.15        70.52        49.51        12.16 
TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-YD-A89C TCGA-YD-A9TA TCGA-YG-AA3P TCGA-Z2-A8RT 
       40.41        24.99         6.90        49.18        14.43        27.58 

  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              0.2               0.2 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
           369.93            368.78 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
           54.510            49.495 
[1] "0.2 - 369.9 (54.5)" "0.2 - 368.8 (49.5)"
[1] "hr=" "1.2"
D16V3, continuous
                   vv
clus                I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  8Q GAIN MUTATED             5       1      16        7       12       14
  8Q GAIN WILD-TYPE           8       6      13       11       16       11
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  8Q GAIN MUTATED           6         5         8        26         10
  8Q GAIN WILD-TYPE         8        14         7        14          5
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  8Q GAIN MUTATED           15         20       10
  8Q GAIN WILD-TYPE         18         35       11
D16V4, multiclass
             clus
vv            8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  I OR II NOS               5                 8
  STAGE 0                   1                 6
  STAGE I                  16                13
  STAGE IA                  7                11
  STAGE IB                 12                16
  STAGE II                 14                11
  STAGE IIA                 6                 8
  STAGE IIB                 5                14
  STAGE IIC                 8                 7
  STAGE III                26                14
  STAGE IIIA               10                 5
  STAGE IIIB               15                18
  STAGE IIIC               20                35
  STAGE IV                 10                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 33 30
  8Q GAIN WILD-TYPE    27 37 45 40
D16V5, multiclass
       clus
vv      8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  T0+T1              37                27
  T2                 36                37
  T3                 33                45
  T4                 30                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"
                   vv
clus                 N0  N1  N2  N3
  8Q GAIN MUTATED    77  34  23  18
  8Q GAIN WILD-TYPE 100  31  16  27
D16V6, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  N0              77               100
  N1              34                31
  N2              23                16
  N3              18                27
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V7, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED   149  10
  8Q GAIN WILD-TYPE 169  12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED    149   10
  8Q GAIN WILD-TYPE  169   12
   clus
vv  8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  0             149               169
  1              10                12
[1] 2 2
[1] FALSE
D16V8, binary
                   cls
clus                 0  1
  8Q GAIN MUTATED   58 40
  8Q GAIN WILD-TYPE 76 50
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     58   40
  8Q GAIN WILD-TYPE   76   50
     clus
vv    8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  NO               58                76
  YES              40                50
[1] 2 2
[1] FALSE
D16V9, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED    28 141
  8Q GAIN WILD-TYPE  19 178
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     28  141
  8Q GAIN WILD-TYPE   19  178
     clus
vv    8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  NO               28                19
  YES             141               178
[1] 2 2
[1] FALSE
D16V10, continuous
D16V11, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED    62 107
  8Q GAIN WILD-TYPE  75 122
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     62  107
  8Q GAIN WILD-TYPE   75  122
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  FEMALE              62                75
  MALE               107               122
[1] 2 2
[1] FALSE
D16V12, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED   149  19
  8Q GAIN WILD-TYPE 168  28
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED    149   19
  8Q GAIN WILD-TYPE  168   28
     clus
vv    8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  NO              149               168
  YES              19                28
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  8Q GAIN MUTATED       4                         0   161
  8Q GAIN WILD-TYPE     1                         1   191
D16V13, multiclass
                           clus
vv                          8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  ASIAN                                   4                 1
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                 161               191
[1] 3 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     3 162
  8Q GAIN WILD-TYPE   4 189
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      3  162
  8Q GAIN WILD-TYPE    4  189
                        clus
vv                       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                 4
  NOT HISPANIC OR LATINO             162               189
[1] 2 2
[1] FALSE

Clustering(17) Variable = 9P GAIN MUTATION ANALYSIS
D17V1, survival
                   sevent
clus2                 0   1
  9P GAIN MUTATED     5   7
  9P GAIN WILD-TYPE 117 116
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               12               233 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                7               116 
$`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        68.52       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        69.21 
TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 
       22.85        76.34       138.67        53.65       150.61        95.51 
TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A95V 
       45.07        64.83        58.85        30.44       225.11        72.10 
TCGA-DA-A95X TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5SG TCGA-EB-A5UN 
       52.90        14.14        12.30         3.91        33.24        52.41 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 
       18.21        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-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-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD 
      185.19       115.43        30.02        77.98        26.14       239.11 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
       12.95       201.60        68.65        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        89.26       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 
       64.04         4.41        54.51         6.28        67.89       111.85 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 
       45.90         3.35       201.80        19.86       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-A19C TCGA-ER-A19D TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
       39.81        11.47       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-A2ND 
      120.76        49.71        47.18       146.63        47.97         4.70 
TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42L 
       16.87        10.95       173.29        15.48        32.05        74.47 
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-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE 
       49.74         8.35        27.62       312.07        32.78        42.08 
TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT 
       12.92         7.82        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-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        96.92        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-A690 
       59.41        85.05       297.01         7.23        18.05         0.20 
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        65.42 
TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AA9Y 
       12.69        21.90        62.89        10.95        48.39         1.94 
TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-Z2-AA3S 
       31.99        18.31        18.35        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 
            68.01             46.92 
[1] "15.8 - 196.0 (68.0)" "0.0 - 346.5 (46.9)" 
[1] "hr=" "1.1"
D17V2, survival
                   sevent
clus2                 0   1
  9P GAIN MUTATED     7   9
  9P GAIN WILD-TYPE 163 178
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               16               341 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                9               178 
$`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 
       93.01       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-D3-A8GV TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A1X3 
      167.70       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        77.56 
TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 
       22.95        76.57        36.03       144.89        20.38       207.48 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA 
      176.55        35.93       120.00        73.84        53.92        65.92 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 
       40.60        68.09        33.93        10.49       225.96        15.68 
TCGA-DA-A95V TCGA-DA-A95W TCGA-DA-A95X TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q 
       72.10        25.15        61.81        14.14        13.02        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        29.29        58.92         7.04 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 
       36.46        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       115.96        59.64        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       173.79       220.24 
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       180.39 
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        64.04 
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       134.33       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        49.48         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-ER-A42L TCGA-FR-A3YN 
      247.04        46.98        33.21        12.95       149.03        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-A1YX TCGA-FS-A1YY 
       34.82        36.26       104.42       216.92        48.59       228.59 
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-A1ZK 
       53.52        46.45        15.45         9.70        32.75        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-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD 
       66.67        28.73        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        96.92 
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        48.00       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-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-A690 TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 
       18.05         0.20         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        17.95       101.33 
TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-A8ZY 
       58.98        70.52        63.22        11.80        35.80        49.51 
TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YD-A89C TCGA-YD-A9TA 
       12.16        40.41        21.40        24.99         6.90        49.18 
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 

  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 
           79.525            50.890 
[1] "16.4 - 268.9 (79.5)" "0.2 - 369.9 (50.9)" 
[1] "hr=" "1.2"
D17V3, continuous
                   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          13       7      25       17       25       25
                   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        15        39         13
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  9P GAIN MUTATED            1          1        1
  9P GAIN WILD-TYPE         32         54       20
D17V4, multiclass
             clus
vv            9P GAIN MUTATED 9P GAIN WILD-TYPE
  I OR II NOS               0                13
  STAGE 0                   0                 7
  STAGE I                   4                25
  STAGE IA                  1                17
  STAGE IB                  3                25
  STAGE II                  0                25
  STAGE IIA                 0                14
  STAGE IIB                 1                18
  STAGE IIC                 0                15
  STAGE III                 1                39
  STAGE IIIA                2                13
  STAGE IIIB                1                32
  STAGE IIIC                1                54
  STAGE IV                  1                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
  9P GAIN MUTATED       4  6  2  3
  9P GAIN WILD-TYPE    60 67 76 67
D17V5, multiclass
       clus
vv      9P GAIN MUTATED 9P GAIN WILD-TYPE
  T0+T1               4                60
  T2                  6                67
  T3                  2                76
  T4                  3                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
  9P GAIN MUTATED    11   3   1   1
  9P GAIN WILD-TYPE 166  62  38  44
D17V6, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  N0              11               166
  N1               3                62
  N2               1                38
  N3               1                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"
D17V7, binary
                   cls
clus                  0   1
  9P GAIN MUTATED    15   1
  9P GAIN WILD-TYPE 303  21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED     15    1
  9P GAIN WILD-TYPE  303   21
   clus
vv  9P GAIN MUTATED 9P GAIN WILD-TYPE
  0              15               303
  1               1                21
[1] 2 2
[1] FALSE
D17V8, binary
                   cls
clus                  0   1
  9P GAIN MUTATED     9   4
  9P GAIN WILD-TYPE 125  86
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      9    4
  9P GAIN WILD-TYPE  125   86
     clus
vv    9P GAIN MUTATED 9P GAIN WILD-TYPE
  NO                9               125
  YES               4                86
[1] 2 2
[1] FALSE
D17V9, binary
                   cls
clus                  0   1
  9P GAIN MUTATED     0  16
  9P GAIN WILD-TYPE  47 303
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      0   16
  9P GAIN WILD-TYPE   47  303
     clus
vv    9P GAIN MUTATED 9P GAIN WILD-TYPE
  NO                0                47
  YES              16               303
[1] 2 2
[1] FALSE
D17V10, continuous
D17V11, binary
                   cls
clus                  0   1
  9P GAIN MUTATED     6  10
  9P GAIN WILD-TYPE 131 219
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      6   10
  9P GAIN WILD-TYPE  131  219
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  FEMALE               6               131
  MALE                10               219
[1] 2 2
[1] FALSE
D17V12, binary
                   cls
clus                  0   1
  9P GAIN MUTATED    13   3
  9P GAIN WILD-TYPE 304  44
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED     13    3
  9P GAIN WILD-TYPE  304   44
     clus
vv    9P GAIN MUTATED 9P GAIN WILD-TYPE
  NO               13               304
  YES               3                44
[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   336
D17V13, multiclass
                           clus
vv                          9P GAIN MUTATED 9P GAIN WILD-TYPE
  ASIAN                                   0                 5
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  16               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"
D17V14, binary
                   cls
clus                  0   1
  9P GAIN MUTATED     0  16
  9P GAIN WILD-TYPE   7 335
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      0   16
  9P GAIN WILD-TYPE    7  335
                        clus
vv                       9P GAIN MUTATED 9P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 7
  NOT HISPANIC OR LATINO              16               335
[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 118 113
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               14               231 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               10               113 
$`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        69.21        22.85 
TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 
       76.34       138.67        53.65       150.61        95.51        45.07 
TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A95V TCGA-DA-A95X 
       64.83        58.85        30.44       225.11        72.10        52.90 
TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN 
       14.14        12.30         3.91        33.24        50.07        52.41 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 
       18.21        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-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-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD 
      185.19       115.43        30.02        77.98        26.14       239.11 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
       12.95       201.60        68.65        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        89.26       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 
       64.04         4.41        54.51         6.28       111.85        45.90 
TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 
        3.35       201.80        19.86       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-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-A2NE TCGA-ER-A2NG 
       49.71        47.18       146.63        47.97        16.87        10.95 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A729 
      173.29        68.52        15.48        32.05        74.47       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-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG 
       27.62       312.07        32.78        42.08        12.92         7.82 
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-A4F9 TCGA-FS-A4FD 
        5.29         3.06        30.90        66.67        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-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
       53.29       117.93        96.92        17.06        42.48         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-A690 TCGA-RP-A693 TCGA-W3-A824 
      297.01         7.23        18.05         0.20         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        65.42        12.69        21.90 
TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 
       62.89        10.95        48.39         1.94        31.99        18.31 
TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-Z2-AA3S 
       18.35        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            46.920 
[1] "4.7 - 196.0 (69.3)" "0.0 - 346.5 (46.9)"
[1] "hr=" "1.1"
D18V2, survival
                   sevent
clus2                 0   1
  9Q GAIN MUTATED     7  14
  9Q GAIN WILD-TYPE 163 173
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               21               336 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               14               173 
$`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-D3-A8GV 
      161.00       152.75        29.06       129.63       117.17       167.70 
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        77.56        22.95 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 
       76.57        36.03       144.89        20.38       207.48       176.55 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB 
       35.93       120.00        73.84        53.92        65.92        40.60 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-DA-A95V 
       68.09        33.93        10.49       225.96        15.68        72.10 
TCGA-DA-A95W TCGA-DA-A95X TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A44R 
       25.15        61.81        14.14        13.02        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        29.29        58.92         7.04 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 
       36.46        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       115.96        59.64        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       173.79       220.24 
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       180.39       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        64.04        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 
      134.33       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        49.48         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        93.01        46.98 
TCGA-ER-A3PL TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A69P TCGA-FR-A729 
       33.21        12.95       149.03        92.98        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-A1YY TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA 
      216.92       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        46.45        15.45         9.70 
TCGA-FS-A1ZH TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR 
       32.75        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-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-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
      117.93        96.92        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-A4U9 
       48.00       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-QB-AA9O TCGA-RP-A690 TCGA-RP-A693 TCGA-RP-A694 
      297.90         7.23        18.05         0.20         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 
       17.95       101.33        58.98        70.52        63.22        11.80 
TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 
       35.80        49.51        12.16        40.41        21.40        24.99 
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 

  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 
           49.180            53.175 
[1] "13.9 - 268.9 (49.2)" "0.2 - 369.9 (53.2)" 
[1] "hr=" "1"  
D18V3, continuous
                   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          13       6      24       17       25       23
                   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        15        39         14
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  9Q GAIN MUTATED            1          2        1
  9Q GAIN WILD-TYPE         32         53       20
D18V4, multiclass
             clus
vv            9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  I OR II NOS               0                13
  STAGE 0                   1                 6
  STAGE I                   5                24
  STAGE IA                  1                17
  STAGE IB                  3                25
  STAGE II                  2                23
  STAGE IIA                 0                14
  STAGE IIB                 1                18
  STAGE IIC                 0                15
  STAGE III                 1                39
  STAGE IIIA                1                14
  STAGE IIIB                1                32
  STAGE IIIC                2                53
  STAGE IV                  1                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
  9Q GAIN MUTATED       6  6  4  2
  9Q GAIN WILD-TYPE    58 67 74 68
D18V5, multiclass
       clus
vv      9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  T0+T1               6                58
  T2                  6                67
  T3                  4                74
  T4                  2                68
[1] 4 2
[1] TRUE
[1] "dimension of 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 163  63  37  43
D18V6, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  N0              14               163
  N1               2                63
  N2               2                37
  N3               2                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"
D18V7, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED    19   1
  9Q GAIN WILD-TYPE 299  21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     19    1
  9Q GAIN WILD-TYPE  299   21
   clus
vv  9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  0              19               299
  1               1                21
[1] 2 2
[1] FALSE
D18V8, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED    11   4
  9Q GAIN WILD-TYPE 123  86
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     11    4
  9Q GAIN WILD-TYPE  123   86
     clus
vv    9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  NO               11               123
  YES               4                86
[1] 2 2
[1] FALSE
D18V9, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED     0  21
  9Q GAIN WILD-TYPE  47 298
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      0   21
  9Q GAIN WILD-TYPE   47  298
     clus
vv    9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  NO                0                47
  YES              21               298
[1] 2 2
[1] FALSE
D18V10, continuous
D18V11, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED     9  12
  9Q GAIN WILD-TYPE 128 217
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      9   12
  9Q GAIN WILD-TYPE  128  217
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  FEMALE               9               128
  MALE                12               217
[1] 2 2
[1] FALSE
D18V12, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED    18   3
  9Q GAIN WILD-TYPE 299  44
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     18    3
  9Q GAIN WILD-TYPE  299   44
     clus
vv    9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  NO               18               299
  YES               3                44
[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   332
D18V13, multiclass
                           clus
vv                          9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  ASIAN                                   0                 5
  BLACK OR AFRICAN AMERICAN               1                 0
  WHITE                                  20               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"
D18V14, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED     0  21
  9Q GAIN WILD-TYPE   7 330
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      0   21
  9Q GAIN WILD-TYPE    7  330
                        clus
vv                       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 7
  NOT HISPANIC OR LATINO              21               330
[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 119 117
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 9                236 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 6                117 
$`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        69.21       138.67        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        76.34        53.65       150.61        95.51        45.07 
TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A95V TCGA-DA-A95X 
       64.83        58.85        30.44       225.11        72.10        52.90 
TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN 
       14.14        12.30         3.91        33.24        50.07        52.41 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 
       18.21        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-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-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD 
      185.19       115.43        30.02        77.98        26.14       239.11 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
       12.95       201.60        68.65        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        89.26       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 
       64.04         4.41        54.51         6.28        67.89       111.85 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 
       45.90         3.35       201.80        19.86       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-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-A2NC TCGA-ER-A2ND 
       49.71        47.18       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        68.52        15.48        32.05 
TCGA-ER-A42L TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FR-A8YC 
       74.47       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        42.08        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-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
       53.29       117.93        96.92        17.06        42.48         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-RP-A690 TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A825 
      297.01         7.23         0.20         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        65.42        12.69        21.90        62.89 
TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 
       10.95        48.39         1.94        31.99        18.31        18.35 
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 
            138.67             346.49 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
             59.84              46.95 
[1] "13.0 - 138.7 (59.8)" "0.0 - 346.5 (47.0)" 
[1] "hr=" "1.4"
D19V2, survival
                    sevent
clus2                  0   1
  10P GAIN MUTATED     6   6
  10P GAIN WILD-TYPE 164 181
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                12                345 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 6                181 
$`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        77.56       144.89 
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-D3-A8GV TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW 
      129.63       117.17       167.70       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-A1I0 TCGA-DA-A1I1 
       25.18        22.95        76.57        36.03        20.38       207.48 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA 
      176.55        35.93       120.00        73.84        53.92        65.92 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 
       40.60        68.09        33.93        10.49       225.96        15.68 
TCGA-DA-A95V TCGA-DA-A95W TCGA-DA-A95X TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q 
       72.10        25.15        61.81        14.14        13.02        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        29.29        58.92 
TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 
        7.04        36.46        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       115.96        59.64 
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       173.79 
TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
      220.24        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       180.39       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        64.04        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       134.33       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        49.48 
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        93.01        46.98 
TCGA-ER-A3PL TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       33.21        12.95       149.03        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 
       46.45        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-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
       80.68        22.92        55.59        13.51        19.30         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 
        7.23         2.04       139.89       117.93        96.92        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        48.00       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-A690 
        0.23        65.88       368.78       297.90         7.23         0.20 
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        17.95       101.33        58.98        70.52 
TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 
       63.22        11.80        35.80        49.51        12.16        40.41 
TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YD-A89C TCGA-YD-A9TA TCGA-YG-AA3O TCGA-YG-AA3P 
       21.40        24.99         6.90        49.18        37.94        14.43 
TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
       27.58        96.99        15.98 

  10P GAIN MUTATED 10P GAIN WILD-TYPE 
               0.2                0.2 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
            144.89             369.93 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
            53.475             53.160 
[1] "0.2 - 144.9 (53.5)" "0.2 - 369.9 (53.2)"
[1] "hr=" "1.2"
D19V3, continuous
                    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          13       7      28       18       26       25
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  10P GAIN MUTATED           0         1         0         2          1
  10P GAIN WILD-TYPE        14        18        15        38         14
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  10P GAIN MUTATED            1          2        2
  10P GAIN WILD-TYPE         32         53       19
D19V4, multiclass
             clus
vv            10P GAIN MUTATED 10P GAIN WILD-TYPE
  I OR II NOS                0                 13
  STAGE 0                    0                  7
  STAGE I                    1                 28
  STAGE IA                   0                 18
  STAGE IB                   2                 26
  STAGE II                   0                 25
  STAGE IIA                  0                 14
  STAGE IIB                  1                 18
  STAGE IIC                  0                 15
  STAGE III                  2                 38
  STAGE IIIA                 1                 14
  STAGE IIIB                 1                 32
  STAGE IIIC                 2                 53
  STAGE IV                   2                 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
  10P GAIN MUTATED       2  4  3  1
  10P GAIN WILD-TYPE    62 69 75 69
D19V5, multiclass
       clus
vv      10P GAIN MUTATED 10P GAIN WILD-TYPE
  T0+T1                2                 62
  T2                   4                 69
  T3                   3                 75
  T4                   1                 69
[1] 4 2
[1] TRUE
[1] "dimension of 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   4   0   2
  10P GAIN WILD-TYPE 173  61  39  43
D19V6, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  N0                4                173
  N1                4                 61
  N2                0                 39
  N3                2                 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"
D19V7, binary
                    cls
clus                   0   1
  10P GAIN MUTATED     9   2
  10P GAIN WILD-TYPE 309  20
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      9    2
  10P GAIN WILD-TYPE  309   20
   clus
vv  10P GAIN MUTATED 10P GAIN WILD-TYPE
  0                9                309
  1                2                 20
[1] 2 2
[1] FALSE
D19V8, binary
                    cls
clus                   0   1
  10P GAIN MUTATED     4   3
  10P GAIN WILD-TYPE 130  87
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      4    3
  10P GAIN WILD-TYPE  130   87
     clus
vv    10P GAIN MUTATED 10P GAIN WILD-TYPE
  NO                 4                130
  YES                3                 87
[1] 2 2
[1] FALSE
D19V9, binary
                    cls
clus                   0   1
  10P GAIN MUTATED     5   7
  10P GAIN WILD-TYPE  42 312
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      5    7
  10P GAIN WILD-TYPE   42  312
     clus
vv    10P GAIN MUTATED 10P GAIN WILD-TYPE
  NO                 5                 42
  YES                7                312
[1] 2 2
[1] FALSE
D19V10, continuous
D19V11, binary
                    cls
clus                   0   1
  10P GAIN MUTATED     3   9
  10P GAIN WILD-TYPE 134 220
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      3    9
  10P GAIN WILD-TYPE  134  220
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  FEMALE                3                134
  MALE                  9                220
[1] 2 2
[1] FALSE
D19V12, binary
                    cls
clus                   0   1
  10P GAIN MUTATED     9   2
  10P GAIN WILD-TYPE 308  45
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      9    2
  10P GAIN WILD-TYPE  308   45
     clus
vv    10P GAIN MUTATED 10P GAIN WILD-TYPE
  NO                 9                308
  YES                2                 45
[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   340
D19V13, multiclass
                           clus
vv                          10P GAIN MUTATED 10P GAIN WILD-TYPE
  ASIAN                                    0                  5
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   12                340
[1] 3 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   7 339
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      0   12
  10P GAIN WILD-TYPE    7  339
                        clus
vv                       10P GAIN MUTATED 10P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  7
  NOT HISPANIC OR LATINO               12                339
[1] 2 2
[1] FALSE

Clustering(20) Variable = 10Q GAIN MUTATION ANALYSIS
D20V1, survival
                    sevent
clus2                  0   1
  10Q GAIN MUTATED     1   2
  10Q GAIN WILD-TYPE 121 121
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 3                242 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 2                121 
$`10Q GAIN MUTATED`
TCGA-DA-A1HY TCGA-ER-A3ET TCGA-QB-AA9O 
      138.67        68.52        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        69.21        22.85        76.34 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC 
       53.65       150.61        95.51        45.07        64.83        58.85 
TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A95V TCGA-DA-A95X TCGA-DA-A95Y TCGA-DA-A95Z 
       30.44       225.11        72.10        52.90        14.14        12.30 
TCGA-EB-A44Q TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X 
        3.91        33.24        50.07        52.41        18.21        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-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-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-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE 
      115.43        30.02        77.98        26.14       239.11        12.95 
TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN 
      201.60        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        89.26       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        64.04 
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-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 
        3.35       201.80        19.86       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-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
      120.76        49.71        47.18       146.63        47.97        22.36 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3EV TCGA-ER-A3PL 
        4.70        16.87        10.95       173.29        15.48        32.05 
TCGA-ER-A42L TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FR-A8YC 
       74.47       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        42.08        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-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
       53.29       117.93        96.92        17.06        42.48         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-RP-A690 TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A825 
      297.01         7.23         0.20         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        65.42        12.69        21.90        62.89 
TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 
       10.95        48.39         1.94        31.99        18.31        18.35 
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 
            138.67             346.49 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
             68.52              47.08 
[1] "18.1 - 138.7 (68.5)" "0.0 - 346.5 (47.1)" 
[1] "hr=" "1.2"
D20V2, survival
                    sevent
clus2                  0   1
  10Q GAIN MUTATED     1   2
  10Q GAIN WILD-TYPE 169 185
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 3                354 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 2                185 
$`10Q GAIN MUTATED`
TCGA-DA-A1HY TCGA-ER-A3ET TCGA-QB-AA9O 
      144.89        93.01        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-D3-A8GV TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A1X3 
      167.70       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        77.56 
TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 
       22.95        76.57        36.03        20.38       207.48       176.55 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB 
       35.93       120.00        73.84        53.92        65.92        40.60 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-DA-A95V 
       68.09        33.93        10.49       225.96        15.68        72.10 
TCGA-DA-A95W TCGA-DA-A95X TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A44R 
       25.15        61.81        14.14        13.02        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        29.29        58.92         7.04 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 
       36.46        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       115.96        59.64 
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       173.79 
TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
      220.24        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       180.39       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        64.04        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       134.33       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        49.48         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-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A 
       46.98        33.21        12.95       149.03        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-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        46.45        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-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
      117.93        96.92        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-A4U9 
       48.00       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-A690 TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 
      297.90         7.23         0.20         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        17.95 
TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX 
      101.33        58.98        70.52        63.22        11.80        35.80 
TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YD-A89C 
       49.51        12.16        40.41        21.40        24.99         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 

  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
             18.05               0.20 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
            144.89             369.93 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
            93.010             52.255 
[1] "18.1 - 144.9 (93.0)" "0.2 - 369.9 (52.3)" 
[1] "hr=" "1.1"
D20V3, continuous
                    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          13       7      29       18       28       25
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  10Q GAIN MUTATED           0         0         0         1          1
  10Q GAIN WILD-TYPE        14        19        15        39         14
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  10Q GAIN MUTATED            0          1        0
  10Q GAIN WILD-TYPE         33         54       21
D20V4, multiclass
             clus
vv            10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  I OR II NOS                0                 13
  STAGE 0                    0                  7
  STAGE I                    0                 29
  STAGE IA                   0                 18
  STAGE IB                   0                 28
  STAGE II                   0                 25
  STAGE IIA                  0                 14
  STAGE IIB                  0                 19
  STAGE IIC                  0                 15
  STAGE III                  1                 39
  STAGE IIIA                 1                 14
  STAGE IIIB                 0                 33
  STAGE IIIC                 1                 54
  STAGE IV                   0                 21
[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 72 77 70
D20V5, multiclass
[1] "Remove cluster labels:" "10Q GAIN MUTATED"      
clus
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 2                283 
        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-DA-A95V 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DA-A95X         TCGA-DA-A95Y         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-ER-A42L         TCGA-FR-A3YN         TCGA-FR-A3YO 
"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-A3I3         TCGA-FW-A3TV 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-FW-A5DY         TCGA-GF-A3OT         TCGA-GF-A4EO 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-GF-A6C8         TCGA-GN-A267         TCGA-GN-A268 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D         TCGA-GN-A4U3 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-GN-A4U4         TCGA-GN-A4U7         TCGA-GN-A4U9 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-GN-A8LK         TCGA-GN-A8LL         TCGA-GN-A9SD 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-HR-A2OH         TCGA-QB-A6FS         TCGA-W3-A824 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-W3-A825         TCGA-W3-A828         TCGA-W3-AA1R 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-W3-AA1V         TCGA-W3-AA1W         TCGA-W3-AA21 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-WE-A8JZ         TCGA-WE-A8K1         TCGA-WE-A8K5 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-WE-A8ZN         TCGA-WE-A8ZO         TCGA-WE-A8ZQ 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-WE-A8ZT         TCGA-WE-A8ZY         TCGA-WE-AA9Y 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-WE-AAA0         TCGA-WE-AAA3         TCGA-YD-A89C 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-YG-AA3P         TCGA-Z2-A8RT         TCGA-Z2-AA3S 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-Z2-AA3V 
"10Q GAIN WILD-TYPE" 
                    vv
clus                  N0  N1  N2  N3
  10Q GAIN MUTATED     0   2   0   1
  10Q GAIN WILD-TYPE 177  63  39  44
D20V6, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  N0                0                177
  N1                2                 63
  N2                0                 39
  N3                1                 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"
D20V7, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED     3   0
  10Q GAIN WILD-TYPE 315  22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      3    0
  10Q GAIN WILD-TYPE  315   22
   clus
vv  10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  0                3                315
  1                0                 22
[1] 2 2
[1] FALSE
D20V8, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED     0   1
  10Q GAIN WILD-TYPE 134  89
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      0    1
  10Q GAIN WILD-TYPE  134   89
     clus
vv    10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  NO                 0                134
  YES                1                 89
[1] 2 2
[1] FALSE
D20V9, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED     1   2
  10Q GAIN WILD-TYPE  46 317
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      1    2
  10Q GAIN WILD-TYPE   46  317
     clus
vv    10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  NO                 1                 46
  YES                2                317
[1] 2 2
[1] FALSE
D20V10, continuous
[1] "Remove cluster labels:" "10Q GAIN MUTATED"      
clus
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 2                264 
        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-DA-A95V 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DA-A95X         TCGA-DA-A95Y         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-ER-A42L 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FR-A729 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-FR-A7U9         TCGA-FR-A7UA         TCGA-FR-A8YC 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-FR-A8YD         TCGA-FR-A8YE         TCGA-FS-A1YW 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-FS-A1YX         TCGA-FS-A1YY         TCGA-FS-A1Z0 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-FS-A1Z4         TCGA-FS-A1Z7         TCGA-FS-A1ZA 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZB         TCGA-FS-A1ZD         TCGA-FS-A1ZE 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZF         TCGA-FS-A1ZG         TCGA-FS-A1ZH 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZJ         TCGA-FS-A1ZK         TCGA-FS-A1ZM 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZP         TCGA-FS-A1ZR         TCGA-FS-A1ZS 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZT         TCGA-FS-A1ZU         TCGA-FS-A1ZW 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZY         TCGA-FS-A1ZZ         TCGA-FS-A4F0 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-FS-A4F2         TCGA-FS-A4F4         TCGA-FS-A4F5 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-FS-A4F8         TCGA-FS-A4F9         TCGA-FS-A4FB 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FS-A4FD         TCGA-FW-A3TV 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-GF-A6C8         TCGA-GN-A262         TCGA-GN-A264 
"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-W3-A824         TCGA-W3-A825         TCGA-W3-A828 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-W3-AA1V         TCGA-W3-AA1W         TCGA-W3-AA21 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-WE-A8JZ         TCGA-WE-A8K1         TCGA-WE-A8K5 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-WE-A8ZN         TCGA-WE-A8ZO         TCGA-WE-A8ZQ 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-WE-A8ZT         TCGA-WE-A8ZY         TCGA-WE-AA9Y 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-WE-AAA0         TCGA-WE-AAA3         TCGA-YD-A89C 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-YD-A9TA         TCGA-YD-A9TB         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" 
D20V11, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED     1   2
  10Q GAIN WILD-TYPE 136 227
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      1    2
  10Q GAIN WILD-TYPE  136  227
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  FEMALE                1                136
  MALE                  2                227
[1] 2 2
[1] FALSE
D20V12, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED     2   1
  10Q GAIN WILD-TYPE 315  46
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      2    1
  10Q GAIN WILD-TYPE  315   46
     clus
vv    10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  NO                 2                315
  YES                1                 46
[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   349
D20V13, multiclass
                           clus
vv                          10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  ASIAN                                    0                  5
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                    3                349
[1] 3 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   7 348
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      0    3
  10Q GAIN WILD-TYPE    7  348
                        clus
vv                       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  7
  NOT HISPANIC OR LATINO                3                348
[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 110 114
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                21                224 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 9                114 
$`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        69.21 
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       201.60         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        62.89 

$`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        76.34 
TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA 
      138.67        53.65       150.61        95.51        45.07        64.83 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A95V TCGA-DA-A95X TCGA-DA-A95Y 
       58.85        30.44       225.11        72.10        52.90        14.14 
TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A6L9 
       12.30         3.91        33.24        50.07        52.41        18.21 
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-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-A29M TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A2A1 TCGA-EE-A2A2 
       63.12        47.74        27.16        61.12       115.43        30.02 
TCGA-EE-A2A6 TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
       77.98       239.11        12.95        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-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI 
      103.13        15.25         5.75       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        89.26       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        64.04 
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-A3JH TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
        3.35        19.86        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        47.18 
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-ER-A42L TCGA-FR-A44A 
      173.29        68.52        15.48        32.05        74.47       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        42.08        12.92 
TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZT TCGA-FS-A1ZU 
        7.82        36.33        78.61       130.95        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        96.92        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-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A690 TCGA-RP-A693 
       85.05       297.01         7.23        18.05         0.20         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        65.42        12.69        21.90 
TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 
       10.95        48.39         1.94        31.99        18.31        18.35 
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 
             62.37              46.95 
[1] "0.8 - 346.5 (62.4)" "0.0 - 312.1 (47.0)"
[1] "hr=" "1.7"
D21V2, survival
                    sevent
clus2                  0   1
  11P GAIN MUTATED    15  18
  11P GAIN WILD-TYPE 155 169
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                33                324 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                18                169 
$`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 
       77.56        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 
      220.24        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        12.95        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        48.00        21.37        63.02 
TCGA-WE-A8K6 TCGA-WE-A8ZQ TCGA-WE-A8ZX 
       17.95        63.22        35.80 

$`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-D3-A8GV TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A1X3 
      167.70       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 
       76.57        36.03       144.89        20.38       207.48       176.55 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB 
       35.93       120.00        73.84        53.92        65.92        40.60 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-DA-A95V TCGA-DA-A95W 
       68.09        33.93       225.96        15.68        72.10        25.15 
TCGA-DA-A95X TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH 
       61.81        14.14        13.02        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        29.29        58.92         7.04        36.46 
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 
      115.96        59.64        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 
      173.79        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       180.39       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        64.04        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 
      134.33        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        49.48         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-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A 
       93.01        46.98        33.21       149.03        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-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZC TCGA-FS-A1ZE TCGA-FS-A1ZF 
       28.08         7.79        27.72       357.37        46.45        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-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY 
      133.55        11.41        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-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-A26A TCGA-GN-A4U3 
      139.89       117.93        96.92        64.44        32.48       121.91 
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-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-A690 TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A828 TCGA-W3-AA1O 
        0.20         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-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT 
       49.05        61.15       101.33        58.98        70.52        11.80 
TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YD-A89C 
       49.51        12.16        40.41        21.40        24.99         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 

  11P GAIN MUTATED 11P GAIN WILD-TYPE 
             10.13               0.20 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
            369.93             368.78 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
            59.570             50.825 
[1] "10.1 - 369.9 (59.6)" "0.2 - 368.8 (50.8)" 
[1] "hr=" "1.1"
D21V3, continuous
                    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          10       6      23       17       28       23
                    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        12        36         14
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  11P GAIN MUTATED            5          3        0
  11P GAIN WILD-TYPE         28         52       21
D21V4, multiclass
             clus
vv            11P GAIN MUTATED 11P GAIN WILD-TYPE
  I OR II NOS                3                 10
  STAGE 0                    1                  6
  STAGE I                    6                 23
  STAGE IA                   1                 17
  STAGE IB                   0                 28
  STAGE II                   2                 23
  STAGE IIA                  2                 12
  STAGE IIB                  1                 18
  STAGE IIC                  3                 12
  STAGE III                  4                 36
  STAGE IIIA                 1                 14
  STAGE IIIB                 5                 28
  STAGE IIIC                 3                 52
  STAGE IV                   0                 21
[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 64 73 63
D21V5, multiclass
       clus
vv      11P GAIN MUTATED 11P GAIN WILD-TYPE
  T0+T1                5                 59
  T2                   9                 64
  T3                   5                 73
  T4                   7                 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
  11P GAIN MUTATED    19   7   2   3
  11P GAIN WILD-TYPE 158  58  37  42
D21V6, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  N0               19                158
  N1                7                 58
  N2                2                 37
  N3                3                 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"
D21V7, binary
                    cls
clus                   0   1
  11P GAIN MUTATED    32   0
  11P GAIN WILD-TYPE 286  22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED     32    0
  11P GAIN WILD-TYPE  286   22
   clus
vv  11P GAIN MUTATED 11P GAIN WILD-TYPE
  0               32                286
  1                0                 22
[1] 2 2
[1] FALSE
D21V8, binary
                    cls
clus                   0   1
  11P GAIN MUTATED    10   7
  11P GAIN WILD-TYPE 124  83
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED     10    7
  11P GAIN WILD-TYPE  124   83
     clus
vv    11P GAIN MUTATED 11P GAIN WILD-TYPE
  NO                10                124
  YES                7                 83
[1] 2 2
[1] FALSE
D21V9, binary
                    cls
clus                   0   1
  11P GAIN MUTATED     7  28
  11P GAIN WILD-TYPE  40 291
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      7   28
  11P GAIN WILD-TYPE   40  291
     clus
vv    11P GAIN MUTATED 11P GAIN WILD-TYPE
  NO                 7                 40
  YES               28                291
[1] 2 2
[1] FALSE
D21V10, continuous
D21V11, binary
                    cls
clus                   0   1
  11P GAIN MUTATED    13  22
  11P GAIN WILD-TYPE 124 207
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED     13   22
  11P GAIN WILD-TYPE  124  207
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  FEMALE               13                124
  MALE                 22                207
[1] 2 2
[1] FALSE
D21V12, binary
                    cls
clus                   0   1
  11P GAIN MUTATED    27   8
  11P GAIN WILD-TYPE 290  39
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED     27    8
  11P GAIN WILD-TYPE  290   39
     clus
vv    11P GAIN MUTATED 11P GAIN WILD-TYPE
  NO                27                290
  YES                8                 39
[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   318
D21V13, multiclass
                           clus
vv                          11P GAIN MUTATED 11P GAIN WILD-TYPE
  ASIAN                                    0                  5
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   34                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"
D21V14, binary
                    cls
clus                   0   1
  11P GAIN MUTATED     0  35
  11P GAIN WILD-TYPE   7 316
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      0   35
  11P GAIN WILD-TYPE    7  316
                        clus
vv                       11P GAIN MUTATED 11P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  7
  NOT HISPANIC OR LATINO               35                316
[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 110 117
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                18                227 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 6                117 
$`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        69.21       185.19 
TCGA-EE-A2GH TCGA-EE-A2GP TCGA-EE-A2MC TCGA-EE-A3JB TCGA-EE-A3JI TCGA-ER-A19N 
      201.60         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        62.89 

$`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 
       76.34       138.67        53.65       150.61        95.51        45.07 
TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A95V TCGA-DA-A95X 
       64.83        58.85        30.44       225.11        72.10        52.90 
TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN 
       14.14        12.30         3.91        33.24        50.07        52.41 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 
       18.21        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-A29D 
       67.50        75.55       155.90        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-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD 
      346.49       115.43        30.02        77.98        26.14       239.11 
TCGA-EE-A2GE TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN 
       12.95        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-A2MF TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK 
        5.75       209.79        94.19       171.85        63.25        89.26 
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        64.04         4.41        54.51 
TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JH 
        6.28        67.89       111.85        45.90         3.35        19.86 
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-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 
       59.84       120.76        49.71        47.18       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        68.52 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A44A TCGA-FR-A7U8 TCGA-FR-A7UA 
       15.48        32.05        74.47       174.21        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-A1ZM 
      312.07        42.08        12.92         7.82        36.33        78.61 
TCGA-FS-A1ZQ TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ 
      130.95        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-A6C8 TCGA-GN-A262 TCGA-GN-A264 
       11.54        19.30         9.90         1.91        53.29       117.93 
TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 
       96.92        17.06         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-A690 TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1Q 
        0.20         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 
       65.42        12.69        21.90        10.95        48.39         1.94 
TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-Z2-AA3S 
       31.99        18.31        18.35        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 
             66.05              46.92 
[1] "0.8 - 209.2 (66.0)" "0.0 - 346.5 (46.9)"
[1] "hr=" "2.2"
D22V2, survival
                    sevent
clus2                  0   1
  11Q GAIN MUTATED    15  12
  11Q GAIN WILD-TYPE 155 175
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                27                330 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                12                175 
$`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        77.56 
TCGA-DA-A3F3 TCGA-EE-A29W TCGA-EE-A2GH TCGA-EE-A2GP TCGA-EE-A2M5 TCGA-EE-A2MC 
       10.49       195.02       220.24        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        12.95       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 
       17.95        63.22        35.80 

$`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-D3-A8GV TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX 
      117.17       167.70       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        76.57        36.03       144.89        20.38       207.48 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA 
      176.55        35.93       120.00        73.84        53.92        65.92 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-DA-A95V 
       40.60        68.09        33.93       225.96        15.68        72.10 
TCGA-DA-A95W TCGA-DA-A95X TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A44R 
       25.15        61.81        14.14        13.02        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        29.29        58.92         7.04 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 
       36.46        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       115.96        59.64        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       173.79        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       180.39       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        64.04        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       134.33        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        49.48 
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        93.01        46.98 
TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A7U8 
       33.21       149.03        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-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-A1ZC TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ 
      357.37        46.45        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-A1ZT 
       23.93       101.26        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-A4F4 
       26.56        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-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 
        2.04        15.78       139.89       117.93        96.92        10.13 
TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 
       64.44        32.48        48.00       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-A690 
       65.88       368.78       297.90         7.23        18.05         0.20 
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-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT 
       49.05        61.15       101.33        58.98        70.52        11.80 
TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YD-A89C 
       49.51        12.16        40.41        21.40        24.99         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 

  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
              7.23               0.20 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
            220.80             369.93 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
            60.230             50.825 
[1] "7.2 - 220.8 (60.2)" "0.2 - 369.9 (50.8)"
[1] "hr=" "1.3"
D22V3, continuous
                    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          10       6      22       17       28       24
                    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        14        37         14
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  11Q GAIN MUTATED            4          3        0
  11Q GAIN WILD-TYPE         29         52       21
D22V4, multiclass
             clus
vv            11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  I OR II NOS                3                 10
  STAGE 0                    1                  6
  STAGE I                    7                 22
  STAGE IA                   1                 17
  STAGE IB                   0                 28
  STAGE II                   1                 24
  STAGE IIA                  2                 12
  STAGE IIB                  1                 18
  STAGE IIC                  1                 14
  STAGE III                  3                 37
  STAGE IIIA                 1                 14
  STAGE IIIB                 4                 29
  STAGE IIIC                 3                 52
  STAGE IV                   0                 21
[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 65 74 66
D22V5, multiclass
       clus
vv      11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  T0+T1                7                 57
  T2                   8                 65
  T3                   4                 74
  T4                   4                 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
  11Q GAIN MUTATED    17   6   2   3
  11Q GAIN WILD-TYPE 160  59  37  42
D22V6, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  N0               17                160
  N1                6                 59
  N2                2                 37
  N3                3                 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"
D22V7, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED    28   0
  11Q GAIN WILD-TYPE 290  22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED     28    0
  11Q GAIN WILD-TYPE  290   22
   clus
vv  11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  0               28                290
  1                0                 22
[1] 2 2
[1] FALSE
D22V8, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED    10   4
  11Q GAIN WILD-TYPE 124  86
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED     10    4
  11Q GAIN WILD-TYPE  124   86
     clus
vv    11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  NO                10                124
  YES                4                 86
[1] 2 2
[1] FALSE
D22V9, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED     7  22
  11Q GAIN WILD-TYPE  40 297
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      7   22
  11Q GAIN WILD-TYPE   40  297
     clus
vv    11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  NO                 7                 40
  YES               22                297
[1] 2 2
[1] FALSE
D22V10, continuous
D22V11, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED    10  19
  11Q GAIN WILD-TYPE 127 210
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED     10   19
  11Q GAIN WILD-TYPE  127  210
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  FEMALE               10                127
  MALE                 19                210
[1] 2 2
[1] FALSE
D22V12, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED    22   7
  11Q GAIN WILD-TYPE 295  40
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED     22    7
  11Q GAIN WILD-TYPE  295   40
     clus
vv    11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  NO                22                295
  YES                7                 40
[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   324
D22V13, multiclass
                           clus
vv                          11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  ASIAN                                    0                  5
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   28                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"
D22V14, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED     0  29
  11Q GAIN WILD-TYPE   7 322
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      0   29
  11Q GAIN WILD-TYPE    7  322
                        clus
vv                       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  7
  NOT HISPANIC OR LATINO               29                322
[1] 2 2
[1] FALSE

Clustering(23) Variable = 12P GAIN MUTATION ANALYSIS
D23V1, survival
                    sevent
clus2                  0   1
  12P GAIN MUTATED    18  31
  12P GAIN WILD-TYPE 104  92
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                49                196 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                31                 92 
$`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        69.21 
TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A3F5 TCGA-DA-A95V TCGA-DA-A95Z TCGA-EB-A44Q 
       45.07        64.83       225.11        72.10        12.30         3.91 
TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A29D TCGA-EE-A2A6 TCGA-EE-A2GB 
       24.89        62.37       155.90        12.99        77.98        26.14 
TCGA-EE-A2GH TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A3AA TCGA-EE-A3AD TCGA-EE-A3JI 
      201.60        81.99       103.13       124.31         4.41       152.81 
TCGA-ER-A197 TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A3ET 
        1.58        53.29        39.81        99.06        59.84        68.52 
TCGA-ER-A3PL TCGA-FR-A729 TCGA-FS-A1ZM TCGA-FS-A1ZU TCGA-GN-A267 TCGA-GN-A26A 
       32.05       209.23        78.61         4.47        17.06         7.59 
TCGA-GN-A8LK TCGA-W3-A825 TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1W TCGA-W3-AA21 
       43.23         1.97        44.05        79.99       185.13        92.84 
TCGA-YG-AA3O 
       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        76.34 
TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1IC TCGA-DA-A3F2 
      138.67        53.65       150.61        95.51        58.85        30.44 
TCGA-DA-A95X TCGA-DA-A95Y TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A6L9 
       52.90        14.14        33.24        50.07        52.41        18.21 
TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A184 TCGA-EE-A20C TCGA-EE-A29B 
       13.15        20.38         0.00        67.50        75.55        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       115.43        30.02       239.11 
TCGA-EE-A2GE TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN 
       12.95        68.65        10.62        32.48        18.35        31.00 
TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2M7 TCGA-EE-A2M8 
      118.32         0.76         0.20        71.31        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        89.26 
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-A3AE TCGA-EE-A3AF TCGA-EE-A3J3 
       53.26       122.73        64.04        54.51         6.28        67.89 
TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH TCGA-ER-A193 
      111.85        45.90         3.35       201.80        19.86        14.56 
TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19D TCGA-ER-A19G 
       34.45        47.31         7.82         4.54        11.47       151.46 
TCGA-ER-A19H TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W 
      150.12        42.48       120.76        49.71        47.18       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-A42L TCGA-FR-A44A TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FR-A8YC 
       15.48        74.47       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        42.08        12.92         7.82        36.33       130.95 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 
      136.27        35.28        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-A268 TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-GN-A9SD 
       96.92        42.48       120.53        34.49        46.92        59.41 
TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A690 TCGA-RP-A693 
       85.05       297.01         7.23        18.05         0.20         0.33 
TCGA-W3-A824 TCGA-W3-A828 TCGA-W3-AA1V TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8ZM 
      174.12       120.07         8.09         1.15        59.64        65.42 
TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AA9Y 
       12.69        21.90        62.89        10.95        48.39         1.94 
TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-Z2-AA3S 
       31.99        18.31        18.35        91.23 

  12P GAIN MUTATED 12P GAIN WILD-TYPE 
              1.58               0.00 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
            225.11             346.49 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
            59.700             45.945 
[1] "1.6 - 225.1 (59.7)" "0.0 - 346.5 (45.9)"
[1] "hr=" "1.3"
D23V2, survival
                    sevent
clus2                  0   1
  12P GAIN MUTATED    25  40
  12P GAIN WILD-TYPE 145 147
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                65                292 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                40                147 
$`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-D3-A8GV TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-DA-A1HW TCGA-DA-A1I7 
       89.13       167.70         9.90        77.56        36.03        73.84 
TCGA-DA-A1IA TCGA-DA-A3F5 TCGA-DA-A95V TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5KH 
       65.92       225.96        72.10        13.02        13.87        20.35 
TCGA-EB-A5UL TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A29D TCGA-EE-A29X 
       29.29        27.22        94.98       168.26        13.97        17.92 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GH TCGA-EE-A2GU TCGA-EE-A2M5 
       39.29        86.14        59.28       220.24        94.82        21.67 
TCGA-EE-A2M6 TCGA-EE-A3AA TCGA-EE-A3AD TCGA-EE-A3J5 TCGA-EE-A3JE TCGA-EE-A3JI 
      129.27       124.31        28.77        36.95        51.35       152.81 
TCGA-ER-A197 TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
       13.94        98.40        48.89         6.44       131.51        61.05 
TCGA-ER-A3ET TCGA-ER-A3PL TCGA-FR-A729 TCGA-FS-A1ZM TCGA-FS-A1ZU TCGA-FS-A4F2 
       93.01        33.21       220.80       101.26        26.56        50.14 
TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A8LK TCGA-W3-A825 TCGA-W3-AA1Q TCGA-W3-AA1R 
       64.44        32.48        50.10        63.02        69.07       111.09 
TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8ZX TCGA-YG-AA3O TCGA-YG-AA3P 
      219.16       105.04        35.80        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        76.57       144.89        20.38 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A1IB 
      207.48       176.55        35.93       120.00        53.92        40.60 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-DA-A95W TCGA-DA-A95X 
       68.09        33.93        10.49        15.68        25.15        61.81 
TCGA-DA-A95Y TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A5VV 
       14.14        10.36        68.25        54.02        58.92         7.04 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
       36.46        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-A20I 
       68.15         4.96       133.81       151.27        91.56        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-A2A0 TCGA-EE-A2A1 
       61.28       369.93        25.87       195.02        46.82       115.96 
TCGA-EE-A2A2 TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GJ 
       59.64        67.43       340.14       173.79        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-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC 
       42.77        81.21        44.88        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       180.39       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-A3AB 
       43.23       134.40       162.48        71.21        53.26       122.73 
TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 
       64.04        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-A198 TCGA-ER-A199 TCGA-ER-A19A 
      134.33        31.40        35.44        50.76         9.17        77.75 
TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19N 
       12.59        13.02        26.37       268.93       152.35        44.05 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 
      162.08        50.89        49.48         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-A3EV TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A 
      247.04        46.98        12.95       149.03        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-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 
       46.45        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-A1ZW 
       74.73       133.55        11.41       148.80        53.16        49.48 
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-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-A266 TCGA-GN-A268 
       15.78       139.89       117.93        96.92        10.13        62.79 
TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A4U9 
       48.00       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-A690 TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 
        7.23        18.05         0.20         0.33         0.69       228.16 
TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1V TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K5 
      121.08         4.01        42.08        24.03        49.05        61.15 
TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT 
       17.95       101.33        58.98        70.52        63.22        11.80 
TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YD-A89C 
       49.51        12.16        40.41        21.40        24.99         6.90 
TCGA-YD-A9TA TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
       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 
            225.96             369.93 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
            61.050             49.495 
[1] "6.4 - 226.0 (61.0)" "0.2 - 369.9 (49.5)"
[1] "hr=" "1.2"
D23V3, continuous
                    vv
clus                 I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  12P GAIN MUTATED             1       0      10        2        6        3
  12P GAIN WILD-TYPE          12       7      19       16       22       22
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  12P GAIN MUTATED           0         1         4        11          5
  12P GAIN WILD-TYPE        14        18        11        29         10
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  12P GAIN MUTATED           11          5        3
  12P GAIN WILD-TYPE         22         50       18
D23V4, multiclass
             clus
vv            12P GAIN MUTATED 12P GAIN WILD-TYPE
  I OR II NOS                1                 12
  STAGE 0                    0                  7
  STAGE I                   10                 19
  STAGE IA                   2                 16
  STAGE IB                   6                 22
  STAGE II                   3                 22
  STAGE IIA                  0                 14
  STAGE IIB                  1                 18
  STAGE IIC                  4                 11
  STAGE III                 11                 29
  STAGE IIIA                 5                 10
  STAGE IIIB                11                 22
  STAGE IIIC                 5                 50
  STAGE IV                   3                 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 12
  12P GAIN WILD-TYPE    48 58 67 58
D23V5, multiclass
       clus
vv      12P GAIN MUTATED 12P GAIN WILD-TYPE
  T0+T1               16                 48
  T2                  15                 58
  T3                  11                 67
  T4                  12                 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
  12P GAIN MUTATED    29  22   5   5
  12P GAIN WILD-TYPE 148  43  34  40
D23V6, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  N0               29                148
  N1               22                 43
  N2                5                 34
  N3                5                 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"
D23V7, binary
                    cls
clus                   0   1
  12P GAIN MUTATED    58   3
  12P GAIN WILD-TYPE 260  19
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     58    3
  12P GAIN WILD-TYPE  260   19
   clus
vv  12P GAIN MUTATED 12P GAIN WILD-TYPE
  0               58                260
  1                3                 19
[1] 2 2
[1] FALSE
D23V8, binary
                    cls
clus                   0   1
  12P GAIN MUTATED    26  14
  12P GAIN WILD-TYPE 108  76
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     26   14
  12P GAIN WILD-TYPE  108   76
     clus
vv    12P GAIN MUTATED 12P GAIN WILD-TYPE
  NO                26                108
  YES               14                 76
[1] 2 2
[1] FALSE
D23V9, binary
                    cls
clus                   0   1
  12P GAIN MUTATED    10  55
  12P GAIN WILD-TYPE  37 264
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     10   55
  12P GAIN WILD-TYPE   37  264
     clus
vv    12P GAIN MUTATED 12P GAIN WILD-TYPE
  NO                10                 37
  YES               55                264
[1] 2 2
[1] FALSE
D23V10, continuous
D23V11, binary
                    cls
clus                   0   1
  12P GAIN MUTATED    23  42
  12P GAIN WILD-TYPE 114 187
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     23   42
  12P GAIN WILD-TYPE  114  187
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  FEMALE               23                114
  MALE                 42                187
[1] 2 2
[1] FALSE
D23V12, binary
                    cls
clus                   0   1
  12P GAIN MUTATED    57   8
  12P GAIN WILD-TYPE 260  39
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     57    8
  12P GAIN WILD-TYPE  260   39
     clus
vv    12P GAIN MUTATED 12P GAIN WILD-TYPE
  NO                57                260
  YES                8                 39
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  12P GAIN MUTATED       3                         0    60
  12P GAIN WILD-TYPE     2                         1   292
D23V13, multiclass
                           clus
vv                          12P GAIN MUTATED 12P GAIN WILD-TYPE
  ASIAN                                    3                  2
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   60                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"
D23V14, binary
                    cls
clus                   0   1
  12P GAIN MUTATED     2  62
  12P GAIN WILD-TYPE   5 289
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      2   62
  12P GAIN WILD-TYPE    5  289
                        clus
vv                       12P GAIN MUTATED 12P GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  5
  NOT HISPANIC OR LATINO               62                289
[1] 2 2
[1] FALSE

Clustering(24) Variable = 12Q GAIN MUTATION ANALYSIS
D24V1, survival
                    sevent
clus2                  0   1
  12Q GAIN MUTATED    11  18
  12Q GAIN WILD-TYPE 111 105
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                29                216 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                18                105 
$`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-DA-A95V TCGA-DA-A95Z TCGA-EB-A44Q 
      124.08        69.53       225.11        72.10        12.30         3.91 
TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A29D TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GH 
       24.89        62.37        12.99        77.98        26.14       201.60 
TCGA-EE-A3JI TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19L TCGA-FR-A729 TCGA-FS-A1ZM 
      152.81        53.29        39.81        99.06       209.23        78.61 
TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A8LK TCGA-W3-A825 TCGA-YG-AA3O 
       17.06         7.59        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        69.21        22.85        76.34       138.67        53.65 
TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 
      150.61        95.51        45.07        64.83        58.85        30.44 
TCGA-DA-A95X TCGA-DA-A95Y TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A6L9 
       52.90        14.14        33.24        50.07        52.41        18.21 
TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A184 TCGA-EE-A20C TCGA-EE-A20H 
       13.15        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       115.43        30.02 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
      239.11        12.95        68.65        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        89.26       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 
       64.04         4.41        54.51         6.28        67.89       111.85 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 
       45.90         3.35       201.80        19.86        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-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S 
      150.12        59.84        42.48       120.76        49.71        47.18 
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-ER-A42L TCGA-FR-A44A 
      173.29        68.52        15.48        32.05        74.47       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        42.08        12.92 
TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU 
        7.82        36.33       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-A268 
        6.05         1.91        53.29       117.93        96.92        42.48 
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-A690 TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A828 
        7.23        18.05         0.20         0.33       174.12       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-A8ZT 
       59.64        65.42        12.69        21.90        62.89        10.95 
TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-Z2-AA3S 
       48.39         1.94        31.99        18.31        18.35        91.23 

  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
              1.97               0.00 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
            225.11             346.49 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
             53.29              46.95 
[1] "2.0 - 225.1 (53.3)" "0.0 - 346.5 (47.0)"
[1] "hr=" "1.2"
D24V2, survival
                    sevent
clus2                  0   1
  12Q GAIN MUTATED    16  23
  12Q GAIN WILD-TYPE 154 164
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                39                318 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                23                164 
$`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-D3-A8GV TCGA-DA-A1HW 
      135.75        18.18       125.19        89.13       167.70        36.03 
TCGA-DA-A3F5 TCGA-DA-A95V TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5UL TCGA-EE-A17Y 
      225.96        72.10        13.02        13.87        29.29        27.22 
TCGA-EE-A180 TCGA-EE-A29D TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GH TCGA-EE-A2M5 
       94.98        13.97        86.14        59.28       220.24        21.67 
TCGA-EE-A3J5 TCGA-EE-A3JE TCGA-EE-A3JI TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19L 
       36.95        51.35       152.81        98.40        48.89       131.51 
TCGA-FR-A729 TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A8LK 
      220.80        23.93       101.26        64.44        32.48        50.10 
TCGA-W3-A825 TCGA-WE-A8ZX TCGA-YG-AA3O 
       63.02        35.80        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 
       77.56        22.95        76.57       144.89        20.38       207.48 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA 
      176.55        35.93       120.00        73.84        53.92        65.92 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-DA-A95W 
       40.60        68.09        33.93        10.49        15.68        25.15 
TCGA-DA-A95X TCGA-DA-A95Y TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH 
       61.81        14.14        10.36        20.35        68.25        54.02 
TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 
       58.92         7.04        36.46        29.82         8.65        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-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       115.96        59.64        39.29 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
       67.43       340.14       173.79        48.72       107.38        54.74 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR 
       79.66        75.48       102.12       126.81        13.91        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-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       180.39       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        64.04        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-A3JA TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 
       53.19       201.80        27.35       134.33        31.40        35.44 
TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19D TCGA-ER-A19E 
       13.94        50.76         9.17        77.75        12.59        13.02 
TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19M TCGA-ER-A19N 
       26.37       268.93       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        49.48         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-ER-A42L 
      247.04        93.01        46.98        33.21        12.95       149.03 
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        46.45        15.45         9.70        32.75 
TCGA-FS-A1ZJ TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT 
       47.38        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-A268 TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A4U4 
       96.92        10.13        62.79        48.00       121.91        39.35 
TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LL TCGA-GN-A9SD TCGA-HR-A2OG 
       10.42        48.89        22.13        21.37        59.41         0.23 
TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A690 
       65.88       368.78       297.90         7.23        18.05         0.20 
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-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K1 
      111.09        42.08       219.16       105.04        24.03        49.05 
TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ 
       61.15        17.95       101.33        58.98        70.52        63.22 
TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 
       11.80        49.51        12.16        40.41        21.40        24.99 
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 

  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
             13.02               0.20 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
            225.96             369.93 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
            59.280             50.825 
[1] "13.0 - 226.0 (59.3)" "0.2 - 369.9 (50.8)" 
[1] "hr=" "1.1"
D24V3, continuous
                    vv
clus                 I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  12Q GAIN MUTATED             1       0       7        1        3        2
  12Q GAIN WILD-TYPE          12       7      22       17       25       23
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  12Q GAIN MUTATED           0         0         1         6          2
  12Q GAIN WILD-TYPE        14        19        14        34         13
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  12Q GAIN MUTATED            7          4        2
  12Q GAIN WILD-TYPE         26         51       19
D24V4, multiclass
             clus
vv            12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  I OR II NOS                1                 12
  STAGE 0                    0                  7
  STAGE I                    7                 22
  STAGE IA                   1                 17
  STAGE IB                   3                 25
  STAGE II                   2                 23
  STAGE IIA                  0                 14
  STAGE IIB                  0                 19
  STAGE IIC                  1                 14
  STAGE III                  6                 34
  STAGE IIIA                 2                 13
  STAGE IIIB                 7                 26
  STAGE IIIC                 4                 51
  STAGE IV                   2                 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  8
  12Q GAIN WILD-TYPE    55 65 73 62
D24V5, multiclass
       clus
vv      12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  T0+T1                9                 55
  T2                   8                 65
  T3                   5                 73
  T4                   8                 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
  12Q GAIN MUTATED    16  14   2   3
  12Q GAIN WILD-TYPE 161  51  37  42
D24V6, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  N0               16                161
  N1               14                 51
  N2                2                 37
  N3                3                 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"
D24V7, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED    33   2
  12Q GAIN WILD-TYPE 285  20
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     33    2
  12Q GAIN WILD-TYPE  285   20
   clus
vv  12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  0               33                285
  1                2                 20
[1] 2 2
[1] FALSE
D24V8, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED    15   9
  12Q GAIN WILD-TYPE 119  81
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     15    9
  12Q GAIN WILD-TYPE  119   81
     clus
vv    12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  NO                15                119
  YES                9                 81
[1] 2 2
[1] FALSE
D24V9, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED     3  36
  12Q GAIN WILD-TYPE  44 283
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      3   36
  12Q GAIN WILD-TYPE   44  283
     clus
vv    12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  NO                 3                 44
  YES               36                283
[1] 2 2
[1] FALSE
D24V10, continuous
D24V11, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED    11  28
  12Q GAIN WILD-TYPE 126 201
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     11   28
  12Q GAIN WILD-TYPE  126  201
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  FEMALE               11                126
  MALE                 28                201
[1] 2 2
[1] FALSE
D24V12, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED    34   5
  12Q GAIN WILD-TYPE 283  42
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     34    5
  12Q GAIN WILD-TYPE  283   42
     clus
vv    12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  NO                34                283
  YES                5                 42
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  12Q GAIN MUTATED       2                         0    36
  12Q GAIN WILD-TYPE     3                         1   316
D24V13, multiclass
                           clus
vv                          12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  ASIAN                                    2                  3
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   36                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"
D24V14, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED     1  37
  12Q GAIN WILD-TYPE   6 314
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      1   37
  12Q GAIN WILD-TYPE    6  314
                        clus
vv                       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO               37                314
[1] 2 2
[1] FALSE

Clustering(25) Variable = 13Q GAIN MUTATION ANALYSIS
D25V1, survival
                    sevent
clus2                  0   1
  13Q GAIN MUTATED    20  44
  13Q GAIN WILD-TYPE 102  79
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                64                181 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                44                 79 
$`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 
       45.07        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       201.60        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        42.08        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        96.92        17.06        42.48       297.01 
TCGA-QB-AA9O TCGA-W3-A824 TCGA-W3-A825 TCGA-WE-AAA3 
       18.05       174.12         1.97        18.31 

$`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        69.21        22.85        76.34 
TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1IA TCGA-DA-A1IC 
      138.67        53.65       150.61        95.51        64.83        58.85 
TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A95V TCGA-DA-A95X TCGA-DA-A95Y TCGA-DA-A95Z 
       30.44       225.11        72.10        52.90        14.14        12.30 
TCGA-EB-A44Q TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A181 
        3.91        50.07        52.41        18.21        13.15        20.38 
TCGA-EE-A182 TCGA-EE-A184 TCGA-EE-A20C TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
        0.00        67.50        75.55        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       115.43 
TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GJ TCGA-EE-A2GK 
       30.02        77.98       239.11        12.95        68.65        10.62 
TCGA-EE-A2GL TCGA-EE-A2GO TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 
       32.48       118.32         0.20        71.31        81.99       103.13 
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        89.26 
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-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3J4 TCGA-EE-A3J8 
      122.73        64.04         4.41        54.51       111.85         3.35 
TCGA-EE-A3JB TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A19A 
      201.80        19.86        14.56        34.45        47.31         4.54 
TCGA-ER-A19B TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W 
       53.29       151.46       150.12        49.71        47.18       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        68.52 
TCGA-ER-A3EV TCGA-ER-A42L TCGA-FR-A44A TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FS-A1YY 
       15.48        74.47       174.21        26.20         5.65        49.74 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZM TCGA-FS-A1ZS 
      312.07        32.78        12.92         7.82        78.61       136.27 
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-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-A264 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 
       53.29       117.93         7.59       120.53        34.49        46.92 
TCGA-GN-A8LK TCGA-GN-A9SD TCGA-LH-A9QB TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 
       43.23        59.41        85.05         7.23         0.20         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        65.42        12.69        21.90        62.89 
TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-YG-AA3O 
       10.95        48.39         1.94        31.99        18.35        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 
             42.48              49.71 
[1] "0.8 - 297.0 (42.5)" "0.0 - 346.5 (49.7)"
[1] "hr=" "1.5"
D25V2, survival
                    sevent
clus2                  0   1
  13Q GAIN MUTATED    34  55
  13Q GAIN WILD-TYPE 136 132
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                89                268 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                55                132 
$`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-DA-A95W 
       58.52        89.13       107.15        73.84        10.49        25.15 
TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5UL TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A20B 
       10.36        68.25        29.29        27.22        94.98       133.81 
TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29G TCGA-EE-A29P TCGA-EE-A29R 
      168.26        63.35        85.08        72.07        56.42        14.47 
TCGA-EE-A2A5 TCGA-EE-A2GB TCGA-EE-A2GH TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP 
       39.29        59.28       220.24        75.48       102.12        13.91 
TCGA-EE-A2M7 TCGA-EE-A2MF TCGA-EE-A2MP TCGA-EE-A3AA TCGA-EE-A3AF TCGA-EE-A3J3 
       28.83       268.73       248.65       124.31        13.81       172.18 
TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-EE-A3JI TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19C 
       64.08        53.19       152.81        13.94         9.17        48.89 
TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P 
       12.59        13.02       131.51        61.05        44.05       162.08 
TCGA-ER-A2NC TCGA-ER-A3PL TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A8YC TCGA-FS-A1YW 
       43.82        33.21        15.72       220.80        34.82       216.92 
TCGA-FS-A1YX TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZE 
       48.59       202.65        20.91        28.08         7.79        46.45 
TCGA-FS-A1ZJ TCGA-FS-A1ZQ TCGA-FS-A1ZT TCGA-FS-A1ZY TCGA-FS-A4F2 TCGA-FS-A4FD 
       47.38       133.55        53.16        27.09        50.14        80.68 
TCGA-FW-A3TU TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A4U9 TCGA-HR-A2OG 
       55.59        96.92        64.44        62.79        22.13         0.23 
TCGA-OD-A75X TCGA-QB-AA9O TCGA-W3-A824 TCGA-W3-A825 TCGA-WE-A8JZ TCGA-WE-A8K6 
      297.90        18.05       228.16        63.02        24.03        17.95 
TCGA-WE-A8ZX TCGA-WE-AAA3 TCGA-YD-A89C TCGA-YD-A9TA TCGA-Z2-A8RT 
       35.80        21.40         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-D3-A8GV TCGA-D9-A148 TCGA-D9-A149 
       29.06       129.63       117.17       167.70       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        77.56        22.95        76.57        36.03 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
      144.89        20.38       207.48       176.55        35.93       120.00 
TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 
       53.92        65.92        40.60        68.09        33.93       225.96 
TCGA-DA-A3F8 TCGA-DA-A95V TCGA-DA-A95X TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q 
       15.68        72.10        61.81        14.14        13.02        13.87 
TCGA-EB-A5KH TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X 
       20.35        54.02        58.92         7.04        36.46        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-A20C TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
      151.27        91.56        13.55        78.97        13.97        63.78 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29S 
       64.64         2.60        56.84        18.61        66.74        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       115.96 
TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GI 
       59.64        86.14        67.43       340.14       173.79        48.72 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GO TCGA-EE-A2GR TCGA-EE-A2GS 
      107.38        54.74        79.66       126.81        42.77        81.21 
TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M8 TCGA-EE-A2MC 
       44.88        94.82        21.67       129.27        19.76        61.51 
TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ 
       47.28       103.27       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 
      180.39       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        64.04        28.77 
TCGA-EE-A3AE TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J8 
       54.51        41.59       138.81       127.20        36.95        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       134.33        31.40        35.44 
TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H 
       50.76        77.75        98.40        26.37       268.93       152.35 
TCGA-ER-A19J TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 
        6.44        50.89        49.48         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-A42K TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A 
       93.01        46.98        12.95       149.03        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        48.00       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-A690 TCGA-RP-A693 TCGA-RP-A694 
       65.88       368.78         7.23         0.20         0.33         0.69 
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-A8K1 TCGA-WE-A8K5 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO 
      105.04        49.05        61.15       101.33        58.98        70.52 
TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 
       63.22        11.80        49.51        12.16        40.41        24.99 
TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-AA3S TCGA-Z2-AA3V 
       37.94        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 
            55.590             50.825 
[1] "0.2 - 297.9 (55.6)" "0.2 - 369.9 (50.8)"
[1] "hr=" "1.3"
D25V3, continuous
                    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          10       6      17       14       18       21
                    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         9        34         11
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  13Q GAIN MUTATED           12         12        3
  13Q GAIN WILD-TYPE         21         43       18
D25V4, multiclass
             clus
vv            13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  I OR II NOS                3                 10
  STAGE 0                    1                  6
  STAGE I                   12                 17
  STAGE IA                   4                 14
  STAGE IB                  10                 18
  STAGE II                   4                 21
  STAGE IIA                  1                 13
  STAGE IIB                  6                 13
  STAGE IIC                  6                  9
  STAGE III                  6                 34
  STAGE IIIA                 4                 11
  STAGE IIIB                12                 21
  STAGE IIIC                12                 43
  STAGE IV                   3                 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
  13Q GAIN MUTATED      15 26 12 19
  13Q GAIN WILD-TYPE    49 47 66 51
D25V5, multiclass
       clus
vv      13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  T0+T1               15                 49
  T2                  26                 47
  T3                  12                 66
  T4                  19                 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
  13Q GAIN MUTATED    49  19   6   8
  13Q GAIN WILD-TYPE 128  46  33  37
D25V6, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  N0               49                128
  N1               19                 46
  N2                6                 33
  N3                8                 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"
D25V7, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED    82   3
  13Q GAIN WILD-TYPE 236  19
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED     82    3
  13Q GAIN WILD-TYPE  236   19
   clus
vv  13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  0               82                236
  1                3                 19
[1] 2 2
[1] FALSE
D25V8, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED    29  25
  13Q GAIN WILD-TYPE 105  65
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED     29   25
  13Q GAIN WILD-TYPE  105   65
     clus
vv    13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  NO                29                105
  YES               25                 65
[1] 2 2
[1] FALSE
D25V9, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED    13  81
  13Q GAIN WILD-TYPE  34 238
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED     13   81
  13Q GAIN WILD-TYPE   34  238
     clus
vv    13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  NO                13                 34
  YES               81                238
[1] 2 2
[1] FALSE
D25V10, continuous
D25V11, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED    35  59
  13Q GAIN WILD-TYPE 102 170
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED     35   59
  13Q GAIN WILD-TYPE  102  170
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  FEMALE               35                102
  MALE                 59                170
[1] 2 2
[1] FALSE
D25V12, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED    84  10
  13Q GAIN WILD-TYPE 233  37
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED     84   10
  13Q GAIN WILD-TYPE  233   37
     clus
vv    13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  NO                84                233
  YES               10                 37
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  13Q GAIN MUTATED       2                         0    90
  13Q GAIN WILD-TYPE     3                         1   262
D25V13, multiclass
                           clus
vv                          13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  ASIAN                                    2                  3
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   90                262
[1] 3 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   6 263
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      1   88
  13Q GAIN WILD-TYPE    6  263
                        clus
vv                       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO               88                263
[1] 2 2
[1] FALSE

Clustering(26) Variable = 14Q GAIN MUTATION ANALYSIS
D26V1, survival
                    sevent
clus2                  0   1
  14Q GAIN MUTATED    16  15
  14Q GAIN WILD-TYPE 106 108
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                31                214 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                15                108 
$`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 
       45.07        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 
      201.60        18.35       118.32        63.25        53.26        54.51 
TCGA-EE-A3JH TCGA-ER-A19C TCGA-ER-A19L TCGA-ER-A19M TCGA-FR-A729 TCGA-FR-A8YC 
       19.86        39.81        99.06        59.84       209.23        10.06 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-GN-A265 TCGA-GN-A9SD TCGA-QB-AA9O TCGA-W3-A828 
       23.21         5.29        96.92        59.41        18.05       120.07 
TCGA-WE-AAA3 
       18.31 

$`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        69.21        22.85 
TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I5 TCGA-DA-A1IA TCGA-DA-A1IC 
       76.34       138.67        53.65        95.51        64.83        58.85 
TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A95V TCGA-DA-A95X TCGA-DA-A95Y TCGA-DA-A95Z 
       30.44       225.11        72.10        52.90        14.14        12.30 
TCGA-EB-A44Q TCGA-EB-A5SG TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y 
        3.91        33.24        52.41        18.21        13.15        24.89 
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-A29P TCGA-EE-A29Q TCGA-EE-A29T 
        0.26        44.28        63.12        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       115.43        30.02        77.98        26.14       239.11 
TCGA-EE-A2GE TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GP 
       12.95        68.65        10.62        32.48        31.00         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-A2MK TCGA-EE-A2ML 
       23.77       209.79        94.19       171.85        89.26       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-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 
      122.73        64.04         4.41         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-A19B TCGA-ER-A19D 
        1.58        47.31         7.82         4.54        53.29        11.47 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S 
      151.46       150.12        42.48       120.76        49.71        47.18 
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-ER-A42L TCGA-FR-A44A 
      173.29        68.52        15.48        32.05        74.47       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        42.08        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-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-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-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS 
       34.49        46.92        43.23        85.05       297.01         7.23 
TCGA-RP-A690 TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-AA1Q TCGA-W3-AA1R 
        0.20         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        65.42 
TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AA9Y 
       12.69        21.90        62.89        10.95        48.39         1.94 
TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-Z2-AA3S 
       31.99        18.35        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 
             58.06              45.80 
[1] "5.3 - 209.2 (58.1)" "0.0 - 346.5 (45.8)"
[1] "hr=" "1.1"
D26V2, survival
                    sevent
clus2                  0   1
  14Q GAIN MUTATED    18  22
  14Q GAIN WILD-TYPE 152 165
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                40                317 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                22                165 
$`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        73.84        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       220.24        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       134.33        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        96.92        48.00        59.41 
TCGA-QB-AA9O TCGA-W3-A828 TCGA-W3-AA1O TCGA-WE-AAA3 
       18.05       121.08         4.01        21.40 

$`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-D3-A8GV TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A1X3 
      167.70       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        77.56        22.95 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I4 
       76.57        36.03       144.89        20.38       207.48        35.93 
TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
      120.00        53.92        65.92        40.60        68.09        33.93 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-DA-A95V TCGA-DA-A95W TCGA-DA-A95X 
       10.49       225.96        15.68        72.10        25.15        61.81 
TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG 
       14.14        13.02        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 
       29.29        58.92         7.04        36.46        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       115.96        59.64        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       173.79        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 
      180.39       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        64.04 
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 
       49.48         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        93.01 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A 
       46.98        33.21        12.95       149.03        92.98       174.21 
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-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        46.45        15.45         9.70 
TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZR 
       32.75        47.38        23.93       101.26       133.55        11.41 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 
      148.80        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-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-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 
       10.13        64.44        62.79        32.48       121.91        39.35 
TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A8LL TCGA-HR-A2OG 
       10.42        48.89        22.13        50.10        21.37         0.23 
TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 
       65.88       368.78       297.90         7.23         0.20         0.33 
TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1V 
        0.69       228.16        63.02        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        17.95 
TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX 
      101.33        58.98        70.52        63.22        11.80        35.80 
TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-YD-A89C TCGA-YD-A9TA 
       49.51        12.16        40.41        24.99         6.90        49.18 
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 

  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             50.100 
[1] "2.6 - 220.8 (58.7)" "0.2 - 369.9 (50.1)"
[1] "hr=" "1"  
D26V3, continuous
                    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          12       6      24       15       24       22
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  14Q GAIN MUTATED           1         3         3         5          2
  14Q GAIN WILD-TYPE        13        16        12        35         13
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  14Q GAIN MUTATED            3          5        0
  14Q GAIN WILD-TYPE         30         50       21
D26V4, multiclass
             clus
vv            14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  I OR II NOS                1                 12
  STAGE 0                    1                  6
  STAGE I                    5                 24
  STAGE IA                   3                 15
  STAGE IB                   4                 24
  STAGE II                   3                 22
  STAGE IIA                  1                 13
  STAGE IIB                  3                 16
  STAGE IIC                  3                 12
  STAGE III                  5                 35
  STAGE IIIA                 2                 13
  STAGE IIIB                 3                 30
  STAGE IIIC                 5                 50
  STAGE IV                   0                 21
[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 63 69 60
D26V5, multiclass
       clus
vv      14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  T0+T1                5                 59
  T2                  10                 63
  T3                   9                 69
  T4                  10                 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
  14Q GAIN MUTATED    25   4   5   3
  14Q GAIN WILD-TYPE 152  61  34  42
D26V6, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  N0               25                152
  N1                4                 61
  N2                5                 34
  N3                3                 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"
D26V7, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED    37   0
  14Q GAIN WILD-TYPE 281  22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED     37    0
  14Q GAIN WILD-TYPE  281   22
   clus
vv  14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  0               37                281
  1                0                 22
[1] 2 2
[1] FALSE
D26V8, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED    15  13
  14Q GAIN WILD-TYPE 119  77
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED     15   13
  14Q GAIN WILD-TYPE  119   77
     clus
vv    14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  NO                15                119
  YES               13                 77
[1] 2 2
[1] FALSE
D26V9, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED     5  36
  14Q GAIN WILD-TYPE  42 283
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      5   36
  14Q GAIN WILD-TYPE   42  283
     clus
vv    14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  NO                 5                 42
  YES               36                283
[1] 2 2
[1] FALSE
D26V10, continuous
D26V11, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED    14  27
  14Q GAIN WILD-TYPE 123 202
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED     14   27
  14Q GAIN WILD-TYPE  123  202
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  FEMALE               14                123
  MALE                 27                202
[1] 2 2
[1] FALSE
D26V12, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED    38   3
  14Q GAIN WILD-TYPE 279  44
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED     38    3
  14Q GAIN WILD-TYPE  279   44
     clus
vv    14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  NO                38                279
  YES                3                 44
[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   311
D26V13, multiclass
                           clus
vv                          14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  ASIAN                                    0                  5
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   41                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"
D26V14, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED     0  41
  14Q GAIN WILD-TYPE   7 310
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      0   41
  14Q GAIN WILD-TYPE    7  310
                        clus
vv                       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  7
  NOT HISPANIC OR LATINO               41                310
[1] 2 2
[1] FALSE

Clustering(27) Variable = 15Q GAIN MUTATION ANALYSIS
D27V1, survival
                    sevent
clus2                 0  1
  15Q GAIN MUTATED   25 29
  15Q GAIN WILD-TYPE 97 94
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                54                191 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                29                 94 
$`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        45.07 
TCGA-DA-A3F5 TCGA-EE-A17Y TCGA-EE-A20H TCGA-EE-A29D TCGA-EE-A29T TCGA-EE-A29W 
      225.11        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 
      115.43        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-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A19C TCGA-ER-A19M 
       67.89        19.86       152.81        14.56        39.81        59.84 
TCGA-ER-A19P TCGA-ER-A19S TCGA-ER-A42L TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A8YC 
      120.76        47.18        74.47       174.21       209.23        10.06 
TCGA-FS-A1Z3 TCGA-FS-A1ZD TCGA-FS-A1ZY TCGA-FS-A4FD TCGA-GF-A4EO TCGA-GN-A264 
        8.35        32.78         5.29        80.68         6.05       117.93 
TCGA-GN-A267 TCGA-GN-A9SD TCGA-W3-A825 TCGA-W3-A828 TCGA-WE-A8ZM TCGA-WE-A8ZQ 
       17.06        59.41         1.97       120.07        65.42        62.89 

$`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        69.21        22.85 
TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1IA 
       76.34       138.67        53.65       150.61        95.51        64.83 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A95V TCGA-DA-A95X TCGA-DA-A95Y TCGA-DA-A95Z 
       58.85        30.44        72.10        52.90        14.14        12.30 
TCGA-EB-A44Q TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X 
        3.91        33.24        50.07        52.41        18.21        13.15 
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-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-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE 
       61.12        30.02        77.98        26.14       239.11        12.95 
TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GR 
      201.60        68.65        10.62        32.48        31.00         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-A2MT TCGA-EE-A2MU 
      171.85        89.26       104.78       145.45        23.51        53.26 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3J4 TCGA-EE-A3J7 
      122.73        64.04         4.41         6.28       111.85        45.90 
TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 
        3.35       201.80        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-A19Q TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
       42.48        49.71       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        68.52        15.48        32.05 
TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z4 
       26.20         5.65       171.78        49.74       195.98        27.62 
TCGA-FS-A1ZC TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM 
      312.07        42.08        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-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-A6C8 TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A268 
       19.30         9.90         1.91        53.29        96.92        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-QB-AA9O TCGA-RP-A690 TCGA-RP-A693 TCGA-W3-A824 
      297.01         7.23        18.05         0.20         0.33       174.12 
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-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AA9Y 
       59.64        12.69        21.90        10.95        48.39         1.94 
TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-Z2-AA3S 
       31.99        18.31        18.35        28.21        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 
             64.04              44.05 
[1] "0.8 - 346.5 (64.0)" "0.0 - 312.1 (44.0)"
[1] "hr=" "1.2"
D27V2, survival
                    sevent
clus2                  0   1
  15Q GAIN MUTATED    39  42
  15Q GAIN WILD-TYPE 131 145
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                81                276 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                42                145 
$`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        73.84       225.96        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 
      115.96        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       134.33 
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        49.48 
TCGA-ER-A19T TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 
        8.88        12.95       149.03       174.21        15.72       220.80 
TCGA-FR-A7U9 TCGA-FR-A8YC TCGA-FS-A1Z3 TCGA-FS-A1ZD TCGA-FS-A1ZY TCGA-FS-A4F2 
       18.77        34.82        20.91        53.52        27.09        50.14 
TCGA-FS-A4FD TCGA-GF-A4EO TCGA-GF-A6C9 TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A9SD 
       80.68         7.23        15.78       117.93        64.44        59.41 
TCGA-HR-A2OG TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O TCGA-WE-A8K6 TCGA-WE-A8ZM 
        0.23        63.02       121.08         4.01        17.95       101.33 
TCGA-WE-A8ZQ TCGA-WE-A8ZX TCGA-YD-A9TA 
       63.22        35.80        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-D3-A8GV TCGA-D9-A148 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A1X3 
      117.17       167.70       151.53         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        77.56        22.95 
TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 
       76.57       144.89        20.38       207.48       176.55        35.93 
TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
      120.00        53.92        65.92        40.60        68.09        33.93 
TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-DA-A95V TCGA-DA-A95W TCGA-DA-A95X TCGA-DA-A95Y 
       10.49        15.68        72.10        25.15        61.81        14.14 
TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH 
       13.02        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 
       29.29        58.92         7.04        36.46        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        59.64 
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       173.79 
TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GR 
      220.24       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 
      180.39       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        64.04        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 
       93.01        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        46.45 
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        96.92 
TCGA-GN-A266 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A4U4 
       10.13        62.79        32.48        48.00       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-A690 TCGA-RP-A693 
      368.78       297.90         7.23        18.05         0.20         0.33 
TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1V TCGA-W3-AA1W 
        0.69       228.16        69.07       111.09        42.08       219.16 
TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8ZN TCGA-WE-A8ZO 
      105.04        24.03        49.05        61.15        58.98        70.52 
TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 
       11.80        49.51        12.16        40.41        21.40        24.99 
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 

  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 
            59.410             49.805 
[1] "0.2 - 369.9 (59.4)" "0.2 - 368.8 (49.8)"
[1] "hr=" "1.2"
D27V3, continuous
                    vv
clus                 I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  15Q GAIN MUTATED             6       2       9        5        5        9
  15Q GAIN WILD-TYPE           7       5      20       13       23       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        13        32         13
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  15Q GAIN MUTATED           11         10        3
  15Q GAIN WILD-TYPE         22         45       18
D27V4, multiclass
             clus
vv            15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  I OR II NOS                6                  7
  STAGE 0                    2                  5
  STAGE I                    9                 20
  STAGE IA                   5                 13
  STAGE IB                   5                 23
  STAGE II                   9                 16
  STAGE IIA                  2                 12
  STAGE IIB                  4                 15
  STAGE IIC                  2                 13
  STAGE III                  8                 32
  STAGE IIIA                 2                 13
  STAGE IIIB                11                 22
  STAGE IIIC                10                 45
  STAGE IV                   3                 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
  15Q GAIN MUTATED      16 19 17 13
  15Q GAIN WILD-TYPE    48 54 61 57
D27V5, multiclass
       clus
vv      15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  T0+T1               16                 48
  T2                  19                 54
  T3                  17                 61
  T4                  13                 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
  15Q GAIN MUTATED    45  15   7   9
  15Q GAIN WILD-TYPE 132  50  32  36
D27V6, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  N0               45                132
  N1               15                 50
  N2                7                 32
  N3                9                 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"
D27V7, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED    76   3
  15Q GAIN WILD-TYPE 242  19
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED     76    3
  15Q GAIN WILD-TYPE  242   19
   clus
vv  15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  0               76                242
  1                3                 19
[1] 2 2
[1] FALSE
D27V8, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED    30  16
  15Q GAIN WILD-TYPE 104  74
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED     30   16
  15Q GAIN WILD-TYPE  104   74
     clus
vv    15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  NO                30                104
  YES               16                 74
[1] 2 2
[1] FALSE
D27V9, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED    13  72
  15Q GAIN WILD-TYPE  34 247
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED     13   72
  15Q GAIN WILD-TYPE   34  247
     clus
vv    15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  NO                13                 34
  YES               72                247
[1] 2 2
[1] FALSE
D27V10, continuous
D27V11, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED    30  55
  15Q GAIN WILD-TYPE 107 174
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED     30   55
  15Q GAIN WILD-TYPE  107  174
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  FEMALE               30                107
  MALE                 55                174
[1] 2 2
[1] FALSE
D27V12, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED    72  13
  15Q GAIN WILD-TYPE 245  34
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED     72   13
  15Q GAIN WILD-TYPE  245   34
     clus
vv    15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  NO                72                245
  YES               13                 34
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  15Q GAIN MUTATED       1                         0    82
  15Q GAIN WILD-TYPE     4                         1   270
D27V13, multiclass
                           clus
vv                          15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  ASIAN                                    1                  4
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   82                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"
D27V14, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED     1  82
  15Q GAIN WILD-TYPE   6 269
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      1   82
  15Q GAIN WILD-TYPE    6  269
                        clus
vv                       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO               82                269
[1] 2 2
[1] FALSE

Clustering(28) Variable = 16P GAIN MUTATION ANALYSIS
D28V1, survival
                    sevent
clus2                  0   1
  16P GAIN MUTATED    20  21
  16P GAIN WILD-TYPE 102 102
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                41                204 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                21                102 
$`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-DA-A95V TCGA-DA-A95Z TCGA-EE-A17Y TCGA-EE-A20H 
      135.12        36.53        72.10        12.30        24.89       155.90 
TCGA-EE-A29P TCGA-EE-A2A1 TCGA-EE-A2GB TCGA-EE-A2GH TCGA-EE-A2GM TCGA-EE-A2GN 
       27.16       115.43        26.14       201.60        18.35        31.00 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MP TCGA-EE-A3AE TCGA-EE-A3J3 TCGA-EE-A3J7 
      103.13        15.25       227.01        54.51        67.89        45.90 
TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P 
       53.29        39.81        11.47        59.84        42.48       120.76 
TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A729 TCGA-FS-A1ZY TCGA-FS-A4F4 TCGA-FS-A4FD 
       32.05        74.47       209.23         5.29        66.67        80.68 
TCGA-GF-A4EO TCGA-GN-A9SD TCGA-QB-AA9O TCGA-W3-AA1V TCGA-WE-AAA3 
        6.05        59.41        18.05         8.09        18.31 

$`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        69.21        22.85        76.34       138.67        53.65 
TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 
      150.61        95.51        45.07        64.83        58.85        30.44 
TCGA-DA-A3F5 TCGA-DA-A95X TCGA-DA-A95Y TCGA-EB-A44Q TCGA-EB-A5SG TCGA-EB-A5SH 
      225.11        52.90        14.14         3.91        33.24        50.07 
TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 
       52.41        18.21        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-A29Q TCGA-EE-A29T TCGA-EE-A29W 
       44.28        63.12        47.74        61.12       346.49       185.19 
TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GJ TCGA-EE-A2GK 
       30.02        77.98       239.11        12.95        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-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-A2MR TCGA-EE-A2MS TCGA-EE-A2MT 
       89.26       104.78       145.45        25.08       143.93        23.51 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AF 
       53.26       124.31       122.73        64.04         4.41         6.28 
TCGA-EE-A3J4 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 
      111.85         3.35       201.80        19.86       152.81        14.56 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19G 
       34.45         1.58        47.31         7.82         4.54       151.46 
TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 
      150.12        99.06        49.71        47.18       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        68.52 
TCGA-ER-A3EV TCGA-FR-A44A TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FS-A1YW 
       15.48       174.21        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 
       42.08        12.92         7.82        36.33        78.61       130.95 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZZ TCGA-FS-A4F0 
      136.27        35.28         4.47        23.21         3.06        30.90 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
      173.19        13.28        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        96.92        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-A690 TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A825 
      297.01         7.23         0.20         0.33       174.12         1.97 
TCGA-W3-A828 TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 
      120.07        44.05        79.99       185.13        92.84         1.15 
TCGA-WE-A8K5 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT 
       59.64        65.42        12.69        21.90        62.89        10.95 
TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-Z2-AA3S 
       48.39         1.94        31.99        18.35        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 
             53.29              46.95 
[1] "5.3 - 227.0 (53.3)" "0.0 - 346.5 (47.0)"
[1] "hr=" "1"  
D28V2, survival
                    sevent
clus2                  0   1
  16P GAIN MUTATED    27  28
  16P GAIN WILD-TYPE 143 159
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                55                302 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                28                159 
$`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-DA-A95V 
       58.52       241.38       152.75       129.63       117.17        72.10 
TCGA-DA-A95Z TCGA-EE-A17Y TCGA-EE-A20B TCGA-EE-A20H TCGA-EE-A29P TCGA-EE-A29R 
       13.02        27.22       133.81       168.26        56.42        14.47 
TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-EE-A2GB TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GM 
      115.96        39.29        59.28       220.24        48.72        75.48 
TCGA-EE-A2GN TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MP TCGA-EE-A3AE TCGA-EE-A3J3 
      102.12       129.27        28.83       248.65        54.51       172.18 
TCGA-EE-A3J7 TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19M TCGA-ER-A19N 
       64.08        98.40        48.89        12.59        61.05        44.05 
TCGA-ER-A19P TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A69P TCGA-FR-A729 TCGA-FS-A1YX 
      162.08        33.21       149.03        15.72       220.80        48.59 
TCGA-FS-A1ZP TCGA-FS-A1ZY TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4FD TCGA-GF-A4EO 
       74.73        27.09        66.67        28.73        80.68         7.23 
TCGA-GN-A9SD TCGA-HR-A2OG TCGA-QB-AA9O TCGA-W3-AA1V TCGA-WE-A8K6 TCGA-WE-AAA3 
       59.41         0.23        18.05        42.08        17.95        21.40 
TCGA-Z2-AA3V 
       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-D3-A8GV TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX 
       29.06       167.70       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 
       77.56        22.95        76.57        36.03       144.89        20.38 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
      207.48       176.55        35.93       120.00        73.84        53.92 
TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 
       65.92        40.60        68.09        33.93        10.49       225.96 
TCGA-DA-A3F8 TCGA-DA-A95W TCGA-DA-A95X TCGA-DA-A95Y TCGA-EB-A44Q TCGA-EB-A44R 
       15.68        25.15        61.81        14.14        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        29.29        58.92         7.04 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 
       36.46        29.82         8.65        94.98        33.73        14.70 
TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I 
       26.89        68.15         4.96       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-A29Q TCGA-EE-A29S 
       64.64         2.60        56.84        18.61        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        59.64 
TCGA-EE-A2A6 TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GJ TCGA-EE-A2GK 
       86.14        67.43       340.14       173.79       107.38        54.74 
TCGA-EE-A2GL TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT 
       79.66       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       180.39 
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-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
       71.21        53.26       124.31       122.73        64.04        28.77 
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-A3JA TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI 
       53.19       201.80        27.35        51.35       134.33       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-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-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
       50.89        49.48         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-A3YN TCGA-FR-A44A TCGA-FR-A7U8 
       93.01        46.98        12.95        92.98       174.21        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-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        46.45        15.45         9.70 
TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZR 
       32.75        47.38        23.93       101.26       133.55        11.41 
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-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-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        96.92        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        48.00       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-RP-A690 TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 
      297.90         7.23         0.20         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       101.33        58.98 
TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AA9Y 
       70.52        63.22        11.80        35.80        49.51        12.16 
TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-YD-A89C TCGA-YD-A9TA TCGA-YG-AA3O TCGA-YG-AA3P 
       40.41        24.99         6.90        49.18        37.94        14.43 
TCGA-Z2-A8RT TCGA-Z2-AA3S 
       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 
             59.28              50.12 
[1] "0.2 - 248.7 (59.3)" "0.2 - 369.9 (50.1)"
[1] "hr=" "1.1"
D28V3, continuous
                    vv
clus                 I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  16P GAIN MUTATED             2       2       9        5        7        7
  16P GAIN WILD-TYPE          11       5      20       13       21       18
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  16P GAIN MUTATED           1         1         3         4          0
  16P GAIN WILD-TYPE        13        18        12        36         15
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  16P GAIN MUTATED            4          7        2
  16P GAIN WILD-TYPE         29         48       19
D28V4, multiclass
             clus
vv            16P GAIN MUTATED 16P GAIN WILD-TYPE
  I OR II NOS                2                 11
  STAGE 0                    2                  5
  STAGE I                    9                 20
  STAGE IA                   5                 13
  STAGE IB                   7                 21
  STAGE II                   7                 18
  STAGE IIA                  1                 13
  STAGE IIB                  1                 18
  STAGE IIC                  3                 12
  STAGE III                  4                 36
  STAGE IIIA                 0                 15
  STAGE IIIB                 4                 29
  STAGE IIIC                 7                 48
  STAGE IV                   2                 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 11  6
  16P GAIN WILD-TYPE    53 55 67 64
D28V5, multiclass
       clus
vv      16P GAIN MUTATED 16P GAIN WILD-TYPE
  T0+T1               11                 53
  T2                  18                 55
  T3                  11                 67
  T4                   6                 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
  16P GAIN MUTATED    39   7   3   5
  16P GAIN WILD-TYPE 138  58  36  40
D28V6, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  N0               39                138
  N1                7                 58
  N2                3                 36
  N3                5                 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"
D28V7, binary
                    cls
clus                   0   1
  16P GAIN MUTATED    52   2
  16P GAIN WILD-TYPE 266  20
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     52    2
  16P GAIN WILD-TYPE  266   20
   clus
vv  16P GAIN MUTATED 16P GAIN WILD-TYPE
  0               52                266
  1                2                 20
[1] 2 2
[1] FALSE
D28V8, binary
                    cls
clus                   0   1
  16P GAIN MUTATED    17  13
  16P GAIN WILD-TYPE 117  77
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     17   13
  16P GAIN WILD-TYPE  117   77
     clus
vv    16P GAIN MUTATED 16P GAIN WILD-TYPE
  NO                17                117
  YES               13                 77
[1] 2 2
[1] FALSE
D28V9, binary
                    cls
clus                   0   1
  16P GAIN MUTATED     6  52
  16P GAIN WILD-TYPE  41 267
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      6   52
  16P GAIN WILD-TYPE   41  267
     clus
vv    16P GAIN MUTATED 16P GAIN WILD-TYPE
  NO                 6                 41
  YES               52                267
[1] 2 2
[1] FALSE
D28V10, continuous
D28V11, binary
                    cls
clus                   0   1
  16P GAIN MUTATED    24  34
  16P GAIN WILD-TYPE 113 195
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     24   34
  16P GAIN WILD-TYPE  113  195
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  FEMALE               24                113
  MALE                 34                195
[1] 2 2
[1] FALSE
D28V12, binary
                    cls
clus                   0   1
  16P GAIN MUTATED    52   6
  16P GAIN WILD-TYPE 265  41
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     52    6
  16P GAIN WILD-TYPE  265   41
     clus
vv    16P GAIN MUTATED 16P GAIN WILD-TYPE
  NO                52                265
  YES                6                 41
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16P GAIN MUTATED       1                         0    56
  16P GAIN WILD-TYPE     4                         1   296
D28V13, multiclass
                           clus
vv                          16P GAIN MUTATED 16P GAIN WILD-TYPE
  ASIAN                                    1                  4
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   56                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"
D28V14, binary
                    cls
clus                   0   1
  16P GAIN MUTATED     1  54
  16P GAIN WILD-TYPE   6 297
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      1   54
  16P GAIN WILD-TYPE    6  297
                        clus
vv                       16P GAIN MUTATED 16P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO               54                297
[1] 2 2
[1] FALSE

Clustering(29) Variable = 16Q GAIN MUTATION ANALYSIS
D29V1, survival
                    sevent
clus2                  0   1
  16Q GAIN MUTATED    12  18
  16Q GAIN WILD-TYPE 110 105
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                30                215 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                18                105 
$`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-DA-A95Z TCGA-EE-A17Y TCGA-EE-A20H TCGA-EE-A2A1 TCGA-EE-A2GB 
       36.53        12.30        24.89       155.90       115.43        26.14 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MP TCGA-EE-A3J3 
       18.35        31.00       103.13        15.25       227.01        67.89 
TCGA-EE-A3J7 TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19M TCGA-ER-A19P TCGA-ER-A3PL 
       45.90        39.81        11.47        59.84       120.76        32.05 
TCGA-FR-A729 TCGA-FS-A1ZY TCGA-FS-A4F4 TCGA-GF-A4EO TCGA-GN-A9SD TCGA-W3-AA1V 
      209.23         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        69.21        22.85        76.34       138.67 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC 
       53.65       150.61        95.51        45.07        64.83        58.85 
TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A95V TCGA-DA-A95X TCGA-DA-A95Y TCGA-EB-A44Q 
       30.44       225.11        72.10        52.90        14.14         3.91 
TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A180 
       33.24        50.07        52.41        18.21        13.15        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-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-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GD 
       61.12       346.49       185.19        30.02        77.98       239.11 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GO 
       12.95       201.60        68.65        10.62        32.48       118.32 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M8 TCGA-EE-A2MC 
        0.76         0.20        71.31        81.99         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        89.26       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-A3J4 
      122.73        64.04         4.41        54.51         6.28       111.85 
TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 
        3.35       201.80        19.86       152.81        14.56        34.45 
TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19G 
        1.58        47.31         7.82         4.54        53.29       151.46 
TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W 
      150.12        99.06        42.48        49.71        47.18       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-A42L TCGA-FR-A44A TCGA-FR-A7U8 TCGA-FR-A7UA 
       68.52        15.48        74.47       174.21        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        42.08        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-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TU 
        3.06        30.90       173.19        13.28        80.68        55.59 
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-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 
       96.92        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-A690 TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1Q 
        0.20         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        65.42 
TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AA9Y 
       12.69        21.90        62.89        10.95        48.39         1.94 
TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-Z2-AA3S 
       31.99        18.31        18.35        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 
            47.625             47.180 
[1] "5.3 - 227.0 (47.6)" "0.0 - 346.5 (47.2)"
[1] "hr=" "1.2"
D29V2, survival
                    sevent
clus2                  0   1
  16Q GAIN MUTATED    18  22
  16Q GAIN WILD-TYPE 152 165
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                40                317 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                22                165 
$`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-DA-A95Z TCGA-EE-A17Y TCGA-EE-A20B TCGA-EE-A20H 
      152.75       129.63        13.02        27.22       133.81       168.26 
TCGA-EE-A29R TCGA-EE-A2A1 TCGA-EE-A2GB TCGA-EE-A2GI TCGA-EE-A2GM TCGA-EE-A2GN 
       14.47       115.96        59.28        48.72        75.48       102.12 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MP TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-ER-A19C 
      129.27        28.83       248.65       172.18        64.08        48.89 
TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19M TCGA-ER-A19P TCGA-ER-A3PL TCGA-FR-A69P 
       12.59        13.02        61.05       162.08        33.21        15.72 
TCGA-FR-A729 TCGA-FS-A1YX TCGA-FS-A1ZY TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-GF-A4EO 
      220.80        48.59        27.09        66.67        28.73         7.23 
TCGA-GN-A9SD TCGA-HR-A2OG TCGA-W3-AA1V TCGA-WE-A8K6 
       59.41         0.23        42.08        17.95 

$`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-D3-A8GV TCGA-D9-A148 
      107.15       161.00        29.06       117.17       167.70       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        77.56        22.95        76.57 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 
       36.03       144.89        20.38       207.48       176.55        35.93 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
      120.00        73.84        53.92        65.92        40.60        68.09 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-DA-A95V TCGA-DA-A95W 
       33.93        10.49       225.96        15.68        72.10        25.15 
TCGA-DA-A95X TCGA-DA-A95Y TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG 
       61.81        14.14        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        29.29        58.92         7.04        36.46        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-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-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-A2A2 TCGA-EE-A2A5 
       25.87       195.02        17.92        46.82        59.64        39.29 
TCGA-EE-A2A6 TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ 
       86.14        67.43       340.14       173.79       220.24       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-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-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 
      180.39       216.66       167.90        47.54        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        64.04 
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 
      134.33       152.81        31.40        35.44        13.94        50.76 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H 
        9.17        77.75        98.40        26.37       268.93       152.35 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T 
        6.44       131.51        44.05        50.89        49.48         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-A42K 
       31.27        32.05       247.04        93.01        46.98        12.95 
TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA 
      149.03        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        46.45        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        96.92        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        48.00       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-A690 TCGA-RP-A693 TCGA-RP-A694 
      297.90         7.23        18.05         0.20         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       101.33 
TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-A8ZY 
       58.98        70.52        63.22        11.80        35.80        49.51 
TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YD-A89C TCGA-YD-A9TA 
       12.16        40.41        21.40        24.99         6.90        49.18 
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 

  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 
             58.67              51.35 
[1] "0.2 - 248.7 (58.7)" "0.2 - 369.9 (51.4)"
[1] "hr=" "1"  
D29V3, continuous
                    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          11       5      22       16       21       21
                    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        14        36         15
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  16Q GAIN MUTATED            5          4        2
  16Q GAIN WILD-TYPE         28         51       19
D29V4, multiclass
             clus
vv            16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  I OR II NOS                2                 11
  STAGE 0                    2                  5
  STAGE I                    7                 22
  STAGE IA                   2                 16
  STAGE IB                   7                 21
  STAGE II                   4                 21
  STAGE IIA                  1                 13
  STAGE IIB                  1                 18
  STAGE IIC                  1                 14
  STAGE III                  4                 36
  STAGE IIIA                 0                 15
  STAGE IIIB                 5                 28
  STAGE IIIC                 4                 51
  STAGE IV                   2                 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 57 69 67
D29V5, multiclass
       clus
vv      16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  T0+T1                7                 57
  T2                  16                 57
  T3                   9                 69
  T4                   3                 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
  16Q GAIN MUTATED    28   8   2   3
  16Q GAIN WILD-TYPE 149  57  37  42
D29V6, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  N0               28                149
  N1                8                 57
  N2                2                 37
  N3                3                 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"
D29V7, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED    40   2
  16Q GAIN WILD-TYPE 278  20
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     40    2
  16Q GAIN WILD-TYPE  278   20
   clus
vv  16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  0               40                278
  1                2                 20
[1] 2 2
[1] FALSE
D29V8, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED    13  10
  16Q GAIN WILD-TYPE 121  80
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     13   10
  16Q GAIN WILD-TYPE  121   80
     clus
vv    16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  NO                13                121
  YES               10                 80
[1] 2 2
[1] FALSE
D29V9, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED     4  40
  16Q GAIN WILD-TYPE  43 279
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      4   40
  16Q GAIN WILD-TYPE   43  279
     clus
vv    16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  NO                 4                 43
  YES               40                279
[1] 2 2
[1] FALSE
D29V10, continuous
D29V11, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED    20  24
  16Q GAIN WILD-TYPE 117 205
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     20   24
  16Q GAIN WILD-TYPE  117  205
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  FEMALE               20                117
  MALE                 24                205
[1] 2 2
[1] FALSE
D29V12, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED    39   5
  16Q GAIN WILD-TYPE 278  42
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     39    5
  16Q GAIN WILD-TYPE  278   42
     clus
vv    16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  NO                39                278
  YES                5                 42
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16Q GAIN MUTATED       1                         0    42
  16Q GAIN WILD-TYPE     4                         1   310
D29V13, multiclass
                           clus
vv                          16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  ASIAN                                    1                  4
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   42                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"
D29V14, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED     1  40
  16Q GAIN WILD-TYPE   6 311
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      1   40
  16Q GAIN WILD-TYPE    6  311
                        clus
vv                       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO               40                311
[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 110 110
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                25                220 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                13                110 
$`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        69.21        45.07        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       201.60        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        76.34       138.67        53.65 
TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A95V 
      150.61        95.51        58.85        30.44       225.11        72.10 
TCGA-DA-A95X TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5SG TCGA-EB-A5SH 
       52.90        14.14        12.30         3.91        33.24        50.07 
TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A184 
       52.41        18.21        13.15        62.37        20.38        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-A29M TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 
       63.12        47.74        61.12       346.49       185.19       115.43 
TCGA-EE-A2A2 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GJ TCGA-EE-A2GK 
       30.02        26.14       239.11        12.95        68.65        10.62 
TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
       32.48        31.00       118.32         0.76         0.20        71.31 
TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MG 
       81.99       103.13         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        89.26       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 
       64.04         4.41        54.51         6.28        67.89       111.85 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 
       45.90         3.35       201.80        19.86       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-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        47.18       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        68.52        15.48 
TCGA-ER-A42L TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FR-A8YC 
       74.47       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-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZQ TCGA-FS-A1ZT 
       42.08        12.92         7.82        36.33       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        96.92 
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-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A690 
       43.23        85.05       297.01         7.23        18.05         0.20 
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        65.42        12.69 
TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 
       21.90        62.89        10.95        48.39         1.94        31.99 
TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-Z2-AA3S 
       18.31        18.35        28.21        91.23 

  17P GAIN MUTATED 17P GAIN WILD-TYPE 
               0.0                0.2 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
            201.60             346.49 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
            45.070             47.245 
[1] "0.0 - 201.6 (45.1)" "0.2 - 346.5 (47.2)"
[1] "hr=" "1.2"
D30V2, survival
                    sevent
clus2                  0   1
  17P GAIN MUTATED    16  20
  17P GAIN WILD-TYPE 154 167
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                36                321 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                20                167 
$`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        77.56        73.84 
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       220.24        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        48.00        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-D3-A8GV TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW 
      129.63       117.17       167.70       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        76.57        36.03       144.89        20.38 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A1IB 
      207.48       176.55        35.93       120.00        53.92        40.60 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-DA-A95V 
       68.09        33.93        10.49       225.96        15.68        72.10 
TCGA-DA-A95W TCGA-DA-A95X TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A44R 
       25.15        61.81        14.14        13.02        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        29.29        58.92         7.04 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A183 
       36.46        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       115.96        59.64        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       173.79        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       180.39       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        64.04        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       134.33       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 
       49.48       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        93.01        46.98        12.95 
TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 
      149.03        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-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG 
       27.72        48.85       357.37        46.45        15.45         9.70 
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-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-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
      117.93        96.92        10.13        64.44        62.79        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-A6FS 
       21.37         0.23        65.88       368.78       297.90         7.23 
TCGA-QB-AA9O TCGA-RP-A690 TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A828 
       18.05         0.20         0.33         0.69       228.16       121.08 
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        17.95       101.33        58.98        70.52 
TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 
       63.22        11.80        35.80        49.51        12.16        40.41 
TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YD-A89C TCGA-YD-A9TA TCGA-YG-AA3O TCGA-YG-AA3P 
       21.40        24.99         6.90        49.18        37.94        14.43 
TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
       27.58        96.99        15.98 

  17P GAIN MUTATED 17P GAIN WILD-TYPE 
              4.01               0.20 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
            220.24             369.93 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
             54.97              50.89 
[1] "4.0 - 220.2 (55.0)" "0.2 - 369.9 (50.9)"
[1] "hr=" "1.2"
D30V3, continuous
                    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          11       7      26       16       25       23
                    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        12        34         14
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  17P GAIN MUTATED            5          6        2
  17P GAIN WILD-TYPE         28         49       19
D30V4, multiclass
             clus
vv            17P GAIN MUTATED 17P GAIN WILD-TYPE
  I OR II NOS                2                 11
  STAGE 0                    0                  7
  STAGE I                    3                 26
  STAGE IA                   2                 16
  STAGE IB                   3                 25
  STAGE II                   2                 23
  STAGE IIA                  1                 13
  STAGE IIB                  1                 18
  STAGE IIC                  3                 12
  STAGE III                  6                 34
  STAGE IIIA                 1                 14
  STAGE IIIB                 5                 28
  STAGE IIIC                 6                 49
  STAGE IV                   2                 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
  17P GAIN MUTATED      10  9  7  7
  17P GAIN WILD-TYPE    54 64 71 63
D30V5, multiclass
       clus
vv      17P GAIN MUTATED 17P GAIN WILD-TYPE
  T0+T1               10                 54
  T2                   9                 64
  T3                   7                 71
  T4                   7                 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
  17P GAIN MUTATED    17   7   8   4
  17P GAIN WILD-TYPE 160  58  31  41
D30V6, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  N0               17                160
  N1                7                 58
  N2                8                 31
  N3                4                 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"
D30V7, binary
                    cls
clus                   0   1
  17P GAIN MUTATED    34   2
  17P GAIN WILD-TYPE 284  20
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED     34    2
  17P GAIN WILD-TYPE  284   20
   clus
vv  17P GAIN MUTATED 17P GAIN WILD-TYPE
  0               34                284
  1                2                 20
[1] 2 2
[1] FALSE
D30V8, binary
                    cls
clus                   0   1
  17P GAIN MUTATED    11  11
  17P GAIN WILD-TYPE 123  79
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED     11   11
  17P GAIN WILD-TYPE  123   79
     clus
vv    17P GAIN MUTATED 17P GAIN WILD-TYPE
  NO                11                123
  YES               11                 79
[1] 2 2
[1] FALSE
D30V9, binary
                    cls
clus                   0   1
  17P GAIN MUTATED     5  32
  17P GAIN WILD-TYPE  42 287
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      5   32
  17P GAIN WILD-TYPE   42  287
     clus
vv    17P GAIN MUTATED 17P GAIN WILD-TYPE
  NO                 5                 42
  YES               32                287
[1] 2 2
[1] FALSE
D30V10, continuous
D30V11, binary
                    cls
clus                   0   1
  17P GAIN MUTATED    16  21
  17P GAIN WILD-TYPE 121 208
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED     16   21
  17P GAIN WILD-TYPE  121  208
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  FEMALE               16                121
  MALE                 21                208
[1] 2 2
[1] FALSE
D30V12, binary
                    cls
clus                   0   1
  17P GAIN MUTATED    33   4
  17P GAIN WILD-TYPE 284  43
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED     33    4
  17P GAIN WILD-TYPE  284   43
     clus
vv    17P GAIN MUTATED 17P GAIN WILD-TYPE
  NO                33                284
  YES                4                 43
[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   316
D30V13, multiclass
                           clus
vv                          17P GAIN MUTATED 17P GAIN WILD-TYPE
  ASIAN                                    1                  4
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   36                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"
D30V14, binary
                    cls
clus                   0   1
  17P GAIN MUTATED     1  35
  17P GAIN WILD-TYPE   6 316
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      1   35
  17P GAIN WILD-TYPE    6  316
                        clus
vv                       17P GAIN MUTATED 17P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO               35                316
[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 102 102
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                41                204 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                21                102 
$`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        76.34 
TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A182 
       45.07        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       201.60        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        64.04        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        96.92        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        18.31 

$`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        69.21        22.85 
TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A3F2 TCGA-DA-A3F5 
      138.67        53.65       150.61        95.51        30.44       225.11 
TCGA-DA-A95V TCGA-DA-A95X TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5SG 
       72.10        52.90        14.14        12.30         3.91        33.24 
TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A180 TCGA-EE-A20C 
       50.07        52.41        18.21        13.15        62.37        75.55 
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       115.43        30.02 
TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
       26.14       239.11        12.95        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-A2M8 TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI 
      103.13         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-A2MT 
       63.25        89.26       104.78       145.45       227.01        23.51 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
       53.26       124.31       122.73         4.41        54.51         6.28 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH 
       67.89       111.85        45.90         3.35       201.80        19.86 
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        47.18 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A3ES 
      146.63        47.97         4.70        16.87        10.95       173.29 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A42L TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7U8 
       68.52        15.48        74.47       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-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZJ 
       27.62       312.07        42.08        12.92         7.82        36.33 
TCGA-FS-A1ZQ TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 
      130.95        35.28        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-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-LH-A9QB TCGA-OD-A75X TCGA-QB-AA9O TCGA-RP-A690 TCGA-RP-A693 TCGA-W3-A824 
       85.05       297.01        18.05         0.20         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        65.42        12.69        21.90        62.89        10.95 
TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-Z2-AA3S 
       48.39         1.94        31.99        18.35        28.21        91.23 

  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
               0.0                0.2 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
            201.60             346.49 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
            45.070             47.245 
[1] "0.0 - 201.6 (45.1)" "0.2 - 346.5 (47.2)"
[1] "hr=" "1.2"
D31V2, survival
                    sevent
clus2                  0   1
  17Q GAIN MUTATED    32  32
  17Q GAIN WILD-TYPE 138 155
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                64                293 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                32                155 
$`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 
       76.57        73.84        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       220.24 
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        64.04 
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        96.92 
TCGA-GN-A268 TCGA-GN-A26D TCGA-GN-A9SD TCGA-QB-A6FS TCGA-RP-A694 TCGA-W3-A825 
       62.79        48.00        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        21.40 

$`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-D3-A8GV TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JX 
      129.63       117.17       167.70       151.53        54.67         7.10 
TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6EA TCGA-D9-A6EC 
       18.12        15.39        22.29        18.44        25.18        77.56 
TCGA-D9-A6EG TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 
       22.95        36.03       144.89        20.38       207.48       176.55 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-DA-A3F3 
       35.93       120.00        53.92        40.60        33.93        10.49 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-DA-A95V TCGA-DA-A95W TCGA-DA-A95X TCGA-DA-A95Y 
      225.96        15.68        72.10        25.15        61.81        14.14 
TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH 
       13.02        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 
       29.29        58.92         7.04        36.46        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       115.96        59.64        39.29        59.28 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
      340.14       173.79        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       180.39 
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       134.33       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 
       49.48       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        93.01        46.98        12.95 
TCGA-ER-A42L TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 
      149.03       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-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-A1ZB 
      202.65        20.91        28.08         7.79        27.72        48.85 
TCGA-FS-A1ZC TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ 
      357.37        46.45        15.45         9.70        32.75        47.38 
TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZT TCGA-FS-A1ZW 
       23.93        74.73       133.55        11.41        53.16        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-A266 TCGA-GN-A267 
        2.04        15.78       139.89       117.93        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-AA9O TCGA-RP-A690 TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A828 TCGA-W3-AA1Q 
       18.05         0.20         0.33       228.16       121.08        69.07 
TCGA-W3-AA1R TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K5 TCGA-WE-A8K6 
      111.09        42.08       219.16       105.04        61.15        17.95 
TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX 
      101.33        58.98        70.52        63.22        11.80        35.80 
TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-YD-A89C TCGA-YD-A9TA 
       49.51        12.16        40.41        24.99         6.90        49.18 
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 

  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
              0.69               0.20 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
            220.24             369.93 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
            53.355             51.350 
[1] "0.7 - 220.2 (53.4)" "0.2 - 369.9 (51.4)"
[1] "hr=" "1.1"
D31V3, continuous
                    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           9       6      24       16       22       20
                    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        10        33         14
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  17Q GAIN MUTATED            8         10        4
  17Q GAIN WILD-TYPE         25         45       17
D31V4, multiclass
             clus
vv            17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  I OR II NOS                4                  9
  STAGE 0                    1                  6
  STAGE I                    5                 24
  STAGE IA                   2                 16
  STAGE IB                   6                 22
  STAGE II                   5                 20
  STAGE IIA                  1                 13
  STAGE IIB                  4                 15
  STAGE IIC                  5                 10
  STAGE III                  7                 33
  STAGE IIIA                 1                 14
  STAGE IIIB                 8                 25
  STAGE IIIC                10                 45
  STAGE IV                   4                 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
  17Q GAIN MUTATED      12 15 14 15
  17Q GAIN WILD-TYPE    52 58 64 55
D31V5, multiclass
       clus
vv      17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  T0+T1               12                 52
  T2                  15                 58
  T3                  14                 64
  T4                  15                 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
  17Q GAIN MUTATED    33  10  12   7
  17Q GAIN WILD-TYPE 144  55  27  38
D31V6, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  N0               33                144
  N1               10                 55
  N2               12                 27
  N3                7                 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"
D31V7, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED    59   4
  17Q GAIN WILD-TYPE 259  18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     59    4
  17Q GAIN WILD-TYPE  259   18
   clus
vv  17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  0               59                259
  1                4                 18
[1] 2 2
[1] FALSE
D31V8, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED    21  21
  17Q GAIN WILD-TYPE 113  69
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     21   21
  17Q GAIN WILD-TYPE  113   69
     clus
vv    17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  NO                21                113
  YES               21                 69
[1] 2 2
[1] FALSE
D31V9, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED    10  55
  17Q GAIN WILD-TYPE  37 264
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     10   55
  17Q GAIN WILD-TYPE   37  264
     clus
vv    17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  NO                10                 37
  YES               55                264
[1] 2 2
[1] FALSE
D31V10, continuous
D31V11, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED    26  39
  17Q GAIN WILD-TYPE 111 190
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     26   39
  17Q GAIN WILD-TYPE  111  190
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  FEMALE               26                111
  MALE                 39                190
[1] 2 2
[1] FALSE
D31V12, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED    59   6
  17Q GAIN WILD-TYPE 258  41
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     59    6
  17Q GAIN WILD-TYPE  258   41
     clus
vv    17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  NO                59                258
  YES                6                 41
[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   290
D31V13, multiclass
                           clus
vv                          17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  ASIAN                                    1                  4
  BLACK OR AFRICAN AMERICAN                1                  0
  WHITE                                   62                290
[1] 3 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   6 289
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      1   62
  17Q GAIN WILD-TYPE    6  289
                        clus
vv                       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO               62                289
[1] 2 2
[1] FALSE

Clustering(32) Variable = 18P GAIN MUTATION ANALYSIS
D32V1, survival
                    sevent
clus2                  0   1
  18P GAIN MUTATED    21  15
  18P GAIN WILD-TYPE 101 108
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                36                209 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                15                108 
$`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-DA-A95V 
      173.85        31.76       135.12        69.21        53.65        72.10 
TCGA-DA-A95X TCGA-EB-A6L9 TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A29E TCGA-EE-A29P 
       52.90        18.21        62.37        20.38         0.26        27.16 
TCGA-EE-A2GB TCGA-EE-A2GH TCGA-EE-A2GM TCGA-EE-A2MP TCGA-ER-A197 TCGA-ER-A19W 
       26.14       201.60        18.35       227.01         1.58       146.63 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A729 TCGA-FS-A1Z0 TCGA-FS-A1ZC TCGA-FS-A1ZJ 
       15.48        32.05       209.23       195.98       312.07        36.33 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-GF-A4EO TCGA-GN-A267 TCGA-GN-A26A TCGA-WE-AAA3 
       35.28         4.47         6.05        17.06         7.59        18.31 

$`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        76.34       138.67       150.61        95.51        45.07 
TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A95Y TCGA-DA-A95Z 
       64.83        58.85        30.44       225.11        14.14        12.30 
TCGA-EB-A44Q TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y 
        3.91        33.24        50.07        52.41        13.15        24.89 
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-A2GD TCGA-EE-A2GE 
      185.19       115.43        30.02        77.98       239.11        12.95 
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-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        89.26 
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-A3AE TCGA-EE-A3AF 
      124.31       122.73        64.04         4.41        54.51         6.28 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH 
       67.89       111.85        45.90         3.35       201.80        19.86 
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-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-A1A1 
       59.84        42.48       120.76        49.71        47.18        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        68.52 
TCGA-ER-A42L TCGA-FR-A44A TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FS-A1YW 
       74.47       174.21        26.20         5.65        10.06       171.78 
TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF 
       49.74         8.35        27.62        32.78        42.08        12.92 
TCGA-FS-A1ZG TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZW TCGA-FS-A1ZY 
        7.82        78.61       130.95       136.27        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-A268 TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 
      117.93        96.92        42.48       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-A690 TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1Q 
        0.20         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-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZY 
       65.42        12.69        21.90        62.89        10.95        48.39 
TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-Z2-AA3S 
        1.94        31.99        18.35        28.21        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 
             38.17              47.31 
[1] "0.3 - 312.1 (38.2)" "0.0 - 346.5 (47.3)"
[1] "hr=" "1.4"
D32V2, survival
                    sevent
clus2                  0   1
  18P GAIN MUTATED    29  25
  18P GAIN WILD-TYPE 141 162
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                54                303 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                25                162 
$`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-DA-A95V 
       25.18        77.56        36.03        20.38       207.48        72.10 
TCGA-DA-A95X TCGA-EB-A5UL TCGA-EB-A6L9 TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A29E 
       61.81        29.29        36.46        94.98        33.73        63.78 
TCGA-EE-A29L TCGA-EE-A29P TCGA-EE-A2GB TCGA-EE-A2GH TCGA-EE-A2GM TCGA-EE-A2M5 
        2.60        56.42        59.28       220.24        75.48        21.67 
TCGA-EE-A2MP TCGA-EE-A3J5 TCGA-ER-A197 TCGA-ER-A19W TCGA-ER-A3EV TCGA-ER-A3PL 
      248.65        36.95        13.94       148.18        46.98        33.21 
TCGA-FR-A3YN TCGA-FR-A729 TCGA-FS-A1YX TCGA-FS-A1Z0 TCGA-FS-A1ZC TCGA-FS-A1ZJ 
       92.98       220.80        48.59       202.65       357.37        47.38 
TCGA-FS-A1ZK TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A4F2 TCGA-GF-A4EO TCGA-GN-A267 
       23.93        53.16        26.56        50.14         7.23        64.44 
TCGA-GN-A26A TCGA-GN-A26D TCGA-HR-A2OG TCGA-WE-A8K6 TCGA-WE-AAA3 TCGA-YD-A9TA 
       32.48        48.00         0.23        17.95        21.40        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-D3-A8GV TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A1X3 
      167.70       151.53        54.67         3.65         7.10        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        76.57 
TCGA-DA-A1HY TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
      144.89       176.55        35.93       120.00        73.84        53.92 
TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 
       65.92        40.60        68.09        33.93        10.49       225.96 
TCGA-DA-A3F8 TCGA-DA-A95W TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A44R 
       15.68        25.15        14.14        13.02        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        58.92         7.04        29.82 
TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 
       27.22         8.65        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-A29G TCGA-EE-A29H TCGA-EE-A29M 
       85.08        78.97        13.97        72.07        64.64        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       115.96        59.64        39.29 
TCGA-EE-A2A6 TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GJ 
       86.14        67.43       340.14       173.79        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-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 
       81.21        44.88        94.82       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       180.39       216.66       167.90        47.54 
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        64.04        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-A3JA 
      138.81       172.18       127.20        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       134.33       152.81        31.40 
TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C 
       35.44        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        49.48 
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-A42K TCGA-ER-A42L 
       31.27        32.05       247.04        93.01        12.95       149.03 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC 
      174.21        15.72        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-A1Z4 
       36.26       104.42       216.92       228.59        20.91        28.08 
TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF 
        7.79        27.72        48.85        53.52        46.45        15.45 
TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR 
        9.70        32.75       101.26        74.73       133.55        11.41 
TCGA-FS-A1ZS TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 
      148.80        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-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 
        2.04        15.78       139.89       117.93        96.92        10.13 
TCGA-GN-A268 TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A4U9 
       62.79       121.91        39.35        10.42        48.89        22.13 
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-QB-AA9O TCGA-RP-A690 TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 
        7.23        18.05         0.20         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       101.33 
TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-A8ZY 
       58.98        70.52        63.22        11.80        35.80        49.51 
TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-YD-A89C TCGA-YG-AA3O TCGA-YG-AA3P 
       12.16        40.41        24.99         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 
            48.885             53.520 
[1] "0.2 - 357.4 (48.9)" "0.2 - 369.9 (53.5)"
[1] "hr=" "1.2"
D32V3, continuous
                    vv
clus                 I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  18P GAIN MUTATED             4       0       6        1        3        2
  18P GAIN WILD-TYPE           9       7      23       17       25       23
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  18P GAIN MUTATED           0         0         7         9          3
  18P GAIN WILD-TYPE        14        19         8        31         12
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  18P GAIN MUTATED            7          7        3
  18P GAIN WILD-TYPE         26         48       18
D32V4, multiclass
             clus
vv            18P GAIN MUTATED 18P GAIN WILD-TYPE
  I OR II NOS                4                  9
  STAGE 0                    0                  7
  STAGE I                    6                 23
  STAGE IA                   1                 17
  STAGE IB                   3                 25
  STAGE II                   2                 23
  STAGE IIA                  0                 14
  STAGE IIB                  0                 19
  STAGE IIC                  7                  8
  STAGE III                  9                 31
  STAGE IIIA                 3                 12
  STAGE IIIB                 7                 26
  STAGE IIIC                 7                 48
  STAGE IV                   3                 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 GAIN MUTATED       8 12  5 19
  18P GAIN WILD-TYPE    56 61 73 51
D32V5, multiclass
       clus
vv      18P GAIN MUTATED 18P GAIN WILD-TYPE
  T0+T1                8                 56
  T2                  12                 61
  T3                   5                 73
  T4                  19                 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
  18P GAIN MUTATED    26  13   5   8
  18P GAIN WILD-TYPE 151  52  34  37
D32V6, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  N0               26                151
  N1               13                 52
  N2                5                 34
  N3                8                 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"
D32V7, binary
                    cls
clus                   0   1
  18P GAIN MUTATED    47   3
  18P GAIN WILD-TYPE 271  19
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED     47    3
  18P GAIN WILD-TYPE  271   19
   clus
vv  18P GAIN MUTATED 18P GAIN WILD-TYPE
  0               47                271
  1                3                 19
[1] 2 2
[1] FALSE
D32V8, binary
                    cls
clus                   0   1
  18P GAIN MUTATED    17  16
  18P GAIN WILD-TYPE 117  74
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED     17   16
  18P GAIN WILD-TYPE  117   74
     clus
vv    18P GAIN MUTATED 18P GAIN WILD-TYPE
  NO                17                117
  YES               16                 74
[1] 2 2
[1] FALSE
D32V9, binary
                    cls
clus                   0   1
  18P GAIN MUTATED     5  50
  18P GAIN WILD-TYPE  42 269
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      5   50
  18P GAIN WILD-TYPE   42  269
     clus
vv    18P GAIN MUTATED 18P GAIN WILD-TYPE
  NO                 5                 42
  YES               50                269
[1] 2 2
[1] FALSE
D32V10, continuous
D32V11, binary
                    cls
clus                   0   1
  18P GAIN MUTATED    25  30
  18P GAIN WILD-TYPE 112 199
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED     25   30
  18P GAIN WILD-TYPE  112  199
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  FEMALE               25                112
  MALE                 30                199
[1] 2 2
[1] FALSE
D32V12, binary
                    cls
clus                   0   1
  18P GAIN MUTATED    51   4
  18P GAIN WILD-TYPE 266  43
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED     51    4
  18P GAIN WILD-TYPE  266   43
     clus
vv    18P GAIN MUTATED 18P GAIN WILD-TYPE
  NO                51                266
  YES                4                 43
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18P GAIN MUTATED       1                         0    53
  18P GAIN WILD-TYPE     4                         1   299
D32V13, multiclass
                           clus
vv                          18P GAIN MUTATED 18P GAIN WILD-TYPE
  ASIAN                                    1                  4
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   53                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"
D32V14, binary
                    cls
clus                   0   1
  18P GAIN MUTATED     1  53
  18P GAIN WILD-TYPE   6 298
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      1   53
  18P GAIN WILD-TYPE    6  298
                        clus
vv                       18P GAIN MUTATED 18P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO               53                298
[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 105 113
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                27                218 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                10                113 
$`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        53.65        62.37        27.16 
TCGA-EE-A2GB TCGA-EE-A2GH TCGA-EE-A2GM TCGA-EE-A2MP TCGA-ER-A197 TCGA-ER-A3PL 
       26.14       201.60        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        18.31 

$`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 
       69.21        22.85        76.34       138.67       150.61        95.51 
TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A95V 
       45.07        64.83        58.85        30.44       225.11        72.10 
TCGA-DA-A95X TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5SG TCGA-EB-A5SH 
       52.90        14.14        12.30         3.91        33.24        50.07 
TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A182 
       52.41        18.21        13.15        24.89        20.38         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-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-A2A6 TCGA-EE-A2GD TCGA-EE-A2GE 
      185.19       115.43        30.02        77.98       239.11        12.95 
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-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        89.26 
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-A3AE TCGA-EE-A3AF 
      124.31       122.73        64.04         4.41        54.51         6.28 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH 
       67.89       111.85        45.90         3.35       201.80        19.86 
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-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        47.18       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-A42L TCGA-FR-A44A TCGA-FR-A7U8 TCGA-FR-A7UA 
       68.52        15.48        74.47       174.21        26.20         5.65 
TCGA-FR-A8YC TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZD 
       10.06       171.78        49.74         8.35        27.62        32.78 
TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ 
       42.08        12.92         7.82        36.33        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        96.92        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-A690 TCGA-RP-A693 TCGA-W3-A824 
      297.01         7.23        18.05         0.20         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        65.42        12.69        21.90 
TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 
       62.89        10.95        48.39         1.94        31.99        18.35 
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 
            40.010             47.525 
[1] "1.6 - 312.1 (40.0)" "0.0 - 346.5 (47.5)"
[1] "hr=" "1.8"
D33V2, survival
                    sevent
clus2                  0   1
  18Q GAIN MUTATED    25  17
  18Q GAIN WILD-TYPE 145 170
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                42                315 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                17                170 
$`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       207.48        29.29        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       220.24        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        48.00         0.23        24.03        17.95        21.40 

$`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-D3-A8GV TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX 
      117.17       167.70       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        77.56 
TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 
       22.95        76.57       144.89        20.38       176.55        35.93 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
      120.00        73.84        53.92        65.92        40.60        68.09 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-DA-A95V TCGA-DA-A95W 
       33.93        10.49       225.96        15.68        72.10        25.15 
TCGA-DA-A95X TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH 
       61.81        14.14        13.02        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        58.92         7.04        36.46        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       115.96 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE 
       59.64        39.29        86.14        67.43       340.14       173.79 
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       180.39       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        64.04        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       134.33 
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        49.48         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-ER-A42L TCGA-FR-A44A TCGA-FR-A69P 
       93.01        46.98        12.95       149.03       174.21        15.72 
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-A1YY TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA 
      216.92       228.59        20.91        28.08         7.79        27.72 
TCGA-FS-A1ZB TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH 
       48.85        53.52        46.45        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-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 
      148.80        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-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 
        2.04        15.78       139.89       117.93        96.92        10.13 
TCGA-GN-A268 TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A4U9 
       62.79       121.91        39.35        10.42        48.89        22.13 
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-QB-AA9O TCGA-RP-A690 TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 
        7.23        18.05         0.20         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-A8ZM TCGA-WE-A8ZN 
      219.16       105.04        49.05        61.15       101.33        58.98 
TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AA9Y 
       70.52        63.22        11.80        35.80        49.51        12.16 
TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-YD-A89C TCGA-YD-A9TA TCGA-YG-AA3O TCGA-YG-AA3P 
       40.41        24.99         6.90        49.18        37.94        14.43 
TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
       27.58        96.99        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             53.260 
[1] "0.2 - 357.4 (49.4)" "0.2 - 369.9 (53.3)"
[1] "hr=" "1.5"
D33V3, continuous
                    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           9       6      24       17       26       25
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  18Q GAIN MUTATED           0         0         6         7          2
  18Q GAIN WILD-TYPE        14        19         9        33         13
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  18Q GAIN MUTATED            6          7        2
  18Q GAIN WILD-TYPE         27         48       19
D33V4, multiclass
             clus
vv            18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  I OR II NOS                4                  9
  STAGE 0                    1                  6
  STAGE I                    5                 24
  STAGE IA                   1                 17
  STAGE IB                   2                 26
  STAGE II                   0                 25
  STAGE IIA                  0                 14
  STAGE IIB                  0                 19
  STAGE IIC                  6                  9
  STAGE III                  7                 33
  STAGE IIIA                 2                 13
  STAGE IIIB                 6                 27
  STAGE IIIC                 7                 48
  STAGE IV                   2                 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
  18Q GAIN MUTATED       8 10  2 15
  18Q GAIN WILD-TYPE    56 63 76 55
D33V5, multiclass
       clus
vv      18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  T0+T1                8                 56
  T2                  10                 63
  T3                   2                 76
  T4                  15                 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
  18Q GAIN MUTATED    21  11   4   7
  18Q GAIN WILD-TYPE 156  54  35  38
D33V6, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  N0               21                156
  N1               11                 54
  N2                4                 35
  N3                7                 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"
D33V7, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED    40   2
  18Q GAIN WILD-TYPE 278  20
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED     40    2
  18Q GAIN WILD-TYPE  278   20
   clus
vv  18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  0               40                278
  1                2                 20
[1] 2 2
[1] FALSE
D33V8, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED    12  13
  18Q GAIN WILD-TYPE 122  77
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED     12   13
  18Q GAIN WILD-TYPE  122   77
     clus
vv    18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  NO                12                122
  YES               13                 77
[1] 2 2
[1] FALSE
D33V9, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED     5  39
  18Q GAIN WILD-TYPE  42 280
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      5   39
  18Q GAIN WILD-TYPE   42  280
     clus
vv    18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  NO                 5                 42
  YES               39                280
[1] 2 2
[1] FALSE
D33V10, continuous
D33V11, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED    20  24
  18Q GAIN WILD-TYPE 117 205
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED     20   24
  18Q GAIN WILD-TYPE  117  205
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  FEMALE               20                117
  MALE                 24                205
[1] 2 2
[1] FALSE
D33V12, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED    41   3
  18Q GAIN WILD-TYPE 276  44
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED     41    3
  18Q GAIN WILD-TYPE  276   44
     clus
vv    18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  NO                41                276
  YES                3                 44
[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   310
D33V13, multiclass
                           clus
vv                          18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  ASIAN                                    0                  5
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   42                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"
D33V14, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED     1  41
  18Q GAIN WILD-TYPE   6 310
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      1   41
  18Q GAIN WILD-TYPE    6  310
                        clus
vv                       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO               41                310
[1] 2 2
[1] FALSE

Clustering(34) Variable = 19P GAIN MUTATION ANALYSIS
D34V1, survival
                    sevent
clus2                  0   1
  19P GAIN MUTATED    23  21
  19P GAIN WILD-TYPE  99 102
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                44                201 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                21                102 
$`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-DA-A95V TCGA-DA-A95Z 
       66.08        43.53       124.08        69.21        72.10        12.30 
TCGA-EB-A5SH TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A29E TCGA-EE-A29P TCGA-EE-A2GH 
       50.07        24.89        62.37         0.26        27.16       201.60 
TCGA-EE-A2GO TCGA-EE-A2GS TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MM TCGA-EE-A3JI 
      118.32        71.31       103.13        15.25       145.45       152.81 
TCGA-ER-A199 TCGA-ER-A2ND TCGA-ER-A2NG TCGA-ER-A3PL TCGA-FR-A729 TCGA-FS-A1Z3 
        7.82         4.70        10.95        32.05       209.23         8.35 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZM TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZY 
      312.07        32.78        78.61       136.27         4.47         5.29 
TCGA-GN-A267 TCGA-QB-AA9O TCGA-W3-AA21 TCGA-WE-A8ZQ TCGA-WE-A8ZY TCGA-WE-AA9Y 
       17.06        18.05        92.84        62.89        48.39         1.94 
TCGA-WE-AAA3 TCGA-YG-AA3O 
       18.31        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        76.34       138.67        53.65       150.61        95.51 
TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A95X 
       45.07        64.83        58.85        30.44       225.11        52.90 
TCGA-DA-A95Y TCGA-EB-A44Q TCGA-EB-A5SG TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X 
       14.14         3.91        33.24        52.41        18.21        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-A29D TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29Q 
       76.14        12.99        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-A2GB 
      346.49       185.19       115.43        30.02        77.98        26.14 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
      239.11        12.95        68.65        10.62        32.48        18.35 
TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GU TCGA-EE-A2M8 TCGA-EE-A2MC 
       31.00         0.76         0.20        81.99         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        89.26       104.78 
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        64.04         4.41        54.51         6.28        67.89 
TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH TCGA-ER-A193 
      111.85        45.90         3.35       201.80        19.86        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        47.18       146.63        47.97        22.36 
TCGA-ER-A2NE TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A42L TCGA-FR-A44A 
       16.87       173.29        68.52        15.48        74.47       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-A1Z4 TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZQ 
       27.62        42.08        12.92         7.82        36.33       130.95 
TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 
       35.28        23.21         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-A268 
        6.05         1.91        53.29       117.93        96.92        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-A690 TCGA-RP-A693 TCGA-W3-A824 
       85.05       297.01         7.23         0.20         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-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT 
        1.15        59.64        65.42        12.69        21.90        10.95 
TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-Z2-AA3S 
       31.99        18.35        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              46.98 
[1] "0.3 - 312.1 (48.9)" "0.0 - 346.5 (47.0)"
[1] "hr=" "1.1"
D34V2, survival
                    sevent
clus2                  0   1
  19P GAIN MUTATED    29  28
  19P GAIN WILD-TYPE 141 159
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                57                300 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                28                159 
$`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        77.56 
TCGA-DA-A95V TCGA-DA-A95Z TCGA-EB-A5SH TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A29E 
       72.10        13.02        54.02        27.22        94.98        63.78 
TCGA-EE-A29L TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A2GH TCGA-EE-A2GO TCGA-EE-A2GS 
        2.60        56.42        14.47       220.24       126.81        81.21 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MM TCGA-EE-A3JI TCGA-ER-A199 TCGA-ER-A19E 
      129.27        28.83       167.90       152.81         9.17        13.02 
TCGA-ER-A2ND TCGA-ER-A2NG TCGA-ER-A3PL TCGA-FR-A729 TCGA-FS-A1YX TCGA-FS-A1Z3 
       23.34        31.27        33.21       220.80        48.59        20.91 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZM TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZY 
      357.37        53.52       101.26       148.80        26.56        27.09 
TCGA-FS-A4F2 TCGA-FS-A4F5 TCGA-FW-A3I3 TCGA-GF-A6C9 TCGA-GN-A266 TCGA-GN-A267 
       50.14        28.73         0.20        15.78        10.13        64.44 
TCGA-HR-A2OG TCGA-QB-AA9O TCGA-W3-AA21 TCGA-WE-A8ZQ TCGA-WE-A8ZX TCGA-WE-A8ZY 
        0.23        18.05       105.04        63.22        35.80        49.51 
TCGA-WE-AA9Y TCGA-WE-AAA3 TCGA-YG-AA3O 
       12.16        21.40        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-D3-A8GV TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW 
      129.63       117.17       167.70       151.53        54.67         3.65 
TCGA-D9-A1JX TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6EA 
        7.10        18.12        15.39        22.29        18.44        25.18 
TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 
       22.95        76.57        36.03       144.89        20.38       207.48 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA 
      176.55        35.93       120.00        73.84        53.92        65.92 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 
       40.60        68.09        33.93        10.49       225.96        15.68 
TCGA-DA-A95W TCGA-DA-A95X TCGA-DA-A95Y TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH 
       25.15        61.81        14.14        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        29.29        58.92         7.04        36.46        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-A29A 
      133.81       151.27        91.56       168.26        13.55        63.35 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M 
       85.08        78.97        13.97        72.07        64.64        56.84 
TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W 
       18.61        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       115.96        59.64        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       173.79        48.72       107.38 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR 
       54.74        79.66        75.48       102.12        13.91        42.77 
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-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-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR 
      180.39       216.66        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        64.04 
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       134.33        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        49.48         8.88       148.18        79.99 
TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET 
       43.82        20.15        16.37        32.05       247.04        93.01 
TCGA-ER-A3EV TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       46.98        12.95       149.03        92.98       174.21        15.72 
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-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA 
      216.92       228.59       202.65        28.08         7.79        27.72 
TCGA-FS-A1ZB TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ 
       48.85        46.45        15.45         9.70        32.75        47.38 
TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZT TCGA-FS-A1ZW 
       23.93        74.73       133.55        11.41        53.16        49.48 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB 
       27.02        77.82        66.67       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-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        9.90         7.23         2.04       139.89       117.93        96.92 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 
       62.79        32.48        48.00       121.91        39.35        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-A6FS TCGA-RP-A690 TCGA-RP-A693 TCGA-RP-A694 
      368.78       297.90         7.23         0.20         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        17.95 
TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-AAA0 TCGA-WE-AAA4 
      101.33        58.98        70.52        11.80        40.41        24.99 
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 
               0.2                0.2 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
            357.37             369.93 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
            53.520             52.255 
[1] "0.2 - 357.4 (53.5)" "0.2 - 369.9 (52.3)"
[1] "hr=" "1"  
D34V3, continuous
                    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          11       7      21       17       24       23
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  19P GAIN MUTATED           3         1         4         6          4
  19P GAIN WILD-TYPE        11        18        11        34         11
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  19P GAIN MUTATED            4         11        4
  19P GAIN WILD-TYPE         29         44       17
D34V4, multiclass
             clus
vv            19P GAIN MUTATED 19P GAIN WILD-TYPE
  I OR II NOS                2                 11
  STAGE 0                    0                  7
  STAGE I                    8                 21
  STAGE IA                   1                 17
  STAGE IB                   4                 24
  STAGE II                   2                 23
  STAGE IIA                  3                 11
  STAGE IIB                  1                 18
  STAGE IIC                  4                 11
  STAGE III                  6                 34
  STAGE IIIA                 4                 11
  STAGE IIIB                 4                 29
  STAGE IIIC                11                 44
  STAGE IV                   4                 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 12
  19P GAIN WILD-TYPE    56 60 66 58
D34V5, multiclass
       clus
vv      19P GAIN MUTATED 19P GAIN WILD-TYPE
  T0+T1                8                 56
  T2                  13                 60
  T3                  12                 66
  T4                  12                 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
  19P GAIN MUTATED    30   9   4   9
  19P GAIN WILD-TYPE 147  56  35  36
D34V6, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  N0               30                147
  N1                9                 56
  N2                4                 35
  N3                9                 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"
D34V7, binary
                    cls
clus                   0   1
  19P GAIN MUTATED    48   4
  19P GAIN WILD-TYPE 270  18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     48    4
  19P GAIN WILD-TYPE  270   18
   clus
vv  19P GAIN MUTATED 19P GAIN WILD-TYPE
  0               48                270
  1                4                 18
[1] 2 2
[1] FALSE
D34V8, binary
                    cls
clus                   0   1
  19P GAIN MUTATED    21  15
  19P GAIN WILD-TYPE 113  75
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     21   15
  19P GAIN WILD-TYPE  113   75
     clus
vv    19P GAIN MUTATED 19P GAIN WILD-TYPE
  NO                21                113
  YES               15                 75
[1] 2 2
[1] FALSE
D34V9, binary
                    cls
clus                   0   1
  19P GAIN MUTATED    10  47
  19P GAIN WILD-TYPE  37 272
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     10   47
  19P GAIN WILD-TYPE   37  272
     clus
vv    19P GAIN MUTATED 19P GAIN WILD-TYPE
  NO                10                 37
  YES               47                272
[1] 2 2
[1] FALSE
D34V10, continuous
D34V11, binary
                    cls
clus                   0   1
  19P GAIN MUTATED    25  32
  19P GAIN WILD-TYPE 112 197
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     25   32
  19P GAIN WILD-TYPE  112  197
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  FEMALE               25                112
  MALE                 32                197
[1] 2 2
[1] FALSE
D34V12, binary
                    cls
clus                   0   1
  19P GAIN MUTATED    51   5
  19P GAIN WILD-TYPE 266  42
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     51    5
  19P GAIN WILD-TYPE  266   42
     clus
vv    19P GAIN MUTATED 19P GAIN WILD-TYPE
  NO                51                266
  YES                5                 42
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  19P GAIN MUTATED       1                         0    53
  19P GAIN WILD-TYPE     4                         1   299
D34V13, multiclass
                           clus
vv                          19P GAIN MUTATED 19P GAIN WILD-TYPE
  ASIAN                                    1                  4
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   53                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"
D34V14, binary
                    cls
clus                   0   1
  19P GAIN MUTATED     1  54
  19P GAIN WILD-TYPE   6 297
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      1   54
  19P GAIN WILD-TYPE    6  297
                        clus
vv                       19P GAIN MUTATED 19P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO               54                297
[1] 2 2
[1] FALSE

Clustering(35) Variable = 19Q GAIN MUTATION ANALYSIS
D35V1, survival
                    sevent
clus2                  0   1
  19Q GAIN MUTATED    19  24
  19Q GAIN WILD-TYPE 103  99
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                43                202 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                24                 99 
$`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-DA-A95Z TCGA-EB-A5SH 
       66.08        43.53        59.70        69.21        12.30        50.07 
TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A29E TCGA-EE-A29P TCGA-EE-A29T TCGA-EE-A2GD 
       24.89        62.37         0.26        27.16       346.49       239.11 
TCGA-EE-A2GH TCGA-EE-A2GS TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A3JI TCGA-ER-A197 
      201.60        71.31       103.13        15.25       152.81         1.58 
TCGA-ER-A199 TCGA-ER-A2NG TCGA-ER-A3ET TCGA-ER-A3PL TCGA-FS-A1Z3 TCGA-FS-A1ZC 
        7.82        10.95        68.52        32.05         8.35       312.07 
TCGA-FS-A1ZD TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZY 
       32.78        78.61       130.95       136.27         4.47         5.29 
TCGA-GN-A267 TCGA-QB-AA9O TCGA-WE-A8ZQ TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA3 
       17.06        18.05        62.89        48.39         1.94        18.31 
TCGA-YG-AA3O 
       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        76.34       138.67        53.65       150.61        95.51 
TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A95V 
       45.07        64.83        58.85        30.44       225.11        72.10 
TCGA-DA-A95X TCGA-DA-A95Y TCGA-EB-A44Q TCGA-EB-A5SG TCGA-EB-A5UN TCGA-EB-A6L9 
       52.90        14.14         3.91        33.24        52.41        18.21 
TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A184 TCGA-EE-A20C TCGA-EE-A20H 
       13.15        20.38         0.00        67.50        75.55       155.90 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M 
       75.22        76.14        12.99        44.28        63.12        47.74 
TCGA-EE-A29Q TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB 
       61.12       185.19       115.43        30.02        77.98        26.14 
TCGA-EE-A2GE TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN 
       12.95        68.65        10.62        32.48        18.35        31.00 
TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GU TCGA-EE-A2M8 TCGA-EE-A2MC 
      118.32         0.76         0.20        81.99         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        89.26       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        64.04         4.41        54.51         6.28 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH 
       67.89       111.85        45.90         3.35       201.80        19.86 
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-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
      120.76        49.71        47.18       146.63        47.97        22.36 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A3ES TCGA-ER-A3EV TCGA-ER-A42L TCGA-FR-A44A 
        4.70        16.87       173.29        15.48        74.47       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-A1Z4 TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZJ 
      195.98        27.62        42.08        12.92         7.82        36.33 
TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 
       35.28        23.21         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-A268 
        6.05         1.91        53.29       117.93        96.92        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-A690 TCGA-RP-A693 TCGA-W3-A824 
       85.05       297.01         7.23         0.20         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        65.42        12.69        21.90 
TCGA-WE-A8ZT TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-Z2-AA3S 
       10.95        31.99        18.35        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 
            43.530             47.245 
[1] "0.3 - 346.5 (43.5)" "0.0 - 297.0 (47.2)"
[1] "hr=" "1.1"
D35V2, survival
                    sevent
clus2                  0   1
  19Q GAIN MUTATED    26  30
  19Q GAIN WILD-TYPE 144 157
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                56                301 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                30                157 
$`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        77.56 
TCGA-DA-A95Z TCGA-EB-A5SH TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A29E TCGA-EE-A29L 
       13.02        54.02        27.22        94.98        63.78         2.60 
TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A29T TCGA-EE-A2GD TCGA-EE-A2GH TCGA-EE-A2GS 
       56.42        14.47       369.93       340.14       220.24        81.21 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A3JI TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19E 
      129.27        28.83       152.81        13.94         9.17        13.02 
TCGA-ER-A2NG TCGA-ER-A3ET TCGA-ER-A3PL TCGA-FS-A1YX TCGA-FS-A1Z3 TCGA-FS-A1ZC 
       31.27        93.01        33.21        48.59        20.91       357.37 
TCGA-FS-A1ZD TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZY 
       53.52       101.26       133.55       148.80        26.56        27.09 
TCGA-FS-A4F5 TCGA-FW-A3I3 TCGA-GF-A6C9 TCGA-GN-A266 TCGA-GN-A267 TCGA-HR-A2OG 
       28.73         0.20        15.78        10.13        64.44         0.23 
TCGA-QB-AA9O TCGA-WE-A8JZ TCGA-WE-A8ZQ TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AA9Y 
       18.05        24.03        63.22        35.80        49.51        12.16 
TCGA-WE-AAA3 TCGA-YG-AA3O 
       21.40        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-D3-A8GV TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW 
      129.63       117.17       167.70       151.53        54.67         3.65 
TCGA-D9-A1JX TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6EA 
        7.10        18.12        15.39        22.29        18.44        25.18 
TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 
       22.95        76.57        36.03       144.89        20.38       207.48 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA 
      176.55        35.93       120.00        73.84        53.92        65.92 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 
       40.60        68.09        33.93        10.49       225.96        15.68 
TCGA-DA-A95V TCGA-DA-A95W TCGA-DA-A95X TCGA-DA-A95Y TCGA-EB-A44Q TCGA-EB-A44R 
       72.10        25.15        61.81        14.14        13.87        10.36 
TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 
       20.35        68.25        29.29        58.92         7.04        36.46 
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-A29D TCGA-EE-A29G TCGA-EE-A29H 
       63.35        85.08        78.97        13.97        72.07        64.64 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W 
       56.84        18.61        66.74        61.28        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       115.96        59.64        39.29        86.14 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
       59.28        67.43       173.79        48.72       107.38        54.74 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR 
       79.66        75.48       102.12       126.81        13.91        42.77 
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-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 
      180.39       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 
       64.04        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-ER-A193 TCGA-ER-A195 
      201.80        27.35        51.35       134.33        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        49.48         8.88       148.18        79.99 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NH TCGA-ER-A3ES 
       43.82        23.34        20.15        16.37        32.05       247.04 
TCGA-ER-A3EV TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       46.98        12.95       149.03        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        46.45        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 
       96.92        62.79        32.48        48.00       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-A690 TCGA-RP-A693 
       65.88       368.78       297.90         7.23         0.20         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-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-A8ZT TCGA-WE-AAA0 
       17.95       101.33        58.98        70.52        11.80        40.41 
TCGA-WE-AAA4 TCGA-YD-A89C TCGA-YD-A9TA TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S 
       24.99         6.90        49.18        14.43        27.58        96.99 
TCGA-Z2-AA3V 
       15.98 

  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
               0.2                0.2 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
            369.93             368.78 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
             49.05              53.19 
[1] "0.2 - 369.9 (49.0)" "0.2 - 368.8 (53.2)"
[1] "hr=" "1.1"
D35V3, continuous
                    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          10       7      24       17       25       24
                    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        13        34         10
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  19Q GAIN MUTATED            6         11        4
  19Q GAIN WILD-TYPE         27         44       17
D35V4, multiclass
             clus
vv            19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  I OR II NOS                3                 10
  STAGE 0                    0                  7
  STAGE I                    5                 24
  STAGE IA                   1                 17
  STAGE IB                   3                 25
  STAGE II                   1                 24
  STAGE IIA                  3                 11
  STAGE IIB                  2                 17
  STAGE IIC                  2                 13
  STAGE III                  6                 34
  STAGE IIIA                 5                 10
  STAGE IIIB                 6                 27
  STAGE IIIC                11                 44
  STAGE IV                   4                 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 62 66 57
D35V5, multiclass
       clus
vv      19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  T0+T1                6                 58
  T2                  11                 62
  T3                  12                 66
  T4                  13                 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
  19Q GAIN MUTATED    25  13   3   9
  19Q GAIN WILD-TYPE 152  52  36  36
D35V6, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  N0               25                152
  N1               13                 52
  N2                3                 36
  N3                9                 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"
D35V7, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED    48   4
  19Q GAIN WILD-TYPE 270  18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     48    4
  19Q GAIN WILD-TYPE  270   18
   clus
vv  19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  0               48                270
  1                4                 18
[1] 2 2
[1] FALSE
D35V8, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED    17  16
  19Q GAIN WILD-TYPE 117  74
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     17   16
  19Q GAIN WILD-TYPE  117   74
     clus
vv    19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  NO                17                117
  YES               16                 74
[1] 2 2
[1] FALSE
D35V9, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED    10  46
  19Q GAIN WILD-TYPE  37 273
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     10   46
  19Q GAIN WILD-TYPE   37  273
     clus
vv    19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  NO                10                 37
  YES               46                273
[1] 2 2
[1] FALSE
D35V10, continuous
D35V11, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED    24  32
  19Q GAIN WILD-TYPE 113 197
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     24   32
  19Q GAIN WILD-TYPE  113  197
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  FEMALE               24                113
  MALE                 32                197
[1] 2 2
[1] FALSE
D35V12, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED    47   8
  19Q GAIN WILD-TYPE 270  39
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     47    8
  19Q GAIN WILD-TYPE  270   39
     clus
vv    19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  NO                47                270
  YES                8                 39
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  19Q GAIN MUTATED       1                         0    51
  19Q GAIN WILD-TYPE     4                         1   301
D35V13, multiclass
                           clus
vv                          19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  ASIAN                                    1                  4
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   51                301
[1] 3 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  52
  19Q GAIN WILD-TYPE   6 299
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      1   52
  19Q GAIN WILD-TYPE    6  299
                        clus
vv                       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO               52                299
[1] 2 2
[1] FALSE

Clustering(36) Variable = 20P GAIN MUTATION ANALYSIS
D36V1, survival
                    sevent
clus2                 0  1
  20P GAIN MUTATED   47 53
  20P GAIN WILD-TYPE 75 70
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               100                145 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                53                 70 
$`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-DA-A95V TCGA-DA-A95Z 
       69.21       150.61        45.07       225.11        72.10        12.30 
TCGA-EB-A6L9 TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A20H TCGA-EE-A29D 
       18.21        24.89        62.37        20.38       155.90        12.99 
TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE 
      346.49       185.19       115.43        77.98        26.14        12.95 
TCGA-EE-A2GH TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GU 
      201.60        18.35        31.00       118.32         0.76        81.99 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MP TCGA-EE-A2MU TCGA-EE-A3AA 
      103.13        15.25         5.75       227.01        53.26       124.31 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-EE-A3JB 
      122.73        64.04        54.51        67.89        45.90       201.80 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19G TCGA-ER-A19L 
       19.86       152.81         7.82        53.29       151.46        99.06 
TCGA-ER-A19M TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A3EV 
       59.84       120.76        49.71        22.36         4.70        15.48 
TCGA-FR-A44A TCGA-FR-A729 TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD 
      174.21       209.23       195.98        27.62       312.07        32.78 
TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZU 
        7.82        36.33        78.61       130.95       136.27         4.47 
TCGA-FS-A1ZY TCGA-FS-A4F8 TCGA-FS-A4FD TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 
        5.29       173.19        80.68       117.93        17.06        42.48 
TCGA-GN-A26A TCGA-GN-A8LK TCGA-GN-A9SD TCGA-OD-A75X TCGA-QB-A6FS TCGA-W3-A825 
        7.59        43.23        59.41       297.01         7.23         1.97 
TCGA-W3-AA21 TCGA-WE-A8ZQ TCGA-WE-A8ZY TCGA-WE-AAA3 
       92.84        62.89        48.39        18.31 

$`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        76.34       138.67 
TCGA-DA-A1I1 TCGA-DA-A1I5 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A95X 
       53.65        95.51        64.83        58.85        30.44        52.90 
TCGA-DA-A95Y TCGA-EB-A44Q TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EE-A17X 
       14.14         3.91        33.24        50.07        52.41        13.15 
TCGA-EE-A182 TCGA-EE-A184 TCGA-EE-A20C TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E 
        0.00        67.50        75.55        75.22        76.14         0.26 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A2A2 
       44.28        63.12        47.74        27.16        61.12        30.02 
TCGA-EE-A2GD TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GR TCGA-EE-A2GS 
      239.11        68.65        10.62        32.48         0.20        71.31 
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        89.26 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AD 
      104.78       145.45        25.08       143.93        23.51         4.41 
TCGA-EE-A3AF TCGA-EE-A3J4 TCGA-EE-A3J8 TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
        6.28       111.85         3.35        14.56        34.45         1.58 
TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19H TCGA-ER-A19N 
       47.31         4.54        39.81        11.47       150.12        42.48 
TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A3ES 
       47.18       146.63        47.97        16.87        10.95       173.29 
TCGA-ER-A3ET TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FR-A8YC 
       68.52        32.05        74.47        26.20         5.65        10.06 
TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZT 
      171.78        49.74         8.35        42.08        12.92        35.28 
TCGA-FS-A1ZW TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F9 TCGA-FW-A3TU 
       23.21         3.06        30.90        66.67        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-A265 TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-LH-A9QB TCGA-QB-AA9O 
       96.92       120.53        34.49        46.92        85.05        18.05 
TCGA-RP-A690 TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A828 TCGA-W3-AA1Q TCGA-W3-AA1R 
        0.20         0.33       174.12       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        65.42        12.69 
TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-YG-AA3O 
       21.90        10.95         1.94        31.99        18.35        28.21 
TCGA-Z2-AA3S 
       91.23 

  20P GAIN MUTATED 20P GAIN WILD-TYPE 
              0.76               0.00 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
            346.49             239.11 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
            59.555             42.480 
[1] "0.8 - 346.5 (59.6)" "0.0 - 239.1 (42.5)"
[1] "hr=" "1.3"
D36V2, survival
                    sevent
clus2                  0   1
  20P GAIN MUTATED    64  77
  20P GAIN WILD-TYPE 106 110
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               141                216 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                77                110 
$`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        77.56        36.03        20.38       176.55        73.84 
TCGA-DA-A3F5 TCGA-DA-A95V TCGA-DA-A95Z TCGA-EB-A5UL TCGA-EB-A6L9 TCGA-EE-A17Y 
      225.96        72.10        13.02        29.29        36.46        27.22 
TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A20B TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29D 
       94.98        33.73       133.81       168.26        63.35        13.97 
TCGA-EE-A29R TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A5 
       14.47       369.93       195.02        17.92       115.96        39.29 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GM 
       86.14        59.28       173.79       220.24        48.72        75.48 
TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 
      102.12       126.81        13.91        94.82        21.67       129.27 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MH TCGA-EE-A2MP TCGA-EE-A2MU TCGA-EE-A3AA 
       28.83        19.76        16.96       248.65        53.26       124.31 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3J3 TCGA-EE-A3J5 TCGA-EE-A3J7 
      122.73        64.04        54.51       172.18        36.95        64.08 
TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A199 TCGA-ER-A19B 
       53.19       201.80       134.33       152.81         9.17        98.40 
TCGA-ER-A19G TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19P TCGA-ER-A19Q 
      268.93         6.44       131.51        61.05       162.08        50.89 
TCGA-ER-A19T TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A3EV TCGA-ER-A42K TCGA-FR-A3YN 
        8.88        43.82        23.34        46.98        12.95        92.98 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A8YD TCGA-FS-A1YX TCGA-FS-A1Z0 
      174.21        15.72       220.80        36.26        48.59       202.65 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZG 
       28.08         7.79        27.72       357.37        53.52         9.70 
TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZU 
       47.38        23.93       101.26       133.55       148.80        26.56 
TCGA-FS-A1ZY TCGA-FS-A4F2 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4FD TCGA-FW-A3I3 
       27.09        50.14        28.73       174.84        80.68         0.20 
TCGA-GF-A6C9 TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
       15.78       117.93        64.44        62.79        32.48        48.00 
TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A9SD TCGA-HR-A2OH TCGA-OD-A75X TCGA-QB-A6FS 
       22.13        50.10        59.41        65.88       297.90         7.23 
TCGA-W3-A825 TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K6 TCGA-WE-A8ZQ TCGA-WE-A8ZX 
       63.02       105.04        24.03        17.95        63.22        35.80 
TCGA-WE-A8ZY TCGA-WE-AAA3 TCGA-YD-A9TA 
       49.51        21.40        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-D3-A8GV TCGA-D9-A148 TCGA-D9-A149 
       29.06       129.63       117.17       167.70       151.53        54.67 
TCGA-D9-A1JW TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A4Z6 TCGA-D9-A6EG TCGA-DA-A1HV 
        3.65        18.12        15.39        18.44        22.95        76.57 
TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A1IA 
      144.89       207.48        35.93       120.00        53.92        65.92 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-DA-A95W 
       40.60        68.09        33.93        10.49        15.68        25.15 
TCGA-DA-A95X TCGA-DA-A95Y TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG 
       61.81        14.14        13.87        10.36        20.35        68.25 
TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A182 
       54.02        58.92         7.04        29.82         8.65        14.70 
TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I 
       26.89        68.15         4.96       151.27        91.56        13.55 
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-A29P TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29V 
       56.84        18.61        56.42        66.74        61.28        25.87 
TCGA-EE-A2A0 TCGA-EE-A2A2 TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GJ TCGA-EE-A2GK 
       46.82        59.64        67.43       340.14       107.38        54.74 
TCGA-EE-A2GL TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2MC TCGA-EE-A2MD 
       79.66        42.77        81.21        44.88        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       180.39 
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-A3AD TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J4 
       71.21        28.77        13.81        41.59       138.81       127.20 
TCGA-EE-A3J8 TCGA-EE-A3JD TCGA-EE-A3JE TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
       34.32        27.35        51.35        31.40        35.44        13.94 
TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F 
       50.76        77.75        48.89        12.59        13.02        26.37 
TCGA-ER-A19H TCGA-ER-A19N TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NE 
      152.35        44.05        49.48       148.18        79.99        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        93.01        33.21 
TCGA-ER-A42L TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YE 
      149.03        27.85        18.77        38.27        34.82       104.42 
TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1ZB TCGA-FS-A1ZE TCGA-FS-A1ZF 
      216.92       228.59        20.91        48.85        46.45        15.45 
TCGA-FS-A1ZH TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A1ZZ 
       32.75        74.73        11.41        53.16        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-A4EO TCGA-GF-A6C8 
       55.59        13.51        19.30         9.90         7.23         2.04 
TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 
      139.89        96.92        10.13       121.91        39.35        10.42 
TCGA-GN-A4U8 TCGA-GN-A8LL TCGA-HR-A2OG TCGA-LH-A9QB TCGA-QB-AA9O TCGA-RP-A690 
       48.89        21.37         0.23       368.78        18.05         0.20 
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       101.33 
TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 
       58.98        70.52        11.80        12.16        40.41        24.99 
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 
               0.2                0.2 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
            369.93             368.78 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
            58.060             49.265 
[1] "0.2 - 369.9 (58.1)" "0.2 - 368.8 (49.3)"
[1] "hr=" "1.1"
D36V3, continuous
                    vv
clus                 I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  20P GAIN MUTATED             8       2      17        9       14        7
  20P GAIN WILD-TYPE           5       5      12        9       14       18
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  20P GAIN MUTATED           5         3         6        18          7
  20P GAIN WILD-TYPE         9        16         9        22          8
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  20P GAIN MUTATED           15         19        6
  20P GAIN WILD-TYPE         18         36       15
D36V4, multiclass
             clus
vv            20P GAIN MUTATED 20P GAIN WILD-TYPE
  I OR II NOS                8                  5
  STAGE 0                    2                  5
  STAGE I                   17                 12
  STAGE IA                   9                  9
  STAGE IB                  14                 14
  STAGE II                   7                 18
  STAGE IIA                  5                  9
  STAGE IIB                  3                 16
  STAGE IIC                  6                  9
  STAGE III                 18                 22
  STAGE IIIA                 7                  8
  STAGE IIIB                15                 18
  STAGE IIIC                19                 36
  STAGE IV                   6                 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 30
  20P GAIN WILD-TYPE    33 38 56 40
D36V5, multiclass
       clus
vv      20P GAIN MUTATED 20P GAIN WILD-TYPE
  T0+T1               31                 33
  T2                  35                 38
  T3                  22                 56
  T4                  30                 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"
                    vv
clus                  N0  N1  N2  N3
  20P GAIN MUTATED    77  28  14  16
  20P GAIN WILD-TYPE 100  37  25  29
D36V6, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  N0               77                100
  N1               28                 37
  N2               14                 25
  N3               16                 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"
D36V7, binary
                    cls
clus                   0   1
  20P GAIN MUTATED   132   6
  20P GAIN WILD-TYPE 186  16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED    132    6
  20P GAIN WILD-TYPE  186   16
   clus
vv  20P GAIN MUTATED 20P GAIN WILD-TYPE
  0              132                186
  1                6                 16
[1] 2 2
[1] FALSE
D36V8, binary
                    cls
clus                  0  1
  20P GAIN MUTATED   58 32
  20P GAIN WILD-TYPE 76 58
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     58   32
  20P GAIN WILD-TYPE   76   58
     clus
vv    20P GAIN MUTATED 20P GAIN WILD-TYPE
  NO                58                 76
  YES               32                 58
[1] 2 2
[1] FALSE
D36V9, binary
                    cls
clus                   0   1
  20P GAIN MUTATED    16 131
  20P GAIN WILD-TYPE  31 188
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     16  131
  20P GAIN WILD-TYPE   31  188
     clus
vv    20P GAIN MUTATED 20P GAIN WILD-TYPE
  NO                16                 31
  YES              131                188
[1] 2 2
[1] FALSE
D36V10, continuous
D36V11, binary
                    cls
clus                   0   1
  20P GAIN MUTATED    57  90
  20P GAIN WILD-TYPE  80 139
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     57   90
  20P GAIN WILD-TYPE   80  139
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  FEMALE               57                 80
  MALE                 90                139
[1] 2 2
[1] FALSE
D36V12, binary
                    cls
clus                   0   1
  20P GAIN MUTATED   128  18
  20P GAIN WILD-TYPE 189  29
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED    128   18
  20P GAIN WILD-TYPE  189   29
     clus
vv    20P GAIN MUTATED 20P GAIN WILD-TYPE
  NO               128                189
  YES               18                 29
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  20P GAIN MUTATED       2                         0   142
  20P GAIN WILD-TYPE     3                         1   210
D36V13, multiclass
                           clus
vv                          20P GAIN MUTATED 20P GAIN WILD-TYPE
  ASIAN                                    2                  3
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                  142                210
[1] 3 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     2 141
  20P GAIN WILD-TYPE   5 210
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      2  141
  20P GAIN WILD-TYPE    5  210
                        clus
vv                       20P GAIN MUTATED 20P GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  5
  NOT HISPANIC OR LATINO              141                210
[1] 2 2
[1] FALSE

Clustering(37) Variable = 20Q GAIN MUTATION ANALYSIS
D37V1, survival
                    sevent
clus2                 0  1
  20Q GAIN MUTATED   62 62
  20Q GAIN WILD-TYPE 60 61
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               124                121 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                62                 61 
$`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        69.21 
TCGA-DA-A1HV TCGA-DA-A1I2 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A3F5 TCGA-DA-A95V 
       76.34       150.61        45.07        64.83       225.11        72.10 
TCGA-DA-A95Z TCGA-EB-A5SH TCGA-EB-A6L9 TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A184 
       12.30        50.07        18.21        24.89        62.37        67.50 
TCGA-EE-A20H TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29P TCGA-EE-A29T TCGA-EE-A29W 
      155.90        12.99         0.26        27.16       346.49       185.19 
TCGA-EE-A2A1 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GM 
      115.43        77.98        26.14        12.95       201.60        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-A2MG TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AA 
        5.75        94.19       227.01       143.93        53.26       124.31 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3J3 TCGA-EE-A3J7 
      122.73        64.04         4.41        54.51        67.89        45.90 
TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19B 
      201.80        19.86       152.81         1.58         7.82        53.29 
TCGA-ER-A19G TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19W 
      151.46        99.06        59.84       120.76        49.71       146.63 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NG TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A44A 
       22.36         4.70        10.95        15.48        32.05       174.21 
TCGA-FR-A729 TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZG 
      209.23       195.98        27.62       312.07        32.78         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-A1ZY TCGA-FS-A4F8 TCGA-FS-A4FD TCGA-GF-A4EO TCGA-GN-A264 TCGA-GN-A265 
        5.29       173.19        80.68         6.05       117.93        96.92 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A8LK TCGA-GN-A9SD TCGA-OD-A75X 
       17.06        42.48         7.59        43.23        59.41       297.01 
TCGA-QB-A6FS TCGA-QB-AA9O TCGA-W3-A825 TCGA-W3-AA1R TCGA-W3-AA21 TCGA-WE-A8ZM 
        7.23        18.05         1.97        79.99        92.84        65.42 
TCGA-WE-A8ZQ TCGA-WE-A8ZY TCGA-WE-AAA3 TCGA-YG-AA3O 
       62.89        48.39        18.31        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       138.67 
TCGA-DA-A1I1 TCGA-DA-A1I5 TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A95X TCGA-DA-A95Y 
       53.65        95.51        58.85        30.44        52.90        14.14 
TCGA-EB-A44Q TCGA-EB-A5SG TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A182 
        3.91        33.24        52.41        13.15        20.38         0.00 
TCGA-EE-A20C TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M 
       75.55        75.22        76.14        44.28        63.12        47.74 
TCGA-EE-A29Q TCGA-EE-A2A2 TCGA-EE-A2GD TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
       61.12        30.02       239.11        68.65        10.62        32.48 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MI TCGA-EE-A2MJ 
        0.20        71.31        23.77       209.79       171.85        63.25 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A3AF 
       89.26       104.78       145.45        25.08        23.51         6.28 
TCGA-EE-A3J4 TCGA-EE-A3J8 TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A19A 
      111.85         3.35        14.56        34.45        47.31         4.54 
TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19H TCGA-ER-A19N TCGA-ER-A19S TCGA-ER-A1A1 
       39.81        11.47       150.12        42.48        47.18        47.97 
TCGA-ER-A2NE TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A42L TCGA-FR-A7U8 TCGA-FR-A7UA 
       16.87       173.29        68.52        74.47        26.20         5.65 
TCGA-FR-A8YC TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1ZE TCGA-FS-A1ZF 
       10.06       171.78        49.74         8.35        42.08        12.92 
TCGA-FS-A1ZW TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F9 TCGA-FW-A3TU 
       23.21         3.06        30.90        66.67        13.28        55.59 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A4U3 
       11.54        19.30         9.90         1.91        53.29       120.53 
TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-LH-A9QB TCGA-RP-A690 TCGA-RP-A693 TCGA-W3-A824 
       34.49        46.92        85.05         0.20         0.33       174.12 
TCGA-W3-A828 TCGA-W3-AA1Q TCGA-W3-AA1V TCGA-W3-AA1W TCGA-WE-A8K1 TCGA-WE-A8K5 
      120.07        44.05         8.09       185.13         1.15        59.64 
TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 
       12.69        21.90        10.95         1.94        31.99        18.35 
TCGA-Z2-AA3S 
       91.23 

  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
              0.26               0.00 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
            346.49             239.11 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
            59.555             42.050 
[1] "0.3 - 346.5 (59.6)" "0.0 - 239.1 (42.0)"
[1] "hr=" "1.4"
D37V2, survival
                    sevent
clus2                 0  1
  20Q GAIN MUTATED   81 92
  20Q GAIN WILD-TYPE 89 95
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               173                184 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                92                 95 
$`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        77.56        76.57 
TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A3F5 
       36.03        20.38       176.55        73.84        65.92       225.96 
TCGA-DA-A95V TCGA-DA-A95Z TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A6L9 TCGA-EE-A17Y 
       72.10        13.02        54.02        29.29        36.46        27.22 
TCGA-EE-A180 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A20B TCGA-EE-A20H TCGA-EE-A29A 
       94.98        26.89        68.15       133.81       168.26        63.35 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29L TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A29T 
       13.97        63.78         2.60        56.42        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       115.96        39.29        86.14        59.28 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO 
      173.79       220.24        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-A2MG TCGA-EE-A2MH TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AA 
      103.20        16.96       248.65       162.48        53.26       124.31 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AG TCGA-EE-A3J3 
      122.73        64.04        28.77        54.51        41.59       172.18 
TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI 
       36.95        64.08        53.19       201.80       134.33       152.81 
TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19G TCGA-ER-A19J TCGA-ER-A19L 
       13.94         9.17        98.40       268.93         6.44       131.51 
TCGA-ER-A19M TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A2NC 
       61.05       162.08        50.89         8.88       148.18        43.82 
TCGA-ER-A2ND TCGA-ER-A2NG TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN 
       23.34        31.27        46.98        33.21        12.95        92.98 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A8YD TCGA-FS-A1YX TCGA-FS-A1Z0 
      174.21        15.72       220.80        36.26        48.59       202.65 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZG 
       28.08         7.79        27.72       357.37        53.52         9.70 
TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT 
       47.38        23.93       101.26       133.55       148.80        53.16 
TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A4F2 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4FD 
       26.56        27.09        50.14        28.73       174.84        80.68 
TCGA-FW-A3I3 TCGA-GF-A4EO TCGA-GF-A6C9 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 
        0.20         7.23        15.78       117.93        96.92        64.44 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A8LL 
       62.79        32.48        48.00        22.13        50.10        21.37 
TCGA-GN-A9SD TCGA-HR-A2OH TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O TCGA-W3-A825 
       59.41        65.88       297.90         7.23        18.05        63.02 
TCGA-W3-AA1R TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZQ 
      111.09       105.04        24.03        17.95       101.33        63.22 
TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AAA3 TCGA-YD-A9TA TCGA-YG-AA3O 
       35.80        49.51        21.40        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-D3-A8GV TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1X3 TCGA-D9-A3Z1 
      117.17       167.70        54.67         3.65        18.12        15.39 
TCGA-D9-A4Z6 TCGA-D9-A6EG TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I4 TCGA-DA-A1I5 
       18.44        22.95       144.89       207.48        35.93       120.00 
TCGA-DA-A1I8 TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 
       53.92        40.60        68.09        33.93        10.49        15.68 
TCGA-DA-A95W TCGA-DA-A95X TCGA-DA-A95Y TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH 
       25.15        61.81        14.14        13.87        10.36        20.35 
TCGA-EB-A5SG TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 
       68.25        58.92         7.04        29.82         8.65        33.73 
TCGA-EE-A182 TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29B 
       14.70         4.96       151.27        91.56        13.55        85.08 
TCGA-EE-A29C TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29Q 
       78.97        72.07        64.64        56.84        18.61        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        59.64        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-A2MI TCGA-EE-A2MJ 
       61.51        47.28       103.27       268.73       204.66        96.23 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MR 
      180.39       216.66       167.90        47.54        43.23       134.40 
TCGA-EE-A2MT TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J8 TCGA-EE-A3JD 
       71.21        13.81       138.81       127.20        34.32        27.35 
TCGA-EE-A3JE TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19C 
       51.35        31.40        35.44        50.76        77.75        48.89 
TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19H TCGA-ER-A19N TCGA-ER-A19S 
       12.59        13.02        26.37       152.35        44.05        49.48 
TCGA-ER-A1A1 TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET 
       79.99        20.15        16.37        32.05       247.04        93.01 
TCGA-ER-A42L TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YE 
      149.03        27.85        18.77        38.27        34.82       104.42 
TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1ZB TCGA-FS-A1ZE TCGA-FS-A1ZF 
      216.92       228.59        20.91        48.85        46.45        15.45 
TCGA-FS-A1ZH TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZW TCGA-FS-A1ZZ TCGA-FS-A4F0 
       32.75        74.73        11.41        49.48        27.02        77.82 
TCGA-FS-A4F4 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FW-A3R5 TCGA-FW-A3TU 
       66.67        34.03        26.73        54.41        22.92        55.59 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A266 
       13.51        19.30         9.90         2.04       139.89        10.13 
TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-HR-A2OG TCGA-LH-A9QB 
      121.91        39.35        10.42        48.89         0.23       368.78 
TCGA-RP-A690 TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A828 TCGA-W3-AA1O 
        0.20         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 
       70.52        11.80        12.16        40.41        24.99         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 
               0.2                0.2 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
            369.93             368.78 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
             58.06              48.87 
[1] "0.2 - 369.9 (58.1)" "0.2 - 368.8 (48.9)"
[1] "hr=" "1.1"
D37V3, continuous
                    vv
clus                 I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  20Q GAIN MUTATED             9       3      18       10       15       10
  20Q GAIN WILD-TYPE           4       4      11        8       13       15
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  20Q GAIN MUTATED           5         3         8        23          8
  20Q GAIN WILD-TYPE         9        16         7        17          7
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  20Q GAIN MUTATED           21         24        7
  20Q GAIN WILD-TYPE         12         31       14
D37V4, multiclass
             clus
vv            20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  I OR II NOS                9                  4
  STAGE 0                    3                  4
  STAGE I                   18                 11
  STAGE IA                  10                  8
  STAGE IB                  15                 13
  STAGE II                  10                 15
  STAGE IIA                  5                  9
  STAGE IIB                  3                 16
  STAGE IIC                  8                  7
  STAGE III                 23                 17
  STAGE IIIA                 8                  7
  STAGE IIIB                21                 12
  STAGE IIIC                24                 31
  STAGE IV                   7                 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 36
  20Q GAIN WILD-TYPE    26 33 50 34
D37V5, multiclass
       clus
vv      20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  T0+T1               38                 26
  T2                  40                 33
  T3                  28                 50
  T4                  36                 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"
                    vv
clus                 N0 N1 N2 N3
  20Q GAIN MUTATED   87 35 18 22
  20Q GAIN WILD-TYPE 90 30 21 23
D37V6, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  N0               87                 90
  N1               35                 30
  N2               18                 21
  N3               22                 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"
D37V7, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED   159   8
  20Q GAIN WILD-TYPE 159  14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED    159    8
  20Q GAIN WILD-TYPE  159   14
   clus
vv  20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  0              159                159
  1                8                 14
[1] 2 2
[1] FALSE
D37V8, binary
                    cls
clus                  0  1
  20Q GAIN MUTATED   67 39
  20Q GAIN WILD-TYPE 67 51
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     67   39
  20Q GAIN WILD-TYPE   67   51
     clus
vv    20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  NO                67                 67
  YES               39                 51
[1] 2 2
[1] FALSE
D37V9, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED    24 155
  20Q GAIN WILD-TYPE  23 164
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     24  155
  20Q GAIN WILD-TYPE   23  164
     clus
vv    20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  NO                24                 23
  YES              155                164
[1] 2 2
[1] FALSE
D37V10, continuous
D37V11, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED    67 112
  20Q GAIN WILD-TYPE  70 117
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     67  112
  20Q GAIN WILD-TYPE   70  117
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  FEMALE               67                 70
  MALE                112                117
[1] 2 2
[1] FALSE
D37V12, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED   157  21
  20Q GAIN WILD-TYPE 160  26
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED    157   21
  20Q GAIN WILD-TYPE  160   26
     clus
vv    20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  NO               157                160
  YES               21                 26
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  20Q GAIN MUTATED       2                         0   173
  20Q GAIN WILD-TYPE     3                         1   179
D37V13, multiclass
                           clus
vv                          20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  ASIAN                                    2                  3
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                  173                179
[1] 3 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     3 172
  20Q GAIN WILD-TYPE   4 179
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      3  172
  20Q GAIN WILD-TYPE    4  179
                        clus
vv                       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                  4
  NOT HISPANIC OR LATINO              172                179
[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  97 104
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                44                201 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                19                104 
$`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 
       69.21        18.21        67.50       155.90        12.99       115.43 
TCGA-EE-A2GH TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2MP TCGA-EE-A3AA TCGA-EE-A3J3 
      201.60        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 
       65.42        18.31 

$`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        76.34       138.67 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC 
       53.65       150.61        95.51        45.07        64.83        58.85 
TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A95V TCGA-DA-A95X TCGA-DA-A95Y TCGA-DA-A95Z 
       30.44       225.11        72.10        52.90        14.14        12.30 
TCGA-EB-A44Q TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y 
        3.91        33.24        50.07        52.41        13.15        24.89 
TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A20C TCGA-EE-A29B TCGA-EE-A29C 
       62.37        20.38         0.00        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-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD 
      346.49       185.19        30.02        77.98        26.14       239.11 
TCGA-EE-A2GE TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GO TCGA-EE-A2GP 
       12.95        68.65        10.62        32.48       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        89.26 
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-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J4 
      122.73        64.04         4.41        54.51         6.28       111.85 
TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 
        3.35       201.80        19.86       152.81        14.56        34.45 
TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19C TCGA-ER-A19G 
        1.58        47.31         7.82         4.54        39.81       151.46 
TCGA-ER-A19H TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W 
      150.12        59.84        42.48        49.71        47.18       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        68.52 
TCGA-ER-A3EV TCGA-ER-A42L TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FS-A1YW TCGA-FS-A1YY 
       15.48        74.47         5.65        10.06       171.78        49.74 
TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1ZC TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG 
      195.98         8.35       312.07        42.08        12.92         7.82 
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-A268 TCGA-GN-A26A TCGA-GN-A4U3 
      117.93        96.92        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-A690 TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A828 TCGA-W3-AA1Q 
       18.05         0.20         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 
       21.90        62.89        10.95        48.39         1.94        31.99 
TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-Z2-AA3S 
       18.35        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              47.18 
[1] "2.0 - 227.0 (49.6)" "0.0 - 346.5 (47.2)"
[1] "hr=" "1.4"
D38V2, survival
                    sevent
clus2                  0   1
  21Q GAIN MUTATED    34  29
  21Q GAIN WILD-TYPE 136 158
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                63                294 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                29                158 
$`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        77.56        36.46 
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       115.96        39.29       220.24        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 
       12.95        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 
       48.00        50.10        63.02       219.16        24.03        17.95 
TCGA-WE-A8ZM TCGA-WE-A8ZX TCGA-WE-AAA3 
      101.33        35.80        21.40 

$`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-D3-A8GV TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW 
      129.63       117.17       167.70       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        76.57        36.03       144.89        20.38 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
      207.48       176.55        35.93       120.00        73.84        53.92 
TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 
       65.92        40.60        68.09        33.93        10.49       225.96 
TCGA-DA-A3F8 TCGA-DA-A95V TCGA-DA-A95W TCGA-DA-A95X TCGA-DA-A95Y TCGA-DA-A95Z 
       15.68        72.10        25.15        61.81        14.14        13.02 
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        29.29 
TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 
       58.92         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        59.64        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       173.79        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       180.39       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        64.04 
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 
      134.33       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        49.48 
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-ER-A42L TCGA-FR-A69P 
       32.05       247.04        93.01        46.98       149.03        15.72 
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-A1Z7 TCGA-FS-A1ZA 
       48.59       228.59       202.65        20.91         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        46.45        15.45         9.70        32.75 
TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZT 
       23.93       101.26        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-A4F4 
       26.56        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-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        96.92        10.13        64.44 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 
       62.79        32.48       121.91        39.35        10.42        48.89 
TCGA-GN-A4U9 TCGA-GN-A8LL TCGA-GN-A9SD TCGA-HR-A2OG TCGA-HR-A2OH TCGA-LH-A9QB 
       22.13        21.37        59.41         0.23        65.88       368.78 
TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A690 TCGA-RP-A693 TCGA-RP-A694 
      297.90         7.23        18.05         0.20         0.33         0.69 
TCGA-W3-A824 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1V 
      228.16       121.08         4.01        69.07       111.09        42.08 
TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ 
      105.04        49.05        61.15        58.98        70.52        63.22 
TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-YD-A89C 
       11.80        49.51        12.16        40.41        24.99         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 

  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
               0.2                0.2 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
            248.65             369.93 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
            59.570             50.135 
[1] "0.2 - 248.7 (59.6)" "0.2 - 369.9 (50.1)"
[1] "hr=" "1.3"
D38V3, continuous
                    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           9       7      20       16       19       22
                    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        10        38         12
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  21Q GAIN MUTATED            6         14        2
  21Q GAIN WILD-TYPE         27         41       19
D38V4, multiclass
             clus
vv            21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  I OR II NOS                4                  9
  STAGE 0                    0                  7
  STAGE I                    9                 20
  STAGE IA                   2                 16
  STAGE IB                   9                 19
  STAGE II                   3                 22
  STAGE IIA                  3                 11
  STAGE IIB                  1                 18
  STAGE IIC                  5                 10
  STAGE III                  2                 38
  STAGE IIIA                 3                 12
  STAGE IIIB                 6                 27
  STAGE IIIC                14                 41
  STAGE IV                   2                 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
  21Q GAIN MUTATED      11 19 13 13
  21Q GAIN WILD-TYPE    53 54 65 57
D38V5, multiclass
       clus
vv      21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  T0+T1               11                 53
  T2                  19                 54
  T3                  13                 65
  T4                  13                 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
  21Q GAIN MUTATED    39  10   5  10
  21Q GAIN WILD-TYPE 138  55  34  35
D38V6, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  N0               39                138
  N1               10                 55
  N2                5                 34
  N3               10                 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"
D38V7, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED    61   2
  21Q GAIN WILD-TYPE 257  20
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED     61    2
  21Q GAIN WILD-TYPE  257   20
   clus
vv  21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  0               61                257
  1                2                 20
[1] 2 2
[1] FALSE
D38V8, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED    20  23
  21Q GAIN WILD-TYPE 114  67
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED     20   23
  21Q GAIN WILD-TYPE  114   67
     clus
vv    21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  NO                20                114
  YES               23                 67
[1] 2 2
[1] FALSE
D38V9, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED     8  59
  21Q GAIN WILD-TYPE  39 260
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      8   59
  21Q GAIN WILD-TYPE   39  260
     clus
vv    21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  NO                 8                 39
  YES               59                260
[1] 2 2
[1] FALSE
D38V10, continuous
D38V11, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED    26  41
  21Q GAIN WILD-TYPE 111 188
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED     26   41
  21Q GAIN WILD-TYPE  111  188
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  FEMALE               26                111
  MALE                 41                188
[1] 2 2
[1] FALSE
D38V12, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED    57   9
  21Q GAIN WILD-TYPE 260  38
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED     57    9
  21Q GAIN WILD-TYPE  260   38
     clus
vv    21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  NO                57                260
  YES                9                 38
[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   287
D38V13, multiclass
                           clus
vv                          21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  ASIAN                                    1                  4
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   65                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"
D38V14, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED     1  64
  21Q GAIN WILD-TYPE   6 287
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      1   64
  21Q GAIN WILD-TYPE    6  287
                        clus
vv                       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO               64                287
[1] 2 2
[1] FALSE

Clustering(39) Variable = 22Q GAIN MUTATION ANALYSIS
D39V1, survival
                    sevent
clus2                 0  1
  22Q GAIN MUTATED   44 40
  22Q GAIN WILD-TYPE 78 83
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                84                161 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                40                 83 
$`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        69.21 
TCGA-DA-A1HV TCGA-DA-A1I1 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A3F5 TCGA-DA-A95V 
       76.34        53.65        45.07        64.83       225.11        72.10 
TCGA-DA-A95Z TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A6L9 TCGA-EE-A17Y TCGA-EE-A180 
       12.30        33.24        50.07        18.21        24.89        62.37 
TCGA-EE-A20H TCGA-EE-A29M TCGA-EE-A29Q TCGA-EE-A29W TCGA-EE-A2GB TCGA-EE-A2GH 
      155.90        47.74        61.12       185.19        26.14       201.60 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MJ 
       18.35        31.00       118.32       103.13        15.25        63.25 
TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AD 
       25.08       143.93        53.26       124.31       122.73         4.41 
TCGA-EE-A3AE TCGA-EE-A3J7 TCGA-EE-A3JB TCGA-ER-A19C TCGA-ER-A19G TCGA-ER-A19L 
       54.51        45.90       201.80        39.81       151.46        99.06 
TCGA-ER-A19M TCGA-ER-A19W TCGA-ER-A2NG TCGA-ER-A3ET TCGA-FR-A44A TCGA-FR-A729 
       59.84       146.63        10.95        68.52       174.21       209.23 
TCGA-FR-A7UA TCGA-FS-A1YY TCGA-FS-A1ZD TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS 
        5.65        49.74        32.78        78.61       130.95       136.27 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A4FD TCGA-FW-A3TU TCGA-GN-A264 
       35.28         4.47        23.21        80.68        55.59       117.93 
TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A8LK TCGA-QB-A6FS 
       96.92        17.06        42.48         7.59        43.23         7.23 
TCGA-W3-AA1R TCGA-WE-A8K5 TCGA-WE-A8ZM TCGA-WE-A8ZY TCGA-WE-AAA3 TCGA-YG-AA3O 
       79.99        59.64        65.42        48.39        18.31        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       138.67 
TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A95X TCGA-DA-A95Y 
      150.61        95.51        58.85        30.44        52.90        14.14 
TCGA-EB-A44Q TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A184 
        3.91        52.41        13.15        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-A29P TCGA-EE-A29T TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 
       63.12        27.16       346.49       115.43        30.02        77.98 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GP 
      239.11        12.95        68.65        10.62        32.48         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-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP 
       94.19       171.85        89.26       104.78       145.45       227.01 
TCGA-EE-A2MT TCGA-EE-A3AC TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J8 
       23.51        64.04         6.28        67.89       111.85         3.35 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
       19.86       152.81        14.56        34.45         1.58        47.31 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19H TCGA-ER-A19N 
        7.82         4.54        53.29        11.47       150.12        42.48 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
      120.76        49.71        47.18        47.97        22.36         4.70 
TCGA-ER-A2NE TCGA-ER-A3ES TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A7U8 
       16.87       173.29        15.48        32.05        74.47        26.20 
TCGA-FR-A8YC TCGA-FS-A1YW TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZC 
       10.06       171.78       195.98         8.35        27.62       312.07 
TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZY TCGA-FS-A1ZZ 
       42.08        12.92         7.82        36.33         5.29         3.06 
TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FW-A3TV TCGA-FW-A5DY 
       30.90        66.67       173.19        13.28        11.54        19.30 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A4U3 TCGA-GN-A4U4 
        9.90         6.05         1.91        53.29       120.53        34.49 
TCGA-GN-A4U8 TCGA-GN-A9SD TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-AA9O TCGA-RP-A690 
       46.92        59.41        85.05       297.01        18.05         0.20 
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-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ 
      185.13        92.84         1.15        12.69        21.90        62.89 
TCGA-WE-A8ZT TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-Z2-AA3S 
       10.95         1.94        31.99        18.35        91.23 

  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
              4.41               0.00 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
            225.11             346.49 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
            53.455             42.480 
[1] "4.4 - 225.1 (53.5)" "0.0 - 346.5 (42.5)"
[1] "hr=" "1.1"
D39V2, survival
                    sevent
clus2                  0   1
  22Q GAIN MUTATED    60  62
  22Q GAIN WILD-TYPE 110 125
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
               122                235 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                62                125 
$`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        77.56        76.57        36.03        20.38       207.48 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A3F5 TCGA-DA-A95V 
       73.84        53.92        65.92        40.60       225.96        72.10 
TCGA-DA-A95Z TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A6L9 
       13.02        20.35        68.25        54.02        29.29        36.46 
TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N 
       27.22        94.98       168.26         2.60        56.84        18.61 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A5 TCGA-EE-A2GB 
       66.74        14.47       195.02        17.92        39.29        59.28 
TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2M6 
      220.24        48.72        75.48       102.12       126.81       129.27 
TCGA-EE-A2M7 TCGA-EE-A2MJ TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MU 
       28.83        96.23        43.23       134.40       162.48        53.26 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AG TCGA-EE-A3J5 
      124.31       122.73        28.77        54.51        41.59        36.95 
TCGA-EE-A3J7 TCGA-EE-A3JB TCGA-EE-A3JD TCGA-ER-A19C TCGA-ER-A19G TCGA-ER-A19L 
       64.08       201.80        27.35        48.89       268.93       131.51 
TCGA-ER-A19M TCGA-ER-A19W TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ET TCGA-FR-A3YN 
       61.05       148.18        16.37        31.27        93.01        92.98 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7UA TCGA-FS-A1YY TCGA-FS-A1Z7 
      174.21        15.72       220.80        38.27       228.59         7.79 
TCGA-FS-A1ZA TCGA-FS-A1ZD TCGA-FS-A1ZH TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS 
       27.72        53.52        32.75       101.26       133.55       148.80 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A4F2 TCGA-FS-A4F5 TCGA-FS-A4FD 
       53.16        26.56        49.48        50.14        28.73        80.68 
TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 
        0.20        55.59       117.93        96.92        64.44        62.79 
TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U7 TCGA-GN-A8LK TCGA-HR-A2OH TCGA-QB-A6FS 
       32.48        48.00        10.42        50.10        65.88         7.23 
TCGA-W3-AA1R TCGA-WE-A8JZ TCGA-WE-A8K5 TCGA-WE-A8ZM TCGA-WE-A8ZY TCGA-WE-AAA3 
      111.09        24.03        61.15       101.33        49.51        21.40 
TCGA-YD-A89C TCGA-YG-AA3O 
        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-D3-A8GV TCGA-D9-A149 TCGA-D9-A1JW 
      152.75       129.63       117.17       167.70        54.67         3.65 
TCGA-D9-A1JX TCGA-D9-A1X3 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6EG TCGA-DA-A1HY 
        7.10        18.12        22.29        18.44        22.95       144.89 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
      176.55        35.93       120.00        68.09        33.93        10.49 
TCGA-DA-A3F8 TCGA-DA-A95W TCGA-DA-A95X TCGA-DA-A95Y TCGA-EB-A44Q TCGA-EB-A44R 
       15.68        25.15        61.81        14.14        13.87        10.36 
TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 
       58.92         7.04        29.82         8.65        33.73        14.70 
TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F 
       26.89        68.15         4.96       133.81       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-A29P TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V 
       72.07        64.64        56.42        61.28       369.93        25.87 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GC TCGA-EE-A2GD 
       46.82       115.96        59.64        86.14        67.43       340.14 
TCGA-EE-A2GE TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GP TCGA-EE-A2GR 
      173.79       107.38        54.74        79.66        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-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MT 
      180.39       216.66       167.90        47.54       248.65        71.21 
TCGA-EE-A3AC TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J8 
       64.04        13.81       138.81       172.18       127.20        34.32 
TCGA-EE-A3JA TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 
       53.19        51.35       134.33       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-A19E TCGA-ER-A19F TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19N TCGA-ER-A19P 
       13.02        26.37       152.35         6.44        44.05       162.08 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
       50.89        49.48         8.88        79.99        43.82        23.34 
TCGA-ER-A2NE TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K 
       20.15        32.05       247.04        46.98        33.21        12.95 
TCGA-ER-A42L TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE 
      149.03        27.85        18.77        34.82        36.26       104.42 
TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZB 
      216.92        48.59       202.65        20.91        28.08        48.85 
TCGA-FS-A1ZC TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZK 
      357.37        46.45        15.45         9.70        47.38        23.93 
TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 
       74.73        11.41        27.09        27.02        77.82        66.67 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FW-A3R5 TCGA-FW-A3TV 
      174.84        34.03        26.73        54.41        22.92        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-A266 TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LL 
       10.13       121.91        39.35        48.89        22.13        21.37 
TCGA-GN-A9SD TCGA-HR-A2OG TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-AA9O TCGA-RP-A690 
       59.41         0.23       368.78       297.90        18.05         0.20 
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        17.95 
TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-AA9Y 
       58.98        70.52        63.22        11.80        35.80        12.16 
TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-YD-A9TA TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S 
       40.41        24.99        49.18        14.43        27.58        96.99 
TCGA-Z2-AA3V 
       15.98 

  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
               0.2                0.2 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
            268.93             369.93 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
             55.05              49.05 
[1] "0.2 - 268.9 (55.0)" "0.2 - 369.9 (49.0)"
[1] "hr=" "1"  
D39V3, continuous
                    vv
clus                 I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  22Q GAIN MUTATED             3       2      10        5        9        6
  22Q GAIN WILD-TYPE          10       5      19       13       19       19
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  22Q GAIN MUTATED           4         3         7        18          9
  22Q GAIN WILD-TYPE        10        16         8        22          6
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  22Q GAIN MUTATED           13         20        7
  22Q GAIN WILD-TYPE         20         35       14
D39V4, multiclass
             clus
vv            22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  I OR II NOS                3                 10
  STAGE 0                    2                  5
  STAGE I                   10                 19
  STAGE IA                   5                 13
  STAGE IB                   9                 19
  STAGE II                   6                 19
  STAGE IIA                  4                 10
  STAGE IIB                  3                 16
  STAGE IIC                  7                  8
  STAGE III                 18                 22
  STAGE IIIA                 9                  6
  STAGE IIIB                13                 20
  STAGE IIIC                20                 35
  STAGE IV                   7                 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 23
  22Q GAIN WILD-TYPE    39 43 55 47
D39V5, multiclass
       clus
vv      22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  T0+T1               25                 39
  T2                  30                 43
  T3                  23                 55
  T4                  23                 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
  22Q GAIN MUTATED    51  26  18  18
  22Q GAIN WILD-TYPE 126  39  21  27
D39V6, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  N0               51                126
  N1               26                 39
  N2               18                 21
  N3               18                 27
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V7, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED   106   8
  22Q GAIN WILD-TYPE 212  14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED    106    8
  22Q GAIN WILD-TYPE  212   14
   clus
vv  22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  0              106                212
  1                8                 14
[1] 2 2
[1] FALSE
D39V8, binary
                    cls
clus                  0  1
  22Q GAIN MUTATED   48 33
  22Q GAIN WILD-TYPE 86 57
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED     48   33
  22Q GAIN WILD-TYPE   86   57
     clus
vv    22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  NO                48                 86
  YES               33                 57
[1] 2 2
[1] FALSE
D39V9, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED    16 110
  22Q GAIN WILD-TYPE  31 209
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED     16  110
  22Q GAIN WILD-TYPE   31  209
     clus
vv    22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  NO                16                 31
  YES              110                209
[1] 2 2
[1] FALSE
D39V10, continuous
D39V11, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED    52  74
  22Q GAIN WILD-TYPE  85 155
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED     52   74
  22Q GAIN WILD-TYPE   85  155
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  FEMALE               52                 85
  MALE                 74                155
[1] 2 2
[1] FALSE
D39V12, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED   108  17
  22Q GAIN WILD-TYPE 209  30
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED    108   17
  22Q GAIN WILD-TYPE  209   30
     clus
vv    22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  NO               108                209
  YES               17                 30
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  22Q GAIN MUTATED       3                         0   120
  22Q GAIN WILD-TYPE     2                         1   232
D39V13, multiclass
                           clus
vv                          22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  ASIAN                                    3                  2
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                  120                232
[1] 3 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     1 122
  22Q GAIN WILD-TYPE   6 229
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      1  122
  22Q GAIN WILD-TYPE    6  229
                        clus
vv                       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO              122                229
[1] 2 2
[1] FALSE

Clustering(40) Variable = XP GAIN MUTATION ANALYSIS
D40V1, survival
                   sevent
clus2                 0   1
  XP GAIN MUTATED    10  12
  XP GAIN WILD-TYPE 112 111
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               22               223 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               12               111 
$`XP GAIN MUTATED`
TCGA-D3-A1Q3 TCGA-D3-A2JA TCGA-D3-A2JE TCGA-D3-A3CE TCGA-D3-A3MU TCGA-DA-A95V 
       15.72        15.75         9.76        59.70        23.67        72.10 
TCGA-DA-A95Z TCGA-EE-A184 TCGA-EE-A2GN TCGA-EE-A2MU TCGA-EE-A3J7 TCGA-ER-A19M 
       12.30        67.50        31.00        53.26        45.90        59.84 
TCGA-ER-A2NC TCGA-FR-A729 TCGA-FR-A8YC TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A4FD 
       22.36       209.23        10.06         4.47         5.29        80.68 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A4U3 TCGA-W3-AA1W 
      117.93        96.92       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        69.21        22.85 
TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 
       76.34       138.67        53.65       150.61        95.51        45.07 
TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A95X TCGA-DA-A95Y 
       64.83        58.85        30.44       225.11        52.90        14.14 
TCGA-EB-A44Q TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X 
        3.91        33.24        50.07        52.41        18.21        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-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       115.43 
TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
       30.02        77.98        26.14       239.11        12.95       201.60 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GO TCGA-EE-A2GP 
       68.65        10.62        32.48        18.35       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        89.26 
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-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
      124.31       122.73        64.04         4.41        54.51         6.28 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI 
       67.89       111.85         3.35       201.80        19.86       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-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 
       42.48       120.76        49.71        47.18       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        68.52        15.48 
TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A44A TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FS-A1YW 
       32.05        74.47       174.21        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-A1ZM TCGA-FS-A1ZQ 
       42.08        12.92         7.82        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-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
      173.19        13.28        55.59        11.54        19.30         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
        6.05         1.91        53.29        17.06        42.48         7.59 
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-A690 TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A825 
        7.23        18.05         0.20         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-A8K5 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT 
       59.64        65.42        12.69        21.90        62.89        10.95 
TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O 
       48.39         1.94        31.99        18.31        18.35        28.21 
TCGA-Z2-AA3S 
       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             47.18 
[1] "4.5 - 209.2 (49.6)" "0.0 - 346.5 (47.2)"
[1] "hr=" "1.2"
D40V2, survival
                   sevent
clus2                 0   1
  XP GAIN MUTATED    15  24
  XP GAIN WILD-TYPE 155 163
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               39               318 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               24               163 
$`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-DA-A95V TCGA-DA-A95Z TCGA-EB-A5KH 
       45.30        29.06        10.49        72.10        13.02        20.35 
TCGA-EE-A184 TCGA-EE-A29A TCGA-EE-A29R TCGA-EE-A2GN TCGA-EE-A2MU TCGA-EE-A3AG 
       68.15        63.35        14.47       102.12        53.26        41.59 
TCGA-EE-A3J7 TCGA-ER-A19M TCGA-ER-A2NC TCGA-FR-A3YN TCGA-FR-A729 TCGA-FR-A8YC 
       64.08        61.05        43.82        92.98       220.80        34.82 
TCGA-FR-A8YD TCGA-FS-A1ZA TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZU TCGA-FS-A1ZY 
       36.26        27.72        23.93        74.73        26.56        27.09 
TCGA-FS-A4FD TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A26D TCGA-GN-A4U3 TCGA-W3-AA1O 
       80.68       117.93        96.92        48.00       121.91         4.01 
TCGA-W3-AA1W TCGA-WE-A8K6 TCGA-YD-A89C 
      219.16        17.95         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-D3-A8GV TCGA-D9-A148 
      161.00       152.75       129.63       117.17       167.70       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        77.56        22.95        76.57 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 
       36.03       144.89        20.38       207.48       176.55        35.93 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
      120.00        73.84        53.92        65.92        40.60        68.09 
TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-DA-A95W TCGA-DA-A95X TCGA-DA-A95Y 
       33.93       225.96        15.68        25.15        61.81        14.14 
TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN 
       13.87        10.36        68.25        54.02        29.29        58.92 
TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 
        7.04        36.46        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-A20H TCGA-EE-A20I TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D 
       91.56       168.26        13.55        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-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       115.96        59.64        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       173.79       220.24        48.72 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GO TCGA-EE-A2GP 
      107.38        54.74        79.66        75.48       126.81        13.91 
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-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML 
      103.20        16.96       204.66        96.23       180.39       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-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
       71.21       124.31       122.73        64.04        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-A3JA TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI 
       53.19       201.80        27.35        51.35       134.33       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-A19N TCGA-ER-A19P TCGA-ER-A19Q 
      152.35         6.44       131.51        44.05       162.08        50.89 
TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2ND TCGA-ER-A2NE 
       49.48         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-A3EV 
       16.37        31.27        32.05       247.04        93.01        46.98 
TCGA-ER-A3PL TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A7U8 
       33.21        12.95       149.03       174.21        15.72        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-A1ZB TCGA-FS-A1ZC 
      202.65        20.91        28.08         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        46.45        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-A1ZW 
      101.26       133.55        11.41       148.80        53.16        49.48 
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-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-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-A4U4 
      139.89        10.13        64.44        62.79        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-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O 
        0.23        65.88       368.78       297.90         7.23        18.05 
TCGA-RP-A690 TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 
        0.20         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       101.33        58.98        70.52        63.22        11.80 
TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 
       35.80        49.51        12.16        40.41        21.40        24.99 
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 
            43.82             53.72 
[1] "4.0 - 220.8 (43.8)" "0.2 - 369.9 (53.7)"
[1] "hr=" "1.5"
D40V3, continuous
                   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          12       6      27       15       24       21
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  XP GAIN MUTATED           1         2         5         5          3
  XP GAIN WILD-TYPE        13        17        10        35         12
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  XP GAIN MUTATED            4          3        1
  XP GAIN WILD-TYPE         29         52       20
D40V4, multiclass
             clus
vv            XP GAIN MUTATED XP GAIN WILD-TYPE
  I OR II NOS               1                12
  STAGE 0                   1                 6
  STAGE I                   2                27
  STAGE IA                  3                15
  STAGE IB                  4                24
  STAGE II                  4                21
  STAGE IIA                 1                13
  STAGE IIB                 2                17
  STAGE IIC                 5                10
  STAGE III                 5                35
  STAGE IIIA                3                12
  STAGE IIIB                4                29
  STAGE IIIC                3                52
  STAGE IV                  1                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  7
  XP GAIN WILD-TYPE    56 64 69 63
D40V5, multiclass
       clus
vv      XP GAIN MUTATED XP GAIN WILD-TYPE
  T0+T1               8                56
  T2                  9                64
  T3                  9                69
  T4                  7                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
  XP GAIN MUTATED    22   7   6   2
  XP GAIN WILD-TYPE 155  58  33  43
D40V6, multiclass
    clus
vv   XP GAIN MUTATED XP GAIN WILD-TYPE
  N0              22               155
  N1               7                58
  N2               6                33
  N3               2                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"
D40V7, binary
                   cls
clus                  0   1
  XP GAIN MUTATED    36   1
  XP GAIN WILD-TYPE 282  21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED     36    1
  XP GAIN WILD-TYPE  282   21
   clus
vv  XP GAIN MUTATED XP GAIN WILD-TYPE
  0              36               282
  1               1                21
[1] 2 2
[1] FALSE
D40V8, binary
                   cls
clus                  0   1
  XP GAIN MUTATED    14  12
  XP GAIN WILD-TYPE 120  78
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED     14   12
  XP GAIN WILD-TYPE  120   78
     clus
vv    XP GAIN MUTATED XP GAIN WILD-TYPE
  NO               14               120
  YES              12                78
[1] 2 2
[1] FALSE
D40V9, binary
                   cls
clus                  0   1
  XP GAIN MUTATED     6  35
  XP GAIN WILD-TYPE  41 284
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED      6   35
  XP GAIN WILD-TYPE   41  284
     clus
vv    XP GAIN MUTATED XP GAIN WILD-TYPE
  NO                6                41
  YES              35               284
[1] 2 2
[1] FALSE
D40V10, continuous
D40V11, binary
                   cls
clus                  0   1
  XP GAIN MUTATED    12  29
  XP GAIN WILD-TYPE 125 200
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED     12   29
  XP GAIN WILD-TYPE  125  200
        clus
vv       XP GAIN MUTATED XP GAIN WILD-TYPE
  FEMALE              12               125
  MALE                29               200
[1] 2 2
[1] FALSE
D40V12, binary
                   cls
clus                  0   1
  XP GAIN MUTATED    38   3
  XP GAIN WILD-TYPE 279  44
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED     38    3
  XP GAIN WILD-TYPE  279   44
     clus
vv    XP GAIN MUTATED XP GAIN WILD-TYPE
  NO               38               279
  YES               3                44
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  XP GAIN MUTATED       1                         0    40
  XP GAIN WILD-TYPE     4                         1   312
D40V13, multiclass
                           clus
vv                          XP GAIN MUTATED XP GAIN WILD-TYPE
  ASIAN                                   1                 4
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  40               312
[1] 3 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  40
  XP GAIN WILD-TYPE   7 311
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED      0   40
  XP GAIN WILD-TYPE    7  311
                        clus
vv                       XP GAIN MUTATED XP GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 7
  NOT HISPANIC OR LATINO              40               311
[1] 2 2
[1] FALSE

Clustering(41) Variable = XQ GAIN MUTATION ANALYSIS
D41V1, survival
                   sevent
clus2                 0   1
  XQ GAIN MUTATED     9  16
  XQ GAIN WILD-TYPE 113 107
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               25               220 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               16               107 
$`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-DA-A95V TCGA-DA-A95Z TCGA-EE-A184 TCGA-EE-A2GN TCGA-EE-A2MU TCGA-EE-A3J7 
       72.10        12.30        67.50        31.00        53.26        45.90 
TCGA-ER-A19M TCGA-ER-A2NC TCGA-ER-A2ND TCGA-FR-A729 TCGA-FR-A8YC TCGA-FS-A1ZG 
       59.84        22.36         4.70       209.23        10.06         7.82 
TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A4FD TCGA-FW-A3TV TCGA-GN-A264 TCGA-GN-A268 
        4.47         5.29        80.68        11.54       117.93        42.48 
TCGA-WE-A8ZT 
       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        69.21        22.85        76.34 
TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA 
      138.67        53.65       150.61        95.51        45.07        64.83 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A95X TCGA-DA-A95Y TCGA-EB-A44Q 
       58.85        30.44       225.11        52.90        14.14         3.91 
TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y 
       33.24        50.07        52.41        18.21        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       115.43        30.02 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ 
       77.98        26.14       239.11        12.95       201.60        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        89.26       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        64.04         4.41        54.51         6.28        67.89 
TCGA-EE-A3J4 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 
      111.85         3.35       201.80        19.86       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-A19C TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19N 
       39.81        11.47       151.46       150.12        99.06        42.48 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NE 
      120.76        49.71        47.18       146.63        47.97        16.87 
TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42L 
       10.95       173.29        68.52        15.48        32.05        74.47 
TCGA-FR-A44A TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 
      174.21        26.20         5.65       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        42.08        12.92 
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-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A265 
       19.30         9.90         6.05         1.91        53.29        96.92 
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-A690 
       59.41        85.05       297.01         7.23        18.05         0.20 
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        65.42 
TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 
       12.69        21.90        62.89        48.39         1.94        31.99 
TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-Z2-AA3S 
       18.31        18.35        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 
            23.67             48.18 
[1] "4.5 - 209.2 (23.7)" "0.0 - 346.5 (48.2)"
[1] "hr=" "2"  
D41V2, survival
                   sevent
clus2                 0   1
  XQ GAIN MUTATED    15  27
  XQ GAIN WILD-TYPE 155 160
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               42               315 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               27               160 
$`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-DA-A95V TCGA-DA-A95Z 
       39.75        45.30        29.06        10.49        72.10        13.02 
TCGA-EB-A5KH TCGA-EE-A184 TCGA-EE-A29A TCGA-EE-A29R TCGA-EE-A2GN TCGA-EE-A2MU 
       20.35        68.15        63.35        14.47       102.12        53.26 
TCGA-EE-A3AG TCGA-EE-A3J7 TCGA-ER-A19M TCGA-ER-A2NC TCGA-ER-A2ND TCGA-FR-A3YN 
       41.59        64.08        61.05        43.82        23.34        92.98 
TCGA-FR-A729 TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FS-A1ZG TCGA-FS-A1ZK TCGA-FS-A1ZP 
      220.80        34.82        36.26         9.70        23.93        74.73 
TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A4FD TCGA-FW-A3TV TCGA-GF-A6C9 TCGA-GN-A264 
       26.56        27.09        80.68        13.51        15.78       117.93 
TCGA-GN-A268 TCGA-GN-A26D TCGA-W3-AA1O TCGA-WE-A8K6 TCGA-WE-A8ZT TCGA-YD-A89C 
       62.79        48.00         4.01        17.95        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-D3-A8GV TCGA-D9-A148 TCGA-D9-A149 
      152.75       129.63       117.17       167.70       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        77.56        22.95        76.57        36.03 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
      144.89        20.38       207.48       176.55        35.93       120.00 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
       73.84        53.92        65.92        40.60        68.09        33.93 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-DA-A95W TCGA-DA-A95X TCGA-DA-A95Y TCGA-EB-A44Q 
      225.96        15.68        25.15        61.81        14.14        13.87 
TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV 
       10.36        68.25        54.02        29.29        58.92         7.04 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 
       36.46        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-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
      168.26        13.55        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-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-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
       46.82       115.96        59.64        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       173.79       220.24        48.72       107.38 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR 
       54.74        79.66        75.48       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-A2MG 
       19.76        61.51        47.28       103.27       268.73       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       180.39       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-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
      124.31       122.73        64.04        28.77        54.51        13.81 
TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J8 TCGA-EE-A3JA 
      138.81       172.18       127.20        36.95        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       134.33       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-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S 
        6.44       131.51        44.05       162.08        50.89        49.48 
TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
        8.88       148.18        79.99        20.15        16.37        31.27 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K 
       32.05       247.04        93.01        46.98        33.21        12.95 
TCGA-ER-A42L TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA 
      149.03       174.21        15.72        27.85        18.77        38.27 
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-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ 
       46.45        15.45        32.75        47.38       101.26       133.55 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A1ZZ TCGA-FS-A4F0 
       11.41       148.80        53.16        49.48        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-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A5DY TCGA-GF-A3OT 
       54.41         0.20        22.92        55.59        19.30         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 
        7.23         2.04       139.89        96.92        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-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-QB-AA9O TCGA-RP-A690 TCGA-RP-A693 TCGA-RP-A694 
      297.90         7.23        18.05         0.20         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       101.33 
TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AA9Y 
       58.98        70.52        63.22        35.80        49.51        12.16 
TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YD-A9TA TCGA-YG-AA3O TCGA-YG-AA3P 
       40.41        21.40        24.99        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 
           38.005            54.410 
[1] "4.0 - 220.8 (38.0)" "0.2 - 369.9 (54.4)"
[1] "hr=" "1.9"
D41V3, continuous
                   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          13       6      27       15       24       22
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  XQ GAIN MUTATED           1         3         5         5          4
  XQ GAIN WILD-TYPE        13        16        10        35         11
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  XQ GAIN MUTATED            4          5        2
  XQ GAIN WILD-TYPE         29         50       19
D41V4, multiclass
             clus
vv            XQ GAIN MUTATED XQ GAIN WILD-TYPE
  I OR II NOS               0                13
  STAGE 0                   1                 6
  STAGE I                   2                27
  STAGE IA                  3                15
  STAGE IB                  4                24
  STAGE II                  3                22
  STAGE IIA                 1                13
  STAGE IIB                 3                16
  STAGE IIC                 5                10
  STAGE III                 5                35
  STAGE IIIA                4                11
  STAGE IIIB                4                29
  STAGE IIIC                5                50
  STAGE IV                  2                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  8
  XQ GAIN WILD-TYPE    54 64 69 62
D41V5, multiclass
       clus
vv      XQ GAIN MUTATED XQ GAIN WILD-TYPE
  T0+T1              10                54
  T2                  9                64
  T3                  9                69
  T4                  8                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
  XQ GAIN MUTATED    21   8   7   3
  XQ GAIN WILD-TYPE 156  57  32  42
D41V6, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  N0              21               156
  N1               8                57
  N2               7                32
  N3               3                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"
D41V7, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED    37   2
  XQ GAIN WILD-TYPE 281  20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     37    2
  XQ GAIN WILD-TYPE  281   20
   clus
vv  XQ GAIN MUTATED XQ GAIN WILD-TYPE
  0              37               281
  1               2                20
[1] 2 2
[1] FALSE
D41V8, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED    15  13
  XQ GAIN WILD-TYPE 119  77
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     15   13
  XQ GAIN WILD-TYPE  119   77
     clus
vv    XQ GAIN MUTATED XQ GAIN WILD-TYPE
  NO               15               119
  YES              13                77
[1] 2 2
[1] FALSE
D41V9, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED     6  37
  XQ GAIN WILD-TYPE  41 282
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      6   37
  XQ GAIN WILD-TYPE   41  282
     clus
vv    XQ GAIN MUTATED XQ GAIN WILD-TYPE
  NO                6                41
  YES              37               282
[1] 2 2
[1] FALSE
D41V10, continuous
D41V11, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED    16  27
  XQ GAIN WILD-TYPE 121 202
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     16   27
  XQ GAIN WILD-TYPE  121  202
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  FEMALE              16               121
  MALE                27               202
[1] 2 2
[1] FALSE
D41V12, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED    41   2
  XQ GAIN WILD-TYPE 276  45
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     41    2
  XQ GAIN WILD-TYPE  276   45
     clus
vv    XQ GAIN MUTATED XQ GAIN WILD-TYPE
  NO               41               276
  YES               2                45
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  XQ GAIN MUTATED       1                         0    42
  XQ GAIN WILD-TYPE     4                         1   310
D41V13, multiclass
                           clus
vv                          XQ GAIN MUTATED XQ GAIN WILD-TYPE
  ASIAN                                   1                 4
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  42               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"
D41V14, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED     0  42
  XQ GAIN WILD-TYPE   7 309
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      0   42
  XQ GAIN WILD-TYPE    7  309
                        clus
vv                       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 7
  NOT HISPANIC OR LATINO              42               309
[1] 2 2
[1] FALSE

Clustering(42) Variable = 1P LOSS MUTATION ANALYSIS
D42V1, survival
                   sevent
clus2                 0   1
  1P LOSS MUTATED    21  17
  1P LOSS WILD-TYPE 101 106
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               38               207 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               17               106 
$`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-A95V TCGA-EE-A20H TCGA-EE-A2GE 
      150.61        45.07       225.11        72.10       155.90        12.95 
TCGA-EE-A2GH TCGA-EE-A2GO TCGA-EE-A2GR TCGA-EE-A2MK TCGA-EE-A2MP TCGA-EE-A2MS 
      201.60       118.32         0.20        89.26       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        65.42        62.89 
TCGA-WE-AA9Y TCGA-WE-AAA3 
        1.94        18.31 

$`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        69.21        22.85        76.34 
TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I5 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 
      138.67        53.65        95.51        64.83        58.85        30.44 
TCGA-DA-A95X TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5SG TCGA-EB-A5SH 
       52.90        14.14        12.30         3.91        33.24        50.07 
TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A181 
       52.41        18.21        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       115.43        30.02        77.98        26.14 
TCGA-EE-A2GD TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN 
      239.11        68.65        10.62        32.48        18.35        31.00 
TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 
        0.76        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-A2ML 
       23.77       209.79        94.19       171.85        63.25       104.78 
TCGA-EE-A2MM TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB 
      145.45        25.08        23.51        53.26       124.31       122.73 
TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 
       64.04        54.51         6.28       111.85        45.90         3.35 
TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A199 
      201.80        19.86       152.81        34.45        47.31         7.82 
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-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
      120.76        49.71        47.18       146.63        47.97        22.36 
TCGA-ER-A2NE TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A44A 
       16.87       173.29        68.52        32.05        74.47       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        42.08 
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-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F9 
        4.47         5.29         3.06        30.90        66.67        13.28 
TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 
       80.68        55.59        19.30         9.90         6.05         1.91 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
       53.29       117.93        96.92        17.06        42.48         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-RP-A690 TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A825 
      297.01         7.23         0.20         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        21.90        10.95        48.39        31.99 
TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-Z2-AA3S 
       18.35        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 
            39.91             47.97 
[1] "0.2 - 227.0 (39.9)" "0.0 - 346.5 (48.0)"
[1] "hr=" "1.2"
D42V2, survival
                   sevent
clus2                 0   1
  1P LOSS MUTATED    30  22
  1P LOSS WILD-TYPE 140 165
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               52               305 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               22               165 
$`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        73.84        53.92 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-DA-A95V TCGA-EB-A44R TCGA-EE-A20H TCGA-EE-A29R 
      225.96        15.68        72.10        10.36       168.26        14.47 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GO TCGA-EE-A2GR TCGA-EE-A2MK TCGA-EE-A2MP 
      173.79       220.24       126.81        42.77       180.39       248.65 
TCGA-EE-A2MS TCGA-EE-A3AD TCGA-EE-A3J3 TCGA-ER-A193 TCGA-ER-A197 TCGA-ER-A19C 
      162.48        28.77       172.18        31.40        13.94        48.89 
TCGA-ER-A19D TCGA-ER-A19L TCGA-ER-A2ND TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3EV 
       12.59       131.51        23.34        31.27        32.05        46.98 
TCGA-FR-A69P TCGA-FR-A7U9 TCGA-FS-A1Z7 TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A4F8 
       15.72        18.77         7.79        53.16        49.48       174.84 
TCGA-FW-A3TV TCGA-GN-A26D TCGA-QB-AA9O TCGA-WE-A8K5 TCGA-WE-A8ZM TCGA-WE-A8ZQ 
       13.51        48.00        18.05        61.15       101.33        63.22 
TCGA-WE-AA9Y TCGA-WE-AAA3 TCGA-YD-A89C TCGA-YG-AA3P 
       12.16        21.40         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-D3-A8GV 
      161.00       152.75        29.06       129.63       117.17       167.70 
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-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW 
        9.90        25.18        77.56        22.95        76.57        36.03 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1IA 
      144.89        20.38       207.48        35.93       120.00        65.92 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A95W TCGA-DA-A95X 
       40.60        68.09        33.93        10.49        25.15        61.81 
TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH 
       14.14        13.02        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 
       29.29        58.92         7.04        36.46        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-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-A2A1 
      369.93        25.87       195.02        17.92        46.82       115.96 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD 
       59.64        39.29        86.14        59.28        67.43       340.14 
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-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-A2MJ TCGA-EE-A2ML TCGA-EE-A2MM 
      103.20        16.96       204.66        96.23       216.66       167.90 
TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA 
       47.54        43.23       134.40        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        64.04        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-A198 
       27.35        51.35       134.33       152.81        35.44        50.76 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G 
        9.17        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-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE 
       49.48         8.88       148.18        79.99        43.82        20.15 
TCGA-ER-A2NF TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3PL TCGA-ER-A42K TCGA-ER-A42L 
       16.37       247.04        93.01        33.21        12.95       149.03 
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 
       46.45        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        96.92        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-A690 TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 
      297.90         7.23         0.20         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-A8K6 TCGA-WE-A8ZN 
      219.16       105.04        24.03        49.05        17.95        58.98 
TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AAA0 TCGA-WE-AAA4 
       70.52        11.80        35.80        49.51        40.41        24.99 
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 

  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 
            47.49             54.02 
[1] "6.9 - 248.7 (47.5)" "0.2 - 369.9 (54.0)"
[1] "hr=" "1.3"
D42V3, continuous
                   vv
clus                I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  1P LOSS MUTATED             0       0       8        1        2        3
  1P LOSS WILD-TYPE          13       7      21       17       26       22
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  1P LOSS MUTATED           1         2         4         7          0
  1P LOSS WILD-TYPE        13        17        11        33         15
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  1P LOSS MUTATED            8         12        2
  1P LOSS WILD-TYPE         25         43       19
D42V4, multiclass
             clus
vv            1P LOSS MUTATED 1P LOSS WILD-TYPE
  I OR II NOS               0                13
  STAGE 0                   0                 7
  STAGE I                   8                21
  STAGE IA                  1                17
  STAGE IB                  2                26
  STAGE II                  3                22
  STAGE IIA                 1                13
  STAGE IIB                 2                17
  STAGE IIC                 4                11
  STAGE III                 7                33
  STAGE IIIA                0                15
  STAGE IIIB                8                25
  STAGE IIIC               12                43
  STAGE IV                  2                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
  1P LOSS MUTATED      10 14  8 15
  1P LOSS WILD-TYPE    54 59 70 55
D42V5, multiclass
       clus
vv      1P LOSS MUTATED 1P LOSS WILD-TYPE
  T0+T1              10                54
  T2                 14                59
  T3                  8                70
  T4                 15                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
  1P LOSS MUTATED    21  11   9   8
  1P LOSS WILD-TYPE 156  54  30  37
D42V6, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  N0              21               156
  N1              11                54
  N2               9                30
  N3               8                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"
D42V7, binary
                   cls
clus                  0   1
  1P LOSS MUTATED    45   2
  1P LOSS WILD-TYPE 273  20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     45    2
  1P LOSS WILD-TYPE  273   20
   clus
vv  1P LOSS MUTATED 1P LOSS WILD-TYPE
  0              45               273
  1               2                20
[1] 2 2
[1] FALSE
D42V8, binary
                   cls
clus                  0   1
  1P LOSS MUTATED    17  16
  1P LOSS WILD-TYPE 117  74
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     17   16
  1P LOSS WILD-TYPE  117   74
     clus
vv    1P LOSS MUTATED 1P LOSS WILD-TYPE
  NO               17               117
  YES              16                74
[1] 2 2
[1] FALSE
D42V9, binary
                   cls
clus                  0   1
  1P LOSS MUTATED     4  49
  1P LOSS WILD-TYPE  43 270
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      4   49
  1P LOSS WILD-TYPE   43  270
     clus
vv    1P LOSS MUTATED 1P LOSS WILD-TYPE
  NO                4                43
  YES              49               270
[1] 2 2
[1] FALSE
D42V10, continuous
D42V11, binary
                   cls
clus                  0   1
  1P LOSS MUTATED    23  30
  1P LOSS WILD-TYPE 114 199
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     23   30
  1P LOSS WILD-TYPE  114  199
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  FEMALE              23               114
  MALE                30               199
[1] 2 2
[1] FALSE
D42V12, binary
                   cls
clus                  0   1
  1P LOSS MUTATED    48   5
  1P LOSS WILD-TYPE 269  42
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     48    5
  1P LOSS WILD-TYPE  269   42
     clus
vv    1P LOSS MUTATED 1P LOSS WILD-TYPE
  NO               48               269
  YES               5                42
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  1P LOSS MUTATED       1                         0    50
  1P LOSS WILD-TYPE     4                         1   302
D42V13, multiclass
                           clus
vv                          1P LOSS MUTATED 1P LOSS WILD-TYPE
  ASIAN                                   1                 4
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  50               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"
D42V14, binary
                   cls
clus                  0   1
  1P LOSS MUTATED     1  52
  1P LOSS WILD-TYPE   6 299
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      1   52
  1P LOSS WILD-TYPE    6  299
                        clus
vv                       1P LOSS MUTATED 1P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 6
  NOT HISPANIC OR LATINO              52               299
[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 112 113
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               20               225 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               10               113 
$`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        45.07 
TCGA-DA-A95V TCGA-EE-A20H TCGA-EE-A2M6 TCGA-EE-A2MP TCGA-EE-A3J3 TCGA-ER-A193 
       72.10       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 
       62.89        18.31 

$`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        69.21 
TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I5 TCGA-DA-A1IA 
       22.85        76.34       138.67        53.65        95.51        64.83 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A95X TCGA-DA-A95Y TCGA-DA-A95Z 
       58.85        30.44       225.11        52.90        14.14        12.30 
TCGA-EB-A44Q TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X 
        3.91        33.24        50.07        52.41        18.21        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       115.43 
TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
       30.02        77.98        26.14       239.11        12.95       201.60 
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-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-A2MJ TCGA-EE-A2MK 
       23.77       209.79        94.19       171.85        63.25        89.26 
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-A3AE TCGA-EE-A3AF 
      124.31       122.73        64.04         4.41        54.51         6.28 
TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI 
      111.85        45.90         3.35       201.80        19.86       152.81 
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        47.18       146.63        47.97        22.36 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3PL TCGA-ER-A42L 
        4.70        16.87       173.29        68.52        32.05        74.47 
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 
       42.08        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-A3TU TCGA-FW-A3TV 
       30.90        66.67        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 
       96.92        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-A690 TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1Q 
        0.20         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        65.42 
TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 
       12.69        21.90        10.95        48.39         1.94        31.99 
TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-Z2-AA3S 
       18.35        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 
            42.54             47.31 
[1] "8.1 - 227.0 (42.5)" "0.0 - 346.5 (47.3)"
[1] "hr=" "1.1"
D43V2, survival
                   sevent
clus2                 0   1
  1Q LOSS MUTATED    15  13
  1Q LOSS WILD-TYPE 155 174
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               28               329 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               13               174 
$`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-DA-A95V TCGA-EE-A20H 
      176.55        73.84        53.92        15.68        72.10       168.26 
TCGA-EE-A29X TCGA-EE-A2M6 TCGA-EE-A2MP TCGA-EE-A3J3 TCGA-ER-A193 TCGA-ER-A19C 
       17.92       129.27       248.65       172.18        31.40        48.89 
TCGA-ER-A2NG TCGA-ER-A3EV TCGA-FR-A69P TCGA-FR-A7U9 TCGA-FS-A4F8 TCGA-QB-AA9O 
       31.27        46.98        15.72        18.77       174.84        18.05 
TCGA-W3-AA1V TCGA-WE-A8ZQ TCGA-WE-AAA3 TCGA-YD-A89C 
       42.08        63.22        21.40         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-D3-A8GV TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW 
      129.63       117.17       167.70       151.53        54.67         3.65 
TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC 
        7.10        15.39        22.29         9.90        25.18        77.56 
TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 
       22.95        76.57        36.03       144.89        20.38       207.48 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
       35.93       120.00        65.92        40.60        68.09        33.93 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A95W TCGA-DA-A95X TCGA-DA-A95Y TCGA-DA-A95Z 
       10.49       225.96        25.15        61.81        14.14        13.02 
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        29.29 
TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
       58.92         7.04        36.46        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-A29A TCGA-EE-A29B 
      133.81       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-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-A29R TCGA-EE-A29S 
       56.84        18.61        56.42        66.74        14.47        61.28 
TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
      369.93        25.87       195.02        46.82       115.96        59.64 
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       173.79 
TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
      220.24        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-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-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 
      180.39       216.66       167.90        47.54        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        64.04 
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-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-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
       51.35       134.33       152.81        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-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 
      162.08        50.89        49.48         8.88       148.18        79.99 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NH TCGA-ER-A3ES 
       43.82        23.34        20.15        16.37        32.05       247.04 
TCGA-ER-A3ET TCGA-ER-A3PL TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A 
       93.01        33.21        12.95       149.03        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        46.45 
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        96.92        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        48.00       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-A690 
        0.23        65.88       368.78       297.90         7.23         0.20 
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-AA1W TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K1 
       69.07       111.09       219.16       105.04        24.03        49.05 
TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT 
       61.15        17.95       101.33        58.98        70.52        11.80 
TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-YD-A9TA 
       35.80        49.51        12.16        40.41        24.99        49.18 
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 

  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 
            44.53             53.26 
[1] "6.9 - 248.7 (44.5)" "0.2 - 369.9 (53.3)"
[1] "hr=" "1.1"
D43V3, continuous
                   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          13       7      24       17       26       24
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  1Q LOSS MUTATED           1         1         3         3          0
  1Q LOSS WILD-TYPE        13        18        12        37         15
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  1Q LOSS MUTATED            3          6        1
  1Q LOSS WILD-TYPE         30         49       20
D43V4, multiclass
             clus
vv            1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  I OR II NOS               0                13
  STAGE 0                   0                 7
  STAGE I                   5                24
  STAGE IA                  1                17
  STAGE IB                  2                26
  STAGE II                  1                24
  STAGE IIA                 1                13
  STAGE IIB                 1                18
  STAGE IIC                 3                12
  STAGE III                 3                37
  STAGE IIIA                0                15
  STAGE IIIB                3                30
  STAGE IIIC                6                49
  STAGE IV                  1                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
  1Q LOSS MUTATED       6  6  6  8
  1Q LOSS WILD-TYPE    58 67 72 62
D43V5, multiclass
       clus
vv      1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  T0+T1               6                58
  T2                  6                67
  T3                  6                72
  T4                  8                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
  1Q LOSS MUTATED    13   3   6   4
  1Q LOSS WILD-TYPE 164  62  33  41
D43V6, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  N0              13               164
  N1               3                62
  N2               6                33
  N3               4                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"
D43V7, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED    24   1
  1Q LOSS WILD-TYPE 294  21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED     24    1
  1Q LOSS WILD-TYPE  294   21
   clus
vv  1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  0              24               294
  1               1                21
[1] 2 2
[1] FALSE
D43V8, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED     9   9
  1Q LOSS WILD-TYPE 125  81
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      9    9
  1Q LOSS WILD-TYPE  125   81
     clus
vv    1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  NO                9               125
  YES               9                81
[1] 2 2
[1] FALSE
D43V9, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED     3  25
  1Q LOSS WILD-TYPE  44 294
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      3   25
  1Q LOSS WILD-TYPE   44  294
     clus
vv    1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  NO                3                44
  YES              25               294
[1] 2 2
[1] FALSE
D43V10, continuous
D43V11, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED    11  17
  1Q LOSS WILD-TYPE 126 212
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED     11   17
  1Q LOSS WILD-TYPE  126  212
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  FEMALE              11               126
  MALE                17               212
[1] 2 2
[1] FALSE
D43V12, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED    26   2
  1Q LOSS WILD-TYPE 291  45
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED     26    2
  1Q LOSS WILD-TYPE  291   45
     clus
vv    1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  NO               26               291
  YES               2                45
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  1Q LOSS MUTATED       0                         0    27
  1Q LOSS WILD-TYPE     5                         1   325
D43V13, multiclass
                           clus
vv                          1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  ASIAN                                   0                 5
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  27               325
[1] 3 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  28
  1Q LOSS WILD-TYPE   7 323
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      0   28
  1Q LOSS WILD-TYPE    7  323
                        clus
vv                       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 7
  NOT HISPANIC OR LATINO              28               323
[1] 2 2
[1] FALSE

Clustering(44) Variable = 2P LOSS MUTATION ANALYSIS
D44V1, survival
                   sevent
clus2                 0   1
  2P LOSS MUTATED    13  20
  2P LOSS WILD-TYPE 109 103
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               33               212 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               20               103 
$`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-DA-A95V 
       11.34        70.62        10.78        16.90       150.61        72.10 
TCGA-EE-A180 TCGA-EE-A29P TCGA-EE-A2GH TCGA-EE-A2GR TCGA-EE-A2MJ TCGA-EE-A2MK 
       62.37        27.16       201.60         0.20        63.25        89.26 
TCGA-EE-A2MS TCGA-EE-A3AD TCGA-EE-A3J3 TCGA-ER-A19C TCGA-ER-A19P TCGA-ER-A3PL 
      143.93         4.41        67.89        39.81       120.76        32.05 
TCGA-FR-A8YC TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-GN-A264 TCGA-GN-A267 
       10.06       171.78        49.74       195.98       117.93        17.06 
TCGA-OD-A75X TCGA-W3-AA21 TCGA-WE-AA9Y 
      297.01        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        69.21 
TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I5 TCGA-DA-A1I7 
       22.85        76.34       138.67        53.65        95.51        45.07 
TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A95X TCGA-DA-A95Y 
       64.83        58.85        30.44       225.11        52.90        14.14 
TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A6L9 
       12.30         3.91        33.24        50.07        52.41        18.21 
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-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-A29M TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 
       63.12        47.74        61.12       346.49       185.19       115.43 
TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GJ 
       30.02        77.98        26.14       239.11        12.95        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-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-A2ML TCGA-EE-A2MM TCGA-EE-A2MP 
      209.79        94.19       171.85       104.78       145.45       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        64.04 
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-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
       19.86       152.81        14.56        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-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W 
       99.06        59.84        42.48        49.71        47.18       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-A42L TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7U8 
       68.52        15.48        74.47       174.21       209.23        26.20 
TCGA-FR-A7UA TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE 
        5.65         8.35        27.62       312.07        32.78        42.08 
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-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-A265 
       19.30         9.90         6.05         1.91        53.29        96.92 
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-QB-A6FS TCGA-QB-AA9O TCGA-RP-A690 TCGA-RP-A693 
       59.41        85.05         7.23        18.05         0.20         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-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO 
      185.13         1.15        59.64        65.42        12.69        21.90 
TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 
       62.89        10.95        48.39        31.99        18.31        18.35 
TCGA-YG-AA3O TCGA-Z2-AA3S 
       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 
           63.250            45.945 
[1] "0.2 - 297.0 (63.2)" "0.0 - 346.5 (45.9)"
[1] "hr=" "1"  
D44V2, survival
                   sevent
clus2                 0   1
  2P LOSS MUTATED    22  25
  2P LOSS WILD-TYPE 148 162
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               47               310 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               25               162 
$`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-DA-A95V TCGA-EE-A180 TCGA-EE-A20B 
       22.29        25.18       176.55        72.10        94.98       133.81 
TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29P TCGA-EE-A2GC TCGA-EE-A2GH TCGA-EE-A2GR 
       91.56        13.55        56.42        67.43       220.24        42.77 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2MS TCGA-EE-A3AD TCGA-EE-A3J3 TCGA-EE-A3JA 
       96.23       180.39       162.48        28.77       172.18        53.19 
TCGA-EE-A3JE TCGA-ER-A19C TCGA-ER-A19P TCGA-ER-A3PL TCGA-FR-A8YC TCGA-FS-A1YW 
       51.35        48.89       162.08        33.21        34.82       216.92 
TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A26D TCGA-HR-A2OG 
      228.59       202.65       117.93        64.44        48.00         0.23 
TCGA-HR-A2OH TCGA-OD-A75X TCGA-W3-AA21 TCGA-WE-AA9Y TCGA-YG-AA3P 
       65.88       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-D3-A8GV TCGA-D9-A148 TCGA-D9-A1JW TCGA-D9-A1JX 
       29.06       129.63       167.70       151.53         3.65         7.10 
TCGA-D9-A3Z1 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV 
       15.39        18.44         9.90        77.56        22.95        76.57 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I4 TCGA-DA-A1I5 
       36.03       144.89        20.38       207.48        35.93       120.00 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
       73.84        53.92        65.92        40.60        68.09        33.93 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-DA-A95W TCGA-DA-A95X TCGA-DA-A95Y 
       10.49       225.96        15.68        25.15        61.81        14.14 
TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH 
       13.02        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 
       29.29        58.92         7.04        36.46        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-A20C TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D 
      151.27       168.26        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-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       115.96        59.64        39.29        86.14 
TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
       59.28       340.14       173.79        48.72       107.38        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-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-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ 
      204.66       216.66       167.90        47.54       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        64.04 
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-A3JB TCGA-EE-A3JD TCGA-EE-A3JH TCGA-EE-A3JI 
       64.08        34.32       201.80        27.35       134.33       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-A19M TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A19S 
        6.44       131.51        61.05        44.05        50.89        49.48 
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        93.01        46.98 
TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 
       12.95       149.03        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        46.45        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 
       96.92        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-A690 TCGA-RP-A693 TCGA-RP-A694 
      368.78         7.23        18.05         0.20         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        17.95 
TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX 
      101.33        58.98        70.52        63.22        11.80        35.80 
TCGA-WE-A8ZY TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YD-A89C TCGA-YD-A9TA 
       49.51        40.41        21.40        24.99         6.90        49.18 
TCGA-YG-AA3O TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
       37.94        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 
            67.43             49.48 
[1] "0.2 - 297.9 (67.4)" "0.2 - 369.9 (49.5)"
[1] "hr=" "1.3"
D44V3, continuous
                   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          12       7      24       17       24       21
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  2P LOSS MUTATED           1         4         3         7          3
  2P LOSS WILD-TYPE        13        15        12        33         12
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  2P LOSS MUTATED            3          4        3
  2P LOSS WILD-TYPE         30         51       18
D44V4, multiclass
             clus
vv            2P LOSS MUTATED 2P LOSS WILD-TYPE
  I OR II NOS               1                12
  STAGE 0                   0                 7
  STAGE I                   5                24
  STAGE IA                  1                17
  STAGE IB                  4                24
  STAGE II                  4                21
  STAGE IIA                 1                13
  STAGE IIB                 4                15
  STAGE IIC                 3                12
  STAGE III                 7                33
  STAGE IIIA                3                12
  STAGE IIIB                3                30
  STAGE IIIC                4                51
  STAGE IV                  3                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
  2P LOSS MUTATED       7  8 12 15
  2P LOSS WILD-TYPE    57 65 66 55
D44V5, multiclass
       clus
vv      2P LOSS MUTATED 2P LOSS WILD-TYPE
  T0+T1               7                57
  T2                  8                65
  T3                 12                66
  T4                 15                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
  2P LOSS MUTATED    28   8   5   3
  2P LOSS WILD-TYPE 149  57  34  42
D44V6, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  N0              28               149
  N1               8                57
  N2               5                34
  N3               3                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"
D44V7, binary
                   cls
clus                  0   1
  2P LOSS MUTATED    41   3
  2P LOSS WILD-TYPE 277  19
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED     41    3
  2P LOSS WILD-TYPE  277   19
   clus
vv  2P LOSS MUTATED 2P LOSS WILD-TYPE
  0              41               277
  1               3                19
[1] 2 2
[1] FALSE
D44V8, binary
                   cls
clus                  0   1
  2P LOSS MUTATED    21  14
  2P LOSS WILD-TYPE 113  76
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED     21   14
  2P LOSS WILD-TYPE  113   76
     clus
vv    2P LOSS MUTATED 2P LOSS WILD-TYPE
  NO               21               113
  YES              14                76
[1] 2 2
[1] FALSE
D44V9, binary
                   cls
clus                  0   1
  2P LOSS MUTATED     3  48
  2P LOSS WILD-TYPE  44 271
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      3   48
  2P LOSS WILD-TYPE   44  271
     clus
vv    2P LOSS MUTATED 2P LOSS WILD-TYPE
  NO                3                44
  YES              48               271
[1] 2 2
[1] FALSE
D44V10, continuous
D44V11, binary
                   cls
clus                  0   1
  2P LOSS MUTATED    21  30
  2P LOSS WILD-TYPE 116 199
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED     21   30
  2P LOSS WILD-TYPE  116  199
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  FEMALE              21               116
  MALE                30               199
[1] 2 2
[1] FALSE
D44V12, binary
                   cls
clus                  0   1
  2P LOSS MUTATED    46   5
  2P LOSS WILD-TYPE 271  42
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED     46    5
  2P LOSS WILD-TYPE  271   42
     clus
vv    2P LOSS MUTATED 2P LOSS WILD-TYPE
  NO               46               271
  YES               5                42
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  2P LOSS MUTATED       0                         0    48
  2P LOSS WILD-TYPE     5                         1   304
D44V13, multiclass
                           clus
vv                          2P LOSS MUTATED 2P LOSS WILD-TYPE
  ASIAN                                   0                 5
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  48               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"
D44V14, binary
                   cls
clus                  0   1
  2P LOSS MUTATED     2  47
  2P LOSS WILD-TYPE   5 304
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      2   47
  2P LOSS WILD-TYPE    5  304
                        clus
vv                       2P LOSS MUTATED 2P LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                 5
  NOT HISPANIC OR LATINO              47               304
[1] 2 2
[1] FALSE

Clustering(45) Variable = 2Q LOSS MUTATION ANALYSIS
D45V1, survival
                   sevent
clus2                 0   1
  2Q LOSS MUTATED    11  23
  2Q LOSS WILD-TYPE 111 100
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               34               211 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               23               100 
$`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-DA-A95V TCGA-EE-A180 TCGA-EE-A20C TCGA-EE-A29D 
       70.62        10.78        72.10        62.37        75.55        12.99 
TCGA-EE-A29P TCGA-EE-A2GH TCGA-EE-A2GR TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2MS 
       27.16       201.60         0.20        63.25        89.26       143.93 
TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-ER-A19C TCGA-ER-A19P TCGA-ER-A2ND TCGA-ER-A3PL 
        6.28        67.89        39.81       120.76         4.70        32.05 
TCGA-FR-A8YC TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1ZQ TCGA-GN-A267 
       10.06       171.78        49.74       195.98       130.95        17.06 
TCGA-OD-A75X TCGA-W3-A828 TCGA-W3-AA21 TCGA-WE-AA9Y 
      297.01       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        69.21        22.85        76.34       138.67        53.65 
TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 
      150.61        95.51        45.07        64.83        58.85        30.44 
TCGA-DA-A3F5 TCGA-DA-A95X TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5SG 
      225.11        52.90        14.14        12.30         3.91        33.24 
TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A181 
       50.07        52.41        18.21        13.15        24.89        20.38 
TCGA-EE-A182 TCGA-EE-A184 TCGA-EE-A20H TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E 
        0.00        67.50       155.90        75.22        76.14         0.26 
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-A2GB TCGA-EE-A2GD TCGA-EE-A2GE 
      115.43        30.02        77.98        26.14       239.11        12.95 
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-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 
        0.76        71.31        81.99       103.13        15.25         5.75 
TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2ML TCGA-EE-A2MM 
       23.77       209.79        94.19       171.85       104.78       145.45 
TCGA-EE-A2MP TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB 
      227.01        25.08        23.51        53.26       124.31       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 
       64.04         4.41        54.51       111.85        45.90         3.35 
TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
      201.80        19.86       152.81        14.56        34.45         1.58 
TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19G 
       47.31         7.82         4.54        53.29        11.47       151.46 
TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A19S 
      150.12        99.06        59.84        42.48        49.71        47.18 
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-ER-A42L TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7U8 
       68.52        15.48        74.47       174.21       209.23        26.20 
TCGA-FR-A7UA TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE 
        5.65         8.35        27.62       312.07        32.78        42.08 
TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZS TCGA-FS-A1ZT 
       12.92         7.82        36.33        78.61       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        96.92 
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-QB-A6FS TCGA-QB-AA9O TCGA-RP-A690 TCGA-RP-A693 
       59.41        85.05         7.23        18.05         0.20         0.33 
TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1V TCGA-W3-AA1W 
      174.12         1.97        44.05        79.99         8.09       185.13 
TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ 
        1.15        59.64        65.42        12.69        21.90        62.89 
TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O 
       10.95        48.39        31.99        18.31        18.35        28.21 
TCGA-Z2-AA3S 
       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 
            62.81             45.99 
[1] "0.2 - 297.0 (62.8)" "0.0 - 346.5 (46.0)"
[1] "hr=" "1.2"
D45V2, survival
                   sevent
clus2                 0   1
  2Q LOSS MUTATED    20  28
  2Q LOSS WILD-TYPE 150 159
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               48               309 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               28               159 
$`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-DA-A95V TCGA-EE-A180 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I 
       72.10        94.98       133.81       151.27        91.56        13.55 
TCGA-EE-A29D TCGA-EE-A29P TCGA-EE-A2GC TCGA-EE-A2GH TCGA-EE-A2GR TCGA-EE-A2MJ 
       13.97        56.42        67.43       220.24        42.77        96.23 
TCGA-EE-A2MK TCGA-EE-A2MS TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3JA TCGA-EE-A3JE 
      180.39       162.48        13.81       172.18        53.19        51.35 
TCGA-ER-A19C TCGA-ER-A19P TCGA-ER-A2ND TCGA-ER-A3PL TCGA-FR-A8YC TCGA-FS-A1YW 
       48.89       162.08        23.34        33.21        34.82       216.92 
TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1ZQ TCGA-GN-A267 TCGA-GN-A26D TCGA-HR-A2OG 
      228.59       202.65       133.55        64.44        48.00         0.23 
TCGA-HR-A2OH TCGA-OD-A75X TCGA-W3-A828 TCGA-W3-AA21 TCGA-WE-AA9Y TCGA-YG-AA3P 
       65.88       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-D3-A8GV TCGA-D9-A1JW 
      161.00       152.75        29.06       129.63       167.70         3.65 
TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EC 
        7.10        15.39        22.29        18.44         9.90        77.56 
TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 
       22.95        76.57        36.03       144.89        20.38       207.48 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA 
      176.55        35.93       120.00        73.84        53.92        65.92 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 
       40.60        68.09        33.93        10.49       225.96        15.68 
TCGA-DA-A95W TCGA-DA-A95X TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A44R 
       25.15        61.81        14.14        13.02        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        29.29        58.92         7.04 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 
       36.46        29.82        27.22         8.65        33.73        14.70 
TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29B 
       26.89        68.15         4.96       168.26        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-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       115.96        59.64        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       173.79        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-A3AD TCGA-EE-A3AE TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J4 
       64.04        28.77        54.51        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       134.33 
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-A2NE 
       49.48         8.88       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        93.01        46.98 
TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 
       12.95       149.03        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        46.45        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 
       96.92        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-A690 TCGA-RP-A693 TCGA-RP-A694 
      368.78         7.23        18.05         0.20         0.33         0.69 
TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-AA1O TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1V 
      228.16        63.02         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        17.95       101.33 
TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-A8ZY 
       58.98        70.52        63.22        11.80        35.80        49.51 
TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YD-A89C TCGA-YD-A9TA TCGA-YG-AA3O 
       40.41        21.40        24.99         6.90        49.18        37.94 
TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
       27.58        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 
           66.655            49.480 
[1] "0.2 - 297.9 (66.7)" "0.2 - 369.9 (49.5)"
[1] "hr=" "1.1"
D45V3, continuous
                   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          11       6      24       17       24       21
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  2Q LOSS MUTATED           1         4         3         4          3
  2Q LOSS WILD-TYPE        13        15        12        36         12
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  2Q LOSS MUTATED            2          7        3
  2Q LOSS WILD-TYPE         31         48       18
D45V4, multiclass
             clus
vv            2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  I OR II NOS               2                11
  STAGE 0                   1                 6
  STAGE I                   5                24
  STAGE IA                  1                17
  STAGE IB                  4                24
  STAGE II                  4                21
  STAGE IIA                 1                13
  STAGE IIB                 4                15
  STAGE IIC                 3                12
  STAGE III                 4                36
  STAGE IIIA                3                12
  STAGE IIIB                2                31
  STAGE IIIC                7                48
  STAGE IV                  3                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
  2Q LOSS MUTATED       7  8 13 13
  2Q LOSS WILD-TYPE    57 65 65 57
D45V5, multiclass
       clus
vv      2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  T0+T1               7                57
  T2                  8                65
  T3                 13                65
  T4                 13                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
  2Q LOSS MUTATED    30   7   3   6
  2Q LOSS WILD-TYPE 147  58  36  39
D45V6, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  N0              30               147
  N1               7                58
  N2               3                36
  N3               6                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"
D45V7, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED    42   4
  2Q LOSS WILD-TYPE 276  18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED     42    4
  2Q LOSS WILD-TYPE  276   18
   clus
vv  2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  0              42               276
  1               4                18
[1] 2 2
[1] FALSE
D45V8, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED    21  14
  2Q LOSS WILD-TYPE 113  76
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED     21   14
  2Q LOSS WILD-TYPE  113   76
     clus
vv    2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  NO               21               113
  YES              14                76
[1] 2 2
[1] FALSE
D45V9, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED     2  50
  2Q LOSS WILD-TYPE  45 269
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      2   50
  2Q LOSS WILD-TYPE   45  269
     clus
vv    2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  NO                2                45
  YES              50               269
[1] 2 2
[1] FALSE
D45V10, continuous
D45V11, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED    21  31
  2Q LOSS WILD-TYPE 116 198
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED     21   31
  2Q LOSS WILD-TYPE  116  198
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  FEMALE              21               116
  MALE                31               198
[1] 2 2
[1] FALSE
D45V12, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED    44   8
  2Q LOSS WILD-TYPE 273  39
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED     44    8
  2Q LOSS WILD-TYPE  273   39
     clus
vv    2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  NO               44               273
  YES               8                39
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  2Q LOSS MUTATED       0                         0    49
  2Q LOSS WILD-TYPE     5                         1   303
D45V13, multiclass
                           clus
vv                          2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  ASIAN                                   0                 5
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  49               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"
D45V14, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED     2  48
  2Q LOSS WILD-TYPE   5 303
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      2   48
  2Q LOSS WILD-TYPE    5  303
                        clus
vv                       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                 5
  NOT HISPANIC OR LATINO              48               303
[1] 2 2
[1] FALSE

Clustering(46) Variable = 3P LOSS MUTATION ANALYSIS
D46V1, survival
                   sevent
clus2                0  1
  3P LOSS MUTATED   23 25
  3P LOSS WILD-TYPE 99 98
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               48               197 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               25                98 
$`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-DA-A95Y 
       18.44        76.34       150.61        95.51        45.07        14.14 
TCGA-EE-A17Y TCGA-EE-A20C TCGA-EE-A29G TCGA-EE-A29P TCGA-EE-A2GH TCGA-EE-A2M6 
       24.89        75.55        44.28        27.16       201.60       103.13 
TCGA-EE-A2MF TCGA-EE-A3AA TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-EE-A3JB TCGA-ER-A195 
      209.79       124.31        67.89        45.90       201.80        34.45 
TCGA-ER-A197 TCGA-ER-A19H TCGA-ER-A19S TCGA-ER-A2ND TCGA-ER-A2NG TCGA-FR-A8YC 
        1.58       150.12        47.18         4.70        10.95        10.06 
TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A4F8 TCGA-FS-A4FD TCGA-FW-A3TU TCGA-GF-A6C8 
       78.61       130.95       173.19        80.68        55.59         1.91 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 TCGA-WE-AAA4 TCGA-Z2-AA3S 
       53.29       117.93        17.06        42.48        18.35        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        69.21        22.85       138.67        53.65 
TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A95V TCGA-DA-A95X 
       64.83        58.85        30.44       225.11        72.10        52.90 
TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A6L9 
       12.30         3.91        33.24        50.07        52.41        18.21 
TCGA-EE-A17X TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A184 TCGA-EE-A20H 
       13.15        62.37        20.38         0.00        67.50       155.90 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29M 
       75.22        76.14        12.99         0.26        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       115.43        30.02        77.98 
TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
       26.14       239.11        12.95        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-A2MG TCGA-EE-A2MI 
       81.99        15.25         5.75        23.77        94.19       171.85 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MR 
       63.25        89.26       104.78       145.45       227.01        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        64.04         4.41 
TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J4 TCGA-EE-A3J8 TCGA-EE-A3JH TCGA-EE-A3JI 
       54.51         6.28       111.85         3.35        19.86       152.81 
TCGA-ER-A193 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C 
       14.56        47.31         7.82         4.54        53.29        39.81 
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-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A3ES 
       49.71       146.63        47.97        22.36        16.87       173.29 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A44A TCGA-FR-A729 
       68.52        15.48        32.05        74.47       174.21       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-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG 
       27.62       312.07        32.78        42.08        12.92         7.82 
TCGA-FS-A1ZJ TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY 
       36.33       136.27        35.28         4.47        23.21         5.29 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F9 TCGA-FW-A3TV TCGA-FW-A5DY 
        3.06        30.90        66.67        13.28        11.54        19.30 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GN-A265 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 
        9.90         6.05        96.92         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-A690 TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 
       18.05         0.20         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-A8ZT 
       59.64        65.42        12.69        21.90        62.89        10.95 
TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-YG-AA3O 
       48.39         1.94        31.99        18.31        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 
           56.825            45.700 
[1] "1.6 - 209.8 (56.8)" "0.0 - 346.5 (45.7)"
[1] "hr=" "1.1"
D46V2, survival
                   sevent
clus2                 0   1
  3P LOSS MUTATED    30  29
  3P LOSS WILD-TYPE 140 158
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               59               298 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               29               158 
$`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        76.57        36.03 
TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A95Y TCGA-EE-A17Y TCGA-EE-A20C 
      176.55       120.00        73.84        14.14        27.22       151.27 
TCGA-EE-A29G TCGA-EE-A29P TCGA-EE-A2GC TCGA-EE-A2GH TCGA-EE-A2M6 TCGA-EE-A2MF 
       72.07        56.42        67.43       220.24       129.27       268.73 
TCGA-EE-A3AA TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-EE-A3JB TCGA-ER-A195 
      124.31        41.59       172.18        64.08       201.80        35.44 
TCGA-ER-A197 TCGA-ER-A19H TCGA-ER-A19S TCGA-ER-A2ND TCGA-ER-A2NG TCGA-FR-A7U9 
       13.94       152.35        49.48        23.34        31.27        18.77 
TCGA-FR-A8YC TCGA-FS-A1YX TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A4F8 TCGA-FS-A4FD 
       34.82        48.59       101.26       133.55       174.84        80.68 
TCGA-FW-A3TU TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 
       55.59         2.04       139.89       117.93        64.44        62.79 
TCGA-GN-A4U9 TCGA-WE-A8ZX TCGA-WE-AAA4 TCGA-YG-AA3P TCGA-Z2-AA3S 
       22.13        35.80        24.99        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-D3-A8GV TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 
      167.70       151.53        54.67         3.65         7.10        15.39 
TCGA-D9-A3Z3 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 
       22.29        77.56        22.95       144.89        20.38       207.48 
TCGA-DA-A1I4 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
       35.93        53.92        65.92        40.60        68.09        33.93 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-DA-A95V TCGA-DA-A95W TCGA-DA-A95X 
       10.49       225.96        15.68        72.10        25.15        61.81 
TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH 
       13.02        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 
       29.29        58.92         7.04        36.46        29.82         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-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
      133.81        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-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       115.96        59.64        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       173.79        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-A2M5 TCGA-EE-A2M7 
       42.77        81.21        44.88        94.82        21.67        28.83 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH 
       19.76        61.51        47.28       103.27       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       180.39       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-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AH 
      122.73        64.04        28.77        54.51        13.81       138.81 
TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE 
      127.20        36.95        34.32        53.19        27.35        51.35 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A 
      134.33       152.81        31.40        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-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-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NF 
        8.88       148.18        79.99        43.82        20.15        16.37 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K 
       32.05       247.04        93.01        46.98        33.21        12.95 
TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 
      149.03        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        46.45        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        96.92 
TCGA-GN-A266 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 
       10.13        32.48        48.00       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-A690 TCGA-RP-A693 
      368.78       297.90         7.23        18.05         0.20         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-A8JZ TCGA-WE-A8K1 
      111.09        42.08       219.16       105.04        24.03        49.05 
TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ 
       61.15        17.95       101.33        58.98        70.52        63.22 
TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-YD-A89C 
       11.80        49.51        12.16        40.41        21.40         6.90 
TCGA-YD-A9TA TCGA-YG-AA3O TCGA-Z2-A8RT TCGA-Z2-AA3V 
       49.18        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 
           66.480            49.495 
[1] "2.0 - 268.7 (66.5)" "0.2 - 369.9 (49.5)"
[1] "hr=" "1.2"
D46V3, continuous
                   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          11       6      23       17       24       25
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  3P LOSS MUTATED           0         5         2         7          5
  3P LOSS WILD-TYPE        14        14        13        33         10
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  3P LOSS MUTATED            7         10        2
  3P LOSS WILD-TYPE         26         45       19
D46V4, multiclass
             clus
vv            3P LOSS MUTATED 3P LOSS WILD-TYPE
  I OR II NOS               2                11
  STAGE 0                   1                 6
  STAGE I                   6                23
  STAGE IA                  1                17
  STAGE IB                  4                24
  STAGE II                  0                25
  STAGE IIA                 0                14
  STAGE IIB                 5                14
  STAGE IIC                 2                13
  STAGE III                 7                33
  STAGE IIIA                5                10
  STAGE IIIB                7                26
  STAGE IIIC               10                45
  STAGE IV                  2                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 LOSS MUTATED      13 12 12 11
  3P LOSS WILD-TYPE    51 61 66 59
D46V5, multiclass
       clus
vv      3P LOSS MUTATED 3P LOSS WILD-TYPE
  T0+T1              13                51
  T2                 12                61
  T3                 12                66
  T4                 11                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
  3P LOSS MUTATED    23  14   9   7
  3P LOSS WILD-TYPE 154  51  30  38
D46V6, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  N0              23               154
  N1              14                51
  N2               9                30
  N3               7                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"
D46V7, binary
                   cls
clus                  0   1
  3P LOSS MUTATED    52   2
  3P LOSS WILD-TYPE 266  20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     52    2
  3P LOSS WILD-TYPE  266   20
   clus
vv  3P LOSS MUTATED 3P LOSS WILD-TYPE
  0              52               266
  1               2                20
[1] 2 2
[1] FALSE
D46V8, binary
                   cls
clus                  0   1
  3P LOSS MUTATED    20  15
  3P LOSS WILD-TYPE 114  75
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     20   15
  3P LOSS WILD-TYPE  114   75
     clus
vv    3P LOSS MUTATED 3P LOSS WILD-TYPE
  NO               20               114
  YES              15                75
[1] 2 2
[1] FALSE
D46V9, binary
                   cls
clus                  0   1
  3P LOSS MUTATED     7  54
  3P LOSS WILD-TYPE  40 265
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      7   54
  3P LOSS WILD-TYPE   40  265
     clus
vv    3P LOSS MUTATED 3P LOSS WILD-TYPE
  NO                7                40
  YES              54               265
[1] 2 2
[1] FALSE
D46V10, continuous
D46V11, binary
                   cls
clus                  0   1
  3P LOSS MUTATED    27  34
  3P LOSS WILD-TYPE 110 195
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     27   34
  3P LOSS WILD-TYPE  110  195
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  FEMALE              27               110
  MALE                34               195
[1] 2 2
[1] FALSE
D46V12, binary
                   cls
clus                  0   1
  3P LOSS MUTATED    56   5
  3P LOSS WILD-TYPE 261  42
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     56    5
  3P LOSS WILD-TYPE  261   42
     clus
vv    3P LOSS MUTATED 3P LOSS WILD-TYPE
  NO               56               261
  YES               5                42
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3P LOSS MUTATED       1                         0    59
  3P LOSS WILD-TYPE     4                         1   293
D46V13, multiclass
                           clus
vv                          3P LOSS MUTATED 3P LOSS WILD-TYPE
  ASIAN                                   1                 4
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  59               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"
D46V14, binary
                   cls
clus                  0   1
  3P LOSS MUTATED     1  59
  3P LOSS WILD-TYPE   6 292
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      1   59
  3P LOSS WILD-TYPE    6  292
                        clus
vv                       3P LOSS MUTATED 3P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 6
  NOT HISPANIC OR LATINO              59               292
[1] 2 2
[1] FALSE

Clustering(47) Variable = 3Q LOSS MUTATION ANALYSIS
D47V1, survival
                   sevent
clus2                 0   1
  3Q LOSS MUTATED    17  24
  3Q LOSS WILD-TYPE 105  99
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               41               204 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               24                99 
$`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        76.34       150.61 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A95V TCGA-DA-A95Y TCGA-EE-A17Y TCGA-EE-A20C 
       95.51        45.07        72.10        14.14        24.89        75.55 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29P TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A3J3 
       44.28        63.12        27.16       201.60        68.65        67.89 
TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A19H TCGA-ER-A19S TCGA-FR-A8YC 
      152.81        34.45         1.58       150.12        47.18        10.06 
TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A4F8 TCGA-FS-A4FD TCGA-FW-A3TU TCGA-GN-A262 
       78.61       130.95       173.19        80.68        55.59        53.29 
TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 TCGA-WE-AAA4 TCGA-Z2-AA3S 
      117.93        17.06        42.48        18.35        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        69.21 
TCGA-D9-A6EG TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 
       22.85       138.67        53.65        64.83        58.85        30.44 
TCGA-DA-A3F5 TCGA-DA-A95X TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5SG TCGA-EB-A5SH 
      225.11        52.90        12.30         3.91        33.24        50.07 
TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 
       52.41        18.21        13.15        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-A29M TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A2 
       47.74        61.12       346.49       185.19       115.43        30.02 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GK TCGA-EE-A2GL 
       77.98        26.14       239.11        12.95        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        89.26       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-A3J4 
      122.73        64.04         4.41        54.51         6.28       111.85 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A198 
       45.90         3.35       201.80        19.86        14.56        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-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19W 
       99.06        59.84        42.48       120.76        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-ER-A42L TCGA-FR-A44A TCGA-FR-A729 
       68.52        15.48        32.05        74.47       174.21       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-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG 
       27.62       312.07        32.78        42.08        12.92         7.82 
TCGA-FS-A1ZJ TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY 
       36.33       136.27        35.28         4.47        23.21         5.29 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F9 TCGA-FW-A3TV TCGA-FW-A5DY 
        3.06        30.90        66.67        13.28        11.54        19.30 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A265 TCGA-GN-A26A TCGA-GN-A4U3 
        9.90         6.05         1.91        96.92         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-A690 TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A825 
        7.23        18.05         0.20         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        65.42        12.69        21.90        62.89 
TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-YG-AA3O 
       10.95        48.39         1.94        31.99        18.31        28.21 

  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
             1.58              0.00 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
           201.60            346.49 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
           67.890            44.875 
[1] "1.6 - 201.6 (67.9)" "0.0 - 346.5 (44.9)"
[1] "hr=" "1"  
D47V2, survival
                   sevent
clus2                 0   1
  3Q LOSS MUTATED    24  28
  3Q LOSS WILD-TYPE 146 159
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               52               305 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               28               159 
$`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-DA-A95V 
       76.57        36.03       176.55       120.00        73.84        72.10 
TCGA-DA-A95Y TCGA-EE-A17Y TCGA-EE-A20C TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29P 
       14.14        27.22       151.27        72.07        64.64        56.42 
TCGA-EE-A2GC TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3JI 
       67.43       220.24       107.38        41.59       172.18       152.81 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A19H TCGA-ER-A19S TCGA-FR-A7U9 TCGA-FR-A8YC 
       35.44        13.94       152.35        49.48        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-GN-A262 TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A4U9 TCGA-GN-A8LL 
      139.89       117.93        64.44        62.79        22.13        21.37 
TCGA-WE-A8ZX TCGA-WE-AAA4 TCGA-YG-AA3P TCGA-Z2-AA3S 
       35.80        24.99        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-D3-A8GV TCGA-D9-A148 
      107.15       161.00        29.06       117.17       167.70       151.53 
TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6EC 
       54.67         3.65         7.10        15.39        22.29        77.56 
TCGA-D9-A6EG TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I4 TCGA-DA-A1I8 
       22.95       144.89        20.38       207.48        35.93        53.92 
TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 
       65.92        40.60        68.09        33.93        10.49       225.96 
TCGA-DA-A3F8 TCGA-DA-A95W TCGA-DA-A95X TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A44R 
       15.68        25.15        61.81        13.02        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        29.29        58.92         7.04 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 
       36.46        29.82         8.65        94.98        33.73        14.70 
TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H 
       26.89        68.15         4.96       133.81        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-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
        2.60        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       115.96 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE 
       59.64        39.29        86.14        59.28       340.14       173.79 
TCGA-EE-A2GI TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO 
       48.72        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       180.39 
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        64.04 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J5 
       28.77        54.51        13.81       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-ER-A193 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B 
      134.33        31.40        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-A19T 
      131.51        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        93.01        46.98        33.21 
TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 
       12.95       149.03        92.98       174.21        15.72       220.80 
TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YY 
       27.85        38.27        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-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        46.45        15.45         9.70        32.75 
TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT 
       47.38        23.93        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-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FW-A3I3 
       66.67        28.73        34.03        26.73        54.41         0.20 
TCGA-FW-A3R5 TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 
       22.92        13.51        19.30         9.90         7.23         2.04 
TCGA-GF-A6C9 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U3 
       15.78        96.92        10.13        32.48        48.00       121.91 
TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A8LK TCGA-GN-A9SD TCGA-HR-A2OG 
       39.35        10.42        48.89        50.10        59.41         0.23 
TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A690 
       65.88       368.78       297.90         7.23        18.05         0.20 
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        17.95       101.33        58.98        70.52 
TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 
       63.22        11.80        49.51        12.16        40.41        21.40 
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 
           220.24            369.93 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
            69.75             49.48 
[1] "9.9 - 220.2 (69.8)" "0.2 - 369.9 (49.5)"
[1] "hr=" "1.1"
D47V3, continuous
                   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          11       5      25       15       24       25
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  3Q LOSS MUTATED           0         4         4         4          4
  3Q LOSS WILD-TYPE        14        15        11        36         11
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  3Q LOSS MUTATED            6          7        1
  3Q LOSS WILD-TYPE         27         48       20
D47V4, multiclass
             clus
vv            3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  I OR II NOS               2                11
  STAGE 0                   2                 5
  STAGE I                   4                25
  STAGE IA                  3                15
  STAGE IB                  4                24
  STAGE II                  0                25
  STAGE IIA                 0                14
  STAGE IIB                 4                15
  STAGE IIC                 4                11
  STAGE III                 4                36
  STAGE IIIA                4                11
  STAGE IIIB                6                27
  STAGE IIIC                7                48
  STAGE IV                  1                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
  3Q LOSS MUTATED      11 10  7 12
  3Q LOSS WILD-TYPE    53 63 71 58
D47V5, multiclass
       clus
vv      3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  T0+T1              11                53
  T2                 10                63
  T3                  7                71
  T4                 12                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    25   9   8   5
  3Q LOSS WILD-TYPE 152  56  31  40
D47V6, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  N0              25               152
  N1               9                56
  N2               8                31
  N3               5                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"
D47V7, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED    45   1
  3Q LOSS WILD-TYPE 273  21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED     45    1
  3Q LOSS WILD-TYPE  273   21
   clus
vv  3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  0              45               273
  1               1                21
[1] 2 2
[1] FALSE
D47V8, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED    18  13
  3Q LOSS WILD-TYPE 116  77
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED     18   13
  3Q LOSS WILD-TYPE  116   77
     clus
vv    3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  NO               18               116
  YES              13                77
[1] 2 2
[1] FALSE
D47V9, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED     5  48
  3Q LOSS WILD-TYPE  42 271
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      5   48
  3Q LOSS WILD-TYPE   42  271
     clus
vv    3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  NO                5                42
  YES              48               271
[1] 2 2
[1] FALSE
D47V10, continuous
D47V11, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED    23  30
  3Q LOSS WILD-TYPE 114 199
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED     23   30
  3Q LOSS WILD-TYPE  114  199
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  FEMALE              23               114
  MALE                30               199
[1] 2 2
[1] FALSE
D47V12, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED    47   6
  3Q LOSS WILD-TYPE 270  41
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED     47    6
  3Q LOSS WILD-TYPE  270   41
     clus
vv    3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  NO               47               270
  YES               6                41
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3Q LOSS MUTATED       1                         0    51
  3Q LOSS WILD-TYPE     4                         1   301
D47V13, multiclass
                           clus
vv                          3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  ASIAN                                   1                 4
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  51               301
[1] 3 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  51
  3Q LOSS WILD-TYPE   6 300
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      1   51
  3Q LOSS WILD-TYPE    6  300
                        clus
vv                       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 6
  NOT HISPANIC OR LATINO              51               300
[1] 2 2
[1] FALSE

Clustering(48) Variable = 4P LOSS MUTATION ANALYSIS
D48V1, survival
                   sevent
clus2                0  1
  4P LOSS MUTATED   24 27
  4P LOSS WILD-TYPE 98 96
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               51               194 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               27                96 
$`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-A95X TCGA-EE-A180 TCGA-EE-A20C TCGA-EE-A29B TCGA-EE-A29C 
       69.21        52.90        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       201.60        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        47.18         4.70        10.95 
TCGA-ER-A3EV TCGA-ER-A42L TCGA-FR-A7U8 TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A4F8 
       15.48        74.47        26.20       195.98        27.62       173.19 
TCGA-FW-A3TU TCGA-GF-A6C8 TCGA-GN-A4U3 TCGA-W3-A825 TCGA-W3-AA1R TCGA-W3-AA1V 
       55.59         1.91       120.53         1.97        79.99         8.09 
TCGA-WE-AA9Y TCGA-WE-AAA3 TCGA-YG-AA3O 
        1.94        18.31        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        76.34       138.67 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC 
       53.65       150.61        95.51        45.07        64.83        58.85 
TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A95V TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q 
       30.44       225.11        72.10        14.14        12.30         3.91 
TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y 
       33.24        50.07        52.41        18.21        13.15        24.89 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A184 TCGA-EE-A20H TCGA-EE-A29E TCGA-EE-A29G 
       20.38         0.00        67.50       155.90         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       115.43        30.02        77.98 
TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
       26.14       239.11        12.95        68.65        10.62        32.48 
TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M7 
       31.00         0.76         0.20        71.31        81.99        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-A2MP TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A2MU 
       89.26       104.78       227.01        25.08        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        64.04         4.41        54.51         6.28 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI 
       67.89       111.85        45.90       201.80        19.86       152.81 
TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19C TCGA-ER-A19G 
       34.45        47.31         7.82         4.54        39.81       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-A2NE TCGA-ER-A3ES TCGA-ER-A3ET 
      146.63        47.97        22.36        16.87       173.29        68.52 
TCGA-ER-A3PL TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FS-A1YW 
       32.05       174.21       209.23         5.65        10.06       171.78 
TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF 
       49.74         8.35       312.07        32.78        42.08        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-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-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
       53.29       117.93        96.92        17.06        42.48         7.59 
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-A690 TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A828 
        7.23        18.05         0.20         0.33       174.12       120.07 
TCGA-W3-AA1Q TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8ZM 
       44.05       185.13        92.84         1.15        59.64        65.42 
TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AAA0 
       12.69        21.90        62.89        10.95        48.39        31.99 
TCGA-WE-AAA4 TCGA-Z2-AA3S 
       18.35        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 
            47.74             46.95 
[1] "1.6 - 346.5 (47.7)" "0.0 - 312.1 (47.0)"
[1] "hr=" "1.1"
D48V2, survival
                   sevent
clus2                 0   1
  4P LOSS MUTATED    40  38
  4P LOSS WILD-TYPE 130 149
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               78               279 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               38               149 
$`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-DA-A95X TCGA-EB-A44R 
        9.90        77.56        36.03        15.68        61.81        10.36 
TCGA-EB-A5KH TCGA-EE-A180 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A29B TCGA-EE-A29C 
       20.35        94.98       133.81       151.27        85.08        78.97 
TCGA-EE-A29D TCGA-EE-A29M TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A5 TCGA-EE-A2GH 
       13.97        56.84       369.93       195.02        39.29       220.24 
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        49.48         8.88        23.34 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3EV TCGA-ER-A42L TCGA-FR-A7U8 TCGA-FS-A1Z0 
       31.27        32.05        46.98       149.03        27.85       202.65 
TCGA-FS-A1Z4 TCGA-FS-A1ZA TCGA-FS-A4F8 TCGA-FW-A3TU TCGA-GF-A6C8 TCGA-GF-A6C9 
       28.08        27.72       174.84        55.59         2.04        15.78 
TCGA-GN-A266 TCGA-GN-A4U3 TCGA-W3-A825 TCGA-W3-AA1R TCGA-W3-AA1V TCGA-WE-A8JZ 
       10.13       121.91        63.02       111.09        42.08        24.03 
TCGA-WE-A8ZX TCGA-WE-AA9Y TCGA-WE-AAA3 TCGA-YD-A9TA TCGA-YG-AA3O TCGA-Z2-A8RT 
       35.80        12.16        21.40        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-D3-A8GV TCGA-D9-A1JW 
      152.75        29.06       129.63       117.17       167.70         3.65 
TCGA-D9-A1JX TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A6EA TCGA-D9-A6EG TCGA-DA-A1HV 
        7.10        18.12        15.39        25.18        22.95        76.57 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
      144.89        20.38       207.48       176.55        35.93       120.00 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
       73.84        53.92        65.92        40.60        68.09        33.93 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A95V TCGA-DA-A95W TCGA-DA-A95Y TCGA-DA-A95Z 
       10.49       225.96        72.10        25.15        14.14        13.02 
TCGA-EB-A44Q TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV 
       13.87        68.25        54.02        29.29        58.92         7.04 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 
       36.46        29.82        27.22         8.65        33.73        14.70 
TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I 
       26.89        68.15         4.96        91.56       168.26        13.55 
TCGA-EE-A29A TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N 
       63.35        63.78        72.07        64.64         2.60        18.61 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29X 
       56.42        66.74        14.47        61.28        25.87        17.92 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC 
       46.82       115.96        59.64        86.14        59.28        67.43 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
      340.14       173.79        48.72       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       180.39       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        64.04        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       134.33       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        93.01 
TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 
       33.21        12.95        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        46.45        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        96.92        64.44        62.79 
TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A4U9 
       32.48        48.00        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-QB-AA9O TCGA-RP-A690 TCGA-RP-A693 TCGA-RP-A694 
      297.90         7.23        18.05         0.20         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        17.95       101.33        58.98        70.52 
TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-YD-A89C 
       63.22        11.80        49.51        40.41        24.99         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 
            48.08             53.52 
[1] "2.0 - 369.9 (48.1)" "0.2 - 368.8 (53.5)"
[1] "hr=" "1"  
D48V3, continuous
                   vv
clus                I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  4P LOSS MUTATED             1       2       6        2        6        7
  4P LOSS WILD-TYPE          12       5      23       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        13        33         10
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  4P LOSS MUTATED           11         13        3
  4P LOSS WILD-TYPE         22         42       18
D48V4, multiclass
             clus
vv            4P LOSS MUTATED 4P LOSS WILD-TYPE
  I OR II NOS               1                12
  STAGE 0                   2                 5
  STAGE I                   6                23
  STAGE IA                  2                16
  STAGE IB                  6                22
  STAGE II                  7                18
  STAGE IIA                 0                14
  STAGE IIB                 6                13
  STAGE IIC                 2                13
  STAGE III                 7                33
  STAGE IIIA                5                10
  STAGE IIIB               11                22
  STAGE IIIC               13                42
  STAGE IV                  3                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
  4P LOSS MUTATED      13 15 22 12
  4P LOSS WILD-TYPE    51 58 56 58
D48V5, multiclass
       clus
vv      4P LOSS MUTATED 4P LOSS WILD-TYPE
  T0+T1              13                51
  T2                 15                58
  T3                 22                56
  T4                 12                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
  4P LOSS MUTATED    34  19   7  11
  4P LOSS WILD-TYPE 143  46  32  34
D48V6, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  N0              34               143
  N1              19                46
  N2               7                32
  N3              11                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"
D48V7, binary
                   cls
clus                  0   1
  4P LOSS MUTATED    70   4
  4P LOSS WILD-TYPE 248  18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     70    4
  4P LOSS WILD-TYPE  248   18
   clus
vv  4P LOSS MUTATED 4P LOSS WILD-TYPE
  0              70               248
  1               4                18
[1] 2 2
[1] FALSE
D48V8, binary
                   cls
clus                  0   1
  4P LOSS MUTATED    33  18
  4P LOSS WILD-TYPE 101  72
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     33   18
  4P LOSS WILD-TYPE  101   72
     clus
vv    4P LOSS MUTATED 4P LOSS WILD-TYPE
  NO               33               101
  YES              18                72
[1] 2 2
[1] FALSE
D48V9, binary
                   cls
clus                  0   1
  4P LOSS MUTATED    10  70
  4P LOSS WILD-TYPE  37 249
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     10   70
  4P LOSS WILD-TYPE   37  249
     clus
vv    4P LOSS MUTATED 4P LOSS WILD-TYPE
  NO               10                37
  YES              70               249
[1] 2 2
[1] FALSE
D48V10, continuous
D48V11, binary
                   cls
clus                  0   1
  4P LOSS MUTATED    32  48
  4P LOSS WILD-TYPE 105 181
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     32   48
  4P LOSS WILD-TYPE  105  181
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  FEMALE              32               105
  MALE                48               181
[1] 2 2
[1] FALSE
D48V12, binary
                   cls
clus                  0   1
  4P LOSS MUTATED    70  10
  4P LOSS WILD-TYPE 247  37
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     70   10
  4P LOSS WILD-TYPE  247   37
     clus
vv    4P LOSS MUTATED 4P LOSS WILD-TYPE
  NO               70               247
  YES              10                37
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  4P LOSS MUTATED       2                         0    76
  4P LOSS WILD-TYPE     3                         1   276
D48V13, multiclass
                           clus
vv                          4P LOSS MUTATED 4P LOSS WILD-TYPE
  ASIAN                                   2                 3
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  76               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"
D48V14, binary
                   cls
clus                  0   1
  4P LOSS MUTATED     1  78
  4P LOSS WILD-TYPE   6 273
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      1   78
  4P LOSS WILD-TYPE    6  273
                        clus
vv                       4P LOSS MUTATED 4P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 6
  NOT HISPANIC OR LATINO              78               273
[1] 2 2
[1] FALSE

Clustering(49) Variable = 4Q LOSS MUTATION ANALYSIS
D49V1, survival
                   sevent
clus2                0  1
  4Q LOSS MUTATED   25 29
  4Q LOSS WILD-TYPE 97 94
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               54               191 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               29                94 
$`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-A95V TCGA-DA-A95X TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A181 
       18.44        72.10        52.90        24.89        62.37        20.38 
TCGA-EE-A20C TCGA-EE-A29C TCGA-EE-A29M TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2GH 
       75.55        76.14        47.74       346.49       185.19       201.60 
TCGA-EE-A2GM TCGA-EE-A2GO TCGA-EE-A2M6 TCGA-EE-A2MM TCGA-EE-A2MS TCGA-EE-A3J8 
       18.35       118.32       103.13       145.45       143.93         3.35 
TCGA-ER-A193 TCGA-ER-A197 TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19S TCGA-ER-A2ND 
       14.56         1.58        53.29        11.47        47.18         4.70 
TCGA-ER-A2NG TCGA-ER-A3EV TCGA-ER-A42L TCGA-FR-A7U8 TCGA-FS-A1Z0 TCGA-FS-A1Z4 
       10.95        15.48        74.47        26.20       195.98        27.62 
TCGA-FS-A4F8 TCGA-FW-A3TU TCGA-GF-A6C8 TCGA-GN-A4U3 TCGA-GN-A8LK TCGA-QB-AA9O 
      173.19        55.59         1.91       120.53        43.23        18.05 
TCGA-W3-A825 TCGA-W3-AA1R TCGA-W3-AA1V TCGA-WE-AA9Y TCGA-WE-AAA3 TCGA-YG-AA3O 
        1.97        79.99         8.09         1.94        18.31        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        69.21        22.85        76.34       138.67 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC 
       53.65       150.61        95.51        45.07        64.83        58.85 
TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5SG 
       30.44       225.11        14.14        12.30         3.91        33.24 
TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A182 TCGA-EE-A184 
       50.07        52.41        18.21        13.15         0.00        67.50 
TCGA-EE-A20H TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H 
      155.90        75.22        12.99         0.26        44.28        63.12 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB 
       27.16        61.12       115.43        30.02        77.98        26.14 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN 
      239.11        12.95        68.65        10.62        32.48        31.00 
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-A2MJ TCGA-EE-A2MK 
       23.77       209.79        94.19       171.85        63.25        89.26 
TCGA-EE-A2ML TCGA-EE-A2MP TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA 
      104.78       227.01        25.08        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        64.04         4.41        54.51         6.28        67.89 
TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 
      111.85        45.90       201.80        19.86       152.81        34.45 
TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19C TCGA-ER-A19G TCGA-ER-A19H 
       47.31         7.82         4.54        39.81       151.46       150.12 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19W 
       99.06        59.84        42.48       120.76        49.71       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        68.52        32.05 
TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FS-A1YW TCGA-FS-A1YY 
      174.21       209.23         5.65        10.06       171.78        49.74 
TCGA-FS-A1Z3 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG 
        8.35       312.07        32.78        42.08        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-A4F9 
       23.21         5.29         3.06        30.90        66.67        13.28 
TCGA-FS-A4FD TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GN-A262 
       80.68        11.54        19.30         9.90         6.05        53.29 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U4 
      117.93        96.92        17.06        42.48         7.59        34.49 
TCGA-GN-A4U8 TCGA-GN-A9SD TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 
       46.92        59.41        85.05       297.01         7.23         0.20 
TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A828 TCGA-W3-AA1Q TCGA-W3-AA1W TCGA-W3-AA21 
        0.33       174.12       120.07        44.05       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        65.42        12.69        21.90        62.89 
TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-Z2-AA3S 
       10.95        48.39        31.99        18.35        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 
           45.105            47.970 
[1] "1.6 - 346.5 (45.1)" "0.0 - 312.1 (48.0)"
[1] "hr=" "1.2"
D49V2, survival
                   sevent
clus2                 0   1
  4Q LOSS MUTATED    43  41
  4Q LOSS WILD-TYPE 127 146
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               84               273 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               41               146 
$`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-DA-A95V TCGA-DA-A95X 
       18.44         9.90        36.03        15.68        72.10        61.81 
TCGA-EB-A44R TCGA-EB-A5KH TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A20B 
       10.36        20.35        27.22        94.98        33.73       133.81 
TCGA-EE-A20C TCGA-EE-A29C TCGA-EE-A29M TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A5 
      151.27        78.97        56.84       369.93       195.02        39.29 
TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GM TCGA-EE-A2GO TCGA-EE-A2M5 TCGA-EE-A2M6 
      220.24        48.72        75.48       126.81        21.67       129.27 
TCGA-EE-A2MM TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A3AG TCGA-EE-A3J8 TCGA-EE-A3JE 
      167.90        43.23       162.48        41.59        34.32        51.35 
TCGA-ER-A193 TCGA-ER-A197 TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19S 
       31.40        13.94        98.40        12.59        13.02        49.48 
TCGA-ER-A19T TCGA-ER-A2ND TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3EV TCGA-ER-A42L 
        8.88        23.34        31.27        32.05        46.98       149.03 
TCGA-FR-A7U8 TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1ZA TCGA-FS-A4F8 TCGA-FW-A3TU 
       27.85       202.65        28.08        27.72       174.84        55.59 
TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A266 TCGA-GN-A4U3 TCGA-GN-A8LK TCGA-HR-A2OH 
        2.04        15.78        10.13       121.91        50.10        65.88 
TCGA-QB-AA9O TCGA-W3-A825 TCGA-W3-AA1R TCGA-W3-AA1V TCGA-WE-A8JZ TCGA-WE-A8K6 
       18.05        63.02       111.09        42.08        24.03        17.95 
TCGA-WE-A8ZX TCGA-WE-AA9Y TCGA-WE-AAA3 TCGA-YD-A9TA TCGA-YG-AA3O TCGA-Z2-A8RT 
       35.80        12.16        21.40        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-D3-A8GV TCGA-D9-A1JW TCGA-D9-A1JX 
       29.06       129.63       117.17       167.70         3.65         7.10 
TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV 
       18.12        15.39        25.18        77.56        22.95        76.57 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
      144.89        20.38       207.48       176.55        35.93       120.00 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
       73.84        53.92        65.92        40.60        68.09        33.93 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A95W TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q 
       10.49       225.96        25.15        14.14        13.02        13.87 
TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 
       68.25        54.02        29.29        58.92         7.04        36.46 
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-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29D 
       91.56       168.26        13.55        63.35        85.08        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-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-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD 
      115.96        59.64        86.14        59.28        67.43       340.14 
TCGA-EE-A2GE TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GP 
      173.79       107.38        54.74        79.66       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-A2MK TCGA-EE-A2ML TCGA-EE-A2MN TCGA-EE-A2MP 
      204.66        96.23       180.39       216.66        47.54       248.65 
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        64.04 
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-A3J7 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JH 
       36.95        64.08        53.19       201.80        27.35       134.33 
TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19C 
      152.81        35.44        50.76         9.17        77.75        48.89 
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-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
       44.05       162.08        50.89       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        93.01        33.21        12.95 
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-A1YW TCGA-FS-A1YX TCGA-FS-A1YY 
       34.82        36.26       104.42       216.92        48.59       228.59 
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        46.45 
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-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GN-A262 
       22.92        13.51        19.30         9.90         7.23       139.89 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
      117.93        96.92        64.44        62.79        32.48        48.00 
TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LL TCGA-GN-A9SD 
       39.35        10.42        48.89        22.13        21.37        59.41 
TCGA-HR-A2OG TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 
        0.23       368.78       297.90         7.23         0.20         0.33 
TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1Q TCGA-W3-AA1W 
        0.69       228.16       121.08         4.01        69.07       219.16 
TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO 
      105.04        49.05        61.15       101.33        58.98        70.52 
TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-YD-A89C 
       63.22        11.80        49.51        40.41        24.99         6.90 
TCGA-YG-AA3P TCGA-Z2-AA3S TCGA-Z2-AA3V 
       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 
            46.98             54.41 
[1] "2.0 - 369.9 (47.0)" "0.2 - 368.8 (54.4)"
[1] "hr=" "1"  
D49V3, continuous
                   vv
clus                I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  4Q LOSS MUTATED             0       2       6        3        7        8
  4Q LOSS WILD-TYPE          13       5      23       15       21       17
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  4Q LOSS MUTATED           0         4         3         8          4
  4Q LOSS WILD-TYPE        14        15        12        32         11
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  4Q LOSS MUTATED           14         13        4
  4Q LOSS WILD-TYPE         19         42       17
D49V4, multiclass
             clus
vv            4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  I OR II NOS               0                13
  STAGE 0                   2                 5
  STAGE I                   6                23
  STAGE IA                  3                15
  STAGE IB                  7                21
  STAGE II                  8                17
  STAGE IIA                 0                14
  STAGE IIB                 4                15
  STAGE IIC                 3                12
  STAGE III                 8                32
  STAGE IIIA                4                11
  STAGE IIIB               14                19
  STAGE IIIC               13                42
  STAGE IV                  4                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
  4Q LOSS MUTATED      17 14 21 13
  4Q LOSS WILD-TYPE    47 59 57 57
D49V5, multiclass
       clus
vv      4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  T0+T1              17                47
  T2                 14                59
  T3                 21                57
  T4                 13                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
  4Q LOSS MUTATED    34  20   8  13
  4Q LOSS WILD-TYPE 143  45  31  32
D49V6, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  N0              34               143
  N1              20                45
  N2               8                31
  N3              13                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"
D49V7, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED    72   5
  4Q LOSS WILD-TYPE 246  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     72    5
  4Q LOSS WILD-TYPE  246   17
   clus
vv  4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  0              72               246
  1               5                17
[1] 2 2
[1] FALSE
D49V8, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED    34  18
  4Q LOSS WILD-TYPE 100  72
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     34   18
  4Q LOSS WILD-TYPE  100   72
     clus
vv    4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  NO               34               100
  YES              18                72
[1] 2 2
[1] FALSE
D49V9, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED    13  72
  4Q LOSS WILD-TYPE  34 247
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     13   72
  4Q LOSS WILD-TYPE   34  247
     clus
vv    4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  NO               13                34
  YES              72               247
[1] 2 2
[1] FALSE
D49V10, continuous
D49V11, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED    35  50
  4Q LOSS WILD-TYPE 102 179
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     35   50
  4Q LOSS WILD-TYPE  102  179
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  FEMALE              35               102
  MALE                50               179
[1] 2 2
[1] FALSE
D49V12, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED    73  12
  4Q LOSS WILD-TYPE 244  35
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     73   12
  4Q LOSS WILD-TYPE  244   35
     clus
vv    4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  NO               73               244
  YES              12                35
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  4Q LOSS MUTATED       3                         0    79
  4Q LOSS WILD-TYPE     2                         1   273
D49V13, multiclass
                           clus
vv                          4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  ASIAN                                   3                 2
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  79               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"
D49V14, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED     1  81
  4Q LOSS WILD-TYPE   6 270
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      1   81
  4Q LOSS WILD-TYPE    6  270
                        clus
vv                       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 6
  NOT HISPANIC OR LATINO              81               270
[1] 2 2
[1] FALSE

Clustering(50) Variable = 5P LOSS MUTATION ANALYSIS
D50V1, survival
                   sevent
clus2                0  1
  5P LOSS MUTATED   24 31
  5P LOSS WILD-TYPE 98 92
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               55               190 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               31                92 
$`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        76.34 
TCGA-DA-A3F5 TCGA-DA-A95Y TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A184 TCGA-EE-A29C 
      225.11        14.14        13.15        24.89        67.50        76.14 
TCGA-EE-A29E TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A2A2 TCGA-EE-A2GB TCGA-EE-A2GD 
        0.26        47.74        27.16        30.02        26.14       239.11 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GR TCGA-EE-A2MM TCGA-EE-A2MU 
       12.95       201.60        68.65         0.20       145.45        53.26 
TCGA-EE-A3AD TCGA-EE-A3J7 TCGA-EE-A3JB TCGA-ER-A199 TCGA-ER-A2NE TCGA-ER-A2NG 
        4.41        45.90       201.80         7.82        16.87        10.95 
TCGA-FS-A1ZD TCGA-FS-A1ZG TCGA-FS-A1ZM TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A1ZY 
       32.78         7.82        78.61        35.28        23.21         5.29 
TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A267 TCGA-GN-A268 
       66.67       173.19         1.91        53.29        17.06        42.48 
TCGA-GN-A4U3 TCGA-GN-A8LK TCGA-OD-A75X TCGA-W3-AA1R TCGA-WE-A8ZM TCGA-WE-A8ZY 
      120.53        43.23       297.01        79.99        65.42        48.39 
TCGA-WE-AAA4 
       18.35 

$`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        69.21        22.85 
TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA 
      138.67        53.65       150.61        95.51        45.07        64.83 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A95V TCGA-DA-A95X TCGA-DA-A95Z TCGA-EB-A44Q 
       58.85        30.44        72.10        52.90        12.30         3.91 
TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A180 TCGA-EE-A181 
       33.24        50.07        52.41        18.21        62.37        20.38 
TCGA-EE-A182 TCGA-EE-A20C TCGA-EE-A20H TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29G 
        0.00        75.55       155.90        75.22        12.99        44.28 
TCGA-EE-A29H TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A6 
       63.12        61.12       346.49       185.19       115.43        77.98 
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-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        89.26       104.78 
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-A3AE TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J8 
       64.04        54.51         6.28        67.89       111.85         3.35 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
       19.86       152.81        14.56        34.45         1.58        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        47.18 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A3ES TCGA-ER-A3ET 
      146.63        47.97        22.36         4.70       173.29        68.52 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7U8 
       15.48        32.05        74.47       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-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZJ TCGA-FS-A1ZQ 
       27.62       312.07        42.08        12.92        36.33       130.95 
TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F9 TCGA-FS-A4FD 
      136.27         4.47         3.06        30.90        13.28        80.68 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GN-A264 
       55.59        11.54        19.30         9.90         6.05       117.93 
TCGA-GN-A265 TCGA-GN-A26A TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-GN-A9SD TCGA-LH-A9QB 
       96.92         7.59        34.49        46.92        59.41        85.05 
TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A690 TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A825 
        7.23        18.05         0.20         0.33       174.12         1.97 
TCGA-W3-A828 TCGA-W3-AA1Q TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 
      120.07        44.05         8.09       185.13        92.84         1.15 
TCGA-WE-A8K5 TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-AA9Y 
       59.64        12.69        21.90        62.89        10.95         1.94 
TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-YG-AA3O TCGA-Z2-AA3S 
       31.99        18.31        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 
            40.01             49.53 
[1] "0.2 - 297.0 (40.0)" "0.0 - 346.5 (49.5)"
[1] "hr=" "1.2"
D50V2, survival
                   sevent
clus2                 0   1
  5P LOSS MUTATED    35  41
  5P LOSS WILD-TYPE 135 146
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               76               281 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               41               146 
$`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        76.57        36.03       225.96 
TCGA-DA-A95Y TCGA-EB-A5KH TCGA-EB-A5UL TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A184 
       14.14        20.35        29.29        29.82        27.22        68.15 
TCGA-EE-A185 TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A2A2 
        4.96        78.97        63.78        56.84        56.42        59.64 
TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       59.28       340.14       173.79       220.24        48.72       107.38 
TCGA-EE-A2GR TCGA-EE-A2GT TCGA-EE-A2MM TCGA-EE-A2MQ TCGA-EE-A2MU TCGA-EE-A3AD 
       42.77        44.88       167.90        43.23        53.26        28.77 
TCGA-EE-A3AH TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3JB TCGA-ER-A199 TCGA-ER-A2NE 
      138.81        36.95        64.08       201.80         9.17        20.15 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-FR-A69P TCGA-FS-A1ZD TCGA-FS-A1ZG TCGA-FS-A1ZM 
       31.27        32.05        15.72        53.52         9.70       101.26 
TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F8 
       53.16        49.48        27.09        50.14        66.67       174.84 
TCGA-FS-A4FB TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
       26.73         2.04       139.89        10.13        64.44        62.79 
TCGA-GN-A4U3 TCGA-GN-A8LK TCGA-HR-A2OG TCGA-HR-A2OH TCGA-OD-A75X TCGA-W3-AA1R 
      121.91        50.10         0.23        65.88       297.90       111.09 
TCGA-WE-A8ZM TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AAA4 
      101.33        35.80        49.51        24.99 

$`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-D3-A8GV 
      107.15       152.75        29.06       129.63       117.17       167.70 
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-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HY TCGA-DA-A1I0 
        9.90        25.18        77.56        22.95       144.89        20.38 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
      207.48       176.55        35.93       120.00        73.84        53.92 
TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 
       65.92        40.60        68.09        33.93        10.49        15.68 
TCGA-DA-A95V TCGA-DA-A95W TCGA-DA-A95X TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A44R 
       72.10        25.15        61.81        13.02        13.87        10.36 
TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17Z 
       68.25        54.02        58.92         7.04        36.46         8.65 
TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20C 
       94.98        33.73        14.70        26.89       133.81       151.27 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29D 
       91.56       168.26        13.55        63.35        85.08        13.97 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29R 
       72.07        64.64         2.60        18.61        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-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GC TCGA-EE-A2GK TCGA-EE-A2GL 
      115.96        39.29        86.14        67.43        54.74        79.66 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2GU 
       75.48       102.12       126.81        13.91        81.21        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-A2MN TCGA-EE-A2MP TCGA-EE-A2MR TCGA-EE-A2MS 
      180.39       216.66        47.54       248.65       134.40       162.48 
TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3AF 
       71.21       124.31       122.73        64.04        54.51        13.81 
TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD 
       41.59       172.18       127.20        34.32        53.19        27.35 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
       51.35       134.33       152.81        31.40        35.44        13.94 
TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E 
       50.76        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-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        49.48         8.88       148.18 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NF TCGA-ER-A3ES TCGA-ER-A3ET 
       79.99        43.82        23.34        16.37       247.04        93.01 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A 
       46.98        33.21        12.95       149.03        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        46.45 
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 
       96.92        32.48        48.00        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-A690 TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 
        0.20         0.33         0.69       228.16        63.02       121.08 
TCGA-W3-AA1O TCGA-W3-AA1Q TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8JZ 
        4.01        69.07        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        17.95        58.98        70.52        63.22 
TCGA-WE-A8ZT TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-YD-A89C TCGA-YD-A9TA 
       11.80        12.16        40.41        21.40         6.90        49.18 
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 

  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 
            51.65             53.19 
[1] "0.2 - 340.1 (51.6)" "0.2 - 369.9 (53.2)"
[1] "hr=" "1"  
D50V3, continuous
                   vv
clus                I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  5P LOSS MUTATED             4       2       6        4        4        5
  5P LOSS WILD-TYPE           9       5      23       14       24       20
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  5P LOSS MUTATED           3         4         4         9          4
  5P LOSS WILD-TYPE        11        15        11        31         11
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  5P LOSS MUTATED           11         13        0
  5P LOSS WILD-TYPE         22         42       21
D50V4, multiclass
             clus
vv            5P LOSS MUTATED 5P LOSS WILD-TYPE
  I OR II NOS               4                 9
  STAGE 0                   2                 5
  STAGE I                   6                23
  STAGE IA                  4                14
  STAGE IB                  4                24
  STAGE II                  5                20
  STAGE IIA                 3                11
  STAGE IIB                 4                15
  STAGE IIC                 4                11
  STAGE III                 9                31
  STAGE IIIA                4                11
  STAGE IIIB               11                22
  STAGE IIIC               13                42
  STAGE IV                  0                21
[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 18
  5P LOSS WILD-TYPE    52 57 61 52
D50V5, multiclass
       clus
vv      5P LOSS MUTATED 5P LOSS WILD-TYPE
  T0+T1              12                52
  T2                 16                57
  T3                 17                61
  T4                 18                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
  5P LOSS MUTATED    33  22   7   9
  5P LOSS WILD-TYPE 144  43  32  36
D50V6, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  N0              33               144
  N1              22                43
  N2               7                32
  N3               9                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"
D50V7, binary
                   cls
clus                  0   1
  5P LOSS MUTATED    72   0
  5P LOSS WILD-TYPE 246  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED     72    0
  5P LOSS WILD-TYPE  246   22
   clus
vv  5P LOSS MUTATED 5P LOSS WILD-TYPE
  0              72               246
  1               0                22
[1] 2 2
[1] FALSE
D50V8, binary
                   cls
clus                  0   1
  5P LOSS MUTATED    25  24
  5P LOSS WILD-TYPE 109  66
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED     25   24
  5P LOSS WILD-TYPE  109   66
     clus
vv    5P LOSS MUTATED 5P LOSS WILD-TYPE
  NO               25               109
  YES              24                66
[1] 2 2
[1] FALSE
D50V9, binary
                   cls
clus                  0   1
  5P LOSS MUTATED     6  73
  5P LOSS WILD-TYPE  41 246
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      6   73
  5P LOSS WILD-TYPE   41  246
     clus
vv    5P LOSS MUTATED 5P LOSS WILD-TYPE
  NO                6                41
  YES              73               246
[1] 2 2
[1] FALSE
D50V10, continuous
D50V11, binary
                   cls
clus                  0   1
  5P LOSS MUTATED    32  47
  5P LOSS WILD-TYPE 105 182
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED     32   47
  5P LOSS WILD-TYPE  105  182
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  FEMALE              32               105
  MALE                47               182
[1] 2 2
[1] FALSE
D50V12, binary
                   cls
clus                  0   1
  5P LOSS MUTATED    67  12
  5P LOSS WILD-TYPE 250  35
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED     67   12
  5P LOSS WILD-TYPE  250   35
     clus
vv    5P LOSS MUTATED 5P LOSS WILD-TYPE
  NO               67               250
  YES              12                35
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  5P LOSS MUTATED       2                         1    74
  5P LOSS WILD-TYPE     3                         0   278
D50V13, multiclass
                           clus
vv                          5P LOSS MUTATED 5P LOSS WILD-TYPE
  ASIAN                                   2                 3
  BLACK OR AFRICAN AMERICAN               1                 0
  WHITE                                  74               278
[1] 3 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  74
  5P LOSS WILD-TYPE   7 277
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      0   74
  5P LOSS WILD-TYPE    7  277
                        clus
vv                       5P LOSS MUTATED 5P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 7
  NOT HISPANIC OR LATINO              74               277
[1] 2 2
[1] FALSE

Clustering(51) Variable = 5Q LOSS MUTATION ANALYSIS
D51V1, survival
                   sevent
clus2                0  1
  5Q LOSS MUTATED   32 37
  5Q LOSS WILD-TYPE 90 86
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               69               176 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               37                86 
$`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        69.21        76.34 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A3F5 TCGA-DA-A95Y TCGA-EE-A17X TCGA-EE-A17Y 
       95.51        45.07       225.11        14.14        13.15        24.89 
TCGA-EE-A20H TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A2A2 
      155.90        76.14         0.26        47.74        27.16        30.02 
TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GM 
       26.14       239.11        12.95       201.60        68.65        18.35 
TCGA-EE-A2GR TCGA-EE-A2M6 TCGA-EE-A2MJ TCGA-EE-A2MM TCGA-EE-A3AB TCGA-EE-A3AD 
        0.20       103.13        63.25       145.45       122.73         4.41 
TCGA-EE-A3J7 TCGA-EE-A3JB TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A2NE TCGA-FR-A44A 
       45.90       201.80         7.82        53.29        16.87       174.21 
TCGA-FS-A1ZG TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A1ZY 
        7.82        78.61       130.95        35.28        23.21         5.29 
TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A267 TCGA-GN-A268 
       66.67       173.19         1.91        53.29        17.06        42.48 
TCGA-GN-A4U3 TCGA-GN-A8LK TCGA-OD-A75X TCGA-W3-A825 TCGA-W3-AA1R TCGA-W3-AA1V 
      120.53        43.23       297.01         1.97        79.99         8.09 
TCGA-WE-A8ZM TCGA-WE-A8ZY TCGA-WE-AAA4 
       65.42        48.39        18.35 

$`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 
      138.67        53.65       150.61        64.83        58.85        30.44 
TCGA-DA-A95V TCGA-DA-A95X TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5SG TCGA-EB-A5SH 
       72.10        52.90        12.30         3.91        33.24        50.07 
TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A184 
       52.41        18.21        62.37        20.38         0.00        67.50 
TCGA-EE-A20C TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29Q 
       75.55        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       115.43        77.98        10.62        32.48 
TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M7 
       31.00       118.32         0.76        71.31        81.99        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        89.26 
TCGA-EE-A2ML TCGA-EE-A2MP TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU 
      104.78       227.01        25.08       143.93        23.51        53.26 
TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 
      124.31        64.04        54.51         6.28        67.89       111.85 
TCGA-EE-A3J8 TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
        3.35        19.86       152.81        14.56        34.45         1.58 
TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19H 
       47.31         4.54        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        47.18 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NG TCGA-ER-A3ES 
      146.63        47.97        22.36         4.70        10.95       173.29 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A729 TCGA-FR-A7U8 
       68.52        15.48        32.05        74.47       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-A1ZJ 
       27.62       312.07        32.78        42.08        12.92        36.33 
TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F9 TCGA-FS-A4FD 
      136.27         4.47         3.06        30.90        13.28        80.68 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GN-A264 
       55.59        11.54        19.30         9.90         6.05       117.93 
TCGA-GN-A265 TCGA-GN-A26A TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-GN-A9SD TCGA-LH-A9QB 
       96.92         7.59        34.49        46.92        59.41        85.05 
TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A690 TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A828 
        7.23        18.05         0.20         0.33       174.12       120.07 
TCGA-W3-AA1Q TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8ZN 
       44.05       185.13        92.84         1.15        59.64        12.69 
TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 
       21.90        62.89        10.95         1.94        31.99        18.31 
TCGA-YG-AA3O TCGA-Z2-AA3S 
       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 
            45.07             48.66 
[1] "0.2 - 297.0 (45.1)" "0.0 - 346.5 (48.7)"
[1] "hr=" "1.1"
D51V2, survival
                   sevent
clus2                 0   1
  5Q LOSS MUTATED    42  53
  5Q LOSS WILD-TYPE 128 134
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               95               262 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               53               134 
$`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        77.56        76.57        36.03 
TCGA-DA-A1I0 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A3F5 TCGA-DA-A95Y TCGA-EB-A5KH 
       20.38       120.00        73.84       225.96        14.14        20.35 
TCGA-EB-A5UL TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A185 TCGA-EE-A20H TCGA-EE-A29C 
       29.29        29.82        27.22         4.96       168.26        78.97 
TCGA-EE-A29E TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29V TCGA-EE-A2A2 TCGA-EE-A2GB 
       63.78        56.84        56.42        25.87        59.64        59.28 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GM 
      340.14       173.79       220.24        48.72       107.38        75.48 
TCGA-EE-A2GR TCGA-EE-A2GT TCGA-EE-A2M6 TCGA-EE-A2MJ TCGA-EE-A2MM TCGA-EE-A2MQ 
       42.77        44.88       129.27        96.23       167.90        43.23 
TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AH TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3JB 
      122.73        28.77       138.81        36.95        64.08       201.80 
TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A2NE TCGA-ER-A2NH TCGA-FR-A44A TCGA-FR-A69P 
        9.17        98.40        20.15        32.05       174.21        15.72 
TCGA-FS-A1YX TCGA-FS-A1ZB TCGA-FS-A1ZG TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZT 
       48.59        48.85         9.70       101.26       133.55        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-A825 TCGA-W3-AA1R 
       50.10         0.23        65.88       297.90        63.02       111.09 
TCGA-W3-AA1V TCGA-WE-A8ZM TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AAA4 
       42.08       101.33        35.80        49.51        24.99 

$`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-D3-A8GV TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A3Z3 
      117.17       167.70       151.53        54.67         3.65        22.29 
TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EG TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 
        9.90        25.18        22.95       144.89       207.48       176.55 
TCGA-DA-A1I4 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
       35.93        53.92        65.92        40.60        68.09        33.93 
TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-DA-A95V TCGA-DA-A95W TCGA-DA-A95X TCGA-DA-A95Z 
       10.49        15.68        72.10        25.15        61.81        13.02 
TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A5VV 
       13.87        10.36        68.25        54.02        58.92         7.04 
TCGA-EB-A6L9 TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
       36.46         8.65        94.98        33.73        14.70        26.89 
TCGA-EE-A184 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29A 
       68.15       133.81       151.27        91.56        13.55        63.35 
TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N 
       85.08        13.97        72.07        64.64         2.60        18.61 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A29X 
       66.74        14.47        61.28       369.93       195.02        17.92 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GC TCGA-EE-A2GK 
       46.82       115.96        39.29        86.14        67.43        54.74 
TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2GU 
       79.66       102.12       126.81        13.91        81.21        94.82 
TCGA-EE-A2M5 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME 
       21.67        28.83        19.76        61.51        47.28       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       180.39       216.66 
TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU 
       47.54       248.65       134.40       162.48        71.21        53.26 
TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3J3 
      124.31        64.04        54.51        13.81        41.59       172.18 
TCGA-EE-A3J4 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH 
      127.20        34.32        53.19        27.35        51.35       134.33 
TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A19A 
      152.81        31.40        35.44        13.94        50.76        77.75 
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-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
       49.48         8.88       148.18        79.99        43.82        23.34 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL 
       16.37        31.27       247.04        93.01        46.98        33.21 
TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 
       12.95       149.03        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        46.45        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        96.92        32.48        48.00        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-A690 TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A828 
       18.05         0.20         0.33         0.69       228.16       121.08 
TCGA-W3-AA1O TCGA-W3-AA1Q TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K1 
        4.01        69.07       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        17.95        58.98        70.52        63.22        11.80 
TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-YD-A89C TCGA-YD-A9TA TCGA-YG-AA3O 
       12.16        40.41        21.40         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 

  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 
           56.840            50.825 
[1] "0.2 - 340.1 (56.8)" "0.2 - 369.9 (50.8)"
[1] "hr=" "1"  
D51V3, continuous
                   vv
clus                I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  5Q LOSS MUTATED             4       3      10        4        5        9
  5Q LOSS WILD-TYPE           9       4      19       14       23       16
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  5Q LOSS MUTATED           2         4         5        11          5
  5Q LOSS WILD-TYPE        12        15        10        29         10
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  5Q LOSS MUTATED           11         14        4
  5Q LOSS WILD-TYPE         22         41       17
D51V4, multiclass
             clus
vv            5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  I OR II NOS               4                 9
  STAGE 0                   3                 4
  STAGE I                  10                19
  STAGE IA                  4                14
  STAGE IB                  5                23
  STAGE II                  9                16
  STAGE IIA                 2                12
  STAGE IIB                 4                15
  STAGE IIC                 5                10
  STAGE III                11                29
  STAGE IIIA                5                10
  STAGE IIIB               11                22
  STAGE IIIC               14                41
  STAGE IV                  4                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 LOSS MUTATED      17 19 21 23
  5Q LOSS WILD-TYPE    47 54 57 47
D51V5, multiclass
       clus
vv      5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  T0+T1              17                47
  T2                 19                54
  T3                 21                57
  T4                 23                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
  5Q LOSS MUTATED    46  23  10  10
  5Q LOSS WILD-TYPE 131  42  29  35
D51V6, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  N0              46               131
  N1              23                42
  N2              10                29
  N3              10                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"
D51V7, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED    88   4
  5Q LOSS WILD-TYPE 230  18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     88    4
  5Q LOSS WILD-TYPE  230   18
   clus
vv  5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  0              88               230
  1               4                18
[1] 2 2
[1] FALSE
D51V8, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED    33  26
  5Q LOSS WILD-TYPE 101  64
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     33   26
  5Q LOSS WILD-TYPE  101   64
     clus
vv    5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  NO               33               101
  YES              26                64
[1] 2 2
[1] FALSE
D51V9, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED     8  91
  5Q LOSS WILD-TYPE  39 228
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      8   91
  5Q LOSS WILD-TYPE   39  228
     clus
vv    5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  NO                8                39
  YES              91               228
[1] 2 2
[1] FALSE
D51V10, continuous
D51V11, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED    38  61
  5Q LOSS WILD-TYPE  99 168
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     38   61
  5Q LOSS WILD-TYPE   99  168
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  FEMALE              38                99
  MALE                61               168
[1] 2 2
[1] FALSE
D51V12, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED    81  18
  5Q LOSS WILD-TYPE 236  29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     81   18
  5Q LOSS WILD-TYPE  236   29
     clus
vv    5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  NO               81               236
  YES              18                29
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  5Q LOSS MUTATED       2                         1    94
  5Q LOSS WILD-TYPE     3                         0   258
D51V13, multiclass
                           clus
vv                          5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  ASIAN                                   2                 3
  BLACK OR AFRICAN AMERICAN               1                 0
  WHITE                                  94               258
[1] 3 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  94
  5Q LOSS WILD-TYPE   7 257
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      0   94
  5Q LOSS WILD-TYPE    7  257
                        clus
vv                       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 7
  NOT HISPANIC OR LATINO              94               257
[1] 2 2
[1] FALSE

Clustering(52) Variable = 6P LOSS MUTATION ANALYSIS
D52V1, survival
                   sevent
clus2                 0   1
  6P LOSS MUTATED    20  25
  6P LOSS WILD-TYPE 102  98
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               45               200 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               25                98 
$`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        69.21        22.85       138.67        53.65        58.85 
TCGA-DA-A3F5 TCGA-DA-A95X TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A29D TCGA-EE-A29G 
      225.11        52.90        24.89        62.37        12.99        44.28 
TCGA-EE-A29Q TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2GL TCGA-EE-A2M6 TCGA-EE-A2M7 
       61.12       185.19       115.43        32.48       103.13        15.25 
TCGA-EE-A2MC TCGA-EE-A3J4 TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A2NE TCGA-ER-A42L 
       23.77       111.85        53.29        11.47        16.87        74.47 
TCGA-FR-A8YC TCGA-FS-A1ZG TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FW-A3TU 
       10.06         7.82       130.95       136.27        35.28        55.59 
TCGA-GN-A4U4 TCGA-QB-A6FS TCGA-WE-A8ZM 
       34.49         7.23        65.42 

$`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        76.34       150.61        95.51        45.07 
TCGA-DA-A1IA TCGA-DA-A3F2 TCGA-DA-A95V TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q 
       64.83        30.44        72.10        14.14        12.30         3.91 
TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A181 
       33.24        50.07        52.41        18.21        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-A29E TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29T TCGA-EE-A2A2 
        0.26        63.12        47.74        27.16       346.49        30.02 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ 
       77.98        26.14       239.11        12.95       201.60        68.65 
TCGA-EE-A2GK TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR 
       10.62        18.35        31.00       118.32         0.76         0.20 
TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M8 TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI 
       71.31        81.99         5.75       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        89.26       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        64.04 
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-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
      201.80        19.86       152.81        14.56        34.45         1.58 
TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19C TCGA-ER-A19G TCGA-ER-A19H 
       47.31         7.82         4.54        39.81       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        47.18 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NG TCGA-ER-A3ES 
      146.63        47.97        22.36         4.70        10.95       173.29 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7U8 
       68.52        15.48        32.05       174.21       209.23        26.20 
TCGA-FR-A7UA TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 
        5.65       171.78        49.74       195.98         8.35        27.62 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZJ TCGA-FS-A1ZM 
      312.07        32.78        42.08        12.92        36.33        78.61 
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-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
      173.19        13.28        80.68        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        96.92        17.06 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U8 TCGA-GN-A8LK TCGA-GN-A9SD 
       42.48         7.59       120.53        46.92        43.23        59.41 
TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-AA9O TCGA-RP-A690 TCGA-RP-A693 TCGA-W3-A824 
       85.05       297.01        18.05         0.20         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-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ 
       92.84         1.15        59.64        12.69        21.90        62.89 
TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 
       10.95        48.39         1.94        31.99        18.31        18.35 
TCGA-YG-AA3O TCGA-Z2-AA3S 
       28.21        91.23 

  6P LOSS MUTATED 6P LOSS WILD-TYPE 
             7.23              0.00 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
           225.11            346.49 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
            53.29             46.95 
[1] "7.2 - 225.1 (53.3)" "0.0 - 346.5 (47.0)"
[1] "hr=" "1.2"
D52V2, survival
                   sevent
clus2                 0   1
  6P LOSS MUTATED    28  38
  6P LOSS WILD-TYPE 142 149
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               66               291 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               38               149 
$`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        77.56        22.95       144.89       207.48        35.93 
TCGA-DA-A1I8 TCGA-DA-A1IC TCGA-DA-A3F5 TCGA-DA-A95X TCGA-EE-A17Y TCGA-EE-A180 
       53.92        68.09       225.96        61.81        27.22        94.98 
TCGA-EE-A29A TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29Q TCGA-EE-A29W TCGA-EE-A29X 
       63.35        13.97        72.07        66.74       195.02        17.92 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2GL TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 
       46.82       115.96        79.66        21.67       129.27        28.83 
TCGA-EE-A2MC TCGA-EE-A3J4 TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19J TCGA-ER-A19T 
       61.51       127.20        98.40        12.59         6.44         8.88 
TCGA-ER-A2NE TCGA-ER-A42L TCGA-FR-A69P TCGA-FR-A8YC TCGA-FS-A1YX TCGA-FS-A1ZB 
       20.15       149.03        15.72        34.82        48.59        48.85 
TCGA-FS-A1ZG TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FW-A3TU 
        9.70       133.55        11.41       148.80        53.16        55.59 
TCGA-GN-A4U4 TCGA-HR-A2OG TCGA-QB-A6FS TCGA-WE-A8JZ TCGA-WE-A8ZM TCGA-YG-AA3P 
       39.35         0.23         7.23        24.03       101.33        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-D3-A8GV TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A1X3 
      167.70       151.53        54.67         3.65         7.10        18.12 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-DA-A1HV TCGA-DA-A1HW 
       15.39        22.29        18.44         9.90        76.57        36.03 
TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IB 
       20.38       176.55       120.00        73.84        65.92        40.60 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-DA-A95V TCGA-DA-A95W TCGA-DA-A95Y 
       33.93        10.49        15.68        72.10        25.15        14.14 
TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH 
       13.02        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 
       29.29        58.92         7.04        36.46        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-A20H TCGA-EE-A20I TCGA-EE-A29B TCGA-EE-A29C 
      151.27        91.56       168.26        13.55        85.08        78.97 
TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P 
       63.78        64.64         2.60        56.84        18.61        56.42 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A2A2 TCGA-EE-A2A5 
       14.47        61.28       369.93        25.87        59.64        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       173.79       220.24 
TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO 
       48.72       107.38        54.74        75.48       102.12       126.81 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M8 
       13.91        42.77        81.21        44.88        94.82        19.76 
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       180.39       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        64.04        28.77        54.51        13.81        41.59 
TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA 
      138.81       172.18        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       134.33       152.81        31.40 
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-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M 
       13.02        26.37       268.93       152.35       131.51        61.05 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 
       44.05       162.08        50.89        49.48       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-A3PL TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A 
       93.01        46.98        33.21        12.95        92.98       174.21 
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-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 
      216.92       228.59       202.65        20.91        28.08         7.79 
TCGA-FS-A1ZA TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZH 
       27.72       357.37        53.52        46.45        15.45        32.75 
TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZU TCGA-FS-A1ZW 
       47.38        23.93       101.26        74.73        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-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 
       22.92        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        96.92        10.13        64.44 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A4U7 TCGA-GN-A4U8 
       62.79        32.48        48.00       121.91        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-AA9O TCGA-RP-A690 TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 
      297.90        18.05         0.20         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        17.95        58.98 
TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AA9Y 
       70.52        63.22        11.80        35.80        49.51        12.16 
TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YD-A89C TCGA-YD-A9TA TCGA-YG-AA3O 
       40.41        21.40        24.99         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 
           225.96            369.93 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
            53.54             51.35 
[1] "0.2 - 226.0 (53.5)" "0.2 - 369.9 (51.4)"
[1] "hr=" "1.2"
D52V3, continuous
                   vv
clus                I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  6P LOSS MUTATED             5       2       6        1        5        5
  6P LOSS WILD-TYPE           8       5      23       17       23       20
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  6P LOSS MUTATED           3         5         1         7          5
  6P LOSS WILD-TYPE        11        14        14        33         10
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  6P LOSS MUTATED            6         11        3
  6P LOSS WILD-TYPE         27         44       18
D52V4, multiclass
             clus
vv            6P LOSS MUTATED 6P LOSS WILD-TYPE
  I OR II NOS               5                 8
  STAGE 0                   2                 5
  STAGE I                   6                23
  STAGE IA                  1                17
  STAGE IB                  5                23
  STAGE II                  5                20
  STAGE IIA                 3                11
  STAGE IIB                 5                14
  STAGE IIC                 1                14
  STAGE III                 7                33
  STAGE IIIA                5                10
  STAGE IIIB                6                27
  STAGE IIIC               11                44
  STAGE IV                  3                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
  6P LOSS MUTATED      10 14 18 12
  6P LOSS WILD-TYPE    54 59 60 58
D52V5, multiclass
       clus
vv      6P LOSS MUTATED 6P LOSS WILD-TYPE
  T0+T1              10                54
  T2                 14                59
  T3                 18                60
  T4                 12                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
  6P LOSS MUTATED    34  14   9   8
  6P LOSS WILD-TYPE 143  51  30  37
D52V6, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  N0              34               143
  N1              14                51
  N2               9                30
  N3               8                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"
D52V7, binary
                   cls
clus                  0   1
  6P LOSS MUTATED    62   3
  6P LOSS WILD-TYPE 256  19
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     62    3
  6P LOSS WILD-TYPE  256   19
   clus
vv  6P LOSS MUTATED 6P LOSS WILD-TYPE
  0              62               256
  1               3                19
[1] 2 2
[1] FALSE
D52V8, binary
                   cls
clus                  0   1
  6P LOSS MUTATED    23  20
  6P LOSS WILD-TYPE 111  70
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     23   20
  6P LOSS WILD-TYPE  111   70
     clus
vv    6P LOSS MUTATED 6P LOSS WILD-TYPE
  NO               23               111
  YES              20                70
[1] 2 2
[1] FALSE
D52V9, binary
                   cls
clus                  0   1
  6P LOSS MUTATED     9  59
  6P LOSS WILD-TYPE  38 260
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      9   59
  6P LOSS WILD-TYPE   38  260
     clus
vv    6P LOSS MUTATED 6P LOSS WILD-TYPE
  NO                9                38
  YES              59               260
[1] 2 2
[1] FALSE
D52V10, continuous
D52V11, binary
                   cls
clus                  0   1
  6P LOSS MUTATED    22  46
  6P LOSS WILD-TYPE 115 183
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     22   46
  6P LOSS WILD-TYPE  115  183
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  FEMALE              22               115
  MALE                46               183
[1] 2 2
[1] FALSE
D52V12, binary
                   cls
clus                  0   1
  6P LOSS MUTATED    58  10
  6P LOSS WILD-TYPE 259  37
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     58   10
  6P LOSS WILD-TYPE  259   37
     clus
vv    6P LOSS MUTATED 6P LOSS WILD-TYPE
  NO               58               259
  YES              10                37
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  6P LOSS MUTATED       1                         0    64
  6P LOSS WILD-TYPE     4                         1   288
D52V13, multiclass
                           clus
vv                          6P LOSS MUTATED 6P LOSS WILD-TYPE
  ASIAN                                   1                 4
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  64               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"
D52V14, binary
                   cls
clus                  0   1
  6P LOSS MUTATED     1  63
  6P LOSS WILD-TYPE   6 288
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      1   63
  6P LOSS WILD-TYPE    6  288
                        clus
vv                       6P LOSS MUTATED 6P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 6
  NOT HISPANIC OR LATINO              63               288
[1] 2 2
[1] FALSE

Clustering(53) Variable = 6Q LOSS MUTATION ANALYSIS
D53V1, survival
                   sevent
clus2                0  1
  6Q LOSS MUTATED   62 58
  6Q LOSS WILD-TYPE 60 65
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
              120               125 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               58                65 
$`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        69.21        22.85 
TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC 
       76.34       138.67        53.65        45.07        64.83        58.85 
TCGA-DA-A3F5 TCGA-DA-A95V TCGA-DA-A95X TCGA-DA-A95Y TCGA-EB-A5UN TCGA-EE-A17Y 
      225.11        72.10        52.90        14.14        52.41        24.89 
TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A184 TCGA-EE-A29C TCGA-EE-A29D 
       62.37        20.38         0.00        67.50        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-A2GB TCGA-EE-A2GD TCGA-EE-A2GE 
      115.43        30.02        77.98        26.14       239.11        12.95 
TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GU TCGA-EE-A2M6 
       32.48        31.00       118.32         0.76        81.99       103.13 
TCGA-EE-A2M7 TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MP TCGA-EE-A2MT TCGA-EE-A3AC 
       15.25        23.77       209.79       227.01        23.51        64.04 
TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3JB TCGA-EE-A3JH 
        4.41         6.28       111.85        45.90       201.80        19.86 
TCGA-ER-A195 TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19N TCGA-ER-A19P 
       34.45         7.82        53.29        11.47        42.48       120.76 
TCGA-ER-A2NE TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A7U8 TCGA-FR-A8YC TCGA-FS-A1Z0 
       16.87        32.05        74.47        26.20        10.06       195.98 
TCGA-FS-A1ZC TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ 
      312.07        12.92         7.82        36.33        78.61       130.95 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZZ TCGA-FW-A3TU 
      136.27        35.28         4.47        23.21         3.06        55.59 
TCGA-GF-A4EO TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 
        6.05       117.93        17.06        42.48         7.59       120.53 
TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A693 
       34.49        46.92        85.05       297.01         7.23         0.33 
TCGA-W3-AA1R TCGA-WE-A8ZM TCGA-WE-A8ZQ TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O 
       79.99        65.42        62.89        18.31        18.35        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-A95Z TCGA-EB-A44Q TCGA-EB-A5SG TCGA-EB-A5SH 
       95.51        30.44        12.30         3.91        33.24        50.07 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A20C TCGA-EE-A20H TCGA-EE-A29B TCGA-EE-A29E 
       18.21        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       201.60        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        89.26 
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        47.18       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        68.52        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        42.08         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        96.92        43.23        59.41        18.05 
TCGA-RP-A690 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1Q TCGA-W3-AA1V 
        0.20       174.12         1.97       120.07        44.05         8.09 
TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8ZN TCGA-WE-A8ZO 
      185.13        92.84         1.15        59.64        12.69        21.90 
TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-Z2-AA3S 
       10.95        48.39         1.94        31.99        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 
            47.33             47.18 
[1] "0.0 - 346.5 (47.3)" "0.2 - 209.2 (47.2)"
[1] "hr=" "1.2"
D53V2, survival
                   sevent
clus2                0  1
  6Q LOSS MUTATED   78 89
  6Q LOSS WILD-TYPE 92 98
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
              167               190 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               89                98 
$`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        77.56        22.95        76.57 
TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I4 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA 
      144.89       207.48        35.93        73.84        53.92        65.92 
TCGA-DA-A1IC TCGA-DA-A3F5 TCGA-DA-A95V TCGA-DA-A95W TCGA-DA-A95X TCGA-DA-A95Y 
       68.09       225.96        72.10        25.15        61.81        14.14 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 
       29.29        58.92        27.22        94.98        33.73        14.70 
TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20I TCGA-EE-A29A 
       26.89        68.15         4.96       133.81        13.55        63.35 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29Q 
       78.97        13.97        72.07        64.64        56.84        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-A2GD 
      115.96        59.64        39.29        86.14        59.28       340.14 
TCGA-EE-A2GE TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GU 
      173.79        79.66       102.12       126.81        13.91        94.82 
TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MP 
       21.67       129.27        28.83        61.51       268.73       248.65 
TCGA-EE-A2MT TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3J4 
       71.21        64.04        28.77        13.81        41.59       127.20 
TCGA-EE-A3J7 TCGA-EE-A3JB TCGA-EE-A3JH TCGA-ER-A195 TCGA-ER-A199 TCGA-ER-A19B 
       64.08       201.80       134.33        35.44         9.17        98.40 
TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19T 
       12.59        26.37         6.44        44.05       162.08         8.88 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A3PL TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A69P 
       20.15        16.37        33.21        12.95       149.03        15.72 
TCGA-FR-A7U8 TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FS-A1YX TCGA-FS-A1Z0 TCGA-FS-A1ZB 
       27.85        34.82        36.26        48.59       202.65        48.85 
TCGA-FS-A1ZC TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZM 
      357.37        15.45         9.70        32.75        47.38       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-A4F5 TCGA-FS-A4FB TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-GF-A4EO 
       27.02        28.73        26.73        22.92        55.59         7.23 
TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 
      117.93        64.44        62.79        32.48       121.91        39.35 
TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LL TCGA-HR-A2OG TCGA-LH-A9QB 
       10.42        48.89        22.13        21.37         0.23       368.78 
TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A693 TCGA-W3-AA1R TCGA-WE-A8JZ TCGA-WE-A8ZM 
      297.90         7.23         0.33       111.09        24.03       101.33 
TCGA-WE-A8ZQ TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-YG-AA3P 
       63.22        21.40        24.99        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-D3-A8GV TCGA-D9-A149 TCGA-D9-A1X3 TCGA-D9-A3Z1 
      129.63       117.17       167.70        54.67        18.12        15.39 
TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I5 
       18.44         9.90        36.03        20.38       176.55       120.00 
TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-DA-A95Z TCGA-EB-A44Q 
       40.60        33.93        10.49        15.68        13.02        13.87 
TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5VV TCGA-EB-A6L9 
       10.36        20.35        68.25        54.02         7.04        36.46 
TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29B 
       29.82         8.65       151.27        91.56       168.26        85.08 
TCGA-EE-A29E TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A2GC 
       63.78         2.60        18.61        56.42        14.47        67.43 
TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GM TCGA-EE-A2GR 
      220.24        48.72       107.38        54.74        75.48        42.77 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2M8 TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG 
       81.21        44.88        19.76        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       180.39       216.66       167.90 
TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AA 
       47.54        43.23       134.40       162.48        53.26       124.31 
TCGA-EE-A3AB TCGA-EE-A3AE TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J5 TCGA-EE-A3J8 
      122.73        54.51       138.81       172.18        36.95        34.32 
TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A197 
       53.19        27.35        51.35       152.81        31.40        13.94 
TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19C TCGA-ER-A19E TCGA-ER-A19G TCGA-ER-A19H 
       50.76        77.75        48.89        13.02       268.93       152.35 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 
      131.51        61.05        50.89        49.48       148.18        79.99 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET 
       43.82        23.34        31.27        32.05       247.04        93.01 
TCGA-ER-A3EV TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7U9 TCGA-FR-A7UA 
       46.98        92.98       174.21       220.80        18.77        38.27 
TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 
      104.42       216.92       228.59        20.91        28.08         7.79 
TCGA-FS-A1ZA TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZY 
       27.72        53.52        46.45        23.93        74.73        27.09 
TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FC 
       77.82        50.14        66.67       174.84        34.03        54.41 
TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 
       80.68         0.20        13.51        19.30         9.90         2.04 
TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A26D TCGA-GN-A8LK 
       15.78       139.89        96.92        10.13        48.00        50.10 
TCGA-GN-A9SD TCGA-HR-A2OH TCGA-QB-AA9O TCGA-RP-A690 TCGA-RP-A694 TCGA-W3-A824 
       59.41        65.88        18.05         0.20         0.69       228.16 
TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1Q TCGA-W3-AA1V TCGA-W3-AA1W 
       63.02       121.08         4.01        69.07        42.08       219.16 
TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZN TCGA-WE-A8ZO 
      105.04        49.05        61.15        17.95        58.98        70.52 
TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-YD-A89C 
       11.80        35.80        49.51        12.16        40.41         6.90 
TCGA-YD-A9TA TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
       49.18        27.58        96.99        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 
           55.590            50.825 
[1] "0.2 - 369.9 (55.6)" "0.2 - 268.9 (50.8)"
[1] "hr=" "1"  
D53V3, continuous
                   vv
clus                I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  6Q LOSS MUTATED             7       4      12        7       14        9
  6Q LOSS WILD-TYPE           6       3      17       11       14       16
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  6Q LOSS MUTATED           7         8         8        19          8
  6Q LOSS WILD-TYPE         7        11         7        21          7
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  6Q LOSS MUTATED           16         28        7
  6Q LOSS WILD-TYPE         17         27       14
D53V4, multiclass
             clus
vv            6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  I OR II NOS               7                 6
  STAGE 0                   4                 3
  STAGE I                  12                17
  STAGE IA                  7                11
  STAGE IB                 14                14
  STAGE II                  9                16
  STAGE IIA                 7                 7
  STAGE IIB                 8                11
  STAGE IIC                 8                 7
  STAGE III                19                21
  STAGE IIIA                8                 7
  STAGE IIIB               16                17
  STAGE IIIC               28                27
  STAGE IV                  7                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
  6Q LOSS MUTATED      28 39 34 31
  6Q LOSS WILD-TYPE    36 34 44 39
D53V5, multiclass
       clus
vv      6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  T0+T1              28                36
  T2                 39                34
  T3                 34                44
  T4                 31                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   78 35 20 21
  6Q LOSS WILD-TYPE 99 30 19 24
D53V6, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  N0              78                99
  N1              35                30
  N2              20                19
  N3              21                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"
D53V7, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED   153   8
  6Q LOSS WILD-TYPE 165  14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED    153    8
  6Q LOSS WILD-TYPE  165   14
   clus
vv  6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  0             153               165
  1               8                14
[1] 2 2
[1] FALSE
D53V8, binary
                   cls
clus                 0  1
  6Q LOSS MUTATED   57 49
  6Q LOSS WILD-TYPE 77 41
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     57   49
  6Q LOSS WILD-TYPE   77   41
     clus
vv    6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  NO               57                77
  YES              49                41
[1] 2 2
[1] FALSE
D53V9, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED    22 150
  6Q LOSS WILD-TYPE  25 169
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     22  150
  6Q LOSS WILD-TYPE   25  169
     clus
vv    6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  NO               22                25
  YES             150               169
[1] 2 2
[1] FALSE
D53V10, continuous
D53V11, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED    69 103
  6Q LOSS WILD-TYPE  68 126
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     69  103
  6Q LOSS WILD-TYPE   68  126
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  FEMALE              69                68
  MALE               103               126
[1] 2 2
[1] FALSE
D53V12, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED   148  24
  6Q LOSS WILD-TYPE 169  23
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED    148   24
  6Q LOSS WILD-TYPE  169   23
     clus
vv    6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  NO              148               169
  YES              24                23
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  6Q LOSS MUTATED       1                         1   165
  6Q LOSS WILD-TYPE     4                         0   187
D53V13, multiclass
                           clus
vv                          6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  ASIAN                                   1                 4
  BLACK OR AFRICAN AMERICAN               1                 0
  WHITE                                 165               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"
D53V14, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED     3 164
  6Q LOSS WILD-TYPE   4 187
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      3  164
  6Q LOSS WILD-TYPE    4  187
                        clus
vv                       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   3                 4
  NOT HISPANIC OR LATINO             164               187
[1] 2 2
[1] FALSE

Clustering(54) Variable = 7P LOSS MUTATION ANALYSIS
D54V1, survival
                   sevent
clus2                 0   1
  7P LOSS MUTATED     5   6
  7P LOSS WILD-TYPE 117 117
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               11               234 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                6               117 
$`7P LOSS MUTATED`
TCGA-D3-A1QA TCGA-D3-A3CE TCGA-EE-A20C TCGA-EE-A29M TCGA-EE-A3JI TCGA-ER-A198 
       76.41        59.70        75.55        47.74       152.81        47.31 
TCGA-FR-A7U8 TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-W3-A828 
       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        69.21        22.85        76.34       138.67        53.65 
TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 
      150.61        95.51        45.07        64.83        58.85        30.44 
TCGA-DA-A3F5 TCGA-DA-A95V TCGA-DA-A95X TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q 
      225.11        72.10        52.90        14.14        12.30         3.91 
TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y 
       33.24        50.07        52.41        18.21        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-A29G TCGA-EE-A29H TCGA-EE-A29P 
       76.14        12.99         0.26        44.28        63.12        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       115.43        30.02        77.98 
TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK 
       26.14       239.11        12.95       201.60        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        89.26       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        64.04         4.41        54.51         6.28 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH 
       67.89       111.85        45.90         3.35       201.80        19.86 
TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B 
       14.56        34.45         1.58         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        47.18       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        68.52 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7UA 
       15.48        32.05        74.47       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        42.08        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 
       96.92        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-A690 TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-AA1Q 
       18.05         0.20         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 
       65.42        12.69        21.90        62.89        10.95        48.39 
TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-Z2-AA3S 
        1.94        31.99        18.31        18.35        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 
           59.700            46.455 
[1] "4.5 - 152.8 (59.7)" "0.0 - 346.5 (46.5)"
[1] "hr=" "1"  
D54V2, survival
                   sevent
clus2                 0   1
  7P LOSS MUTATED     7  11
  7P LOSS WILD-TYPE 163 176
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               18               339 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               11               176 
$`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-D3-A8GV TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW 
      129.63       117.17       167.70       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        77.56        22.95        76.57        36.03       144.89 
TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 
       20.38       207.48       176.55        35.93       120.00        73.84 
TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
       53.92        65.92        40.60        68.09        33.93        10.49 
TCGA-DA-A3F5 TCGA-DA-A95V TCGA-DA-A95W TCGA-DA-A95X TCGA-DA-A95Y TCGA-DA-A95Z 
      225.96        72.10        25.15        61.81        14.14        13.02 
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        29.29        58.92 
TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 
        7.04        36.46        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       115.96        59.64        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       173.79       220.24        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       180.39 
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        64.04 
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       134.33        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        49.48         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-ER-A42L 
      247.04        93.01        46.98        33.21        12.95       149.03 
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-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        46.45        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-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-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        96.92 
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        48.00       121.91 
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-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-A690 TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-AA1O 
        0.20         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-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO 
       49.05        61.15        17.95       101.33        58.98        70.52 
TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 
       63.22        11.80        35.80        49.51        12.16        40.41 
TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YD-A89C TCGA-YD-A9TA TCGA-YG-AA3O TCGA-YG-AA3P 
       21.40        24.99         6.90        49.18        37.94        14.43 
TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
       27.58        96.99        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            51.350 
[1] "10.4 - 152.8 (53.2)" "0.2 - 369.9 (51.4)" 
[1] "hr=" "1.3"
D54V3, continuous
                   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          13       6      27       17       24       24
                   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        13        38         15
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  7P LOSS MUTATED            3          1        0
  7P LOSS WILD-TYPE         30         54       21
D54V4, multiclass
             clus
vv            7P LOSS MUTATED 7P LOSS WILD-TYPE
  I OR II NOS               0                13
  STAGE 0                   1                 6
  STAGE I                   2                27
  STAGE IA                  1                17
  STAGE IB                  4                24
  STAGE II                  1                24
  STAGE IIA                 0                14
  STAGE IIB                 0                19
  STAGE IIC                 2                13
  STAGE III                 2                38
  STAGE IIIA                0                15
  STAGE IIIB                3                30
  STAGE IIIC                1                54
  STAGE IV                  0                21
[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 64 77 68
D54V5, multiclass
       clus
vv      7P LOSS MUTATED 7P LOSS WILD-TYPE
  T0+T1               2                62
  T2                  9                64
  T3                  1                77
  T4                  2                68
[1] 4 2
[1] TRUE
[1] "dimension of 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 167  63  36  44
D54V6, multiclass
    clus
vv   7P LOSS MUTATED 7P LOSS WILD-TYPE
  N0              10               167
  N1               2                63
  N2               3                36
  N3               1                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"
D54V7, binary
                   cls
clus                  0   1
  7P LOSS MUTATED    18   0
  7P LOSS WILD-TYPE 300  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED     18    0
  7P LOSS WILD-TYPE  300   22
   clus
vv  7P LOSS MUTATED 7P LOSS WILD-TYPE
  0              18               300
  1               0                22
[1] 2 2
[1] FALSE
D54V8, binary
                   cls
clus                  0   1
  7P LOSS MUTATED     7   4
  7P LOSS WILD-TYPE 127  86
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      7    4
  7P LOSS WILD-TYPE  127   86
     clus
vv    7P LOSS MUTATED 7P LOSS WILD-TYPE
  NO                7               127
  YES               4                86
[1] 2 2
[1] FALSE
D54V9, binary
                   cls
clus                  0   1
  7P LOSS MUTATED     2  16
  7P LOSS WILD-TYPE  45 303
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      2   16
  7P LOSS WILD-TYPE   45  303
     clus
vv    7P LOSS MUTATED 7P LOSS WILD-TYPE
  NO                2                45
  YES              16               303
[1] 2 2
[1] FALSE
D54V10, continuous
D54V11, binary
                   cls
clus                  0   1
  7P LOSS MUTATED     5  13
  7P LOSS WILD-TYPE 132 216
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      5   13
  7P LOSS WILD-TYPE  132  216
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  FEMALE               5               132
  MALE                13               216
[1] 2 2
[1] FALSE
D54V12, binary
                   cls
clus                  0   1
  7P LOSS MUTATED    16   2
  7P LOSS WILD-TYPE 301  45
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED     16    2
  7P LOSS WILD-TYPE  301   45
     clus
vv    7P LOSS MUTATED 7P LOSS WILD-TYPE
  NO               16               301
  YES               2                45
[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   335
D54V13, multiclass
                           clus
vv                          7P LOSS MUTATED 7P LOSS WILD-TYPE
  ASIAN                                   1                 4
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  17               335
[1] 3 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   7 333
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      0   18
  7P LOSS WILD-TYPE    7  333
                        clus
vv                       7P LOSS MUTATED 7P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 7
  NOT HISPANIC OR LATINO              18               333
[1] 2 2
[1] FALSE

Clustering(55) Variable = 7Q LOSS MUTATION ANALYSIS
D55V1, survival
                   sevent
clus2                 0   1
  7Q LOSS MUTATED     5   8
  7Q LOSS WILD-TYPE 117 115
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               13               232 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                8               115 
$`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        42.08        35.28         4.47        30.90       120.07 
TCGA-WE-A8ZM 
       65.42 

$`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        69.21        22.85        76.34       138.67        53.65 
TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 
      150.61        95.51        45.07        64.83        58.85        30.44 
TCGA-DA-A3F5 TCGA-DA-A95V TCGA-DA-A95X TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q 
      225.11        72.10        52.90        14.14        12.30         3.91 
TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y 
       33.24        50.07        52.41        18.21        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-A29P 
       75.22        76.14         0.26        44.28        63.12        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       115.43        30.02        77.98 
TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK 
       26.14       239.11        12.95       201.60        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        89.26       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        64.04         4.41        54.51         6.28        67.89 
TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH TCGA-ER-A193 
      111.85        45.90         3.35       201.80        19.86        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-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-A1A1 TCGA-ER-A2NC 
       42.48       120.76        49.71        47.18        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        68.52        15.48 
TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7UA 
       32.05        74.47       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-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM 
      312.07        32.78        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-A4F4 
      130.95       136.27        23.21         5.29         3.06        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        96.92 
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-A690 TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-AA1Q TCGA-W3-AA1R 
        0.20         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 
       21.90        62.89        10.95        48.39         1.94        31.99 
TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-Z2-AA3S 
       18.31        18.35        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 
            47.74             47.08 
[1] "4.5 - 152.8 (47.7)" "0.0 - 346.5 (47.1)"
[1] "hr=" "1.3"
D55V2, survival
                   sevent
clus2                 0   1
  7Q LOSS MUTATED     5  12
  7Q LOSS WILD-TYPE 165 175
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               17               340 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               12               175 
$`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        46.45        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       101.33 

$`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-D3-A8GV TCGA-D9-A148 
      152.75        29.06       129.63       117.17       167.70       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        77.56        22.95        76.57 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 
       36.03       144.89        20.38       207.48       176.55        35.93 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
      120.00        73.84        53.92        65.92        40.60        68.09 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-DA-A95V TCGA-DA-A95W 
       33.93        10.49       225.96        15.68        72.10        25.15 
TCGA-DA-A95X TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5SG 
       61.81        14.14        13.02        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        29.29        58.92         7.04        36.46        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 
      115.96        59.64        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 
      173.79       220.24        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       180.39       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        64.04        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       134.33        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        49.48 
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        93.01        46.98        33.21 
TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 
       12.95       149.03        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-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ 
      133.55        11.41       148.80        49.48        27.09        27.02 
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-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
      117.93        96.92        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-A4U9 
       48.00       121.91        39.35        10.42        48.89        22.13 
TCGA-GN-A8LK TCGA-GN-A9SD TCGA-HR-A2OG TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X 
       50.10        59.41         0.23        65.88       368.78       297.90 
TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A690 TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 
        7.23        18.05         0.20         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-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZN 
      105.04        24.03        49.05        61.15        17.95        58.98 
TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AA9Y 
       70.52        63.22        11.80        35.80        49.51        12.16 
TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YD-A89C TCGA-YD-A9TA TCGA-YG-AA3O 
       40.41        21.40        24.99         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 

  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 
           56.840            50.825 
[1] "10.4 - 152.8 (56.8)" "0.2 - 369.9 (50.8)" 
[1] "hr=" "1.5"
D55V3, continuous
                   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          13       7      28       18       24       24
                   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        12        38         15
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  7Q LOSS MUTATED            2          1        0
  7Q LOSS WILD-TYPE         31         54       21
D55V4, multiclass
             clus
vv            7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  I OR II NOS               0                13
  STAGE 0                   0                 7
  STAGE I                   1                28
  STAGE IA                  0                18
  STAGE IB                  4                24
  STAGE II                  1                24
  STAGE IIA                 1                13
  STAGE IIB                 1                18
  STAGE IIC                 3                12
  STAGE III                 2                38
  STAGE IIIA                0                15
  STAGE IIIB                2                31
  STAGE IIIC                1                54
  STAGE IV                  0                21
[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 66 76 66
D55V5, multiclass
       clus
vv      7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  T0+T1               1                63
  T2                  7                66
  T3                  2                76
  T4                  4                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
  7Q LOSS MUTATED    10   4   1   0
  7Q LOSS WILD-TYPE 167  61  38  45
D55V6, multiclass
    clus
vv   7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  N0              10               167
  N1               4                61
  N2               1                38
  N3               0                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"
D55V7, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED    16   0
  7Q LOSS WILD-TYPE 302  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED     16    0
  7Q LOSS WILD-TYPE  302   22
   clus
vv  7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  0              16               302
  1               0                22
[1] 2 2
[1] FALSE
D55V8, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED     7   5
  7Q LOSS WILD-TYPE 127  85
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      7    5
  7Q LOSS WILD-TYPE  127   85
     clus
vv    7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  NO                7               127
  YES               5                85
[1] 2 2
[1] FALSE
D55V9, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED     1  16
  7Q LOSS WILD-TYPE  46 303
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      1   16
  7Q LOSS WILD-TYPE   46  303
     clus
vv    7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  NO                1                46
  YES              16               303
[1] 2 2
[1] FALSE
D55V10, continuous
D55V11, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED     6  11
  7Q LOSS WILD-TYPE 131 218
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      6   11
  7Q LOSS WILD-TYPE  131  218
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  FEMALE               6               131
  MALE                11               218
[1] 2 2
[1] FALSE
D55V12, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED    14   3
  7Q LOSS WILD-TYPE 303  44
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED     14    3
  7Q LOSS WILD-TYPE  303   44
     clus
vv    7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  NO               14               303
  YES               3                44
[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   336
D55V13, multiclass
                           clus
vv                          7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  ASIAN                                   1                 4
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  16               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"
D55V14, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED     0  17
  7Q LOSS WILD-TYPE   7 334
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      0   17
  7Q LOSS WILD-TYPE    7  334
                        clus
vv                       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 7
  NOT HISPANIC OR LATINO              17               334
[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 103  90
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               52               193 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               33                90 
$`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        18.21        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        64.04        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        47.18         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        96.92       297.01         7.23        18.05        79.99 
TCGA-WE-A8ZY TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-Z2-AA3S 
       48.39        31.99        18.31        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        69.21        22.85        76.34 
TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IC 
      138.67        53.65       150.61        95.51        45.07        58.85 
TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A95V TCGA-DA-A95X TCGA-DA-A95Y TCGA-DA-A95Z 
       30.44       225.11        72.10        52.90        14.14        12.30 
TCGA-EB-A44Q TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y 
        3.91        33.24        50.07        52.41        13.15        24.89 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A184 TCGA-EE-A20H TCGA-EE-A29B TCGA-EE-A29D 
       20.38         0.00        67.50       155.90        75.22        12.99 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W 
        0.26        44.28        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 
      115.43        30.02        77.98        26.14       239.11        12.95 
TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN 
      201.60        68.65        10.62        32.48        18.35        31.00 
TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 
      118.32         0.76         0.20        81.99       103.13        15.25 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MR 
        5.75        23.77        63.25        89.26       104.78        25.08 
TCGA-EE-A2MT TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J4 
       23.51       122.73         4.41        54.51         6.28       111.85 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 
       45.90         3.35       201.80        19.86        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-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET 
      146.63        47.97        22.36        10.95       173.29        68.52 
TCGA-ER-A3EV TCGA-ER-A42L TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7UA 
       15.48        74.47       174.21       209.23        26.20         5.65 
TCGA-FS-A1YW TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF 
      171.78         8.35        27.62        32.78        42.08        12.92 
TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZU 
        7.82        36.33        78.61       130.95       136.27         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-A267 TCGA-GN-A268 TCGA-GN-A26A 
        6.05         1.91        53.29        17.06        42.48         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-RP-A690 TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1Q 
        0.20         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        65.42 
TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-AA9Y TCGA-WE-AAA4 
       12.69        21.90        62.89        10.95         1.94        18.35 
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 
           62.745            44.050 
[1] "1.6 - 312.1 (62.7)" "0.0 - 346.5 (44.0)"
[1] "hr=" "1.1"
D56V2, survival
                   sevent
clus2                 0   1
  8P LOSS MUTATED    28  39
  8P LOSS WILD-TYPE 142 148
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               67               290 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               39               148 
$`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        36.46 
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        64.04       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 
       49.48         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        96.92       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        40.41        21.40        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-D3-A8GV 
      161.00       152.75        29.06       129.63       117.17       167.70 
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-A6E9 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY 
        9.90        77.56        22.95        76.57        36.03       144.89 
TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 
       20.38       207.48       176.55        35.93       120.00        73.84 
TCGA-DA-A1I8 TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 
       53.92        40.60        68.09        33.93        10.49       225.96 
TCGA-DA-A3F8 TCGA-DA-A95V TCGA-DA-A95W TCGA-DA-A95X TCGA-DA-A95Y TCGA-DA-A95Z 
       15.68        72.10        25.15        61.81        14.14        13.02 
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        29.29 
TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A181 
       58.92         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       115.96        59.64 
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       173.79       220.24 
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       180.39       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       134.33        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        93.01        46.98        12.95 
TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 
      149.03        92.98       174.21        15.72       220.80        27.85 
TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YX 
       18.77        38.27        36.26       104.42       216.92        48.59 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZB TCGA-FS-A1ZD TCGA-FS-A1ZE 
       20.91        28.08         7.79        48.85        53.52        46.45 
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-A1ZU TCGA-FS-A1ZW 
       74.73       133.55        11.41       148.80        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-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
       15.78       139.89        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-A4U9 
       48.00       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-RP-A690 TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 
        0.20         0.33         0.69       228.16        63.02       121.08 
TCGA-W3-AA1O TCGA-W3-AA1Q TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 
        4.01        69.07        42.08       219.16       105.04        49.05 
TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ 
       61.15        17.95       101.33        58.98        70.52        63.22 
TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-AA9Y TCGA-WE-AAA4 TCGA-YD-A89C TCGA-YG-AA3O 
       11.80        35.80        12.16        24.99         6.90        37.94 
TCGA-Z2-A8RT TCGA-Z2-AA3V 
       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 
            53.26             51.12 
[1] "3.6 - 357.4 (53.3)" "0.2 - 369.9 (51.1)"
[1] "hr=" "1.1"
D56V3, continuous
                   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          11       4      22       12       22       23
                   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        15        34         13
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  8P LOSS MUTATED            4         12        3
  8P LOSS WILD-TYPE         29         43       18
D56V4, multiclass
             clus
vv            8P LOSS MUTATED 8P LOSS WILD-TYPE
  I OR II NOS               2                11
  STAGE 0                   3                 4
  STAGE I                   7                22
  STAGE IA                  6                12
  STAGE IB                  6                22
  STAGE II                  2                23
  STAGE IIA                 2                12
  STAGE IIB                 5                14
  STAGE IIC                 0                15
  STAGE III                 6                34
  STAGE IIIA                2                13
  STAGE IIIB                4                29
  STAGE IIIC               12                43
  STAGE IV                  3                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
  8P LOSS MUTATED      14 15 10 11
  8P LOSS WILD-TYPE    50 58 68 59
D56V5, multiclass
       clus
vv      8P LOSS MUTATED 8P LOSS WILD-TYPE
  T0+T1              14                50
  T2                 15                58
  T3                 10                68
  T4                 11                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
  8P LOSS MUTATED    34   8   7  12
  8P LOSS WILD-TYPE 143  57  32  33
D56V6, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  N0              34               143
  N1               8                57
  N2               7                32
  N3              12                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"
D56V7, binary
                   cls
clus                  0   1
  8P LOSS MUTATED    59   4
  8P LOSS WILD-TYPE 259  18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     59    4
  8P LOSS WILD-TYPE  259   18
   clus
vv  8P LOSS MUTATED 8P LOSS WILD-TYPE
  0              59               259
  1               4                18
[1] 2 2
[1] FALSE
D56V8, binary
                   cls
clus                  0   1
  8P LOSS MUTATED    28  12
  8P LOSS WILD-TYPE 106  78
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     28   12
  8P LOSS WILD-TYPE  106   78
     clus
vv    8P LOSS MUTATED 8P LOSS WILD-TYPE
  NO               28               106
  YES              12                78
[1] 2 2
[1] FALSE
D56V9, binary
                   cls
clus                  0   1
  8P LOSS MUTATED     8  59
  8P LOSS WILD-TYPE  39 260
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      8   59
  8P LOSS WILD-TYPE   39  260
     clus
vv    8P LOSS MUTATED 8P LOSS WILD-TYPE
  NO                8                39
  YES              59               260
[1] 2 2
[1] FALSE
D56V10, continuous
D56V11, binary
                   cls
clus                  0   1
  8P LOSS MUTATED    23  44
  8P LOSS WILD-TYPE 114 185
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     23   44
  8P LOSS WILD-TYPE  114  185
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  FEMALE              23               114
  MALE                44               185
[1] 2 2
[1] FALSE
D56V12, binary
                   cls
clus                  0   1
  8P LOSS MUTATED    58   9
  8P LOSS WILD-TYPE 259  38
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     58    9
  8P LOSS WILD-TYPE  259   38
     clus
vv    8P LOSS MUTATED 8P LOSS WILD-TYPE
  NO               58               259
  YES               9                38
[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   288
D56V13, multiclass
                           clus
vv                          8P LOSS MUTATED 8P LOSS WILD-TYPE
  ASIAN                                   1                 4
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  64               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"
D56V14, binary
                   cls
clus                  0   1
  8P LOSS MUTATED     1  65
  8P LOSS WILD-TYPE   6 286
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      1   65
  8P LOSS WILD-TYPE    6  286
                        clus
vv                       8P LOSS MUTATED 8P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 6
  NOT HISPANIC OR LATINO              65               286
[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 116 108
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               21               224 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               15               108 
$`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        69.21 
TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 
       22.85        76.34       138.67        53.65       150.61        95.51 
TCGA-DA-A1I7 TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A95V TCGA-DA-A95X 
       45.07        58.85        30.44       225.11        72.10        52.90 
TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN 
       14.14        12.30         3.91        33.24        50.07        52.41 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A184 
       18.21        13.15        24.89        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       115.43 
TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
       30.02        77.98        26.14       239.11        12.95       201.60 
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-A2MG TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML 
        5.75        23.77        94.19        63.25        89.26       104.78 
TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
       25.08        23.51       124.31       122.73        64.04         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-A3JH TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
      201.80        19.86        14.56        34.45         1.58        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        47.18 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NG TCGA-ER-A3ES 
      146.63        47.97        22.36         4.70        10.95       173.29 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A42L TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7U8 
       68.52        15.48        74.47       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-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZJ 
       27.62        32.78        42.08        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        96.92        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-A690 TCGA-RP-A693 
       85.05       297.01         7.23        18.05         0.20         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        65.42        12.69        21.90 
TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 
       62.89        10.95         1.94        31.99        18.31        18.35 
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 
           75.550            44.675 
[1] "7.3 - 312.1 (75.5)" "0.0 - 346.5 (44.7)"
[1] "hr=" "1.2"
D57V2, survival
                   sevent
clus2                 0   1
  8Q LOSS MUTATED    10  17
  8Q LOSS WILD-TYPE 160 170
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               27               330 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               17               170 
$`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-D3-A8GV TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW 
      129.63       117.17       167.70       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-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 
       77.56        22.95        76.57        36.03       144.89        20.38 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
      207.48       176.55        35.93       120.00        73.84        53.92 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 
       40.60        68.09        33.93        10.49       225.96        15.68 
TCGA-DA-A95V TCGA-DA-A95W TCGA-DA-A95X TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q 
       72.10        25.15        61.81        14.14        13.02        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        29.29        58.92 
TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A181 
        7.04        36.46        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       115.96        59.64        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       173.79       220.24        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       180.39       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        64.04 
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       134.33        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        49.48         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-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A 
       93.01        46.98        12.95       149.03        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-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-A1ZD TCGA-FS-A1ZE 
       20.91        28.08         7.79        48.85        53.52        46.45 
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-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        96.92        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        48.00       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-A690 TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 
        0.20         0.33         0.69       228.16        63.02       121.08 
TCGA-W3-AA1O TCGA-W3-AA1Q TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 
        4.01        69.07        42.08       219.16       105.04        49.05 
TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ 
       61.15        17.95       101.33        58.98        70.52        63.22 
TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 
       11.80        35.80        12.16        40.41        21.40        24.99 
TCGA-YD-A89C TCGA-YD-A9TA TCGA-YG-AA3O TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
        6.90        49.18        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 
           65.920            50.825 
[1] "9.2 - 357.4 (65.9)" "0.2 - 369.9 (50.8)"
[1] "hr=" "1.2"
D57V3, continuous
                   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          11       5      25       17       26       23
                   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        15        38         15
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  8Q LOSS MUTATED            3          4        1
  8Q LOSS WILD-TYPE         30         51       20
D57V4, multiclass
             clus
vv            8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  I OR II NOS               2                11
  STAGE 0                   2                 5
  STAGE I                   4                25
  STAGE IA                  1                17
  STAGE IB                  2                26
  STAGE II                  2                23
  STAGE IIA                 1                13
  STAGE IIB                 3                16
  STAGE IIC                 0                15
  STAGE III                 2                38
  STAGE IIIA                0                15
  STAGE IIIB                3                30
  STAGE IIIC                4                51
  STAGE IV                  1                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
  8Q LOSS MUTATED       1  7  5  8
  8Q LOSS WILD-TYPE    63 66 73 62
D57V5, multiclass
       clus
vv      8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  T0+T1               1                63
  T2                  7                66
  T3                  5                73
  T4                  8                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
  8Q LOSS MUTATED    18   3   2   3
  8Q LOSS WILD-TYPE 159  62  37  42
D57V6, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  N0              18               159
  N1               3                62
  N2               2                37
  N3               3                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"
D57V7, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED    26   1
  8Q LOSS WILD-TYPE 292  21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED     26    1
  8Q LOSS WILD-TYPE  292   21
   clus
vv  8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  0              26               292
  1               1                21
[1] 2 2
[1] FALSE
D57V8, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED    10   6
  8Q LOSS WILD-TYPE 124  84
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED     10    6
  8Q LOSS WILD-TYPE  124   84
     clus
vv    8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  NO               10               124
  YES               6                84
[1] 2 2
[1] FALSE
D57V9, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED     1  26
  8Q LOSS WILD-TYPE  46 293
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      1   26
  8Q LOSS WILD-TYPE   46  293
     clus
vv    8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  NO                1                46
  YES              26               293
[1] 2 2
[1] FALSE
D57V10, continuous
D57V11, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED    10  17
  8Q LOSS WILD-TYPE 127 212
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED     10   17
  8Q LOSS WILD-TYPE  127  212
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  FEMALE              10               127
  MALE                17               212
[1] 2 2
[1] FALSE
D57V12, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED    23   4
  8Q LOSS WILD-TYPE 294  43
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED     23    4
  8Q LOSS WILD-TYPE  294   43
     clus
vv    8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  NO               23               294
  YES               4                43
[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   327
D57V13, multiclass
                           clus
vv                          8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  ASIAN                                   0                 5
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  25               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"
D57V14, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED     1  25
  8Q LOSS WILD-TYPE   6 326
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      1   25
  8Q LOSS WILD-TYPE    6  326
                        clus
vv                       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 6
  NOT HISPANIC OR LATINO              25               326
[1] 2 2
[1] FALSE

Clustering(58) Variable = 9P LOSS MUTATION ANALYSIS
D58V1, survival
                   sevent
clus2                0  1
  9P LOSS MUTATED   73 87
  9P LOSS WILD-TYPE 49 36
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              160                85 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               87                36 
$`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 
       76.34       138.67        53.65       150.61        95.51        64.83 
TCGA-DA-A1IC TCGA-DA-A3F5 TCGA-DA-A95X TCGA-DA-A95Y TCGA-EB-A44Q TCGA-EB-A5SG 
       58.85       225.11        52.90        14.14         3.91        33.24 
TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 
       52.41        13.15        24.89        62.37        20.38         0.00 
TCGA-EE-A20C TCGA-EE-A20H TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G 
       75.55       155.90        76.14        12.99         0.26        44.28 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29W TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE 
       27.16        61.12       185.19        26.14       239.11        12.95 
TCGA-EE-A2GH TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP 
      201.60        32.48        18.35        31.00       118.32         0.76 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M8 TCGA-EE-A2MF 
        0.20        71.31        81.99       103.13         5.75       209.79 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MR TCGA-EE-A2MS 
       89.26       104.78       145.45       227.01        25.08       143.93 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J3 
      124.31       122.73         4.41        54.51         6.28        67.89 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 
       45.90         3.35       201.80        19.86       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-A19L TCGA-ER-A19M TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S 
      150.12        99.06        59.84       120.76        49.71        47.18 
TCGA-ER-A19W TCGA-ER-A2ND TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3EV TCGA-ER-A3PL 
      146.63         4.70        10.95       173.29        15.48        32.05 
TCGA-ER-A42L TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A8YC TCGA-FS-A1YW TCGA-FS-A1YY 
       74.47       174.21       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-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F9 
      136.27        23.21         5.29        30.90        66.67        13.28 
TCGA-FW-A3TU TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A268 
       55.59         6.05         1.91        53.29        96.92        42.48 
TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A8LK TCGA-GN-A9SD TCGA-OD-A75X TCGA-QB-A6FS 
        7.59       120.53        43.23        59.41       297.01         7.23 
TCGA-RP-A693 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1R TCGA-W3-AA1V TCGA-W3-AA21 
        0.33         1.97       120.07        79.99         8.09        92.84 
TCGA-WE-A8K5 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZY 
       59.64        65.42        12.69        21.90        62.89        48.39 
TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-Z2-AA3S 
       18.31        18.35        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        69.21        45.07 
TCGA-DA-A3F2 TCGA-DA-A95V TCGA-DA-A95Z TCGA-EB-A5SH TCGA-EB-A6L9 TCGA-EE-A184 
       30.44        72.10        12.30        50.07        18.21        67.50 
TCGA-EE-A29B TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29T TCGA-EE-A2A1 TCGA-EE-A2A2 
       75.22        63.12        47.74       346.49       115.43        30.02 
TCGA-EE-A2A6 TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2M7 TCGA-EE-A2MC TCGA-EE-A2MG 
       77.98        68.65        10.62        15.25        23.77        94.19 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AC TCGA-EE-A3J4 
      171.85        63.25        23.51        53.26        64.04       111.85 
TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19G TCGA-ER-A19N TCGA-ER-A1A1 TCGA-ER-A2NC 
       47.31         4.54       151.46        42.48        47.97        22.36 
TCGA-ER-A2NE TCGA-ER-A3ET TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FS-A1Z0 TCGA-FS-A1Z4 
       16.87        68.52        26.20         5.65       195.98        27.62 
TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZZ 
       42.08         7.82        36.33        35.28         4.47         3.06 
TCGA-FS-A4F8 TCGA-FS-A4FD TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GN-A264 
      173.19        80.68        11.54        19.30         9.90       117.93 
TCGA-GN-A267 TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-LH-A9QB TCGA-QB-AA9O TCGA-RP-A690 
       17.06        34.49        46.92        85.05        18.05         0.20 
TCGA-W3-A824 TCGA-W3-AA1Q TCGA-W3-AA1W TCGA-WE-A8K1 TCGA-WE-A8ZT TCGA-WE-AA9Y 
      174.12        44.05       185.13         1.15        10.95         1.94 
TCGA-WE-AAA0 
       31.99 

  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              0.0               0.2 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
           312.07            346.49 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
           47.785            46.920 
[1] "0.0 - 312.1 (47.8)" "0.2 - 346.5 (46.9)"
[1] "hr=" "1.2"
D58V2, survival
                   sevent
clus2                 0   1
  9P LOSS MUTATED    99 129
  9P LOSS WILD-TYPE  71  58
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              228               129 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              129                58 
$`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-D3-A8GV TCGA-D9-A148 TCGA-D9-A149 
      152.75       129.63       117.17       167.70       151.53        54.67 
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-A1HW TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 
       76.57        36.03       144.89       207.48       176.55        35.93 
TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F5 TCGA-DA-A95X 
      120.00        53.92        65.92        68.09       225.96        61.81 
TCGA-DA-A95Y TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5UL TCGA-EB-A5UN 
       14.14        13.87        10.36        68.25        29.29        58.92 
TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A185 
       29.82        27.22        94.98        33.73        14.70         4.96 
TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29C 
      133.81       151.27        91.56       168.26        13.55        78.97 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P 
       13.97        63.78        72.07         2.60        18.61        56.42 
TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 
       66.74        61.28        25.87       195.02        17.92        46.82 
TCGA-EE-A2A5 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
       39.29        59.28        67.43       340.14       173.79       220.24 
TCGA-EE-A2GI TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP 
       48.72        79.66        75.48       102.12       126.81        13.91 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M8 TCGA-EE-A2MD 
       42.77        81.21        94.82       129.27        19.76        47.28 
TCGA-EE-A2MF TCGA-EE-A2MH TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN 
      268.73        16.96       180.39       216.66       167.90        47.54 
TCGA-EE-A2MP TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AD 
      248.65       134.40       162.48       124.31       122.73        28.77 
TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J7 
       54.51        13.81        41.59       138.81       172.18        64.08 
TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 
       34.32        53.19       201.80       134.33       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-A19E TCGA-ER-A19F TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19P 
       13.02        26.37       152.35       131.51        61.05       162.08 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A2ND TCGA-ER-A2NG 
       50.89        49.48         8.88       148.18        23.34        31.27 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-ER-A42L 
       32.05       247.04        46.98        33.21        12.95       149.03 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A8YC TCGA-FS-A1YW 
       92.98       174.21        15.72       220.80        34.82       216.92 
TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB 
       48.59       228.59        20.91         7.79        27.72        48.85 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-FS-A1ZM TCGA-FS-A1ZQ 
      357.37        53.52        15.45        32.75       101.26       133.55 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F0 TCGA-FS-A4F2 
       11.41       148.80        49.48        27.09        77.82        50.14 
TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FW-A3I3 
       66.67        28.73        34.03        26.73        54.41         0.20 
TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 
       22.92        55.59         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 
       96.92        62.79        32.48        48.00       121.91        10.42 
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-OD-A75X TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A825 TCGA-W3-A828 
      297.90         7.23         0.33         0.69        63.02       121.08 
TCGA-W3-AA1R TCGA-W3-AA1V TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K5 TCGA-WE-A8K6 
      111.09        42.08       105.04        24.03        61.15        17.95 
TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZX TCGA-WE-A8ZY 
      101.33        58.98        70.52        63.22        35.80        49.51 
TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
       21.40        24.99        37.94        27.58        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 
       77.56        20.38        73.84        40.60        33.93        10.49 
TCGA-DA-A3F8 TCGA-DA-A95V TCGA-DA-A95W TCGA-DA-A95Z TCGA-EB-A5KH TCGA-EB-A5SH 
       15.68        72.10        25.15        13.02        20.35        54.02 
TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17Z TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A29A 
        7.04        36.46         8.65        26.89        68.15        63.35 
TCGA-EE-A29B TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29R TCGA-EE-A29T TCGA-EE-A2A1 
       85.08        64.64        56.84        14.47       369.93       115.96 
TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GT TCGA-EE-A2M5 
       59.64        86.14       107.38        54.74        44.88        21.67 
TCGA-EE-A2M7 TCGA-EE-A2MC TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ 
       28.83        61.51       103.27       103.20       204.66        96.23 
TCGA-EE-A2MQ TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AC TCGA-EE-A3J4 TCGA-EE-A3J5 
       43.23        71.21        53.26        64.04       127.20        36.95 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19G TCGA-ER-A19J 
       27.35        51.35        50.76        77.75       268.93         6.44 
TCGA-ER-A19N TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A3ET 
       44.05        79.99        43.82        20.15        16.37        93.01 
TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1Z0 
       27.85        18.77        38.27        36.26       104.42       202.65 
TCGA-FS-A1Z4 TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZP 
       28.08        46.45         9.70        47.38        23.93        74.73 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZZ TCGA-FS-A4F8 TCGA-FS-A4FD TCGA-FW-A3TV 
       53.16        26.56        27.02       174.84        80.68        13.51 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GN-A264 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A4U4 
       19.30         9.90       117.93        10.13        64.44        39.35 
TCGA-GN-A4U8 TCGA-LH-A9QB TCGA-QB-AA9O TCGA-RP-A690 TCGA-W3-A824 TCGA-W3-AA1O 
       48.89       368.78        18.05         0.20       228.16         4.01 
TCGA-W3-AA1Q TCGA-W3-AA1W TCGA-WE-A8K1 TCGA-WE-A8ZT TCGA-WE-AA9Y TCGA-WE-AAA0 
       69.07       219.16        49.05        11.80        12.16        40.41 
TCGA-YD-A89C TCGA-YD-A9TA TCGA-YG-AA3P 
        6.90        49.18        14.43 

  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              0.2               0.2 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
           357.37            369.93 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
            54.59             48.89 
[1] "0.2 - 357.4 (54.6)" "0.2 - 369.9 (48.9)"
[1] "hr=" "1.1"
D58V3, continuous
                   vv
clus                I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  9P LOSS MUTATED            11       4      19        9       18       18
  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        10        27          7
  9P LOSS WILD-TYPE         5         7         5        13          8
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  9P LOSS MUTATED           24         32       14
  9P LOSS WILD-TYPE          9         23        7
D58V4, multiclass
             clus
vv            9P LOSS MUTATED 9P LOSS WILD-TYPE
  I OR II NOS              11                 2
  STAGE 0                   4                 3
  STAGE I                  19                10
  STAGE IA                  9                 9
  STAGE IB                 18                10
  STAGE II                 18                 7
  STAGE IIA                 9                 5
  STAGE IIB                12                 7
  STAGE IIC                10                 5
  STAGE III                27                13
  STAGE IIIA                7                 8
  STAGE IIIB               24                 9
  STAGE IIIC               32                23
  STAGE IV                 14                 7
[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 49 53 46
  9P LOSS WILD-TYPE    25 24 25 24
D58V5, multiclass
       clus
vv      9P LOSS MUTATED 9P LOSS WILD-TYPE
  T0+T1              39                25
  T2                 49                24
  T3                 53                25
  T4                 46                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"
                   vv
clus                 N0  N1  N2  N3
  9P LOSS MUTATED   117  43  24  26
  9P LOSS WILD-TYPE  60  22  15  19
D58V6, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  N0             117                60
  N1              43                22
  N2              24                15
  N3              26                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"
D58V7, binary
                   cls
clus                  0   1
  9P LOSS MUTATED   204  15
  9P LOSS WILD-TYPE 114   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED    204   15
  9P LOSS WILD-TYPE  114    7
   clus
vv  9P LOSS MUTATED 9P LOSS WILD-TYPE
  0             204               114
  1              15                 7
[1] 2 2
[1] FALSE
D58V8, binary
                   cls
clus                 0  1
  9P LOSS MUTATED   85 59
  9P LOSS WILD-TYPE 49 31
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     85   59
  9P LOSS WILD-TYPE   49   31
     clus
vv    9P LOSS MUTATED 9P LOSS WILD-TYPE
  NO               85                49
  YES              59                31
[1] 2 2
[1] FALSE
D58V9, binary
                   cls
clus                  0   1
  9P LOSS MUTATED    26 210
  9P LOSS WILD-TYPE  21 109
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     26  210
  9P LOSS WILD-TYPE   21  109
     clus
vv    9P LOSS MUTATED 9P LOSS WILD-TYPE
  NO               26                21
  YES             210               109
[1] 2 2
[1] FALSE
D58V10, continuous
D58V11, binary
                   cls
clus                  0   1
  9P LOSS MUTATED    99 137
  9P LOSS WILD-TYPE  38  92
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     99  137
  9P LOSS WILD-TYPE   38   92
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  FEMALE              99                38
  MALE               137                92
[1] 2 2
[1] FALSE
D58V12, binary
                   cls
clus                  0   1
  9P LOSS MUTATED   209  26
  9P LOSS WILD-TYPE 108  21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED    209   26
  9P LOSS WILD-TYPE  108   21
     clus
vv    9P LOSS MUTATED 9P LOSS WILD-TYPE
  NO              209               108
  YES              26                21
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  9P LOSS MUTATED       3                         1   225
  9P LOSS WILD-TYPE     2                         0   127
D58V13, multiclass
                           clus
vv                          9P LOSS MUTATED 9P LOSS WILD-TYPE
  ASIAN                                   3                 2
  BLACK OR AFRICAN AMERICAN               1                 0
  WHITE                                 225               127
[1] 3 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     2 228
  9P LOSS WILD-TYPE   5 123
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      2  228
  9P LOSS WILD-TYPE    5  123
                        clus
vv                       9P LOSS MUTATED 9P LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                 5
  NOT HISPANIC OR LATINO             228               123
[1] 2 2
[1] FALSE

Clustering(59) Variable = 9Q LOSS MUTATION ANALYSIS
D59V1, survival
                   sevent
clus2                0  1
  9Q LOSS MUTATED   60 68
  9Q LOSS WILD-TYPE 62 55
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
              128               117 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               68                55 
$`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 
       76.34        53.65       150.61        95.51        64.83        58.85 
TCGA-DA-A3F5 TCGA-DA-A95X TCGA-EB-A5SG TCGA-EB-A5UN TCGA-EE-A17Y TCGA-EE-A180 
      225.11        52.90        33.24        52.41        24.89        62.37 
TCGA-EE-A181 TCGA-EE-A20C TCGA-EE-A20H TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29P 
       20.38        75.55       155.90        12.99        44.28        27.16 
TCGA-EE-A29Q TCGA-EE-A29W TCGA-EE-A2A2 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE 
       61.12       185.19        30.02        26.14       239.11        12.95 
TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP 
      201.60        68.65        32.48        18.35        31.00         0.76 
TCGA-EE-A2GS TCGA-EE-A2M6 TCGA-EE-A2M8 TCGA-EE-A2MF TCGA-EE-A2MK TCGA-EE-A2ML 
       71.31       103.13         5.75       209.79        89.26       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-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH 
        4.41        54.51         6.28         3.35       201.80        19.86 
TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19B 
      152.81        14.56        34.45         1.58         7.82        53.29 
TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19H TCGA-ER-A19M TCGA-ER-A19P TCGA-ER-A19Q 
       39.81        11.47       150.12        59.84       120.76        49.71 
TCGA-ER-A19W TCGA-ER-A2NG TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A729 
      146.63        10.95        15.48        32.05        74.47       209.23 
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-A1ZF TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZW TCGA-FS-A1ZY 
       12.92        78.61       130.95       136.27        23.21         5.29 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FW-A3TV TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 
        3.06        30.90        11.54         6.05         1.91        53.29 
TCGA-GN-A265 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A8LK TCGA-GN-A9SD 
       96.92        42.48         7.59       120.53        43.23        59.41 
TCGA-OD-A75X TCGA-RP-A693 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1R TCGA-W3-AA1V 
      297.01         0.33         1.97       120.07        79.99         8.09 
TCGA-W3-AA21 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZY TCGA-WE-AAA4 
       92.84        65.42        12.69        21.90        48.39        18.35 
TCGA-YG-AA3O TCGA-Z2-AA3S 
       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        69.21        22.85       138.67 
TCGA-DA-A1I7 TCGA-DA-A3F2 TCGA-DA-A95V TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q 
       45.07        30.44        72.10        14.14        12.30         3.91 
TCGA-EB-A5SH TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A182 TCGA-EE-A184 TCGA-EE-A29B 
       50.07        18.21        13.15         0.00        67.50        75.22 
TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29T TCGA-EE-A2A1 
       76.14         0.26        63.12        47.74       346.49       115.43 
TCGA-EE-A2A6 TCGA-EE-A2GK TCGA-EE-A2GO TCGA-EE-A2GR TCGA-EE-A2GU TCGA-EE-A2M7 
       77.98        10.62       118.32         0.20        81.99        15.25 
TCGA-EE-A2MC TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MT TCGA-EE-A2MU 
       23.77        94.19       171.85        63.25        23.51        53.26 
TCGA-EE-A3AC TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-ER-A198 TCGA-ER-A19A 
       64.04        67.89       111.85        45.90        47.31         4.54 
TCGA-ER-A19G TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A19S TCGA-ER-A1A1 TCGA-ER-A2NC 
      151.46        99.06        42.48        47.18        47.97        22.36 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A3ES TCGA-ER-A3ET TCGA-FR-A44A TCGA-FR-A7U8 
        4.70        16.87       173.29        68.52       174.21        26.20 
TCGA-FR-A7UA TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ 
        5.65       195.98        27.62        42.08         7.82        36.33 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FD 
       35.28         4.47        66.67       173.19        13.28        80.68 
TCGA-FW-A3TU TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A4U4 
       55.59        19.30         9.90       117.93        17.06        34.49 
TCGA-GN-A4U8 TCGA-LH-A9QB TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A690 TCGA-W3-A824 
       46.92        85.05         7.23        18.05         0.20       174.12 
TCGA-W3-AA1Q TCGA-W3-AA1W TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8ZQ TCGA-WE-A8ZT 
       44.05       185.13         1.15        59.64        62.89        10.95 
TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 
        1.94        31.99        18.31 

  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
             0.33              0.00 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
           312.07            346.49 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
            49.53             45.90 
[1] "0.3 - 312.1 (49.5)" "0.0 - 346.5 (45.9)"
[1] "hr=" "1"  
D59V2, survival
                   sevent
clus2                0  1
  9Q LOSS MUTATED   80 99
  9Q LOSS WILD-TYPE 90 88
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
              179               178 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               99                88 
$`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        76.57        36.03       207.48 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IC 
      176.55        35.93       120.00        53.92        65.92        68.09 
TCGA-DA-A3F5 TCGA-DA-A95X TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5UN TCGA-EE-A17Y 
      225.96        61.81        10.36        68.25        58.92        27.22 
TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H 
       94.98        33.73       133.81       151.27        91.56       168.26 
TCGA-EE-A20I TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P 
       13.55        13.97        72.07         2.60        18.61        56.42 
TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A2 
       66.74        61.28       195.02        17.92        46.82        59.64 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
       59.28        67.43       340.14       173.79       220.24        48.72 
TCGA-EE-A2GJ TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GS 
      107.38        79.66        75.48       102.12        13.91        81.21 
TCGA-EE-A2M6 TCGA-EE-A2M8 TCGA-EE-A2MF TCGA-EE-A2MH TCGA-EE-A2MK TCGA-EE-A2ML 
      129.27        19.76       268.73        16.96       180.39       216.66 
TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A3AA 
      167.90       248.65        43.23       134.40       162.48       124.31 
TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3J5 
      122.73        28.77        54.51        13.81        41.59        36.95 
TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI 
       34.32        53.19       201.80        51.35       134.33       152.81 
TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19C 
       31.40        35.44        13.94         9.17        98.40        48.89 
TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19H TCGA-ER-A19M TCGA-ER-A19P TCGA-ER-A19Q 
       12.59        26.37       152.35        61.05       162.08        50.89 
TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3EV TCGA-ER-A3PL 
        8.88       148.18        31.27        32.05        46.98        33.21 
TCGA-ER-A42L TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A8YC TCGA-FS-A1YW TCGA-FS-A1YY 
      149.03        15.72       220.80        34.82       216.92       228.59 
TCGA-FS-A1Z3 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZF 
       20.91        27.72        48.85       357.37        53.52        15.45 
TCGA-FS-A1ZH TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZW 
       32.75       101.26       133.55        11.41       148.80        49.48 
TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F5 TCGA-FS-A4FB 
       27.09        27.02        77.82        50.14        28.73        26.73 
TCGA-FS-A4FC TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TV TCGA-GF-A4EO TCGA-GF-A6C8 
       54.41         0.20        22.92        13.51         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        96.92        62.79        32.48        48.00 
TCGA-GN-A4U3 TCGA-GN-A4U7 TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A9SD TCGA-HR-A2OG 
      121.91        10.42        22.13        50.10        59.41         0.23 
TCGA-HR-A2OH TCGA-OD-A75X TCGA-RP-A693 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1R 
       65.88       297.90         0.33        63.02       121.08       111.09 
TCGA-W3-AA1V TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO 
       42.08       105.04        24.03       101.33        58.98        70.52 
TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-Z2-AA3S 
       35.80        49.51        24.99        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-D3-A8GV TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       29.06       167.70         3.65         7.10        15.39        22.29 
TCGA-D9-A4Z6 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HY TCGA-DA-A1I0 
       18.44        25.18        77.56        22.95       144.89        20.38 
TCGA-DA-A1I7 TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-DA-A95V 
       73.84        40.60        33.93        10.49        15.68        72.10 
TCGA-DA-A95W TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5SH 
       25.15        14.14        13.02        13.87        20.35        54.02 
TCGA-EB-A5UL TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A182 
       29.29         7.04        36.46        29.82         8.65        14.70 
TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C 
       26.89        68.15         4.96        63.35        85.08        78.97 
TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29R TCGA-EE-A29T TCGA-EE-A29V 
       63.78        64.64        56.84        14.47       369.93        25.87 
TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GK TCGA-EE-A2GO TCGA-EE-A2GR 
      115.96        39.29        86.14        54.74       126.81        42.77 
TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M7 TCGA-EE-A2MC TCGA-EE-A2MD 
       44.88        94.82        21.67        28.83        61.51        47.28 
TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MN TCGA-EE-A2MT 
      103.27       103.20       204.66        96.23        47.54        71.21 
TCGA-EE-A2MU TCGA-EE-A3AC TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 
       53.26        64.04       138.81       172.18       127.20        64.08 
TCGA-EE-A3JD TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19E TCGA-ER-A19G TCGA-ER-A19J 
       27.35        50.76        77.75        13.02       268.93         6.44 
TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A19S TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
      131.51        44.05        49.48        79.99        43.82        23.34 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A42K TCGA-FR-A3YN 
       20.15        16.37       247.04        93.01        12.95        92.98 
TCGA-FR-A44A TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YD TCGA-FR-A8YE 
      174.21        27.85        18.77        38.27        36.26       104.42 
TCGA-FS-A1YX TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZE TCGA-FS-A1ZG 
       48.59       202.65        28.08         7.79        46.45         9.70 
TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A4F4 
       47.38        23.93        74.73        53.16        26.56        66.67 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A5DY TCGA-GF-A3OT 
      174.84        34.03        80.68        55.59        19.30         9.90 
TCGA-GN-A264 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-GN-A8LL 
      117.93        10.13        64.44        39.35        48.89        21.37 
TCGA-LH-A9QB TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A690 TCGA-RP-A694 TCGA-W3-A824 
      368.78         7.23        18.05         0.20         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        17.95 
TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-YD-A89C 
       63.22        11.80        12.16        40.41        21.40         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 
              0.2               0.2 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
           357.37            369.93 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
           58.920            46.865 
[1] "0.2 - 357.4 (58.9)" "0.2 - 369.9 (46.9)"
[1] "hr=" "1.1"
D59V3, continuous
                   vv
clus                I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  9Q LOSS MUTATED             8       3      16        6       14       12
  9Q LOSS WILD-TYPE           5       4      13       12       14       13
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  9Q LOSS MUTATED           8        11         8        24          6
  9Q LOSS WILD-TYPE         6         8         7        16          9
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  9Q LOSS MUTATED           21         18       12
  9Q LOSS WILD-TYPE         12         37        9
D59V4, multiclass
             clus
vv            9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  I OR II NOS               8                 5
  STAGE 0                   3                 4
  STAGE I                  16                13
  STAGE IA                  6                12
  STAGE IB                 14                14
  STAGE II                 12                13
  STAGE IIA                 8                 6
  STAGE IIB                11                 8
  STAGE IIC                 8                 7
  STAGE III                24                16
  STAGE IIIA                6                 9
  STAGE IIIB               21                12
  STAGE IIIC               18                37
  STAGE IV                 12                 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
  9Q LOSS MUTATED      33 37 42 36
  9Q LOSS WILD-TYPE    31 36 36 34
D59V5, multiclass
       clus
vv      9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  T0+T1              33                31
  T2                 37                36
  T3                 42                36
  T4                 36                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"
                   vv
clus                N0 N1 N2 N3
  9Q LOSS MUTATED   94 32 22 17
  9Q LOSS WILD-TYPE 83 33 17 28
D59V6, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  N0              94                83
  N1              32                33
  N2              22                17
  N3              17                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"
D59V7, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED   159  13
  9Q LOSS WILD-TYPE 159   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED    159   13
  9Q LOSS WILD-TYPE  159    9
   clus
vv  9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  0             159               159
  1              13                 9
[1] 2 2
[1] FALSE
D59V8, binary
                   cls
clus                 0  1
  9Q LOSS MUTATED   70 42
  9Q LOSS WILD-TYPE 64 48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     70   42
  9Q LOSS WILD-TYPE   64   48
     clus
vv    9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  NO               70                64
  YES              42                48
[1] 2 2
[1] FALSE
D59V9, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED    22 163
  9Q LOSS WILD-TYPE  25 156
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     22  163
  9Q LOSS WILD-TYPE   25  156
     clus
vv    9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  NO               22                25
  YES             163               156
[1] 2 2
[1] FALSE
D59V10, continuous
D59V11, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED    79 106
  9Q LOSS WILD-TYPE  58 123
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     79  106
  9Q LOSS WILD-TYPE   58  123
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  FEMALE              79                58
  MALE               106               123
[1] 2 2
[1] FALSE
D59V12, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED   159  25
  9Q LOSS WILD-TYPE 158  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED    159   25
  9Q LOSS WILD-TYPE  158   22
     clus
vv    9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  NO              159               158
  YES              25                22
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  9Q LOSS MUTATED       2                         0   177
  9Q LOSS WILD-TYPE     3                         1   175
D59V13, multiclass
                           clus
vv                          9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  ASIAN                                   2                 3
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                 177               175
[1] 3 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     3 178
  9Q LOSS WILD-TYPE   4 173
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      3  178
  9Q LOSS WILD-TYPE    4  173
                        clus
vv                       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   3                 4
  NOT HISPANIC OR LATINO             178               173
[1] 2 2
[1] FALSE

Clustering(60) Variable = 10P LOSS MUTATION ANALYSIS
D60V1, survival
                    sevent
clus2                 0  1
  10P LOSS MUTATED   69 72
  10P LOSS WILD-TYPE 53 51
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
               141                104 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                72                 51 
$`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 
       53.65       150.61        95.51        45.07        64.83       225.11 
TCGA-DA-A95V TCGA-DA-A95Y TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EE-A180 TCGA-EE-A181 
       72.10        14.14        50.07        52.41        62.37        20.38 
TCGA-EE-A20H TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29Q 
      155.90        44.28        63.12        47.74        27.16        61.12 
TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A2 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH 
      346.49       185.19        30.02        26.14        12.95       201.60 
TCGA-EE-A2GJ TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR 
       68.65        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-A2MG 
       71.31        81.99       103.13        15.25         5.75        94.19 
TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AA 
       89.26       145.45       227.01       143.93        53.26       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-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A199 TCGA-ER-A19D 
        3.35       201.80        19.86       152.81         7.82        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        47.18       146.63        22.36 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL 
        4.70        16.87        10.95        68.52        15.48        32.05 
TCGA-ER-A42L TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FS-A1Z0 TCGA-FS-A1Z3 
       74.47       174.21       209.23        26.20       195.98         8.35 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM 
      312.07        32.78        12.92         7.82        36.33        78.61 
TCGA-FS-A1ZQ TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F4 TCGA-FS-A4FD 
      130.95         4.47        23.21         5.29        66.67        80.68 
TCGA-FW-A3TV TCGA-GF-A4EO TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
       11.54         6.05       117.93        17.06        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-AA21 TCGA-WE-A8ZM TCGA-WE-A8ZQ TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA3 
       92.84        65.42        62.89        48.39         1.94        18.31 
TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-Z2-AA3S 
       18.35        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        69.21        76.34 
TCGA-DA-A1HY TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A95X TCGA-DA-A95Z TCGA-EB-A44Q 
      138.67        58.85        30.44        52.90        12.30         3.91 
TCGA-EB-A5SG TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A182 TCGA-EE-A184 
       33.24        18.21        13.15        24.89         0.00        67.50 
TCGA-EE-A20C TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A2A1 
       75.55        75.22        76.14        12.99         0.26       115.43 
TCGA-EE-A2A6 TCGA-EE-A2GD TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2MC TCGA-EE-A2MF 
       77.98       239.11        10.62        32.48        23.77       209.79 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A3AC 
      171.85        63.25       104.78        25.08        23.51        64.04 
TCGA-EE-A3AF TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A19A 
        6.28        14.56        34.45         1.58        47.31         4.54 
TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19G TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19Q 
       53.29        39.81       151.46        59.84        42.48        49.71 
TCGA-ER-A1A1 TCGA-ER-A3ES TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FS-A1YW TCGA-FS-A1YY 
       47.97       173.29         5.65        10.06       171.78        49.74 
TCGA-FS-A1Z4 TCGA-FS-A1ZE TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZZ TCGA-FS-A4F0 
       27.62        42.08       136.27        35.28         3.06        30.90 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FW-A3TU TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 
      173.19        13.28        55.59        19.30         9.90         1.91 
TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-LH-A9QB TCGA-QB-A6FS 
       53.29        96.92        34.49        46.92        85.05         7.23 
TCGA-QB-AA9O TCGA-RP-A690 TCGA-W3-A824 TCGA-W3-A828 TCGA-W3-AA1Q TCGA-W3-AA1R 
       18.05         0.20       174.12       120.07        44.05        79.99 
TCGA-W3-AA1V TCGA-W3-AA1W TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8ZN TCGA-WE-A8ZO 
        8.09       185.13         1.15        59.64        12.69        21.90 
TCGA-WE-A8ZT TCGA-WE-AAA0 
       10.95        31.99 

  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 
             48.39              45.02 
[1] "0.2 - 346.5 (48.4)" "0.0 - 239.1 (45.0)"
[1] "hr=" "1.1"
D60V2, survival
                    sevent
clus2                  0   1
  10P LOSS MUTATED    94 104
  10P LOSS WILD-TYPE  76  83
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
               198                159 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
               104                 83 
$`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-D3-A8GV TCGA-D9-A149 TCGA-D9-A1X3 
      152.75       129.63       117.17       167.70        54.67        18.12 
TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EG TCGA-DA-A1HW 
       22.29        18.44         9.90        25.18        22.95        36.03 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
      207.48       176.55        35.93       120.00        73.84        53.92 
TCGA-DA-A1IA TCGA-DA-A3F5 TCGA-DA-A95V TCGA-DA-A95W TCGA-DA-A95Y TCGA-EB-A44R 
       65.92       225.96        72.10        25.15        14.14        10.36 
TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 
       54.02        29.29        58.92         8.65        94.98        33.73 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29G 
        4.96       133.81        91.56       168.26        13.55        72.07 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T 
       64.64         2.60        56.84        56.42        66.74       369.93 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2GB TCGA-EE-A2GC 
      195.02        17.92        59.64        39.29        59.28        67.43 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GM TCGA-EE-A2GN 
      173.79       220.24        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-A2MG TCGA-EE-A2MH TCGA-EE-A2MK TCGA-EE-A2MM 
       28.83        19.76       103.20        16.96       180.39       167.90 
TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AD 
      248.65       162.48        53.26       124.31       122.73        28.77 
TCGA-EE-A3AE TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 
       54.51       138.81       172.18       127.20        36.95        64.08 
TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI 
       34.32        53.19       201.80        51.35       134.33       152.81 
TCGA-ER-A199 TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19P 
        9.17        12.59        13.02       152.35       131.51       162.08 
TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
       49.48         8.88       148.18        43.82        23.34        20.15 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K 
       31.27        32.05        93.01        46.98        33.21        12.95 
TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 
      149.03        92.98       174.21        15.72       220.80        27.85 
TCGA-FR-A8YE TCGA-FS-A1YX TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z7 TCGA-FS-A1ZA 
      104.42        48.59       202.65        20.91         7.79        27.72 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ 
      357.37        53.52        15.45         9.70        32.75        47.38 
TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY 
      101.26       133.55        11.41        26.56        49.48        27.09 
TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4FD TCGA-FW-A3TV TCGA-GF-A4EO TCGA-GN-A264 
       66.67        28.73        80.68        13.51         7.23       117.93 
TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U7 
       10.13        64.44        62.79        32.48       121.91        10.42 
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-OD-A75X TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A825 TCGA-W3-AA21 TCGA-WE-A8JZ 
      297.90         0.33         0.69        63.02       105.04        24.03 
TCGA-WE-A8ZM TCGA-WE-A8ZQ TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA3 
      101.33        63.22        35.80        49.51        12.16        21.40 
TCGA-WE-AAA4 TCGA-YD-A9TA TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-AA3S TCGA-Z2-AA3V 
       24.99        49.18        37.94        14.43        96.99        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        77.56        76.57       144.89        20.38        40.60 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-DA-A95X TCGA-DA-A95Z 
       68.09        33.93        10.49        15.68        61.81        13.02 
TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X 
       13.87        20.35        68.25         7.04        36.46        29.82 
TCGA-EE-A17Y TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A20C TCGA-EE-A29A 
       27.22        14.70        26.89        68.15       151.27        63.35 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29N TCGA-EE-A29R 
       85.08        78.97        13.97        63.78        18.61        14.47 
TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A6 TCGA-EE-A2GD 
       61.28        25.87        46.82       115.96        86.14       340.14 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2MC TCGA-EE-A2MD 
       54.74        79.66        44.88        21.67        61.51        47.28 
TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MN 
      103.27       268.73       204.66        96.23       216.66        47.54 
TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A3AC TCGA-EE-A3AF TCGA-EE-A3AG 
       43.23       134.40        71.21        64.04        13.81        41.59 
TCGA-EE-A3JD TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A19A 
       27.35        31.40        35.44        13.94        50.76        77.75 
TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19J TCGA-ER-A19M 
       98.40        48.89        26.37       268.93         6.44        61.05 
TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A1A1 TCGA-ER-A2NF TCGA-ER-A3ES TCGA-FR-A7U9 
       44.05        50.89        79.99        16.37       247.04        18.77 
TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z4 
       38.27        34.82        36.26       216.92       228.59        28.08 
TCGA-FS-A1ZB TCGA-FS-A1ZE TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZS TCGA-FS-A1ZT 
       48.85        46.45        23.93        74.73       148.80        53.16 
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-A5DY TCGA-GF-A3OT 
       54.41         0.20        22.92        55.59        19.30         9.90 
TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A26D TCGA-GN-A4U4 
        2.04        15.78       139.89        96.92        48.00        39.35 
TCGA-GN-A4U8 TCGA-LH-A9QB TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A690 TCGA-W3-A824 
       48.89       368.78         7.23        18.05         0.20       228.16 
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-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT 
       49.05        61.15        17.95        58.98        70.52        11.80 
TCGA-WE-AAA0 TCGA-YD-A89C TCGA-Z2-A8RT 
       40.41         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 
             54.59              48.89 
[1] "0.2 - 369.9 (54.6)" "0.2 - 368.8 (48.9)"
[1] "hr=" "1.1"
D60V3, continuous
                    vv
clus                 I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  10P LOSS MUTATED             8       4      17       12       15       15
  10P LOSS WILD-TYPE           5       3      12        6       13       10
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  10P LOSS MUTATED           5         6         9        26         11
  10P LOSS WILD-TYPE         9        13         6        14          4
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  10P LOSS MUTATED           18         33       10
  10P LOSS WILD-TYPE         15         22       11
D60V4, multiclass
             clus
vv            10P LOSS MUTATED 10P LOSS WILD-TYPE
  I OR II NOS                8                  5
  STAGE 0                    4                  3
  STAGE I                   17                 12
  STAGE IA                  12                  6
  STAGE IB                  15                 13
  STAGE II                  15                 10
  STAGE IIA                  5                  9
  STAGE IIB                  6                 13
  STAGE IIC                  9                  6
  STAGE III                 26                 14
  STAGE IIIA                11                  4
  STAGE IIIB                18                 15
  STAGE IIIC                33                 22
  STAGE IV                  10                 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
  10P LOSS MUTATED      40 42 33 49
  10P LOSS WILD-TYPE    24 31 45 21
D60V5, multiclass
       clus
vv      10P LOSS MUTATED 10P LOSS WILD-TYPE
  T0+T1               40                 24
  T2                  42                 31
  T3                  33                 45
  T4                  49                 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   96 40 24 24
  10P LOSS WILD-TYPE 81 25 15 21
D60V6, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  N0               96                 81
  N1               40                 25
  N2               24                 15
  N3               24                 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"
D60V7, binary
                    cls
clus                   0   1
  10P LOSS MUTATED   181  10
  10P LOSS WILD-TYPE 137  12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED    181   10
  10P LOSS WILD-TYPE  137   12
   clus
vv  10P LOSS MUTATED 10P LOSS WILD-TYPE
  0              181                137
  1               10                 12
[1] 2 2
[1] FALSE
D60V8, binary
                    cls
clus                  0  1
  10P LOSS MUTATED   72 53
  10P LOSS WILD-TYPE 62 37
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     72   53
  10P LOSS WILD-TYPE   62   37
     clus
vv    10P LOSS MUTATED 10P LOSS WILD-TYPE
  NO                72                 62
  YES               53                 37
[1] 2 2
[1] FALSE
D60V9, binary
                    cls
clus                   0   1
  10P LOSS MUTATED    23 181
  10P LOSS WILD-TYPE  24 138
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     23  181
  10P LOSS WILD-TYPE   24  138
     clus
vv    10P LOSS MUTATED 10P LOSS WILD-TYPE
  NO                23                 24
  YES              181                138
[1] 2 2
[1] FALSE
D60V10, continuous
D60V11, binary
                    cls
clus                   0   1
  10P LOSS MUTATED    86 118
  10P LOSS WILD-TYPE  51 111
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     86  118
  10P LOSS WILD-TYPE   51  111
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  FEMALE               86                 51
  MALE                118                111
[1] 2 2
[1] FALSE
D60V12, binary
                    cls
clus                   0   1
  10P LOSS MUTATED   176  28
  10P LOSS WILD-TYPE 141  19
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED    176   28
  10P LOSS WILD-TYPE  141   19
     clus
vv    10P LOSS MUTATED 10P LOSS WILD-TYPE
  NO               176                141
  YES               28                 19
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  10P LOSS MUTATED       1                         0   197
  10P LOSS WILD-TYPE     4                         1   155
D60V13, multiclass
                           clus
vv                          10P LOSS MUTATED 10P LOSS WILD-TYPE
  ASIAN                                    1                  4
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                  197                155
[1] 3 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     4 195
  10P LOSS WILD-TYPE   3 156
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      4  195
  10P LOSS WILD-TYPE    3  156
                        clus
vv                       10P LOSS MUTATED 10P LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                  3
  NOT HISPANIC OR LATINO              195                156
[1] 2 2
[1] FALSE

Clustering(61) Variable = 10Q LOSS MUTATION ANALYSIS
D61V1, survival
                    sevent
clus2                 0  1
  10Q LOSS MUTATED   74 77
  10Q LOSS WILD-TYPE 48 46
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
               151                 94 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                77                 46 
$`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        69.21 
TCGA-D9-A6EG TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA 
       22.85        53.65       150.61        95.51        45.07        64.83 
TCGA-DA-A3F5 TCGA-DA-A95V TCGA-DA-A95Y TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EE-A180 
      225.11        72.10        14.14        50.07        52.41        62.37 
TCGA-EE-A181 TCGA-EE-A20H TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M 
       20.38       155.90        12.99        44.28        63.12        47.74 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A2 TCGA-EE-A2A6 
       27.16        61.12       346.49       185.19        30.02        77.98 
TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GM 
       26.14       239.11        12.95       201.60        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-A2MF TCGA-EE-A2MG TCGA-EE-A2MI 
      103.13        15.25         5.75       209.79        94.19       171.85 
TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB 
       89.26       145.45       227.01        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-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A199 
        3.35       201.80        19.86       152.81        14.56         7.82 
TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19P TCGA-ER-A19S 
       39.81        11.47       150.12        99.06       120.76        47.18 
TCGA-ER-A19W TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A3EV TCGA-ER-A3PL 
      146.63        22.36        16.87        10.95        15.48        32.05 
TCGA-ER-A42L TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FS-A1YY TCGA-FS-A1Z0 
       74.47       174.21       209.23        26.20        49.74       195.98 
TCGA-FS-A1Z3 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZJ TCGA-FS-A1ZM 
        8.35       312.07        32.78        12.92        36.33        78.61 
TCGA-FS-A1ZQ TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F4 TCGA-FS-A4FD 
      130.95         4.47        23.21         5.29        66.67        80.68 
TCGA-FW-A3TV TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A267 
       11.54         6.05         1.91        53.29       117.93        17.06 
TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U8 TCGA-GN-A8LK TCGA-GN-A9SD TCGA-OD-A75X 
        7.59       120.53        46.92        43.23        59.41       297.01 
TCGA-RP-A693 TCGA-W3-A825 TCGA-W3-AA21 TCGA-WE-A8K5 TCGA-WE-A8ZM TCGA-WE-A8ZQ 
        0.33         1.97        92.84        59.64        65.42        62.89 
TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O 
       10.95        48.39         1.94        18.31        18.35        28.21 
TCGA-Z2-AA3S 
       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        76.34       138.67 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A95X TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5SG 
       58.85        30.44        52.90        12.30         3.91        33.24 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A182 TCGA-EE-A184 TCGA-EE-A20C 
       18.21        13.15        24.89         0.00        67.50        75.55 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A2A1 TCGA-EE-A2GK TCGA-EE-A2GL 
       75.22        76.14         0.26       115.43        10.62        32.48 
TCGA-EE-A2MC TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT 
       23.77        63.25       104.78        25.08       143.93        23.51 
TCGA-EE-A3AC TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19B 
       64.04        34.45         1.58        47.31         4.54        53.29 
TCGA-ER-A19G TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A1A1 TCGA-ER-A2ND 
      151.46        59.84        42.48        49.71        47.97         4.70 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FS-A1YW TCGA-FS-A1Z4 
      173.29        68.52         5.65        10.06       171.78        27.62 
TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZZ TCGA-FS-A4F0 
       42.08         7.82       136.27        35.28         3.06        30.90 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FW-A3TU TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GN-A265 
      173.19        13.28        55.59        19.30         9.90        96.92 
TCGA-GN-A268 TCGA-GN-A4U4 TCGA-LH-A9QB TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A690 
       42.48        34.49        85.05         7.23        18.05         0.20 
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-A8ZN TCGA-WE-A8ZO TCGA-WE-AAA0 
        1.15        12.69        21.90        31.99 

  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 
            50.070             42.065 
[1] "0.2 - 346.5 (50.1)" "0.0 - 185.1 (42.1)"
[1] "hr=" "1.2"
D61V2, survival
                    sevent
clus2                  0   1
  10Q LOSS MUTATED   105 112
  10Q LOSS WILD-TYPE  65  75
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
               217                140 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
               112                 75 
$`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-D3-A8GV TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1X3 TCGA-D9-A3Z3 
      117.17       167.70       151.53        54.67        18.12        22.29 
TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HW 
       18.44         9.90        25.18        77.56        22.95        36.03 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
      207.48       176.55        35.93       120.00        73.84        53.92 
TCGA-DA-A1IA TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-DA-A95V TCGA-DA-A95W TCGA-DA-A95Y 
       65.92       225.96        15.68        72.10        25.15        14.14 
TCGA-EB-A44R TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17Z TCGA-EE-A180 
       10.36        54.02        29.29        58.92         8.65        94.98 
TCGA-EE-A181 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I 
       33.73         4.96       133.81        91.56       168.26        13.55 
TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29P 
       13.97        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        59.64        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       173.79       220.24 
TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP 
       48.72       107.38        75.48       102.12       126.81        13.91 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 
       42.77        81.21        94.82       129.27        28.83        19.76 
TCGA-EE-A2MD TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK 
       47.28       268.73       103.20        16.96       204.66       180.39 
TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AD 
      167.90       248.65        53.26       124.31       122.73        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-A3JB TCGA-EE-A3JE 
       36.95        64.08        34.32        53.19       201.80        51.35 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A199 TCGA-ER-A19C TCGA-ER-A19D 
      134.33       152.81        31.40         9.17        48.89        12.59 
TCGA-ER-A19E TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19P TCGA-ER-A19S TCGA-ER-A19T 
       13.02       152.35       131.51       162.08        49.48         8.88 
TCGA-ER-A19W TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3EV 
      148.18        43.82        20.15        31.27        32.05        46.98 
TCGA-ER-A3PL TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       33.21        12.95       149.03        92.98       174.21        15.72 
TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A8YE TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
      220.80        27.85       104.42        48.59       228.59       202.65 
TCGA-FS-A1Z3 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZF 
       20.91         7.79        27.72       357.37        53.52        15.45 
TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZU 
       32.75        47.38       101.26       133.55        11.41        26.56 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4FB TCGA-FS-A4FD 
       49.48        27.09        66.67        28.73        26.73        80.68 
TCGA-FW-A3TV TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A266 
       13.51         7.23         2.04       139.89       117.93        10.13 
TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A4U9 
       64.44        32.48       121.91        10.42        48.89        22.13 
TCGA-GN-A8LK TCGA-GN-A9SD TCGA-HR-A2OG TCGA-HR-A2OH TCGA-OD-A75X TCGA-RP-A693 
       50.10        59.41         0.23        65.88       297.90         0.33 
TCGA-RP-A694 TCGA-W3-A825 TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K5 TCGA-WE-A8K6 
        0.69        63.02       105.04        24.03        61.15        17.95 
TCGA-WE-A8ZM TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AA9Y 
      101.33        63.22        11.80        35.80        49.51        12.16 
TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YD-A9TA TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-AA3S 
       21.40        24.99        49.18        37.94        14.43        96.99 
TCGA-Z2-AA3V 
       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        76.57       144.89        20.38        40.60 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A95X TCGA-DA-A95Z TCGA-EB-A44Q 
       68.09        33.93        10.49        61.81        13.02        13.87 
TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y 
       20.35        68.25         7.04        36.46        29.82        27.22 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A20C TCGA-EE-A29A TCGA-EE-A29B 
       14.70        26.89        68.15       151.27        63.35        85.08 
TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29N TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V 
       78.97        63.78        18.61        14.47        61.28        25.87 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GT TCGA-EE-A2M5 
       46.82       115.96        54.74        79.66        44.88        21.67 
TCGA-EE-A2MC TCGA-EE-A2ME TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MN TCGA-EE-A2MQ 
       61.51       103.27        96.23       216.66        47.54        43.23 
TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AC TCGA-EE-A3JD TCGA-ER-A195 
      134.40       162.48        71.21        64.04        27.35        35.44 
TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19F TCGA-ER-A19G 
       13.94        50.76        77.75        98.40        26.37       268.93 
TCGA-ER-A19J TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A1A1 TCGA-ER-A2ND 
        6.44        61.05        44.05        50.89        79.99        23.34 
TCGA-ER-A2NF TCGA-ER-A3ES TCGA-ER-A3ET TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC 
       16.37       247.04        93.01        18.77        38.27        34.82 
TCGA-FR-A8YD TCGA-FS-A1YW TCGA-FS-A1Z4 TCGA-FS-A1ZB TCGA-FS-A1ZE TCGA-FS-A1ZG 
       36.26       216.92        28.08        48.85        46.45         9.70 
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-A4FC TCGA-FW-A3I3 TCGA-FW-A3R5 
       50.14       174.84        34.03        54.41         0.20        22.92 
TCGA-FW-A3TU TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C9 TCGA-GN-A265 TCGA-GN-A268 
       55.59        19.30         9.90        15.78        96.92        62.79 
TCGA-GN-A26D TCGA-GN-A4U4 TCGA-GN-A8LL TCGA-LH-A9QB TCGA-QB-A6FS TCGA-QB-AA9O 
       48.00        39.35        21.37       368.78         7.23        18.05 
TCGA-RP-A690 TCGA-W3-A824 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1Q TCGA-W3-AA1R 
        0.20       228.16       121.08         4.01        69.07       111.09 
TCGA-W3-AA1V TCGA-W3-AA1W TCGA-WE-A8K1 TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-AAA0 
       42.08       219.16        49.05        58.98        70.52        40.41 
TCGA-YD-A89C TCGA-Z2-A8RT 
        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 
             54.02              48.95 
[1] "0.2 - 369.9 (54.0)" "0.2 - 368.8 (49.0)"
[1] "hr=" "1.2"
D61V3, continuous
                    vv
clus                 I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  10Q LOSS MUTATED            10       3      19       13       16       14
  10Q LOSS WILD-TYPE           3       4      10        5       12       11
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  10Q LOSS MUTATED           5        10         8        29         11
  10Q LOSS WILD-TYPE         9         9         7        11          4
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  10Q LOSS MUTATED           21         32       14
  10Q LOSS WILD-TYPE         12         23        7
D61V4, multiclass
             clus
vv            10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  I OR II NOS               10                  3
  STAGE 0                    3                  4
  STAGE I                   19                 10
  STAGE IA                  13                  5
  STAGE IB                  16                 12
  STAGE II                  14                 11
  STAGE IIA                  5                  9
  STAGE IIB                 10                  9
  STAGE IIC                  8                  7
  STAGE III                 29                 11
  STAGE IIIA                11                  4
  STAGE IIIB                21                 12
  STAGE IIIC                32                 23
  STAGE IV                  14                  7
[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 39 47
  10Q LOSS WILD-TYPE    19 26 39 23
D61V5, multiclass
       clus
vv      10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  T0+T1               45                 19
  T2                  47                 26
  T3                  39                 39
  T4                  47                 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   103  47  25  26
  10Q LOSS WILD-TYPE  74  18  14  19
D61V6, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  N0              103                 74
  N1               47                 18
  N2               25                 14
  N3               26                 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"
D61V7, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED   193  15
  10Q LOSS WILD-TYPE 125   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED    193   15
  10Q LOSS WILD-TYPE  125    7
   clus
vv  10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  0              193                125
  1               15                  7
[1] 2 2
[1] FALSE
D61V8, binary
                    cls
clus                  0  1
  10Q LOSS MUTATED   80 55
  10Q LOSS WILD-TYPE 54 35
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     80   55
  10Q LOSS WILD-TYPE   54   35
     clus
vv    10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  NO                80                 54
  YES               55                 35
[1] 2 2
[1] FALSE
D61V9, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED    28 196
  10Q LOSS WILD-TYPE  19 123
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     28  196
  10Q LOSS WILD-TYPE   19  123
     clus
vv    10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  NO                28                 19
  YES              196                123
[1] 2 2
[1] FALSE
D61V10, continuous
D61V11, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED    92 132
  10Q LOSS WILD-TYPE  45  97
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     92  132
  10Q LOSS WILD-TYPE   45   97
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  FEMALE               92                 45
  MALE                132                 97
[1] 2 2
[1] FALSE
D61V12, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED   193  31
  10Q LOSS WILD-TYPE 124  16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED    193   31
  10Q LOSS WILD-TYPE  124   16
     clus
vv    10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  NO               193                124
  YES               31                 16
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  10Q LOSS MUTATED       1                         0   217
  10Q LOSS WILD-TYPE     4                         1   135
D61V13, multiclass
                           clus
vv                          10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  ASIAN                                    1                  4
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                  217                135
[1] 3 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     4 215
  10Q LOSS WILD-TYPE   3 136
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      4  215
  10Q LOSS WILD-TYPE    3  136
                        clus
vv                       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                  3
  NOT HISPANIC OR LATINO              215                136
[1] 2 2
[1] FALSE

Clustering(62) Variable = 11P LOSS MUTATION ANALYSIS
D62V1, survival
                    sevent
clus2                 0  1
  11P LOSS MUTATED   42 43
  11P LOSS WILD-TYPE 80 80
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                85                160 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                43                 80 
$`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        76.34 
TCGA-DA-A1I1 TCGA-DA-A1I5 TCGA-DA-A3F5 TCGA-DA-A95V TCGA-EB-A5SG TCGA-EB-A5SH 
       53.65        95.51       225.11        72.10        33.24        50.07 
TCGA-EE-A182 TCGA-EE-A20C TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29M TCGA-EE-A29P 
        0.00        75.55        76.14        12.99        47.74        27.16 
TCGA-EE-A29Q TCGA-EE-A2A2 TCGA-EE-A2GE TCGA-EE-A2GM TCGA-EE-A2M6 TCGA-EE-A2MJ 
       61.12        30.02        12.95        18.35       103.13        63.25 
TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE 
      227.01       143.93        53.26       122.73         4.41        54.51 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JH TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19C 
       45.90         3.35        19.86         1.58         7.82        39.81 
TCGA-ER-A19D TCGA-ER-A19L TCGA-ER-A19S TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A3ET 
       11.47        99.06        47.18         4.70        16.87        68.52 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A7UA TCGA-FS-A1Z3 TCGA-FS-A1ZF 
       15.48        32.05        74.47         5.65         8.35        12.92 
TCGA-FS-A1ZM TCGA-FS-A1ZW TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-GN-A262 
       78.61        23.21        66.67       173.19        13.28        53.29 
TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A9SD TCGA-QB-AA9O TCGA-W3-AA1R 
      117.93        17.06         7.59        59.41        18.05        79.99 
TCGA-WE-A8K5 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-AAA3 TCGA-WE-AAA4 
       59.64        65.42        12.69        21.90        18.31        18.35 
TCGA-YG-AA3O 
       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        69.21 
TCGA-DA-A1HY TCGA-DA-A1I2 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 
      138.67       150.61        45.07        64.83        58.85        30.44 
TCGA-DA-A95X TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5UN TCGA-EB-A6L9 
       52.90        14.14        12.30         3.91        52.41        18.21 
TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A184 TCGA-EE-A20H 
       13.15        24.89        62.37        20.38        67.50       155.90 
TCGA-EE-A29B TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29T TCGA-EE-A29W 
       75.22         0.26        44.28        63.12       346.49       185.19 
TCGA-EE-A2A1 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GH TCGA-EE-A2GJ 
      115.43        77.98        26.14       239.11       201.60        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-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-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MR 
       94.19       171.85        89.26       104.78       145.45        25.08 
TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 
       23.51       124.31        64.04         6.28        67.89       111.85 
TCGA-EE-A3JB TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A19A 
      201.80       152.81        14.56        34.45        47.31         4.54 
TCGA-ER-A19B TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P 
       53.29       151.46       150.12        59.84        42.48       120.76 
TCGA-ER-A19Q TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NG TCGA-ER-A3ES 
       49.71       146.63        47.97        22.36        10.95       173.29 
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-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG 
      195.98        27.62       312.07        32.78        42.08         7.82 
TCGA-FS-A1ZJ TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZY 
       36.33       130.95       136.27        35.28         4.47         5.29 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
        3.06        30.90        80.68        55.59        11.54        19.30 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A265 TCGA-GN-A268 TCGA-GN-A4U3 
        9.90         6.05         1.91        96.92        42.48       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-A690 TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1Q 
        0.20         0.33       174.12         1.97       120.07        44.05 
TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8ZQ TCGA-WE-A8ZT 
        8.09       185.13        92.84         1.15        62.89        10.95 
TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-Z2-AA3S 
       48.39         1.94        31.99        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 
             45.99              48.18 
[1] "0.0 - 227.0 (46.0)" "0.2 - 346.5 (48.2)"
[1] "hr=" "1.2"
D62V2, survival
                    sevent
clus2                  0   1
  11P LOSS MUTATED    59  65
  11P LOSS WILD-TYPE 111 122
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
               124                233 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                65                122 
$`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        76.57        36.03       207.48       120.00 
TCGA-DA-A1I8 TCGA-DA-A3F5 TCGA-DA-A95V TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH 
       53.92       225.96        72.10        10.36        68.25        54.02 
TCGA-EB-A5UL TCGA-EE-A182 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20I TCGA-EE-A29C 
       29.29        14.70       133.81       151.27        13.55        78.97 
TCGA-EE-A29D TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
       13.97         2.60        56.84        18.61        56.42        66.74 
TCGA-EE-A29R TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2GC 
       14.47        25.87        17.92        59.64        39.29        67.43 
TCGA-EE-A2GE TCGA-EE-A2GM TCGA-EE-A2M6 TCGA-EE-A2MJ TCGA-EE-A2MN TCGA-EE-A2MP 
      173.79        75.48       129.27        96.23        47.54       248.65 
TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3J5 
      162.48        53.26       122.73        28.77        54.51        36.95 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JH TCGA-ER-A197 TCGA-ER-A199 
       64.08        34.32        53.19       134.33        13.94         9.17 
TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19L TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A2ND 
       48.89        12.59       131.51        49.48         8.88        23.34 
TCGA-ER-A2NE TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A3YN 
       20.15        93.01        46.98        33.21       149.03        92.98 
TCGA-FR-A69P TCGA-FR-A7UA TCGA-FS-A1Z3 TCGA-FS-A1ZA TCGA-FS-A1ZF TCGA-FS-A1ZH 
       15.72        38.27        20.91        27.72        15.45        32.75 
TCGA-FS-A1ZM TCGA-FS-A1ZW TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 
      101.26        49.48        66.67        28.73       174.84        34.03 
TCGA-FW-A3I3 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A4U7 
        0.20       139.89       117.93        64.44        32.48        10.42 
TCGA-GN-A4U9 TCGA-GN-A9SD TCGA-HR-A2OH TCGA-QB-AA9O TCGA-W3-AA1R TCGA-WE-A8JZ 
       22.13        59.41        65.88        18.05       111.09        24.03 
TCGA-WE-A8K5 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-AAA3 TCGA-WE-AAA4 
       61.15       101.33        58.98        70.52        21.40        24.99 
TCGA-YD-A9TA TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-A8RT 
       49.18        37.94        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-D3-A8GV TCGA-D9-A148 
       89.13        29.06       129.63       117.17       167.70       151.53 
TCGA-D9-A1JW TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-DA-A1HY 
        3.65        18.12        15.39         9.90        77.56       144.89 
TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IB 
       20.38       176.55        35.93        73.84        65.92        40.60 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-DA-A95W TCGA-DA-A95X 
       68.09        33.93        10.49        15.68        25.15        61.81 
TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A5VV 
       14.14        13.02        13.87        20.35        58.92         7.04 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 
       36.46        29.82        27.22         8.65        94.98        33.73 
TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A 
       26.89        68.15         4.96        91.56       168.26        63.35 
TCGA-EE-A29B TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29S TCGA-EE-A29T 
       85.08        63.78        72.07        64.64        61.28       369.93 
TCGA-EE-A29W TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD 
      195.02        46.82       115.96        86.14        59.28       340.14 
TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN 
      220.24        48.72       107.38        54.74        79.66       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-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME 
       21.67        28.83        19.76        61.51        47.28       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       180.39       216.66 
TCGA-EE-A2MM TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AC 
      167.90        43.23       134.40        71.21       124.31        64.04 
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-A193 TCGA-ER-A195 TCGA-ER-A198 
       27.35        51.35       152.81        31.40        35.44        50.76 
TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H 
       77.75        98.40        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-A19W 
        6.44        61.05        44.05       162.08        50.89       148.18 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES 
       79.99        43.82        16.37        31.27        32.05       247.04 
TCGA-ER-A42K TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A8YC 
       12.95       174.21       220.80        27.85        18.77        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-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        46.45 
TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR 
        9.70        47.38        23.93        74.73       133.55        11.41 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 
      148.80        53.16        26.56        27.09        27.02        77.82 
TCGA-FS-A4F2 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3R5 TCGA-FW-A3TU 
       50.14        26.73        54.41        80.68        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-A265 TCGA-GN-A266 TCGA-GN-A268 TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A4U4 
       96.92        10.13        62.79        48.00       121.91        39.35 
TCGA-GN-A4U8 TCGA-GN-A8LK TCGA-GN-A8LL TCGA-HR-A2OG TCGA-LH-A9QB TCGA-OD-A75X 
       48.89        50.10        21.37         0.23       368.78       297.90 
TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 
        7.23         0.20         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        17.95        63.22        11.80        35.80        49.51 
TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-YD-A89C TCGA-Z2-AA3S TCGA-Z2-AA3V 
       12.16        40.41         6.90        96.99        15.98 

  11P LOSS MUTATED 11P LOSS WILD-TYPE 
               0.2                0.2 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
            248.65             369.93 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
            51.335             53.160 
[1] "0.2 - 248.7 (51.3)" "0.2 - 369.9 (53.2)"
[1] "hr=" "1.2"
D62V3, continuous
                    vv
clus                 I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  11P LOSS MUTATED             6       3       9        4       12        5
  11P LOSS WILD-TYPE           7       4      20       14       16       20
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  11P LOSS MUTATED           0         7         6        14          5
  11P LOSS WILD-TYPE        14        12         9        26         10
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  11P LOSS MUTATED           14         22       10
  11P LOSS WILD-TYPE         19         33       11
D62V4, multiclass
             clus
vv            11P LOSS MUTATED 11P LOSS WILD-TYPE
  I OR II NOS                6                  7
  STAGE 0                    3                  4
  STAGE I                    9                 20
  STAGE IA                   4                 14
  STAGE IB                  12                 16
  STAGE II                   5                 20
  STAGE IIA                  0                 14
  STAGE IIB                  7                 12
  STAGE IIC                  6                  9
  STAGE III                 14                 26
  STAGE IIIA                 5                 10
  STAGE IIIB                14                 19
  STAGE IIIC                22                 33
  STAGE IV                  10                 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
  11P LOSS MUTATED      21 25 23 30
  11P LOSS WILD-TYPE    43 48 55 40
D62V5, multiclass
       clus
vv      11P LOSS MUTATED 11P LOSS WILD-TYPE
  T0+T1               21                 43
  T2                  25                 48
  T3                  23                 55
  T4                  30                 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"
                    vv
clus                  N0  N1  N2  N3
  11P LOSS MUTATED    57  29  13  15
  11P LOSS WILD-TYPE 120  36  26  30
D62V6, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  N0               57                120
  N1               29                 36
  N2               13                 26
  N3               15                 30
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V7, binary
                    cls
clus                   0   1
  11P LOSS MUTATED   107  10
  11P LOSS WILD-TYPE 211  12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED    107   10
  11P LOSS WILD-TYPE  211   12
   clus
vv  11P LOSS MUTATED 11P LOSS WILD-TYPE
  0              107                211
  1               10                 12
[1] 2 2
[1] FALSE
D62V8, binary
                    cls
clus                  0  1
  11P LOSS MUTATED   44 38
  11P LOSS WILD-TYPE 90 52
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     44   38
  11P LOSS WILD-TYPE   90   52
     clus
vv    11P LOSS MUTATED 11P LOSS WILD-TYPE
  NO                44                 90
  YES               38                 52
[1] 2 2
[1] FALSE
D62V9, binary
                    cls
clus                   0   1
  11P LOSS MUTATED    13 113
  11P LOSS WILD-TYPE  34 206
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     13  113
  11P LOSS WILD-TYPE   34  206
     clus
vv    11P LOSS MUTATED 11P LOSS WILD-TYPE
  NO                13                 34
  YES              113                206
[1] 2 2
[1] FALSE
D62V10, continuous
D62V11, binary
                    cls
clus                   0   1
  11P LOSS MUTATED    58  68
  11P LOSS WILD-TYPE  79 161
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     58   68
  11P LOSS WILD-TYPE   79  161
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  FEMALE               58                 79
  MALE                 68                161
[1] 2 2
[1] FALSE
D62V12, binary
                    cls
clus                   0   1
  11P LOSS MUTATED   112  13
  11P LOSS WILD-TYPE 205  34
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED    112   13
  11P LOSS WILD-TYPE  205   34
     clus
vv    11P LOSS MUTATED 11P LOSS WILD-TYPE
  NO               112                205
  YES               13                 34
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  11P LOSS MUTATED       1                         1   118
  11P LOSS WILD-TYPE     4                         0   234
D62V13, multiclass
                           clus
vv                          11P LOSS MUTATED 11P LOSS WILD-TYPE
  ASIAN                                    1                  4
  BLACK OR AFRICAN AMERICAN                1                  0
  WHITE                                  118                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"
D62V14, binary
                    cls
clus                   0   1
  11P LOSS MUTATED     2 121
  11P LOSS WILD-TYPE   5 230
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      2  121
  11P LOSS WILD-TYPE    5  230
                        clus
vv                       11P LOSS MUTATED 11P LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  5
  NOT HISPANIC OR LATINO              121                230
[1] 2 2
[1] FALSE

Clustering(63) Variable = 11Q LOSS MUTATION ANALYSIS
D63V1, survival
                    sevent
clus2                 0  1
  11Q LOSS MUTATED   55 50
  11Q LOSS WILD-TYPE 67 73
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
               105                140 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                50                 73 
$`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        76.34        53.65 
TCGA-DA-A1I5 TCGA-DA-A3F5 TCGA-DA-A95V TCGA-EB-A44Q TCGA-EB-A5SG TCGA-EB-A5SH 
       95.51       225.11        72.10         3.91        33.24        50.07 
TCGA-EE-A180 TCGA-EE-A182 TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29M TCGA-EE-A29P 
       62.37         0.00        76.14        12.99        47.74        27.16 
TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A2A2 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GM 
       61.12       346.49        30.02        26.14        12.95        18.35 
TCGA-EE-A2M6 TCGA-EE-A2MJ TCGA-EE-A2MP TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB 
      103.13        63.25       227.01        23.51        53.26       122.73 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JH TCGA-ER-A193 
        4.41        54.51        45.90         3.35        19.86        14.56 
TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19L TCGA-ER-A19S 
        1.58         7.82        39.81        11.47        99.06        47.18 
TCGA-ER-A19W TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A3ET TCGA-ER-A3EV 
      146.63         4.70        16.87        10.95        68.52        15.48 
TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A7UA TCGA-FS-A1Z3 TCGA-FS-A1ZE TCGA-FS-A1ZF 
       32.05        74.47         5.65         8.35        42.08        12.92 
TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZW TCGA-FS-A1ZZ TCGA-FS-A4F4 TCGA-FS-A4FD 
       36.33        78.61        23.21         3.06        66.67        80.68 
TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A9SD TCGA-LH-A9QB 
      117.93        17.06         7.59       120.53        59.41        85.05 
TCGA-QB-A6FS TCGA-QB-AA9O TCGA-W3-AA1R TCGA-W3-AA1V TCGA-WE-A8K1 TCGA-WE-A8K5 
        7.23        18.05        79.99         8.09         1.15        59.64 
TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 
       65.42        12.69        21.90        48.39         1.94        31.99 
TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O 
       18.31        18.35        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 
       69.21       138.67       150.61        45.07        64.83        58.85 
TCGA-DA-A3F2 TCGA-DA-A95X TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A5UN TCGA-EB-A6L9 
       30.44        52.90        14.14        12.30        52.41        18.21 
TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A184 TCGA-EE-A20C TCGA-EE-A20H 
       13.15        24.89        20.38        67.50        75.55       155.90 
TCGA-EE-A29B TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29W TCGA-EE-A2A1 
       75.22         0.26        44.28        63.12       185.19       115.43 
TCGA-EE-A2A6 TCGA-EE-A2GD TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
       77.98       239.11       201.60        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-A2MS TCGA-EE-A3AA 
       89.26       104.78       145.45        25.08       143.93       124.31 
TCGA-EE-A3AC TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3JB TCGA-EE-A3JI 
       64.04         6.28        67.89       111.85       201.80       152.81 
TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19G TCGA-ER-A19H 
       34.45        47.31         4.54        53.29       151.46       150.12 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A1A1 TCGA-ER-A2NC 
       59.84        42.48       120.76        49.71        47.97        22.36 
TCGA-ER-A3ES TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A8YC TCGA-FS-A1YW 
      173.29       174.21       209.23        26.20        10.06       171.78 
TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZG 
       49.74       195.98        27.62       312.07        32.78         7.82 
TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A4F0 
      130.95       136.27        35.28         4.47         5.29        30.90 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
      173.19        13.28        55.59        11.54        19.30         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A268 TCGA-GN-A4U4 
        6.05         1.91        53.29        96.92        42.48        34.49 
TCGA-GN-A4U8 TCGA-GN-A8LK TCGA-OD-A75X TCGA-RP-A690 TCGA-RP-A693 TCGA-W3-A824 
       46.92        43.23       297.01         0.20         0.33       174.12 
TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1Q TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8ZQ 
        1.97       120.07        44.05       185.13        92.84        62.89 
TCGA-WE-A8ZT TCGA-Z2-AA3S 
       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 
            42.080             51.075 
[1] "0.0 - 346.5 (42.1)" "0.2 - 312.1 (51.1)"
[1] "hr=" "1.1"
D63V2, survival
                    sevent
clus2                  0   1
  11Q LOSS MUTATED    71  74
  11Q LOSS WILD-TYPE  99 113
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
               145                212 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                74                113 
$`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        76.57        36.03       207.48       120.00        53.92 
TCGA-DA-A3F5 TCGA-DA-A95V TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH 
      225.96        72.10        13.87        10.36        68.25        54.02 
TCGA-EB-A5UL TCGA-EE-A180 TCGA-EE-A182 TCGA-EE-A20B TCGA-EE-A29C TCGA-EE-A29D 
       29.29        94.98        14.70       133.81        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-A29T TCGA-EE-A29V TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2GB TCGA-EE-A2GC 
      369.93        25.87        59.64        39.29        59.28        67.43 
TCGA-EE-A2GE TCGA-EE-A2GM TCGA-EE-A2M6 TCGA-EE-A2MD TCGA-EE-A2MJ TCGA-EE-A2MN 
      173.79        75.48       129.27        47.28        96.23        47.54 
TCGA-EE-A2MP TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE 
      248.65        71.21        53.26       122.73        28.77        54.51 
TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JH TCGA-ER-A193 
       36.95        64.08        34.32        53.19       134.33        31.40 
TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19L TCGA-ER-A19S 
       13.94         9.17        48.89        12.59       131.51        49.48 
TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A3ET 
        8.88       148.18        23.34        20.15        31.27        93.01 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A69P TCGA-FR-A7UA 
       46.98        33.21       149.03        92.98        15.72        38.27 
TCGA-FS-A1Z3 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZH 
       20.91         7.79        27.72        46.45        15.45        32.75 
TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZW TCGA-FS-A1ZZ TCGA-FS-A4F4 TCGA-FS-A4F5 
       47.38       101.26        49.48        27.02        66.67        28.73 
TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-GN-A264 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A26A 
       80.68         0.20       117.93        10.13        64.44        32.48 
TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A4U7 TCGA-GN-A4U9 TCGA-GN-A9SD TCGA-HR-A2OH 
       48.00       121.91        10.42        22.13        59.41        65.88 
TCGA-LH-A9QB TCGA-QB-A6FS TCGA-QB-AA9O TCGA-W3-AA1R TCGA-W3-AA1V TCGA-WE-A8JZ 
      368.78         7.23        18.05       111.09        42.08        24.03 
TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZY 
       49.05        61.15       101.33        58.98        70.52        49.51 
TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-YG-AA3P 
       12.16        40.41        21.40        24.99        37.94        14.43 
TCGA-Z2-A8RT 
       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-D3-A8GV TCGA-D9-A148 
      170.20        89.13        29.06       117.17       167.70       151.53 
TCGA-D9-A1JW TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EC 
        3.65        18.12        15.39        18.44         9.90        77.56 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I7 TCGA-DA-A1IA 
      144.89        20.38       176.55        35.93        73.84        65.92 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-DA-A95W 
       40.60        68.09        33.93        10.49        15.68        25.15 
TCGA-DA-A95X TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A5VV 
       61.81        14.14        13.02        20.35        58.92         7.04 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A183 
       36.46        29.82        27.22         8.65        33.73        26.89 
TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I 
       68.15         4.96       151.27        91.56       168.26        13.55 
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-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A6 TCGA-EE-A2GD 
      195.02        17.92        46.82       115.96        86.14       340.14 
TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN 
      220.24        48.72       107.38        54.74        79.66       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-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-A2MM 
      103.20        16.96       204.66       180.39       216.66       167.90 
TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AF 
       43.23       134.40       162.48       124.31        64.04        13.81 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3JB TCGA-EE-A3JD 
       41.59       138.81       172.18       127.20       201.80        27.35 
TCGA-EE-A3JE TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19B 
       51.35       152.81        35.44        50.76        77.75        98.40 
TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19M 
       13.02        26.37       268.93       152.35         6.44        61.05 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NF 
       44.05       162.08        50.89        79.99        43.82        16.37 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A42K TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7U8 
       32.05       247.04        12.95       174.21       220.80        27.85 
TCGA-FR-A7U9 TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YX 
       18.77        34.82        36.26       104.42       216.92        48.59 
TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD 
      228.59       202.65        28.08        48.85       357.37        53.52 
TCGA-FS-A1ZG TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS 
        9.70        23.93        74.73       133.55        11.41       148.80 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F8 
       53.16        26.56        27.09        77.82        50.14       174.84 
TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV 
       34.03        26.73        54.41        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-A268 TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-GN-A8LK TCGA-GN-A8LL 
       96.92        62.79        39.35        48.89        50.10        21.37 
TCGA-HR-A2OG TCGA-OD-A75X TCGA-RP-A690 TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 
        0.23       297.90         0.20         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 
       17.95        63.22        11.80        35.80         6.90        49.18 
TCGA-Z2-AA3S TCGA-Z2-AA3V 
       96.99        15.98 

  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
               0.2                0.2 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
            369.93             357.37 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
            49.480             53.965 
[1] "0.2 - 369.9 (49.5)" "0.2 - 357.4 (54.0)"
[1] "hr=" "1"  
D63V3, continuous
                    vv
clus                 I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  11Q LOSS MUTATED             6       3       9        5       13        7
  11Q LOSS WILD-TYPE           7       4      20       13       15       18
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  11Q LOSS MUTATED           1         9         8        17          5
  11Q LOSS WILD-TYPE        13        10         7        23         10
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  11Q LOSS MUTATED           15         28       10
  11Q LOSS WILD-TYPE         18         27       11
D63V4, multiclass
             clus
vv            11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  I OR II NOS                6                  7
  STAGE 0                    3                  4
  STAGE I                    9                 20
  STAGE IA                   5                 13
  STAGE IB                  13                 15
  STAGE II                   7                 18
  STAGE IIA                  1                 13
  STAGE IIB                  9                 10
  STAGE IIC                  8                  7
  STAGE III                 17                 23
  STAGE IIIA                 5                 10
  STAGE IIIB                15                 18
  STAGE IIIC                28                 27
  STAGE IV                  10                 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
  11Q LOSS MUTATED      24 29 30 34
  11Q LOSS WILD-TYPE    40 44 48 36
D63V5, multiclass
       clus
vv      11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  T0+T1               24                 40
  T2                  29                 44
  T3                  30                 48
  T4                  34                 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"
                    vv
clus                  N0  N1  N2  N3
  11Q LOSS MUTATED    65  31  14  21
  11Q LOSS WILD-TYPE 112  34  25  24
D63V6, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  N0               65                112
  N1               31                 34
  N2               14                 25
  N3               21                 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"
D63V7, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED   126  10
  11Q LOSS WILD-TYPE 192  12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED    126   10
  11Q LOSS WILD-TYPE  192   12
   clus
vv  11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  0              126                192
  1               10                 12
[1] 2 2
[1] FALSE
D63V8, binary
                    cls
clus                  0  1
  11Q LOSS MUTATED   54 46
  11Q LOSS WILD-TYPE 80 44
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     54   46
  11Q LOSS WILD-TYPE   80   44
     clus
vv    11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  NO                54                 80
  YES               46                 44
[1] 2 2
[1] FALSE
D63V9, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED    16 132
  11Q LOSS WILD-TYPE  31 187
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     16  132
  11Q LOSS WILD-TYPE   31  187
     clus
vv    11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  NO                16                 31
  YES              132                187
[1] 2 2
[1] FALSE
D63V10, continuous
D63V11, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED    70  78
  11Q LOSS WILD-TYPE  67 151
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     70   78
  11Q LOSS WILD-TYPE   67  151
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  FEMALE               70                 67
  MALE                 78                151
[1] 2 2
[1] FALSE
D63V12, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED   126  21
  11Q LOSS WILD-TYPE 191  26
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED    126   21
  11Q LOSS WILD-TYPE  191   26
     clus
vv    11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  NO               126                191
  YES               21                 26
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  11Q LOSS MUTATED       2                         1   139
  11Q LOSS WILD-TYPE     3                         0   213
D63V13, multiclass
                           clus
vv                          11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  ASIAN                                    2                  3
  BLACK OR AFRICAN AMERICAN                1                  0
  WHITE                                  139                213
[1] 3 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     3 142
  11Q LOSS WILD-TYPE   4 209
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      3  142
  11Q LOSS WILD-TYPE    4  209
                        clus
vv                       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  4
  NOT HISPANIC OR LATINO              142                209
[1] 2 2
[1] FALSE

Clustering(64) Variable = 12P LOSS MUTATION ANALYSIS
D64V1, survival
                    sevent
clus2                  0   1
  12P LOSS MUTATED    21  12
  12P LOSS WILD-TYPE 101 111
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                33                212 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                12                111 
$`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-DA-A95X TCGA-EB-A5SH TCGA-EE-A20C TCGA-EE-A29G TCGA-EE-A29Q 
       53.65        52.90        50.07        75.55        44.28        61.12 
TCGA-EE-A2A2 TCGA-EE-A2GP TCGA-EE-A2MG TCGA-EE-A2MK TCGA-EE-A2MP TCGA-EE-A2MS 
       30.02         0.76        94.19        89.26       227.01       143.93 
TCGA-EE-A2MU TCGA-EE-A3AE TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-ER-A19S TCGA-ER-A2NG 
       53.26        54.51        67.89        45.90        47.18        10.95 
TCGA-FS-A1Z4 TCGA-FS-A1ZQ TCGA-FS-A1ZT TCGA-GN-A4U3 TCGA-LH-A9QB TCGA-OD-A75X 
       27.62       130.95        35.28       120.53        85.05       297.01 
TCGA-RP-A693 TCGA-W3-AA1V TCGA-WE-A8ZY 
        0.33         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        69.21        22.85        76.34 
TCGA-DA-A1HY TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC 
      138.67       150.61        95.51        45.07        64.83        58.85 
TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A95V TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q 
       30.44       225.11        72.10        14.14        12.30         3.91 
TCGA-EB-A5SG TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A180 
       33.24        52.41        18.21        13.15        24.89        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-A29P TCGA-EE-A29T 
       12.99         0.26        63.12        47.74        27.16       346.49 
TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE 
      185.19       115.43        77.98        26.14       239.11        12.95 
TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN 
      201.60        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-A2MI TCGA-EE-A2MJ TCGA-EE-A2ML 
        5.75        23.77       209.79       171.85        63.25       104.78 
TCGA-EE-A2MM TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC 
      145.45        25.08        23.51       124.31       122.73        64.04 
TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3J4 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH 
        4.41         6.28       111.85         3.35       201.80        19.86 
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-A19W 
       99.06        59.84        42.48       120.76        49.71       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        68.52 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7U8 
       15.48        32.05        74.47       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        42.08        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        96.92        17.06        42.48         7.59        34.49 
TCGA-GN-A4U8 TCGA-GN-A8LK TCGA-GN-A9SD TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A690 
       46.92        43.23        59.41         7.23        18.05         0.20 
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        65.42        12.69        21.90 
TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 
       62.89        10.95         1.94        31.99        18.31        18.35 
TCGA-YG-AA3O TCGA-Z2-AA3S 
       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 
            53.260             45.385 
[1] "0.3 - 297.0 (53.3)" "0.0 - 346.5 (45.4)"
[1] "hr=" "1.6"
D64V2, survival
                    sevent
clus2                  0   1
  12P LOSS MUTATED    30  25
  12P LOSS WILD-TYPE 140 162
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                55                302 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                25                162 
$`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-DA-A95X TCGA-EB-A5SH TCGA-EE-A20B TCGA-EE-A20C 
       25.18       207.48        61.81        54.02       133.81       151.27 
TCGA-EE-A29G TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A2A2 TCGA-EE-A2GP TCGA-EE-A2MG 
       72.07        66.74        61.28        59.64        13.91       103.20 
TCGA-EE-A2MK TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AE TCGA-EE-A3J3 
      180.39       248.65       162.48        53.26        54.51       172.18 
TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-ER-A19E TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A2NG 
       64.08        53.19        13.02        49.48         8.88        31.27 
TCGA-ER-A42K TCGA-FS-A1YX TCGA-FS-A1Z4 TCGA-FS-A1ZA TCGA-FS-A1ZH TCGA-FS-A1ZQ 
       12.95        48.59        28.08        27.72        32.75       133.55 
TCGA-FS-A1ZT TCGA-FS-A4F5 TCGA-FW-A3R5 TCGA-GN-A4U3 TCGA-GN-A8LL TCGA-HR-A2OH 
       53.16        28.73        22.92       121.91        21.37        65.88 
TCGA-LH-A9QB TCGA-OD-A75X TCGA-RP-A693 TCGA-W3-AA1V TCGA-WE-A8JZ TCGA-WE-A8ZY 
      368.78       297.90         0.33        42.08        24.03        49.51 
TCGA-YD-A9TA 
       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-D3-A8GV TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX 
      117.17       167.70       151.53        54.67         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        77.56        22.95 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 
       76.57        36.03       144.89        20.38       176.55        35.93 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
      120.00        73.84        53.92        65.92        40.60        68.09 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-DA-A95V TCGA-DA-A95W 
       33.93        10.49       225.96        15.68        72.10        25.15 
TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG 
       14.14        13.02        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 
       29.29        58.92         7.04        36.46        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-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
       17.92        46.82       115.96        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       173.79       220.24        48.72       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-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-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MQ 
      204.66        96.23       216.66       167.90        47.54        43.23 
TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
      134.40        71.21       124.31       122.73        64.04        28.77 
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       134.33       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-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J 
       48.89        12.59        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-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-A42L TCGA-FR-A3YN 
      247.04        93.01        46.98        33.21       149.03        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        46.45 
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 
       96.92        10.13        64.44        62.79        32.48        48.00 
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-A690 TCGA-RP-A694 TCGA-W3-A824 
        0.23         7.23        18.05         0.20         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-A8K1 TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN 
      105.04        49.05        61.15        17.95       101.33        58.98 
TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-AA9Y TCGA-WE-AAA0 
       70.52        63.22        11.80        35.80        12.16        40.41 
TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YD-A89C TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-A8RT 
       21.40        24.99         6.90        37.94        14.43        27.58 
TCGA-Z2-AA3S TCGA-Z2-AA3V 
       96.99        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 
            53.260             50.825 
[1] "0.3 - 368.8 (53.3)" "0.2 - 369.9 (50.8)"
[1] "hr=" "1.4"
D64V3, continuous
                    vv
clus                 I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  12P LOSS MUTATED             4       1       5        3        5        4
  12P LOSS WILD-TYPE           9       6      24       15       23       21
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  12P LOSS MUTATED           2         2         1         7          1
  12P LOSS WILD-TYPE        12        17        14        33         14
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  12P LOSS MUTATED            5          6        6
  12P LOSS WILD-TYPE         28         49       15
D64V4, multiclass
             clus
vv            12P LOSS MUTATED 12P LOSS WILD-TYPE
  I OR II NOS                4                  9
  STAGE 0                    1                  6
  STAGE I                    5                 24
  STAGE IA                   3                 15
  STAGE IB                   5                 23
  STAGE II                   4                 21
  STAGE IIA                  2                 12
  STAGE IIB                  2                 17
  STAGE IIC                  1                 14
  STAGE III                  7                 33
  STAGE IIIA                 1                 14
  STAGE IIIB                 5                 28
  STAGE IIIC                 6                 49
  STAGE IV                   6                 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
  12P LOSS MUTATED       8 10 12 14
  12P LOSS WILD-TYPE    56 63 66 56
D64V5, multiclass
       clus
vv      12P LOSS MUTATED 12P LOSS WILD-TYPE
  T0+T1                8                 56
  T2                  10                 63
  T3                  12                 66
  T4                  14                 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
  12P LOSS MUTATED    27   8   7   7
  12P LOSS WILD-TYPE 150  57  32  38
D64V6, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  N0               27                150
  N1                8                 57
  N2                7                 32
  N3                7                 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"
D64V7, binary
                    cls
clus                   0   1
  12P LOSS MUTATED    47   6
  12P LOSS WILD-TYPE 271  16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     47    6
  12P LOSS WILD-TYPE  271   16
   clus
vv  12P LOSS MUTATED 12P LOSS WILD-TYPE
  0               47                271
  1                6                 16
[1] 2 2
[1] FALSE
D64V8, binary
                    cls
clus                   0   1
  12P LOSS MUTATED    21  16
  12P LOSS WILD-TYPE 113  74
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     21   16
  12P LOSS WILD-TYPE  113   74
     clus
vv    12P LOSS MUTATED 12P LOSS WILD-TYPE
  NO                21                113
  YES               16                 74
[1] 2 2
[1] FALSE
D64V9, binary
                    cls
clus                   0   1
  12P LOSS MUTATED     5  54
  12P LOSS WILD-TYPE  42 265
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      5   54
  12P LOSS WILD-TYPE   42  265
     clus
vv    12P LOSS MUTATED 12P LOSS WILD-TYPE
  NO                 5                 42
  YES               54                265
[1] 2 2
[1] FALSE
D64V10, continuous
D64V11, binary
                    cls
clus                   0   1
  12P LOSS MUTATED    25  34
  12P LOSS WILD-TYPE 112 195
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     25   34
  12P LOSS WILD-TYPE  112  195
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  FEMALE               25                112
  MALE                 34                195
[1] 2 2
[1] FALSE
D64V12, binary
                    cls
clus                   0   1
  12P LOSS MUTATED    52   7
  12P LOSS WILD-TYPE 265  40
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     52    7
  12P LOSS WILD-TYPE  265   40
     clus
vv    12P LOSS MUTATED 12P LOSS WILD-TYPE
  NO                52                265
  YES                7                 40
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  12P LOSS MUTATED       0                         0    57
  12P LOSS WILD-TYPE     5                         1   295
D64V13, multiclass
                           clus
vv                          12P LOSS MUTATED 12P LOSS WILD-TYPE
  ASIAN                                    0                  5
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   57                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"
D64V14, binary
                    cls
clus                   0   1
  12P LOSS MUTATED     0  57
  12P LOSS WILD-TYPE   7 294
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      0   57
  12P LOSS WILD-TYPE    7  294
                        clus
vv                       12P LOSS MUTATED 12P LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  7
  NOT HISPANIC OR LATINO               57                294
[1] 2 2
[1] FALSE

Clustering(65) Variable = 12Q LOSS MUTATION ANALYSIS
D65V1, survival
                    sevent
clus2                  0   1
  12Q LOSS MUTATED    24  18
  12Q LOSS WILD-TYPE  98 105
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                42                203 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                18                105 
$`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-DA-A95X TCGA-EB-A5SH 
       78.21        10.78        69.21        53.65        52.90        50.07 
TCGA-EE-A20C TCGA-EE-A29G TCGA-EE-A29Q TCGA-EE-A2A2 TCGA-EE-A2GP TCGA-EE-A2GR 
       75.55        44.28        61.12        30.02         0.76         0.20 
TCGA-EE-A2GU TCGA-EE-A2MG TCGA-EE-A2MK TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MU 
       81.99        94.19        89.26       227.01       143.93        53.26 
TCGA-EE-A3AA TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-ER-A199 
      124.31         4.41        54.51        67.89        45.90         7.82 
TCGA-ER-A19S TCGA-ER-A3PL TCGA-FS-A1Z4 TCGA-FS-A1ZQ TCGA-FS-A1ZT TCGA-GN-A4U3 
       47.18        32.05        27.62       130.95        35.28       120.53 
TCGA-LH-A9QB TCGA-OD-A75X TCGA-RP-A693 TCGA-W3-AA1R TCGA-WE-A8ZM TCGA-WE-A8ZY 
       85.05       297.01         0.33        79.99        65.42        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        76.34       138.67       150.61        95.51 
TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A95V 
       45.07        64.83        58.85        30.44       225.11        72.10 
TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5SG TCGA-EB-A5UN TCGA-EB-A6L9 
       14.14        12.30         3.91        33.24        52.41        18.21 
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-A29H 
      155.90        75.22        76.14        12.99         0.26        63.12 
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       115.43        77.98 
TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK 
       26.14       239.11        12.95       201.60        68.65        10.62 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GS TCGA-EE-A2M6 
       32.48        18.35        31.00       118.32        71.31       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-A2ML TCGA-EE-A2MM TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A3AB TCGA-EE-A3AC 
      104.78       145.45        25.08        23.51       122.73        64.04 
TCGA-EE-A3AF TCGA-EE-A3J4 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI 
        6.28       111.85         3.35       201.80        19.86       152.81 
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-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-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        68.52        15.48 
TCGA-ER-A42L TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FR-A8YC 
       74.47       174.21       209.23        26.20         5.65        10.06 
TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1ZC TCGA-FS-A1ZD 
      171.78        49.74       195.98         8.35       312.07        32.78 
TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZS 
       42.08        12.92         7.82        36.33        78.61       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-A264 TCGA-GN-A265 
        9.90         6.05         1.91        53.29       117.93        96.92 
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-QB-A6FS TCGA-QB-AA9O TCGA-RP-A690 TCGA-W3-A824 TCGA-W3-A825 
       59.41         7.23        18.05         0.20       174.12         1.97 
TCGA-W3-A828 TCGA-W3-AA1Q TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 
      120.07        44.05         8.09       185.13        92.84         1.15 
TCGA-WE-A8K5 TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-AA9Y 
       59.64        12.69        21.90        62.89        10.95         1.94 
TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-Z2-AA3S 
       31.99        18.31        18.35        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 
            53.455             45.070 
[1] "0.2 - 297.0 (53.5)" "0.0 - 346.5 (45.1)"
[1] "hr=" "1.3"
D65V2, survival
                    sevent
clus2                  0   1
  12Q LOSS MUTATED    32  32
  12Q LOSS WILD-TYPE 138 155
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                64                293 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                32                155 
$`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-DA-A95X TCGA-EB-A5SH TCGA-EE-A20B 
       25.18        77.56       207.48        61.81        54.02       133.81 
TCGA-EE-A20C TCGA-EE-A29G TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29X TCGA-EE-A2A2 
      151.27        72.07        66.74        61.28        17.92        59.64 
TCGA-EE-A2A5 TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GU TCGA-EE-A2MG TCGA-EE-A2MK 
       39.29        13.91        42.77        94.82       103.20       180.39 
TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AD TCGA-EE-A3AE 
      248.65       162.48        53.26       124.31        28.77        54.51 
TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-ER-A199 TCGA-ER-A19E TCGA-ER-A19S 
      172.18        64.08        53.19         9.17        13.02        49.48 
TCGA-ER-A3PL TCGA-ER-A42K TCGA-FS-A1YX TCGA-FS-A1Z4 TCGA-FS-A1ZA TCGA-FS-A1ZH 
       33.21        12.95        48.59        28.08        27.72        32.75 
TCGA-FS-A1ZQ TCGA-FS-A1ZT TCGA-FS-A4F2 TCGA-FS-A4F5 TCGA-FW-A3R5 TCGA-GN-A4U3 
      133.55        53.16        50.14        28.73        22.92       121.91 
TCGA-GN-A8LL TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X TCGA-RP-A693 TCGA-W3-AA1R 
       21.37        65.88       368.78       297.90         0.33       111.09 
TCGA-WE-A8JZ TCGA-WE-A8ZM TCGA-WE-A8ZY TCGA-YD-A9TA 
       24.03       101.33        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-D3-A8GV TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX 
      117.17       167.70       151.53        54.67         3.65         7.10 
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        76.57 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
       36.03       144.89        20.38       176.55        35.93       120.00 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
       73.84        53.92        65.92        40.60        68.09        33.93 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-DA-A95V TCGA-DA-A95W TCGA-DA-A95Y 
       10.49       225.96        15.68        72.10        25.15        14.14 
TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5UL 
       13.02        13.87        10.36        20.35        68.25        29.29 
TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
       58.92         7.04        36.46        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-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-A29R TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A2A0 
       56.42        14.47       369.93        25.87       195.02        46.82 
TCGA-EE-A2A1 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE 
      115.96        86.14        59.28        67.43       340.14       173.79 
TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
      220.24        48.72       107.38        54.74        79.66        75.48 
TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2M6 
      102.12       126.81        81.21        44.88        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-A3AB TCGA-EE-A3AC TCGA-EE-A3AF 
       43.23       134.40        71.21       122.73        64.04        13.81 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J8 TCGA-EE-A3JB 
       41.59       138.81       127.20        36.95        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       134.33       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-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-A19T TCGA-ER-A19W TCGA-ER-A1A1 
       44.05       162.08        50.89         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-A42L TCGA-FR-A3YN TCGA-FR-A44A 
      247.04        93.01        46.98       149.03        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        46.45        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        96.92        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        48.00        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-A690 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 
       18.05         0.20         0.69       228.16        63.02       121.08 
TCGA-W3-AA1O TCGA-W3-AA1Q TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 
        4.01        69.07        42.08       219.16       105.04        49.05 
TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT 
       61.15        17.95        58.98        70.52        63.22        11.80 
TCGA-WE-A8ZX TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YD-A89C 
       35.80        12.16        40.41        21.40        24.99         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 

  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 
            54.265             50.100 
[1] "0.3 - 368.8 (54.3)" "0.2 - 369.9 (50.1)"
[1] "hr=" "1.2"
D65V3, continuous
                    vv
clus                 I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  12Q LOSS MUTATED             4       1       5        4        7        5
  12Q LOSS WILD-TYPE           9       6      24       14       21       20
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  12Q LOSS MUTATED           2         2         3         9          3
  12Q LOSS WILD-TYPE        12        17        12        31         12
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  12Q LOSS MUTATED            5          6        4
  12Q LOSS WILD-TYPE         28         49       17
D65V4, multiclass
             clus
vv            12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  I OR II NOS                4                  9
  STAGE 0                    1                  6
  STAGE I                    5                 24
  STAGE IA                   4                 14
  STAGE IB                   7                 21
  STAGE II                   5                 20
  STAGE IIA                  2                 12
  STAGE IIB                  2                 17
  STAGE IIC                  3                 12
  STAGE III                  9                 31
  STAGE IIIA                 3                 12
  STAGE IIIB                 5                 28
  STAGE IIIC                 6                 49
  STAGE IV                   4                 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
  12Q LOSS MUTATED      11 13 12 16
  12Q LOSS WILD-TYPE    53 60 66 54
D65V5, multiclass
       clus
vv      12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  T0+T1               11                 53
  T2                  13                 60
  T3                  12                 66
  T4                  16                 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
  12Q LOSS MUTATED    34  10   8   6
  12Q LOSS WILD-TYPE 143  55  31  39
D65V6, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  N0               34                143
  N1               10                 55
  N2                8                 31
  N3                6                 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"
D65V7, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED    57   4
  12Q LOSS WILD-TYPE 261  18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED     57    4
  12Q LOSS WILD-TYPE  261   18
   clus
vv  12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  0               57                261
  1                4                 18
[1] 2 2
[1] FALSE
D65V8, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED    23  17
  12Q LOSS WILD-TYPE 111  73
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED     23   17
  12Q LOSS WILD-TYPE  111   73
     clus
vv    12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  NO                23                111
  YES               17                 73
[1] 2 2
[1] FALSE
D65V9, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED     8  59
  12Q LOSS WILD-TYPE  39 260
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      8   59
  12Q LOSS WILD-TYPE   39  260
     clus
vv    12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  NO                 8                 39
  YES               59                260
[1] 2 2
[1] FALSE
D65V10, continuous
D65V11, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED    28  39
  12Q LOSS WILD-TYPE 109 190
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED     28   39
  12Q LOSS WILD-TYPE  109  190
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  FEMALE               28                109
  MALE                 39                190
[1] 2 2
[1] FALSE
D65V12, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED    60   7
  12Q LOSS WILD-TYPE 257  40
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED     60    7
  12Q LOSS WILD-TYPE  257   40
     clus
vv    12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  NO                60                257
  YES                7                 40
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  12Q LOSS MUTATED       0                         0    65
  12Q LOSS WILD-TYPE     5                         1   287
D65V13, multiclass
                           clus
vv                          12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  ASIAN                                    0                  5
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   65                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"
D65V14, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED     0  65
  12Q LOSS WILD-TYPE   7 286
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      0   65
  12Q LOSS WILD-TYPE    7  286
                        clus
vv                       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  7
  NOT HISPANIC OR LATINO               65                286
[1] 2 2
[1] FALSE

Clustering(66) Variable = 13Q LOSS MUTATION ANALYSIS
D66V1, survival
                    sevent
clus2                  0   1
  13Q LOSS MUTATED    33  22
  13Q LOSS WILD-TYPE  89 101
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                55                190 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                22                101 
$`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        76.34       150.61        95.51 
TCGA-DA-A1IC TCGA-DA-A95V TCGA-DA-A95X TCGA-EB-A5UN TCGA-EE-A181 TCGA-EE-A184 
       58.85        72.10        52.90        52.41        20.38        67.50 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29M TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W 
       76.14        12.99        47.74        61.12       346.49       185.19 
TCGA-EE-A2A6 TCGA-EE-A2GE TCGA-EE-A2GJ TCGA-EE-A2MG TCGA-EE-A2MR TCGA-EE-A2MS 
       77.98        12.95        68.65        94.19        25.08       143.93 
TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3JB TCGA-EE-A3JH 
       53.26       122.73         4.41        54.51       201.80        19.86 
TCGA-ER-A193 TCGA-ER-A19B TCGA-ER-A19H TCGA-ER-A2NG TCGA-FS-A4F4 TCGA-GN-A8LK 
       14.56        53.29       150.12        10.95        66.67        43.23 
TCGA-GN-A9SD TCGA-RP-A693 TCGA-W3-AA1V TCGA-WE-A8ZM TCGA-WE-A8ZQ TCGA-WE-A8ZY 
       59.41         0.33         8.09        65.42        62.89        48.39 
TCGA-YG-AA3O 
       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 
       69.21        22.85       138.67        53.65        45.07        64.83 
TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5SG 
       30.44       225.11        14.14        12.30         3.91        33.24 
TCGA-EB-A5SH TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A182 
       50.07        18.21        13.15        24.89        62.37         0.00 
TCGA-EE-A20C TCGA-EE-A20H TCGA-EE-A29B TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H 
       75.55       155.90        75.22         0.26        44.28        63.12 
TCGA-EE-A29P TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GH 
       27.16       115.43        30.02        26.14       239.11       201.60 
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-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML 
       23.77       209.79       171.85        63.25        89.26       104.78 
TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AF 
      145.45       227.01        23.51       124.31        64.04         6.28 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JI TCGA-ER-A195 
       67.89       111.85        45.90         3.35       152.81        34.45 
TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19C TCGA-ER-A19D 
        1.58        47.31         7.82         4.54        39.81        11.47 
TCGA-ER-A19G TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
      151.46        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 
       47.18       146.63        47.97        22.36         4.70        16.87 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A44A 
      173.29        68.52        15.48        32.05        74.47       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        42.08 
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-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        96.92 
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-QB-AA9O TCGA-RP-A690 TCGA-W3-A824 
       85.05       297.01         7.23        18.05         0.20       174.12 
TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1W TCGA-W3-AA21 
        1.97       120.07        44.05        79.99       185.13        92.84 
TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-AA9Y 
        1.15        59.64        12.69        21.90        10.95         1.94 
TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-Z2-AA3S 
       31.99        18.31        18.35        91.23 

  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
              0.33               0.00 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
            346.49             312.07 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
            53.290             44.165 
[1] "0.3 - 346.5 (53.3)" "0.0 - 312.1 (44.2)"
[1] "hr=" "1.4"
D66V2, survival
                    sevent
clus2                  0   1
  13Q LOSS MUTATED    41  39
  13Q LOSS WILD-TYPE 129 148
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                80                277 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                39                148 
$`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-D3-A8GV TCGA-D9-A148 
       23.61       170.20       129.63       117.17       167.70       151.53 
TCGA-D9-A149 TCGA-D9-A3Z3 TCGA-D9-A6EA TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I2 
       54.67        22.29        25.18        76.57        36.03       176.55 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A1IC TCGA-DA-A95V TCGA-DA-A95X 
       35.93       120.00        53.92        68.09        72.10        61.81 
TCGA-EB-A5UN TCGA-EE-A181 TCGA-EE-A184 TCGA-EE-A20I TCGA-EE-A29C TCGA-EE-A29D 
       58.92        33.73        68.15        13.55        78.97        13.97 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A6 
       56.84        18.61        66.74       369.93       195.02        86.14 
TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2M5 TCGA-EE-A2MG TCGA-EE-A2MH 
      173.79        48.72       107.38        21.67       103.20        16.96 
TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE 
      134.40       162.48        53.26       122.73        28.77        54.51 
TCGA-EE-A3AH TCGA-EE-A3J5 TCGA-EE-A3JB TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A19B 
      138.81        36.95       201.80       134.33        31.40        98.40 
TCGA-ER-A19H TCGA-ER-A19T TCGA-ER-A2NG TCGA-FR-A3YN TCGA-FR-A7U9 TCGA-FS-A1ZA 
      152.35         8.88        31.27        92.98        18.77        27.72 
TCGA-FS-A1ZH TCGA-FS-A4F4 TCGA-GN-A266 TCGA-GN-A26D TCGA-GN-A4U7 TCGA-GN-A8LK 
       32.75        66.67        10.13        48.00        10.42        50.10 
TCGA-GN-A9SD TCGA-RP-A693 TCGA-W3-AA1V TCGA-WE-A8ZM TCGA-WE-A8ZQ TCGA-WE-A8ZY 
       59.41         0.33        42.08       101.33        63.22        49.51 
TCGA-YG-AA3O TCGA-YG-AA3P 
       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        77.56        22.95       144.89        20.38 
TCGA-DA-A1I1 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-DA-A3F3 
      207.48        73.84        65.92        40.60        33.93        10.49 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-DA-A95W TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q 
      225.96        15.68        25.15        14.14        13.02        13.87 
TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5VV 
       10.36        20.35        68.25        54.02        29.29         7.04 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A182 
       36.46        29.82        27.22         8.65        94.98        14.70 
TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H 
       26.89         4.96       133.81       151.27        91.56       168.26 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L 
       63.35        85.08        63.78        72.07        64.64         2.60 
TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A0 
       56.42        14.47        61.28        25.87        17.92        46.82 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD 
      115.96        59.64        39.29        59.28        67.43       340.14 
TCGA-EE-A2GH TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO 
      220.24        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-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-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN 
      204.66        96.23       180.39       216.66       167.90        47.54 
TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AF 
      248.65        43.23        71.21       124.31        64.04        13.81 
TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA 
       41.59       172.18       127.20        64.08        34.32        53.19 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
       27.35        51.35       152.81        35.44        13.94        50.76 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F 
        9.17        77.75        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-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
       50.89        49.48       148.18        79.99        43.82        23.34 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
       20.15        16.37        32.05       247.04        93.01        46.98 
TCGA-ER-A3PL TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 
       33.21        12.95       149.03       174.21        15.72       220.80 
TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW 
       27.85        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-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG 
       48.85       357.37        53.52        46.45        15.45         9.70 
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-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB 
       77.82        50.14        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-A268 TCGA-GN-A26A TCGA-GN-A4U3 
      117.93        96.92        64.44        62.79        32.48       121.91 
TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LL TCGA-HR-A2OG TCGA-HR-A2OH 
       39.35        48.89        22.13        21.37         0.23        65.88 
TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A690 TCGA-RP-A694 
      368.78       297.90         7.23        18.05         0.20         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-A8K6 
      219.16       105.04        24.03        49.05        61.15        17.95 
TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-AA9Y TCGA-WE-AAA0 
       58.98        70.52        11.80        35.80        12.16        40.41 
TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YD-A89C TCGA-YD-A9TA TCGA-Z2-A8RT TCGA-Z2-AA3S 
       21.40        24.99         6.90        49.18        27.58        96.99 
TCGA-Z2-AA3V 
       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 
             60.61              49.18 
[1] "0.3 - 369.9 (60.6)" "0.2 - 368.8 (49.2)"
[1] "hr=" "1.2"
D66V3, continuous
                    vv
clus                 I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  13Q LOSS MUTATED             3       2       6        6        8        5
  13Q LOSS WILD-TYPE          10       5      23       12       20       20
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  13Q LOSS MUTATED           3         3         4         9          2
  13Q LOSS WILD-TYPE        11        16        11        31         13
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  13Q LOSS MUTATED            7          8        7
  13Q LOSS WILD-TYPE         26         47       14
D66V4, multiclass
             clus
vv            13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  I OR II NOS                3                 10
  STAGE 0                    2                  5
  STAGE I                    6                 23
  STAGE IA                   6                 12
  STAGE IB                   8                 20
  STAGE II                   5                 20
  STAGE IIA                  3                 11
  STAGE IIB                  3                 16
  STAGE IIC                  4                 11
  STAGE III                  9                 31
  STAGE IIIA                 2                 13
  STAGE IIIB                 7                 26
  STAGE IIIC                 8                 47
  STAGE IV                   7                 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
  13Q LOSS MUTATED      18 13 21 13
  13Q LOSS WILD-TYPE    46 60 57 57
D66V5, multiclass
       clus
vv      13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  T0+T1               18                 46
  T2                  13                 60
  T3                  21                 57
  T4                  13                 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
  13Q LOSS MUTATED    41  13   9   8
  13Q LOSS WILD-TYPE 136  52  30  37
D66V6, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  N0               41                136
  N1               13                 52
  N2                9                 30
  N3                8                 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"
D66V7, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED    67   8
  13Q LOSS WILD-TYPE 251  14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     67    8
  13Q LOSS WILD-TYPE  251   14
   clus
vv  13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  0               67                251
  1                8                 14
[1] 2 2
[1] FALSE
D66V8, binary
                    cls
clus                  0  1
  13Q LOSS MUTATED   38 16
  13Q LOSS WILD-TYPE 96 74
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     38   16
  13Q LOSS WILD-TYPE   96   74
     clus
vv    13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  NO                38                 96
  YES               16                 74
[1] 2 2
[1] FALSE
D66V9, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED     8  72
  13Q LOSS WILD-TYPE  39 247
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      8   72
  13Q LOSS WILD-TYPE   39  247
     clus
vv    13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  NO                 8                 39
  YES               72                247
[1] 2 2
[1] FALSE
D66V10, continuous
D66V11, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED    28  52
  13Q LOSS WILD-TYPE 109 177
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     28   52
  13Q LOSS WILD-TYPE  109  177
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  FEMALE               28                109
  MALE                 52                177
[1] 2 2
[1] FALSE
D66V12, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED    68  12
  13Q LOSS WILD-TYPE 249  35
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     68   12
  13Q LOSS WILD-TYPE  249   35
     clus
vv    13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  NO                68                249
  YES               12                 35
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  13Q LOSS MUTATED       0                         0    77
  13Q LOSS WILD-TYPE     5                         1   275
D66V13, multiclass
                           clus
vv                          13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  ASIAN                                    0                  5
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   77                275
[1] 3 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  77
  13Q LOSS WILD-TYPE   5 274
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      2   77
  13Q LOSS WILD-TYPE    5  274
                        clus
vv                       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  5
  NOT HISPANIC OR LATINO               77                274
[1] 2 2
[1] FALSE

Clustering(67) Variable = 14Q LOSS MUTATION ANALYSIS
D67V1, survival
                    sevent
clus2                 0  1
  14Q LOSS MUTATED   35 37
  14Q LOSS WILD-TYPE 87 86
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                72                173 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                37                 86 
$`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        76.34       138.67        53.65 
TCGA-DA-A1I5 TCGA-DA-A3F5 TCGA-DA-A95V TCGA-EE-A181 TCGA-EE-A29C TCGA-EE-A29G 
       95.51       225.11        72.10        20.38        76.14        44.28 
TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GE TCGA-EE-A2GP TCGA-EE-A2M6 TCGA-EE-A2M7 
       30.02        77.98        12.95         0.76       103.13        15.25 
TCGA-EE-A2M8 TCGA-EE-A2MG TCGA-EE-A2MK TCGA-EE-A2MS TCGA-EE-A3AA TCGA-EE-A3J3 
        5.75        94.19        89.26       143.93       124.31        67.89 
TCGA-EE-A3J7 TCGA-EE-A3JB TCGA-EE-A3JI TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19B 
       45.90       201.80       152.81         1.58         7.82        53.29 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19S TCGA-ER-A2ND TCGA-ER-A3PL TCGA-FR-A44A 
      151.46       150.12        47.18         4.70        32.05       174.21 
TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZE TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZT 
       27.62       312.07        42.08        78.61       130.95        35.28 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FW-A3TU TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A264 
      173.19        13.28        55.59         6.05         1.91       117.93 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A8LK TCGA-LH-A9QB 
       17.06        42.48         7.59       120.53        43.23        85.05 
TCGA-OD-A75X TCGA-W3-A825 TCGA-W3-AA1V TCGA-WE-A8ZM TCGA-WE-A8ZY TCGA-YG-AA3O 
      297.01         1.97         8.09        65.42        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 
       69.21        22.85       150.61        45.07        64.83        58.85 
TCGA-DA-A3F2 TCGA-DA-A95X TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5SG 
       30.44        52.90        14.14        12.30         3.91        33.24 
TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A180 
       50.07        52.41        18.21        13.15        24.89        62.37 
TCGA-EE-A182 TCGA-EE-A184 TCGA-EE-A20C TCGA-EE-A20H TCGA-EE-A29B TCGA-EE-A29D 
        0.00        67.50        75.55       155.90        75.22        12.99 
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-A2GB TCGA-EE-A2GD TCGA-EE-A2GH TCGA-EE-A2GJ 
      185.19       115.43        26.14       239.11       201.60        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-A2MC TCGA-EE-A2MF TCGA-EE-A2MI TCGA-EE-A2MJ 
       71.31        81.99        23.77       209.79       171.85        63.25 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A2MU 
      104.78       145.45       227.01        25.08        23.51        53.26 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J4 
      122.73        64.04         4.41        54.51         6.28       111.85 
TCGA-EE-A3J8 TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A19A 
        3.35        19.86        14.56        34.45        47.31         4.54 
TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P 
       39.81        11.47        99.06        59.84        42.48       120.76 
TCGA-ER-A19Q TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NG 
       49.71       146.63        47.97        22.36        16.87        10.95 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A42L TCGA-FR-A729 TCGA-FR-A7U8 
      173.29        68.52        15.48        74.47       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-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZS TCGA-FS-A1ZU 
       32.78        12.92         7.82        36.33       136.27         4.47 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4FD 
       23.21         5.29         3.06        30.90        66.67        80.68 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A4U4 
       11.54        19.30         9.90        53.29        96.92        34.49 
TCGA-GN-A4U8 TCGA-GN-A9SD TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A690 TCGA-RP-A693 
       46.92        59.41         7.23        18.05         0.20         0.33 
TCGA-W3-A824 TCGA-W3-A828 TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1W TCGA-W3-AA21 
      174.12       120.07        44.05        79.99       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        21.90        62.89        10.95 
TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-Z2-AA3S 
        1.94        31.99        18.31        18.35        91.23 

  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
              0.76               0.00 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
            312.07             346.49 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
             54.62              45.07 
[1] "0.8 - 312.1 (54.6)" "0.0 - 346.5 (45.1)"
[1] "hr=" "1.2"
D67V2, survival
                    sevent
clus2                  0   1
  14Q LOSS MUTATED    50  60
  14Q LOSS WILD-TYPE 120 127
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               110                247 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                60                127 
$`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 
       76.57       144.89       207.48       120.00        53.92       225.96 
TCGA-DA-A95V TCGA-EB-A44R TCGA-EB-A5UL TCGA-EE-A181 TCGA-EE-A29C TCGA-EE-A29G 
       72.10        10.36        29.29        33.73        78.97        72.07 
TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GE 
       25.87        17.92        59.64        39.29        86.14       173.79 
TCGA-EE-A2GP TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MD TCGA-EE-A2MG 
       13.91       129.27        28.83        19.76        47.28       103.20 
TCGA-EE-A2MH TCGA-EE-A2MK TCGA-EE-A2MN TCGA-EE-A2MS TCGA-EE-A3AA TCGA-EE-A3AH 
       16.96       180.39        47.54       162.48       124.31       138.81 
TCGA-EE-A3J3 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JE 
      172.18        36.95        64.08        53.19       201.80        51.35 
TCGA-EE-A3JI TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19E TCGA-ER-A19G 
      152.81        13.94         9.17        98.40        13.02       268.93 
TCGA-ER-A19H TCGA-ER-A19S TCGA-ER-A2ND TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A44A 
      152.35        49.48        23.34        33.21        12.95       174.21 
TCGA-FS-A1YX TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZC TCGA-FS-A1ZE 
       48.59        28.08         7.79        27.72       357.37        46.45 
TCGA-FS-A1ZH TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZT TCGA-FS-A4F2 
       32.75       101.26       133.55        11.41        53.16        50.14 
TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FW-A3TU TCGA-GF-A4EO TCGA-GF-A6C8 
       28.73       174.84        34.03        55.59         7.23         2.04 
TCGA-GF-A6C9 TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 
       15.78       117.93        64.44        62.79        32.48       121.91 
TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-HR-A2OG TCGA-LH-A9QB TCGA-OD-A75X TCGA-W3-A825 
       22.13        50.10         0.23       368.78       297.90        63.02 
TCGA-W3-AA1V TCGA-WE-A8JZ TCGA-WE-A8ZM TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-YG-AA3O 
       42.08        24.03       101.33        35.80        49.51        37.94 
TCGA-YG-AA3P TCGA-Z2-A8RT 
       14.43        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-D3-A8GV TCGA-D9-A148 TCGA-D9-A1JW 
      152.75        29.06       129.63       167.70       151.53         3.65 
TCGA-D9-A1JX TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EC 
        7.10        18.12        15.39        22.29         9.90        77.56 
TCGA-D9-A6EG TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I7 
       22.95        36.03        20.38       176.55        35.93        73.84 
TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 
       65.92        40.60        68.09        33.93        10.49        15.68 
TCGA-DA-A95W TCGA-DA-A95X TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5KH 
       25.15        61.81        14.14        13.02        13.87        20.35 
TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X 
       68.25        54.02        58.92         7.04        36.46        29.82 
TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 
       27.22         8.65        94.98        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-A29D TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L 
       63.35        85.08        13.97        63.78        64.64         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-A29T TCGA-EE-A29W TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2GB TCGA-EE-A2GC 
      369.93       195.02        46.82       115.96        59.28        67.43 
TCGA-EE-A2GD TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
      340.14       220.24        48.72       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-A2MC TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MI 
       94.82        21.67        61.51       103.27       268.73       204.66 
TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR 
       96.23       216.66       167.90       248.65        43.23       134.40 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
       71.21        53.26       122.73        64.04        28.77        54.51 
TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3J4 TCGA-EE-A3J8 TCGA-EE-A3JD TCGA-EE-A3JH 
       13.81        41.59       127.20        34.32        27.35       134.33 
TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19C TCGA-ER-A19D 
       31.40        35.44        50.76        77.75        48.89        12.59 
TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P 
       26.37         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-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
       16.37        31.27        32.05       247.04        93.01        46.98 
TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 
      149.03        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        96.92        10.13        48.00        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-A690 TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A828 TCGA-W3-AA1O 
        0.20         0.33         0.69       228.16       121.08         4.01 
TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8K5 
       69.07       111.09       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-AA9Y 
       17.95        58.98        70.52        63.22        11.80        12.16 
TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YD-A89C TCGA-YD-A9TA TCGA-Z2-AA3S 
       40.41        21.40        24.99         6.90        49.18        96.99 
TCGA-Z2-AA3V 
       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 
             55.13              49.18 
[1] "0.2 - 368.8 (55.1)" "0.2 - 369.9 (49.2)"
[1] "hr=" "1.1"
D67V3, continuous
                    vv
clus                 I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  14Q LOSS MUTATED             5       0      12        3        8       10
  14Q LOSS WILD-TYPE           8       7      17       15       20       15
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  14Q LOSS MUTATED           2         5         5        17          3
  14Q LOSS WILD-TYPE        12        14        10        23         12
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  14Q LOSS MUTATED           11         16        4
  14Q LOSS WILD-TYPE         22         39       17
D67V4, multiclass
             clus
vv            14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  I OR II NOS                5                  8
  STAGE 0                    0                  7
  STAGE I                   12                 17
  STAGE IA                   3                 15
  STAGE IB                   8                 20
  STAGE II                  10                 15
  STAGE IIA                  2                 12
  STAGE IIB                  5                 14
  STAGE IIC                  5                 10
  STAGE III                 17                 23
  STAGE IIIA                 3                 12
  STAGE IIIB                11                 22
  STAGE IIIC                16                 39
  STAGE IV                   4                 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
  14Q LOSS MUTATED      24 23 21 23
  14Q LOSS WILD-TYPE    40 50 57 47
D67V5, multiclass
       clus
vv      14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  T0+T1               24                 40
  T2                  23                 50
  T3                  21                 57
  T4                  23                 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
  14Q LOSS MUTATED    53  26   9  12
  14Q LOSS WILD-TYPE 124  39  30  33
D67V6, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  N0               53                124
  N1               26                 39
  N2                9                 30
  N3               12                 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"
D67V7, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED    99   4
  14Q LOSS WILD-TYPE 219  18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     99    4
  14Q LOSS WILD-TYPE  219   18
   clus
vv  14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  0               99                219
  1                4                 18
[1] 2 2
[1] FALSE
D67V8, binary
                    cls
clus                  0  1
  14Q LOSS MUTATED   38 29
  14Q LOSS WILD-TYPE 96 61
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     38   29
  14Q LOSS WILD-TYPE   96   61
     clus
vv    14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  NO                38                 96
  YES               29                 61
[1] 2 2
[1] FALSE
D67V9, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED    15  97
  14Q LOSS WILD-TYPE  32 222
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     15   97
  14Q LOSS WILD-TYPE   32  222
     clus
vv    14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  NO                15                 32
  YES               97                222
[1] 2 2
[1] FALSE
D67V10, continuous
D67V11, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED    46  66
  14Q LOSS WILD-TYPE  91 163
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     46   66
  14Q LOSS WILD-TYPE   91  163
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  FEMALE               46                 91
  MALE                 66                163
[1] 2 2
[1] FALSE
D67V12, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED    99  13
  14Q LOSS WILD-TYPE 218  34
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     99   13
  14Q LOSS WILD-TYPE  218   34
     clus
vv    14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  NO                99                218
  YES               13                 34
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  14Q LOSS MUTATED       1                         0   107
  14Q LOSS WILD-TYPE     4                         1   245
D67V13, multiclass
                           clus
vv                          14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  ASIAN                                    1                  4
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                  107                245
[1] 3 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     3 107
  14Q LOSS WILD-TYPE   4 244
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      3  107
  14Q LOSS WILD-TYPE    4  244
                        clus
vv                       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  4
  NOT HISPANIC OR LATINO              107                244
[1] 2 2
[1] FALSE

Clustering(68) Variable = 15Q LOSS MUTATION ANALYSIS
D68V1, survival
                    sevent
clus2                  0   1
  15Q LOSS MUTATED    16  17
  15Q LOSS WILD-TYPE 106 106
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                33                212 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                17                106 
$`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-DA-A95V TCGA-DA-A95Z TCGA-EB-A5SH 
       69.21        53.65        64.83        72.10        12.30        50.07 
TCGA-EE-A180 TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A2GH TCGA-EE-A2MC TCGA-EE-A2MF 
       62.37        27.16        61.12       201.60        23.77       209.79 
TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3J7 TCGA-ER-A197 
       89.26       145.45        53.26       122.73        45.90         1.58 
TCGA-ER-A199 TCGA-ER-A3EV TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1ZM TCGA-FS-A1ZT 
        7.82        15.48       195.98        27.62        78.61        35.28 
TCGA-GN-A8LK TCGA-W3-AA1R TCGA-W3-AA1V 
       43.23        79.99         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        76.34       138.67 
TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 
      150.61        95.51        45.07        58.85        30.44       225.11 
TCGA-DA-A95X TCGA-DA-A95Y TCGA-EB-A44Q TCGA-EB-A5SG TCGA-EB-A5UN TCGA-EB-A6L9 
       52.90        14.14         3.91        33.24        52.41        18.21 
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-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-A29M TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A2 
       63.12        47.74       346.49       185.19       115.43        30.02 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GJ TCGA-EE-A2GK 
       77.98        26.14       239.11        12.95        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-A2MG 
       71.31        81.99       103.13        15.25         5.75        94.19 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MP TCGA-EE-A2MR TCGA-EE-A2MS 
      171.85        63.25       104.78       227.01        25.08       143.93 
TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
       23.51       124.31        64.04         4.41        54.51         6.28 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI 
       67.89       111.85         3.35       201.80        19.86       152.81 
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-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
      120.76        49.71        47.18       146.63        47.97        22.36 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3PL 
        4.70        16.87        10.95       173.29        68.52        32.05 
TCGA-ER-A42L TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FR-A8YC 
       74.47       174.21       209.23        26.20         5.65        10.06 
TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE 
      171.78        49.74         8.35       312.07        32.78        42.08 
TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZU 
       12.92         7.82        36.33       130.95       136.27         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        96.92        17.06 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-GN-A9SD 
       42.48         7.59       120.53        34.49        46.92        59.41 
TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A690 TCGA-RP-A693 
       85.05       297.01         7.23        18.05         0.20         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-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ 
        1.15        59.64        65.42        12.69        21.90        62.89 
TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 
       10.95        48.39         1.94        31.99        18.31        18.35 
TCGA-YG-AA3O TCGA-Z2-AA3S 
       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 
             53.26              46.95 
[1] "1.6 - 209.8 (53.3)" "0.0 - 346.5 (47.0)"
[1] "hr=" "1"  
D68V2, survival
                    sevent
clus2                  0   1
  15Q LOSS MUTATED    21  30
  15Q LOSS WILD-TYPE 149 157
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                51                306 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                30                157 
$`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        77.56       207.48        53.92 
TCGA-DA-A1IA TCGA-DA-A95V TCGA-DA-A95Z TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SH 
       65.92        72.10        13.02        10.36        20.35        54.02 
TCGA-EE-A180 TCGA-EE-A29L TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A2A5 TCGA-EE-A2GH 
       94.98         2.60        56.42        66.74        39.29       220.24 
TCGA-EE-A2M5 TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MH TCGA-EE-A2MK TCGA-EE-A2MM 
       21.67        61.51       268.73        16.96       180.39       167.90 
TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-EE-A3JE TCGA-ER-A197 
       53.26       122.73        64.08        53.19        51.35        13.94 
TCGA-ER-A199 TCGA-ER-A19E TCGA-ER-A3EV TCGA-FS-A1YX TCGA-FS-A1Z0 TCGA-FS-A1Z4 
        9.17        13.02        46.98        48.59       202.65        28.08 
TCGA-FS-A1ZM TCGA-FS-A1ZT TCGA-GN-A266 TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A8LL 
      101.26        53.16        10.13        22.13        50.10        21.37 
TCGA-W3-AA1R TCGA-W3-AA1V TCGA-WE-A8JZ 
      111.09        42.08        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-D3-A8GV TCGA-D9-A149 
      152.75        29.06       129.63       117.17       167.70        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-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY 
        9.90        25.18        22.95        76.57        36.03       144.89 
TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IB 
       20.38       176.55        35.93       120.00        73.84        40.60 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-DA-A95W 
       68.09        33.93        10.49       225.96        15.68        25.15 
TCGA-DA-A95X TCGA-DA-A95Y TCGA-EB-A44Q TCGA-EB-A5SG TCGA-EB-A5UL TCGA-EB-A5UN 
       61.81        14.14        13.87        68.25        29.29        58.92 
TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A181 
        7.04        36.46        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-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-A29M TCGA-EE-A29N 
       13.97        63.78        72.07        64.64        56.84        18.61 
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-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC 
       46.82       115.96        59.64        86.14        59.28        67.43 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
      340.14       173.79        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-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MD 
       44.88        94.82       129.27        28.83        19.76        47.28 
TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MN 
      103.27       103.20       204.66        96.23       216.66        47.54 
TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AA 
      248.65        43.23       134.40       162.48        71.21       124.31 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH 
       64.04        28.77        54.51        13.81        41.59       138.81 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JD 
      172.18       127.20        36.95        34.32       201.80        27.35 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A19A 
      134.33       152.81        31.40        35.44        50.76        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 
       49.48         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        93.01 
TCGA-ER-A3PL TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       33.21        12.95       149.03        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-A1Z3 TCGA-FS-A1Z7 TCGA-FS-A1ZA 
      104.42       216.92       228.59        20.91         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        46.45        15.45         9.70 
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-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-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-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
      117.93        96.92        64.44        62.79        32.48        48.00 
TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A9SD TCGA-HR-A2OG 
      121.91        39.35        10.42        48.89        59.41         0.23 
TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A690 
       65.88       368.78       297.90         7.23        18.05         0.20 
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        17.95 
TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX 
      101.33        58.98        70.52        63.22        11.80        35.80 
TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YD-A89C 
       49.51        12.16        40.41        21.40        24.99         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 
            53.920             49.825 
[1] "2.6 - 268.7 (53.9)" "0.2 - 369.9 (49.8)"
[1] "hr=" "1.1"
D68V3, continuous
                    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          12       6      20       16       23       22
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  15Q LOSS MUTATED           0         1         5        10          3
  15Q LOSS WILD-TYPE        14        18        10        30         12
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  15Q LOSS MUTATED            5          4        1
  15Q LOSS WILD-TYPE         28         51       20
D68V4, multiclass
             clus
vv            15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  I OR II NOS                1                 12
  STAGE 0                    1                  6
  STAGE I                    9                 20
  STAGE IA                   2                 16
  STAGE IB                   5                 23
  STAGE II                   3                 22
  STAGE IIA                  0                 14
  STAGE IIB                  1                 18
  STAGE IIC                  5                 10
  STAGE III                 10                 30
  STAGE IIIA                 3                 12
  STAGE IIIB                 5                 28
  STAGE IIIC                 4                 51
  STAGE IV                   1                 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 15
  15Q LOSS WILD-TYPE    56 57 72 55
D68V5, multiclass
       clus
vv      15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  T0+T1                8                 56
  T2                  16                 57
  T3                   6                 72
  T4                  15                 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 LOSS MUTATED    31   8   5   5
  15Q LOSS WILD-TYPE 146  57  34  40
D68V6, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  N0               31                146
  N1                8                 57
  N2                5                 34
  N3                5                 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"
D68V7, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED    47   2
  15Q LOSS WILD-TYPE 271  20
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED     47    2
  15Q LOSS WILD-TYPE  271   20
   clus
vv  15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  0               47                271
  1                2                 20
[1] 2 2
[1] FALSE
D68V8, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED    20  14
  15Q LOSS WILD-TYPE 114  76
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED     20   14
  15Q LOSS WILD-TYPE  114   76
     clus
vv    15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  NO                20                114
  YES               14                 76
[1] 2 2
[1] FALSE
D68V9, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED     6  46
  15Q LOSS WILD-TYPE  41 273
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      6   46
  15Q LOSS WILD-TYPE   41  273
     clus
vv    15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  NO                 6                 41
  YES               46                273
[1] 2 2
[1] FALSE
D68V10, continuous
D68V11, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED    19  33
  15Q LOSS WILD-TYPE 118 196
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED     19   33
  15Q LOSS WILD-TYPE  118  196
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  FEMALE               19                118
  MALE                 33                196
[1] 2 2
[1] FALSE
D68V12, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED    47   5
  15Q LOSS WILD-TYPE 270  42
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED     47    5
  15Q LOSS WILD-TYPE  270   42
     clus
vv    15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  NO                47                270
  YES                5                 42
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  15Q LOSS MUTATED       2                         0    49
  15Q LOSS WILD-TYPE     3                         1   303
D68V13, multiclass
                           clus
vv                          15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  ASIAN                                    2                  3
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   49                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"
D68V14, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED     0  51
  15Q LOSS WILD-TYPE   7 300
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      0   51
  15Q LOSS WILD-TYPE    7  300
                        clus
vv                       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  7
  NOT HISPANIC OR LATINO               51                300
[1] 2 2
[1] FALSE

Clustering(69) Variable = 16P LOSS MUTATION ANALYSIS
D69V1, survival
                    sevent
clus2                  0   1
  16P LOSS MUTATED    21  23
  16P LOSS WILD-TYPE 101 100
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                44                201 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                23                100 
$`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        69.21 
TCGA-DA-A1I2 TCGA-DA-A95X TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A29D TCGA-EE-A29M 
      150.61        52.90        62.37        20.38        12.99        47.74 
TCGA-EE-A29W TCGA-EE-A2GO TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MU TCGA-EE-A3AB 
      185.19       118.32        89.26       145.45        53.26       122.73 
TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A197 TCGA-ER-A2ND TCGA-FR-A8YC TCGA-FS-A1Z0 
      152.81        14.56         1.58         4.70        10.06       195.98 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FW-A3TU TCGA-GN-A262 TCGA-GN-A264 
       35.28         4.47        23.21        55.59        53.29       117.93 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A4U3 TCGA-OD-A75X TCGA-WE-A8K5 TCGA-WE-A8ZQ 
       17.06        42.48       120.53       297.01        59.64        62.89 
TCGA-YG-AA3O TCGA-Z2-AA3S 
       28.21        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        76.34 
TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC 
      138.67        53.65        95.51        45.07        64.83        58.85 
TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A95V TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q 
       30.44       225.11        72.10        14.14        12.30         3.91 
TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y 
       33.24        50.07        52.41        18.21        13.15        24.89 
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-A29G TCGA-EE-A29H TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T 
        0.26        44.28        63.12        27.16        61.12       346.49 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE 
      115.43        30.02        77.98        26.14       239.11        12.95 
TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN 
      201.60        68.65        10.62        32.48        18.35        31.00 
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-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-A3AE TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 
       64.04         4.41        54.51         6.28        67.89       111.85 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH TCGA-ER-A195 TCGA-ER-A198 
       45.90         3.35       201.80        19.86        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-A2NE TCGA-ER-A2NG 
       47.18       146.63        47.97        22.36        16.87        10.95 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A44A 
      173.29        68.52        15.48        32.05        74.47       174.21 
TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z3 
      209.23        26.20         5.65       171.78        49.74         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        42.08        12.92         7.82 
TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZY TCGA-FS-A1ZZ 
       36.33        78.61       130.95       136.27         5.29         3.06 
TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TV 
       30.90        66.67       173.19        13.28        80.68        11.54 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A265 TCGA-GN-A26A 
       19.30         9.90         6.05         1.91        96.92         7.59 
TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-GN-A8LK TCGA-GN-A9SD TCGA-LH-A9QB TCGA-QB-A6FS 
       34.49        46.92        43.23        59.41        85.05         7.23 
TCGA-QB-AA9O TCGA-RP-A690 TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 
       18.05         0.20         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-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AA9Y 
       65.42        12.69        21.90        10.95        48.39         1.94 
TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 
       31.99        18.31        18.35 

  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 
             62.63              44.28 
[1] "1.6 - 297.0 (62.6)" "0.0 - 346.5 (44.3)"
[1] "hr=" "1.2"
D69V2, survival
                    sevent
clus2                  0   1
  16P LOSS MUTATED    30  36
  16P LOSS WILD-TYPE 140 151
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                66                291 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                36                151 
$`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-DA-A95X 
      107.15        25.18        77.56        36.03       176.55        61.81 
TCGA-EB-A44R TCGA-EB-A5UL TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A20I 
       10.36        29.29         8.65        94.98        33.73        13.55 
TCGA-EE-A29D TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 
       13.97         2.60        56.84       195.02        17.92        46.82 
TCGA-EE-A2GC TCGA-EE-A2GO TCGA-EE-A2M5 TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MQ 
       67.43       126.81        21.67       180.39       167.90        43.23 
TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3J5 TCGA-EE-A3JA TCGA-EE-A3JI TCGA-ER-A193 
       53.26       122.73        36.95        53.19       152.81        31.40 
TCGA-ER-A197 TCGA-ER-A19E TCGA-ER-A19T TCGA-ER-A2ND TCGA-FR-A8YC TCGA-FS-A1Z0 
       13.94        13.02         8.88        23.34        34.82       202.65 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-GN-A262 
       53.16        26.56        49.48        22.92        55.59       139.89 
TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26D TCGA-GN-A4U3 TCGA-OD-A75X 
      117.93        64.44        62.79        48.00       121.91       297.90 
TCGA-WE-A8JZ TCGA-WE-A8K5 TCGA-WE-A8ZQ TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-AA3S 
       24.03        61.15        63.22        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-D3-A8GV 
      161.00       152.75        29.06       129.63       117.17       167.70 
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        76.57       144.89 
TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
       20.38       207.48        35.93       120.00        73.84        53.92 
TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 
       65.92        40.60        68.09        33.93        10.49       225.96 
TCGA-DA-A3F8 TCGA-DA-A95V TCGA-DA-A95W TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q 
       15.68        72.10        25.15        14.14        13.02        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        58.92         7.04        36.46 
TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 
       29.82        27.22        14.70        26.89        68.15         4.96 
TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29B 
      133.81       151.27        91.56       168.26        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-A2A1 
       66.74        14.47        61.28       369.93        25.87       115.96 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE 
       59.64        39.29        86.14        59.28       340.14       173.79 
TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
      220.24        48.72       107.38        54.74        79.66        75.48 
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-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-A2MN TCGA-EE-A2MP TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AA 
       47.54       248.65       134.40       162.48        71.21       124.31 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH 
       64.04        28.77        54.51        13.81        41.59       138.81 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JD 
      172.18       127.20        64.08        34.32       201.80        27.35 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A 
       51.35       134.33        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-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NF 
       49.48       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-A3PL 
       31.27        32.05       247.04        93.01        46.98        33.21 
TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 
       12.95       149.03        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        46.45        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        96.92        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-A690 
        0.23        65.88       368.78         7.23        18.05         0.20 
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-A8K1 
       69.07       111.09        42.08       219.16       105.04        49.05 
TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-A8ZX 
       17.95       101.33        58.98        70.52        11.80        35.80 
TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YD-A89C 
       49.51        12.16        40.41        21.40        24.99         6.90 
TCGA-YD-A9TA TCGA-Z2-A8RT TCGA-Z2-AA3V 
       49.18        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 
            56.215             50.140 
[1] "2.6 - 297.9 (56.2)" "0.2 - 369.9 (50.1)"
[1] "hr=" "1"  
D69V3, continuous
                    vv
clus                 I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  16P LOSS MUTATED             3       2       3        3        6        2
  16P LOSS WILD-TYPE          10       5      26       15       22       23
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  16P LOSS MUTATED           2         8         3        11          3
  16P LOSS WILD-TYPE        12        11        12        29         12
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  16P LOSS MUTATED            5          7        5
  16P LOSS WILD-TYPE         28         48       16
D69V4, multiclass
             clus
vv            16P LOSS MUTATED 16P LOSS WILD-TYPE
  I OR II NOS                3                 10
  STAGE 0                    2                  5
  STAGE I                    3                 26
  STAGE IA                   3                 15
  STAGE IB                   6                 22
  STAGE II                   2                 23
  STAGE IIA                  2                 12
  STAGE IIB                  8                 11
  STAGE IIC                  3                 12
  STAGE III                 11                 29
  STAGE IIIA                 3                 12
  STAGE IIIB                 5                 28
  STAGE IIIC                 7                 48
  STAGE IV                   5                 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
  16P LOSS MUTATED       9 14 12 18
  16P LOSS WILD-TYPE    55 59 66 52
D69V5, multiclass
       clus
vv      16P LOSS MUTATED 16P LOSS WILD-TYPE
  T0+T1                9                 55
  T2                  14                 59
  T3                  12                 66
  T4                  18                 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
  16P LOSS MUTATED    35  13   6   8
  16P LOSS WILD-TYPE 142  52  33  37
D69V6, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  N0               35                142
  N1               13                 52
  N2                6                 33
  N3                8                 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"
D69V7, binary
                    cls
clus                   0   1
  16P LOSS MUTATED    58   5
  16P LOSS WILD-TYPE 260  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED     58    5
  16P LOSS WILD-TYPE  260   17
   clus
vv  16P LOSS MUTATED 16P LOSS WILD-TYPE
  0               58                260
  1                5                 17
[1] 2 2
[1] FALSE
D69V8, binary
                    cls
clus                   0   1
  16P LOSS MUTATED    32  16
  16P LOSS WILD-TYPE 102  74
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED     32   16
  16P LOSS WILD-TYPE  102   74
     clus
vv    16P LOSS MUTATED 16P LOSS WILD-TYPE
  NO                32                102
  YES               16                 74
[1] 2 2
[1] FALSE
D69V9, binary
                    cls
clus                   0   1
  16P LOSS MUTATED     4  64
  16P LOSS WILD-TYPE  43 255
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      4   64
  16P LOSS WILD-TYPE   43  255
     clus
vv    16P LOSS MUTATED 16P LOSS WILD-TYPE
  NO                 4                 43
  YES               64                255
[1] 2 2
[1] FALSE
D69V10, continuous
D69V11, binary
                    cls
clus                   0   1
  16P LOSS MUTATED    29  39
  16P LOSS WILD-TYPE 108 190
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED     29   39
  16P LOSS WILD-TYPE  108  190
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  FEMALE               29                108
  MALE                 39                190
[1] 2 2
[1] FALSE
D69V12, binary
                    cls
clus                   0   1
  16P LOSS MUTATED    59   9
  16P LOSS WILD-TYPE 258  38
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED     59    9
  16P LOSS WILD-TYPE  258   38
     clus
vv    16P LOSS MUTATED 16P LOSS WILD-TYPE
  NO                59                258
  YES                9                 38
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16P LOSS MUTATED       1                         1    62
  16P LOSS WILD-TYPE     4                         0   290
D69V13, multiclass
                           clus
vv                          16P LOSS MUTATED 16P LOSS WILD-TYPE
  ASIAN                                    1                  4
  BLACK OR AFRICAN AMERICAN                1                  0
  WHITE                                   62                290
[1] 3 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  64
  16P LOSS WILD-TYPE   4 287
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      3   64
  16P LOSS WILD-TYPE    4  287
                        clus
vv                       16P LOSS MUTATED 16P LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  4
  NOT HISPANIC OR LATINO               64                287
[1] 2 2
[1] FALSE

Clustering(70) Variable = 16Q LOSS MUTATION ANALYSIS
D70V1, survival
                    sevent
clus2                 0  1
  16Q LOSS MUTATED   33 34
  16Q LOSS WILD-TYPE 89 89
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                67                178 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                34                 89 
$`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-A95V TCGA-DA-A95X TCGA-EB-A5SG 
       16.90        69.21       150.61        72.10        52.90        33.24 
TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A20C TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29M 
       62.37        20.38        75.55        75.22        12.99        47.74 
TCGA-EE-A29P TCGA-EE-A29W TCGA-EE-A2GH TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2MJ 
       27.16       185.19       201.60       118.32         0.76        63.25 
TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AE TCGA-EE-A3AF 
       89.26       145.45        53.26       122.73        54.51         6.28 
TCGA-EE-A3J4 TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A197 TCGA-ER-A19B TCGA-ER-A19N 
      111.85       152.81        14.56         1.58        53.29        42.48 
TCGA-ER-A19W TCGA-ER-A2ND TCGA-ER-A42L TCGA-FR-A8YC TCGA-FS-A1Z0 TCGA-FS-A1ZF 
      146.63         4.70        74.47        10.06       195.98        12.92 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FW-A3TU TCGA-GN-A262 TCGA-GN-A264 
       35.28         4.47        23.21        55.59        53.29       117.93 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A4U3 TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS 
       17.06        42.48       120.53        85.05       297.01         7.23 
TCGA-QB-AA9O TCGA-W3-AA1R TCGA-WE-A8K5 TCGA-WE-A8ZQ TCGA-WE-AAA3 TCGA-YG-AA3O 
       18.05        79.99        59.64        62.89        18.31        28.21 
TCGA-Z2-AA3S 
       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        76.34       138.67        53.65 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 
       95.51        45.07        64.83        58.85        30.44       225.11 
TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A6L9 
       14.14        12.30         3.91        50.07        52.41        18.21 
TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A182 TCGA-EE-A184 TCGA-EE-A20H TCGA-EE-A29C 
       13.15        24.89         0.00        67.50       155.90        76.14 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A2A1 
        0.26        44.28        63.12        61.12       346.49       115.43 
TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GJ 
       30.02        77.98        26.14       239.11        12.95        68.65 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GR TCGA-EE-A2GS 
       10.62        32.48        18.35        31.00         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-A2ML TCGA-EE-A2MP TCGA-EE-A2MR TCGA-EE-A2MS 
       94.19       171.85       104.78       227.01        25.08       143.93 
TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3J3 TCGA-EE-A3J7 
       23.51       124.31        64.04         4.41        67.89        45.90 
TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A199 
        3.35       201.80        19.86        34.45        47.31         7.82 
TCGA-ER-A19A TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L 
        4.54        39.81        11.47       151.46       150.12        99.06 
TCGA-ER-A19M TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A1A1 TCGA-ER-A2NC 
       59.84       120.76        49.71        47.18        47.97        22.36 
TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL 
       16.87        10.95       173.29        68.52        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-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG 
        8.35        27.62       312.07        32.78        42.08         7.82 
TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZY TCGA-FS-A1ZZ 
       36.33        78.61       130.95       136.27         5.29         3.06 
TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TV 
       30.90        66.67       173.19        13.28        80.68        11.54 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A265 TCGA-GN-A26A 
       19.30         9.90         6.05         1.91        96.92         7.59 
TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-GN-A8LK TCGA-GN-A9SD TCGA-RP-A690 TCGA-RP-A693 
       34.49        46.92        43.23        59.41         0.20         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-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT 
       92.84         1.15        65.42        12.69        21.90        10.95 
TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 
       48.39         1.94        31.99        18.35 

  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 
             62.37              43.79 
[1] "0.8 - 297.0 (62.4)" "0.0 - 346.5 (43.8)"
[1] "hr=" "1.1"
D70V2, survival
                    sevent
clus2                  0   1
  16Q LOSS MUTATED    48  55
  16Q LOSS WILD-TYPE 122 132
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
               103                254 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                55                132 
$`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        77.56        36.03       176.55 
TCGA-DA-A1I4 TCGA-DA-A3F8 TCGA-DA-A95V TCGA-DA-A95X TCGA-EB-A44R TCGA-EB-A5SG 
       35.93        15.68        72.10        61.81        10.36        68.25 
TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A20I 
        8.65        94.98        33.73         4.96       151.27        13.55 
TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29W 
       85.08        13.97         2.60        56.84        56.42       195.02 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A5 TCGA-EE-A2GC TCGA-EE-A2GH TCGA-EE-A2GO 
       17.92        46.82        39.29        67.43       220.24       126.81 
TCGA-EE-A2GP TCGA-EE-A2M5 TCGA-EE-A2MD TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2MM 
       13.91        21.67        47.28        96.23       180.39       167.90 
TCGA-EE-A2MQ TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J4 
       43.23        53.26       122.73        54.51        13.81       127.20 
TCGA-EE-A3J5 TCGA-EE-A3JA TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A197 TCGA-ER-A19B 
       36.95        53.19       152.81        31.40        13.94        98.40 
TCGA-ER-A19N TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A2ND TCGA-ER-A42L TCGA-FR-A8YC 
       44.05         8.88       148.18        23.34       149.03        34.82 
TCGA-FS-A1Z0 TCGA-FS-A1ZB TCGA-FS-A1ZF TCGA-FS-A1ZP TCGA-FS-A1ZT TCGA-FS-A1ZU 
      202.65        48.85        15.45        74.73        53.16        26.56 
TCGA-FS-A1ZW TCGA-FS-A4F2 TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-GN-A262 
       49.48        50.14         0.20        22.92        55.59       139.89 
TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26D TCGA-GN-A4U3 TCGA-LH-A9QB 
      117.93        64.44        62.79        48.00       121.91       368.78 
TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O TCGA-W3-AA1R TCGA-WE-A8JZ TCGA-WE-A8K5 
      297.90         7.23        18.05       111.09        24.03        61.15 
TCGA-WE-A8ZQ TCGA-WE-A8ZX TCGA-WE-AAA3 TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-AA3S 
       63.22        35.80        21.40        37.94        14.43        96.99 
TCGA-Z2-AA3V 
       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-D3-A8GV TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A1X3 TCGA-D9-A3Z1 
      129.63       167.70         3.65         7.10        18.12        15.39 
TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I0 
       18.44         9.90        22.95        76.57       144.89        20.38 
TCGA-DA-A1I1 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB 
      207.48       120.00        73.84        53.92        65.92        40.60 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A95W TCGA-DA-A95Y 
       68.09        33.93        10.49       225.96        25.15        14.14 
TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN 
       13.02        13.87        20.35        54.02        29.29        58.92 
TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A182 TCGA-EE-A183 
        7.04        36.46        29.82        27.22        14.70        26.89 
TCGA-EE-A184 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C 
       68.15       133.81        91.56       168.26        63.35        78.97 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29R 
       63.78        72.07        64.64        18.61        66.74        14.47 
TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 
       61.28       369.93        25.87       115.96        59.64        86.14 
TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
       59.28       340.14       173.79        48.72       107.38        54.74 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT 
       79.66        75.48       102.12        42.77        81.21        44.88 
TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2ME 
       94.82       129.27        28.83        19.76        61.51       103.27 
TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2ML TCGA-EE-A2MN 
      268.73       103.20        16.96       204.66       216.66        47.54 
TCGA-EE-A2MP TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AC 
      248.65       134.40       162.48        71.21       124.31        64.04 
TCGA-EE-A3AD TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-EE-A3J8 
       28.77        41.59       138.81       172.18        64.08        34.32 
TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A195 TCGA-ER-A198 
      201.80        27.35        51.35       134.33        35.44        50.76 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F 
        9.17        77.75        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-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NF 
       50.89        49.48        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-A3PL 
       31.27        32.05       247.04        93.01        46.98        33.21 
TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 
       12.95        92.98       174.21        15.72       220.80        27.85 
TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YX 
       18.77        38.27        36.26       104.42       216.92        48.59 
TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZC 
      228.59        20.91        28.08         7.79        27.72       357.37 
TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK 
       53.52        46.45         9.70        32.75        47.38        23.93 
TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZY TCGA-FS-A1ZZ 
      101.26       133.55        11.41       148.80        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-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
       54.41        80.68        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        96.92        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-RP-A690 TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 
        0.23        65.88         0.20         0.33         0.69       228.16 
TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1Q TCGA-W3-AA1V TCGA-W3-AA1W 
       63.02       121.08         4.01        69.07        42.08       219.16 
TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO 
      105.04        49.05        17.95       101.33        58.98        70.52 
TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-YD-A89C 
       11.80        49.51        12.16        40.41        24.99         6.90 
TCGA-YD-A9TA TCGA-Z2-A8RT 
       49.18        27.58 

  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
               0.2                0.2 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
            368.78             369.93 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
             56.42              49.33 
[1] "0.2 - 368.8 (56.4)" "0.2 - 369.9 (49.3)"
[1] "hr=" "1"  
D70V3, continuous
                    vv
clus                 I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  16Q LOSS MUTATED             3       3       5        7        7        8
  16Q LOSS WILD-TYPE          10       4      24       11       21       17
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  16Q LOSS MUTATED           2         9         7        11          3
  16Q LOSS WILD-TYPE        12        10         8        29         12
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  16Q LOSS MUTATED            9         13        6
  16Q LOSS WILD-TYPE         24         42       15
D70V4, multiclass
             clus
vv            16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  I OR II NOS                3                 10
  STAGE 0                    3                  4
  STAGE I                    5                 24
  STAGE IA                   7                 11
  STAGE IB                   7                 21
  STAGE II                   8                 17
  STAGE IIA                  2                 12
  STAGE IIB                  9                 10
  STAGE IIC                  7                  8
  STAGE III                 11                 29
  STAGE IIIA                 3                 12
  STAGE IIIB                 9                 24
  STAGE IIIC                13                 42
  STAGE IV                   6                 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
  16Q LOSS MUTATED      17 16 21 27
  16Q LOSS WILD-TYPE    47 57 57 43
D70V5, multiclass
       clus
vv      16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  T0+T1               17                 47
  T2                  16                 57
  T3                  21                 57
  T4                  27                 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
  16Q LOSS MUTATED    57  16   9  13
  16Q LOSS WILD-TYPE 120  49  30  32
D70V6, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  N0               57                120
  N1               16                 49
  N2                9                 30
  N3               13                 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"
D70V7, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED    88   7
  16Q LOSS WILD-TYPE 230  15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED     88    7
  16Q LOSS WILD-TYPE  230   15
   clus
vv  16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  0               88                230
  1                7                 15
[1] 2 2
[1] FALSE
D70V8, binary
                    cls
clus                  0  1
  16Q LOSS MUTATED   46 27
  16Q LOSS WILD-TYPE 88 63
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED     46   27
  16Q LOSS WILD-TYPE   88   63
     clus
vv    16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  NO                46                 88
  YES               27                 63
[1] 2 2
[1] FALSE
D70V9, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED    10  96
  16Q LOSS WILD-TYPE  37 223
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED     10   96
  16Q LOSS WILD-TYPE   37  223
     clus
vv    16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  NO                10                 37
  YES               96                223
[1] 2 2
[1] FALSE
D70V10, continuous
D70V11, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED    45  61
  16Q LOSS WILD-TYPE  92 168
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED     45   61
  16Q LOSS WILD-TYPE   92  168
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  FEMALE               45                 92
  MALE                 61                168
[1] 2 2
[1] FALSE
D70V12, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED    91  14
  16Q LOSS WILD-TYPE 226  33
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED     91   14
  16Q LOSS WILD-TYPE  226   33
     clus
vv    16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  NO                91                226
  YES               14                 33
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16Q LOSS MUTATED       1                         1   100
  16Q LOSS WILD-TYPE     4                         0   252
D70V13, multiclass
                           clus
vv                          16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  ASIAN                                    1                  4
  BLACK OR AFRICAN AMERICAN                1                  0
  WHITE                                  100                252
[1] 3 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     3 102
  16Q LOSS WILD-TYPE   4 249
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      3  102
  16Q LOSS WILD-TYPE    4  249
                        clus
vv                       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  4
  NOT HISPANIC OR LATINO              102                249
[1] 2 2
[1] FALSE

Clustering(71) Variable = 17P LOSS MUTATION ANALYSIS
D71V1, survival
                    sevent
clus2                 0  1
  17P LOSS MUTATED   40 42
  17P LOSS WILD-TYPE 82 81
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                82                163 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                42                 81 
$`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        76.34       138.67 
TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A3F5 TCGA-DA-A95X TCGA-EB-A5UN TCGA-EE-A17X 
      150.61        95.51       225.11        52.90        52.41        13.15 
TCGA-EE-A180 TCGA-EE-A184 TCGA-EE-A20C TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G 
       62.37        67.50        75.55        76.14         0.26        44.28 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29T TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2GJ 
       63.12        47.74       346.49       115.43        30.02        68.65 
TCGA-EE-A2GP TCGA-EE-A2M6 TCGA-EE-A2MC TCGA-EE-A2MG TCGA-EE-A2MP TCGA-EE-A2MR 
        0.76       103.13        23.77        94.19       227.01        25.08 
TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3J7 
      143.93        53.26       124.31        64.04        54.51        45.90 
TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A199 
        3.35       201.80        19.86        14.56        34.45         7.82 
TCGA-ER-A19C TCGA-ER-A19S TCGA-ER-A2NG TCGA-ER-A3EV TCGA-FR-A44A TCGA-FR-A729 
       39.81        47.18        10.95        15.48       174.21       209.23 
TCGA-FR-A8YC TCGA-FS-A1Z4 TCGA-FS-A1ZJ TCGA-FS-A1ZQ TCGA-FS-A1ZT TCGA-FS-A1ZU 
       10.06        27.62        36.33       130.95        35.28         4.47 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F9 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 
       23.21         5.29        13.28        96.92        17.06        42.48 
TCGA-GN-A4U3 TCGA-QB-AA9O TCGA-W3-AA1R TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8ZY 
      120.53        18.05        79.99        92.84         1.15        48.39 
TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-YG-AA3O 
        1.94        31.99        18.31        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        69.21 
TCGA-D9-A6EG TCGA-DA-A1I1 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 
       22.85        53.65        45.07        64.83        58.85        30.44 
TCGA-DA-A95V TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5SG TCGA-EB-A5SH 
       72.10        14.14        12.30         3.91        33.24        50.07 
TCGA-EB-A6L9 TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A20H TCGA-EE-A29B 
       18.21        24.89        20.38         0.00       155.90        75.22 
TCGA-EE-A29D TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29W TCGA-EE-A2A6 TCGA-EE-A2GB 
       12.99        27.16        61.12       185.19        77.98        26.14 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
      239.11        12.95       201.60        10.62        32.48        18.35 
TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M7 
       31.00       118.32         0.20        71.31        81.99        15.25 
TCGA-EE-A2M8 TCGA-EE-A2MF TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML 
        5.75       209.79       171.85        63.25        89.26       104.78 
TCGA-EE-A2MM TCGA-EE-A2MT TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3J3 
      145.45        23.51       122.73         4.41         6.28        67.89 
TCGA-EE-A3J4 TCGA-EE-A3JI TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19B 
      111.85       152.81         1.58        47.31         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-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-A3PL TCGA-ER-A42L TCGA-FR-A7U8 
       16.87       173.29        68.52        32.05        74.47        26.20 
TCGA-FR-A7UA TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1ZC 
        5.65       171.78        49.74       195.98         8.35       312.07 
TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZM TCGA-FS-A1ZS 
       32.78        42.08        12.92         7.82        78.61       136.27 
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-A26A TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-GN-A8LK TCGA-GN-A9SD 
      117.93         7.59        34.49        46.92        43.23        59.41 
TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 TCGA-W3-A824 
       85.05       297.01         7.23         0.20         0.33       174.12 
TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1Q TCGA-W3-AA1V TCGA-W3-AA1W TCGA-WE-A8K5 
        1.97       120.07        44.05         8.09       185.13        59.64 
TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-AAA4 
       65.42        12.69        21.90        62.89        10.95        18.35 
TCGA-Z2-AA3S 
       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 
             50.40              45.99 
[1] "0.3 - 346.5 (50.4)" "0.0 - 312.1 (46.0)"
[1] "hr=" "1"  
D71V2, survival
                    sevent
clus2                  0   1
  17P LOSS MUTATED    59  64
  17P LOSS WILD-TYPE 111 123
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               123                234 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                64                123 
$`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        76.57        36.03       144.89       176.55       120.00 
TCGA-DA-A1I8 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A95X TCGA-EB-A44R TCGA-EB-A5UL 
       53.92        10.49       225.96        61.81        10.36        29.29 
TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A180 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20C 
       58.92        29.82        94.98        68.15         4.96       151.27 
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-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A2 
       61.28       369.93        25.87        17.92       115.96        59.64 
TCGA-EE-A2A5 TCGA-EE-A2GC TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GP TCGA-EE-A2GT 
       39.29        67.43        48.72       107.38        13.91        44.88 
TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2MG TCGA-EE-A2MN 
       21.67       129.27        61.51        47.28       103.20        47.54 
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-A3AC TCGA-EE-A3AE TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB 
       64.04        54.51        36.95        64.08        34.32       201.80 
TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A199 TCGA-ER-A19C TCGA-ER-A19S 
      134.33        31.40        35.44         9.17        48.89        49.48 
TCGA-ER-A2NG TCGA-ER-A3EV TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7U9 
       31.27        46.98        92.98       174.21       220.80        18.77 
TCGA-FR-A8YC TCGA-FS-A1YX TCGA-FS-A1Z4 TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZQ 
       34.82        48.59        28.08        32.75        47.38       133.55 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F2 TCGA-FS-A4F9 
       53.16        26.56        49.48        27.09        50.14        34.03 
TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
        0.20        22.92        96.92        10.13        64.44        62.79 
TCGA-GN-A4U3 TCGA-GN-A4U9 TCGA-HR-A2OG TCGA-QB-AA9O TCGA-W3-AA1R TCGA-W3-AA21 
      121.91        22.13         0.23        18.05       111.09       105.04 
TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 
       24.03        49.05        35.80        49.51        12.16        40.41 
TCGA-WE-AAA3 TCGA-YG-AA3O TCGA-Z2-AA3V 
       21.40        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-D3-A8GV TCGA-D9-A149 TCGA-D9-A1JX TCGA-D9-A1X3 
      129.63       117.17       167.70        54.67         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        77.56        22.95 
TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I4 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IB 
       20.38       207.48        35.93        73.84        65.92        40.60 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F8 TCGA-DA-A95V TCGA-DA-A95W TCGA-DA-A95Y 
       68.09        33.93        15.68        72.10        25.15        14.14 
TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5VV 
       13.02        13.87        20.35        68.25        54.02         7.04 
TCGA-EB-A6L9 TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
       36.46        27.22         8.65        33.73        14.70        26.89 
TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
      133.81        91.56       168.26        13.55        63.35        85.08 
TCGA-EE-A29D TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29W 
       13.97        18.61        56.42        66.74        14.47       195.02 
TCGA-EE-A2A0 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
       46.82        86.14        59.28       340.14       173.79       220.24 
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-A2ME TCGA-EE-A2MF 
       81.21        94.82        28.83        19.76       103.27       268.73 
TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM 
       16.96       204.66        96.23       180.39       216.66       167.90 
TCGA-EE-A2MT TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH 
       71.21       122.73        28.77        13.81        41.59       138.81 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JI 
      172.18       127.20        53.19        27.35        51.35       152.81 
TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19E 
       13.94        50.76        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-A19T TCGA-ER-A19W TCGA-ER-A1A1 
       44.05       162.08        50.89         8.88       148.18        79.99 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NH TCGA-ER-A3ES 
       43.82        23.34        20.15        16.37        32.05       247.04 
TCGA-ER-A3ET TCGA-ER-A3PL TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A69P TCGA-FR-A7U8 
       93.01        33.21        12.95       149.03        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 
       46.45        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        48.00        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-A690 TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 
        7.23         0.20         0.33         0.69       228.16        63.02 
TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1Q TCGA-W3-AA1V TCGA-W3-AA1W TCGA-WE-A8K5 
      121.08         4.01        69.07        42.08       219.16        61.15 
TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT 
       17.95       101.33        58.98        70.52        63.22        11.80 
TCGA-WE-AAA4 TCGA-YD-A89C TCGA-YD-A9TA TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S 
       24.99         6.90        49.18        14.43        27.58        96.99 

  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               0.2                0.2 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
            369.93             368.78 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
             49.51              53.77 
[1] "0.2 - 369.9 (49.5)" "0.2 - 368.8 (53.8)"
[1] "hr=" "1.1"
D71V3, continuous
                    vv
clus                 I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  17P LOSS MUTATED             5       3      15       10       10        5
  17P LOSS WILD-TYPE           8       4      14        8       18       20
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  17P LOSS MUTATED           4         7         4        14          7
  17P LOSS WILD-TYPE        10        12        11        26          8
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  17P LOSS MUTATED           11         18        4
  17P LOSS WILD-TYPE         22         37       17
D71V4, multiclass
             clus
vv            17P LOSS MUTATED 17P LOSS WILD-TYPE
  I OR II NOS                5                  8
  STAGE 0                    3                  4
  STAGE I                   15                 14
  STAGE IA                  10                  8
  STAGE IB                  10                 18
  STAGE II                   5                 20
  STAGE IIA                  4                 10
  STAGE IIB                  7                 12
  STAGE IIC                  4                 11
  STAGE III                 14                 26
  STAGE IIIA                 7                  8
  STAGE IIIB                11                 22
  STAGE IIIC                18                 37
  STAGE IV                   4                 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
  17P LOSS MUTATED      23 30 25 25
  17P LOSS WILD-TYPE    41 43 53 45
D71V5, multiclass
       clus
vv      17P LOSS MUTATED 17P LOSS WILD-TYPE
  T0+T1               23                 41
  T2                  30                 43
  T3                  25                 53
  T4                  25                 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"
                    vv
clus                  N0  N1  N2  N3
  17P LOSS MUTATED    63  23  14  15
  17P LOSS WILD-TYPE 114  42  25  30
D71V6, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  N0               63                114
  N1               23                 42
  N2               14                 25
  N3               15                 30
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V7, binary
                    cls
clus                   0   1
  17P LOSS MUTATED   116   5
  17P LOSS WILD-TYPE 202  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED    116    5
  17P LOSS WILD-TYPE  202   17
   clus
vv  17P LOSS MUTATED 17P LOSS WILD-TYPE
  0              116                202
  1                5                 17
[1] 2 2
[1] FALSE
D71V8, binary
                    cls
clus                  0  1
  17P LOSS MUTATED   56 32
  17P LOSS WILD-TYPE 78 58
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     56   32
  17P LOSS WILD-TYPE   78   58
     clus
vv    17P LOSS MUTATED 17P LOSS WILD-TYPE
  NO                56                 78
  YES               32                 58
[1] 2 2
[1] FALSE
D71V9, binary
                    cls
clus                   0   1
  17P LOSS MUTATED    14 113
  17P LOSS WILD-TYPE  33 206
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     14  113
  17P LOSS WILD-TYPE   33  206
     clus
vv    17P LOSS MUTATED 17P LOSS WILD-TYPE
  NO                14                 33
  YES              113                206
[1] 2 2
[1] FALSE
D71V10, continuous
D71V11, binary
                    cls
clus                   0   1
  17P LOSS MUTATED    39  88
  17P LOSS WILD-TYPE  98 141
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     39   88
  17P LOSS WILD-TYPE   98  141
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  FEMALE               39                 98
  MALE                 88                141
[1] 2 2
[1] FALSE
D71V12, binary
                    cls
clus                   0   1
  17P LOSS MUTATED   113  13
  17P LOSS WILD-TYPE 204  34
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED    113   13
  17P LOSS WILD-TYPE  204   34
     clus
vv    17P LOSS MUTATED 17P LOSS WILD-TYPE
  NO               113                204
  YES               13                 34
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  17P LOSS MUTATED       1                         1   122
  17P LOSS WILD-TYPE     4                         0   230
D71V13, multiclass
                           clus
vv                          17P LOSS MUTATED 17P LOSS WILD-TYPE
  ASIAN                                    1                  4
  BLACK OR AFRICAN AMERICAN                1                  0
  WHITE                                  122                230
[1] 3 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     1 123
  17P LOSS WILD-TYPE   6 228
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      1  123
  17P LOSS WILD-TYPE    6  228
                        clus
vv                       17P LOSS MUTATED 17P LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO              123                228
[1] 2 2
[1] FALSE

Clustering(72) Variable = 17Q LOSS MUTATION ANALYSIS
D72V1, survival
                    sevent
clus2                  0   1
  17Q LOSS MUTATED    17  23
  17Q LOSS WILD-TYPE 105 100
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                40                205 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                23                100 
$`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 
       69.21       150.61        95.51        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-EE-A3JH TCGA-ER-A193 
       54.51        45.90         3.35       201.80        19.86        14.56 
TCGA-ER-A19C TCGA-ER-A19L TCGA-ER-A19S TCGA-FR-A729 TCGA-FR-A8YC TCGA-FS-A1Z4 
       39.81        99.06        47.18       209.23        10.06        27.62 
TCGA-FS-A1ZQ TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F9 TCGA-GN-A267 
      130.95        35.28        23.21         5.29        13.28        17.06 
TCGA-QB-AA9O TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-YG-AA3O 
       18.05        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        76.34       138.67 
TCGA-DA-A1I1 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 
       53.65        45.07        64.83        58.85        30.44       225.11 
TCGA-DA-A95V TCGA-DA-A95X TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5SG 
       72.10        52.90        14.14        12.30         3.91        33.24 
TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A181 
       50.07        52.41        18.21        13.15        24.89        20.38 
TCGA-EE-A182 TCGA-EE-A184 TCGA-EE-A20C TCGA-EE-A20H TCGA-EE-A29B TCGA-EE-A29D 
        0.00        67.50        75.55       155.90        75.22        12.99 
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-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD 
      185.19       115.43        30.02        77.98        26.14       239.11 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
       12.95       201.60        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-A2M7 
       31.00       118.32         0.20        71.31        81.99        15.25 
TCGA-EE-A2M8 TCGA-EE-A2MF TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML 
        5.75       209.79       171.85        63.25        89.26       104.78 
TCGA-EE-A2MM TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB 
      145.45        25.08       143.93        23.51        53.26       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3JI 
       64.04         4.41         6.28        67.89       111.85       152.81 
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-A19M TCGA-ER-A19N TCGA-ER-A19P 
       11.47       151.46       150.12        59.84        42.48       120.76 
TCGA-ER-A19Q TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
       49.71       146.63        47.97        22.36         4.70        16.87 
TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42L 
       10.95       173.29        68.52        15.48        32.05        74.47 
TCGA-FR-A44A TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 
      174.21        26.20         5.65       171.78        49.74       195.98 
TCGA-FS-A1Z3 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG 
        8.35       312.07        32.78        42.08        12.92         7.82 
TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZZ TCGA-FS-A4F0 
       36.33        78.61       136.27         4.47         3.06        30.90 
TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
       66.67       173.19        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        96.92 
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-RP-A690 TCGA-RP-A693 
       59.41        85.05       297.01         7.23         0.20         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        65.42        12.69 
TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 
       21.90        62.89        10.95        31.99        18.31        18.35 
TCGA-Z2-AA3S 
       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 
            42.855             47.740 
[1] "0.3 - 227.0 (42.9)" "0.0 - 346.5 (47.7)"
[1] "hr=" "1.3"
D72V2, survival
                    sevent
clus2                  0   1
  17Q LOSS MUTATED    28  32
  17Q LOSS WILD-TYPE 142 155
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                60                297 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                32                155 
$`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        77.56 
TCGA-DA-A1HW TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-EE-A180 TCGA-EE-A29C 
       36.03       176.55       120.00        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       134.33 
TCGA-ER-A193 TCGA-ER-A19C TCGA-ER-A19L TCGA-ER-A19S TCGA-FR-A729 TCGA-FR-A7U9 
       31.40        48.89       131.51        49.48       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        35.80        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-D3-A8GV TCGA-D9-A149 TCGA-D9-A1JW 
       29.06       129.63       117.17       167.70        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-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I4 
       22.95        76.57       144.89        20.38       207.48        35.93 
TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
       73.84        65.92        40.60        68.09        33.93        10.49 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-DA-A95V TCGA-DA-A95W TCGA-DA-A95X TCGA-DA-A95Y 
      225.96        15.68        72.10        25.15        61.81        14.14 
TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH 
       13.02        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 
       29.29        58.92         7.04        36.46        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       115.96        59.64        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       173.79       220.24       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       180.39       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        64.04        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        93.01        46.98        33.21 
TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A7U8 
       12.95       149.03        92.98       174.21        15.72        27.85 
TCGA-FR-A7UA TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY 
       38.27        36.26       104.42       216.92        48.59       228.59 
TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC 
      202.65        20.91         7.79        27.72        48.85       357.37 
TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZK 
       53.52        46.45        15.45         9.70        47.38        23.93 
TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZZ 
      101.26        74.73        11.41       148.80        26.56        27.02 
TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4FB TCGA-FS-A4FC 
       77.82        66.67        28.73       174.84        26.73        54.41 
TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
       80.68        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        96.92        10.13 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 
       62.79        32.48        48.00       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-A690 TCGA-RP-A693 
       65.88       368.78       297.90         7.23         0.20         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-A8JZ TCGA-WE-A8K1 
      111.09        42.08       219.16       105.04        24.03        49.05 
TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ 
       61.15        17.95       101.33        58.98        70.52        63.22 
TCGA-WE-A8ZT TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YD-A89C TCGA-YD-A9TA 
       11.80        40.41        21.40        24.99         6.90        49.18 
TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S 
       14.43        27.58        96.99 

  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
               0.2                0.2 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
            248.65             369.93 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
            49.185             54.410 
[1] "0.2 - 248.7 (49.2)" "0.2 - 369.9 (54.4)"
[1] "hr=" "1.2"
D72V3, continuous
                    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          10       6      20       13       24       25
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  17Q LOSS MUTATED           2         4         2         7          6
  17Q LOSS WILD-TYPE        12        15        13        33          9
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  17Q LOSS MUTATED            5          7        4
  17Q LOSS WILD-TYPE         28         48       17
D72V4, multiclass
             clus
vv            17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  I OR II NOS                3                 10
  STAGE 0                    1                  6
  STAGE I                    9                 20
  STAGE IA                   5                 13
  STAGE IB                   4                 24
  STAGE II                   0                 25
  STAGE IIA                  2                 12
  STAGE IIB                  4                 15
  STAGE IIC                  2                 13
  STAGE III                  7                 33
  STAGE IIIA                 6                  9
  STAGE IIIB                 5                 28
  STAGE IIIC                 7                 48
  STAGE IV                   4                 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
  17Q LOSS MUTATED      13 15 13 11
  17Q LOSS WILD-TYPE    51 58 65 59
D72V5, multiclass
       clus
vv      17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  T0+T1               13                 51
  T2                  15                 58
  T3                  13                 65
  T4                  11                 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
  17Q LOSS MUTATED    30  14   5   8
  17Q LOSS WILD-TYPE 147  51  34  37
D72V6, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  N0               30                147
  N1               14                 51
  N2                5                 34
  N3                8                 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"
D72V7, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED    55   5
  17Q LOSS WILD-TYPE 263  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     55    5
  17Q LOSS WILD-TYPE  263   17
   clus
vv  17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  0               55                263
  1                5                 17
[1] 2 2
[1] FALSE
D72V8, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED    30  14
  17Q LOSS WILD-TYPE 104  76
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     30   14
  17Q LOSS WILD-TYPE  104   76
     clus
vv    17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  NO                30                104
  YES               14                 76
[1] 2 2
[1] FALSE
D72V9, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED     7  57
  17Q LOSS WILD-TYPE  40 262
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      7   57
  17Q LOSS WILD-TYPE   40  262
     clus
vv    17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  NO                 7                 40
  YES               57                262
[1] 2 2
[1] FALSE
D72V10, continuous
D72V11, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED    21  43
  17Q LOSS WILD-TYPE 116 186
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     21   43
  17Q LOSS WILD-TYPE  116  186
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  FEMALE               21                116
  MALE                 43                186
[1] 2 2
[1] FALSE
D72V12, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED    58   5
  17Q LOSS WILD-TYPE 259  42
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     58    5
  17Q LOSS WILD-TYPE  259   42
     clus
vv    17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  NO                58                259
  YES                5                 42
[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   289
D72V13, multiclass
                           clus
vv                          17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  ASIAN                                    0                  5
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   63                289
[1] 3 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   6 288
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      1   63
  17Q LOSS WILD-TYPE    6  288
                        clus
vv                       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO               63                288
[1] 2 2
[1] FALSE

Clustering(73) Variable = 18P LOSS MUTATION ANALYSIS
D73V1, survival
                    sevent
clus2                 0  1
  18P LOSS MUTATED   37 37
  18P LOSS WILD-TYPE 85 86
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                74                171 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                37                 86 
$`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        76.34       150.61        45.07 
TCGA-DA-A3F5 TCGA-EB-A5SG TCGA-EB-A5UN TCGA-EE-A20C TCGA-EE-A29D TCGA-EE-A29G 
      225.11        33.24        52.41        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        12.95         0.76 
TCGA-EE-A2GR TCGA-EE-A2MG TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MS TCGA-EE-A2MU 
        0.20        94.19        89.26       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-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19C 
       19.86       152.81        14.56         7.82        53.29        39.81 
TCGA-ER-A19H TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A42L TCGA-FR-A44A TCGA-FR-A7U8 
      150.12        49.71        47.18        74.47       174.21        26.20 
TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FW-A3TU 
       78.61       130.95       136.27        23.21         5.29        55.59 
TCGA-GN-A268 TCGA-GN-A8LK TCGA-GN-A9SD TCGA-W3-A825 TCGA-WE-A8K1 TCGA-WE-A8ZY 
       42.48        43.23        59.41         1.97         1.15        48.39 
TCGA-WE-AA9Y TCGA-YG-AA3O 
        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        69.21       138.67        53.65        95.51        64.83 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A95V TCGA-DA-A95X TCGA-DA-A95Y TCGA-DA-A95Z 
       58.85        30.44        72.10        52.90        14.14        12.30 
TCGA-EB-A44Q TCGA-EB-A5SH TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A180 
        3.91        50.07        18.21        13.15        24.89        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-A29E TCGA-EE-A29H TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A2A1 TCGA-EE-A2A2 
        0.26        63.12        27.16        61.12       115.43        30.02 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
       77.98        26.14       201.60        68.65        10.62        32.48 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 
       18.35        31.00       118.32        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-A2ML TCGA-EE-A2MP TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A3AC TCGA-EE-A3AF 
      104.78       227.01        25.08        23.51        64.04         6.28 
TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3JB TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
      111.85        45.90       201.80        34.45         1.58        47.31 
TCGA-ER-A19A TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
        4.54        11.47       151.46        99.06        59.84        42.48 
TCGA-ER-A19P TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
      120.76       146.63        47.97        22.36         4.70        16.87 
TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A729 
       10.95       173.29        68.52        15.48        32.05       209.23 
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        42.08        12.92         7.82 
TCGA-FS-A1ZJ TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 
       36.33        35.28         4.47         3.06        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-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 
        6.05         1.91        53.29       117.93        96.92        17.06 
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-RP-A690 TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A828 
        7.23        18.05         0.20         0.33       174.12       120.07 
TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K5 
       44.05        79.99         8.09       185.13        92.84        59.64 
TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-AAA0 
       65.42        12.69        21.90        62.89        10.95        31.99 
TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-Z2-AA3S 
       18.31        18.35        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 
             49.53              44.05 
[1] "0.2 - 346.5 (49.5)" "0.0 - 312.1 (44.0)"
[1] "hr=" "1.1"
D73V2, survival
                    sevent
clus2                  0   1
  18P LOSS MUTATED    45  55
  18P LOSS WILD-TYPE 125 132
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
               100                257 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                55                132 
$`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        76.57       176.55        73.84        53.92 
TCGA-DA-A3F5 TCGA-EB-A5SG TCGA-EB-A5UN TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A29A 
      225.96        68.25        58.92       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       173.79        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       180.39       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       134.33       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-ER-A42L TCGA-FR-A44A 
       50.89        49.48         8.88        12.95       149.03       174.21 
TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FS-A1ZA TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZR 
       15.72        27.85        27.72       101.26       133.55        11.41 
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-WE-A8JZ TCGA-WE-A8K1 
       50.10        21.37        59.41        63.02        24.03        49.05 
TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-YG-AA3O TCGA-Z2-A8RT 
       49.51        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-D3-A8GV TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A3Z1 
       29.06       167.70       151.53        54.67         3.65        15.39 
TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HW 
       22.29        18.44         9.90        25.18        77.56        36.03 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1IA 
      144.89        20.38       207.48        35.93       120.00        65.92 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-DA-A95V 
       40.60        68.09        33.93        10.49        15.68        72.10 
TCGA-DA-A95W TCGA-DA-A95X TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A44R 
       25.15        61.81        14.14        13.02        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        29.29         7.04        36.46        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       115.96        59.64 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK 
       39.29        86.14        59.28       220.24       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        64.04 
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        93.01        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 
       46.45        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        96.92 
TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A4U4 
       10.13        64.44        32.48        48.00       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-A690 TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 
        7.23        18.05         0.20         0.33         0.69       228.16 
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-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO 
      105.04        61.15        17.95       101.33        58.98        70.52 
TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 
       63.22        11.80        35.80        40.41        21.40        24.99 
TCGA-YD-A89C TCGA-YD-A9TA TCGA-YG-AA3P TCGA-Z2-AA3S TCGA-Z2-AA3V 
        6.90        49.18        14.43        96.99        15.98 

  18P LOSS MUTATED 18P LOSS WILD-TYPE 
               7.1                0.2 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
            369.93             368.78 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
            59.165             47.540 
[1] "7.1 - 369.9 (59.2)" "0.2 - 368.8 (47.5)"
[1] "hr=" "1.1"
D73V3, continuous
                    vv
clus                 I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  18P LOSS MUTATED             5       3       8        6       10        8
  18P LOSS WILD-TYPE           8       4      21       12       18       17
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  18P LOSS MUTATED           1         6         3        13          6
  18P LOSS WILD-TYPE        13        13        12        27          9
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  18P LOSS MUTATED            6         16        2
  18P LOSS WILD-TYPE         27         39       19
D73V4, multiclass
             clus
vv            18P LOSS MUTATED 18P LOSS WILD-TYPE
  I OR II NOS                5                  8
  STAGE 0                    3                  4
  STAGE I                    8                 21
  STAGE IA                   6                 12
  STAGE IB                  10                 18
  STAGE II                   8                 17
  STAGE IIA                  1                 13
  STAGE IIB                  6                 13
  STAGE IIC                  3                 12
  STAGE III                 13                 27
  STAGE IIIA                 6                  9
  STAGE IIIB                 6                 27
  STAGE IIIC                16                 39
  STAGE IV                   2                 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
  18P LOSS MUTATED      23 21 18 21
  18P LOSS WILD-TYPE    41 52 60 49
D73V5, multiclass
       clus
vv      18P LOSS MUTATED 18P LOSS WILD-TYPE
  T0+T1               23                 41
  T2                  21                 52
  T3                  18                 60
  T4                  21                 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
  18P LOSS MUTATED    48  16  13  13
  18P LOSS WILD-TYPE 129  49  26  32
D73V6, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  N0               48                129
  N1               16                 49
  N2               13                 26
  N3               13                 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"
D73V7, binary
                    cls
clus                   0   1
  18P LOSS MUTATED    94   2
  18P LOSS WILD-TYPE 224  20
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     94    2
  18P LOSS WILD-TYPE  224   20
   clus
vv  18P LOSS MUTATED 18P LOSS WILD-TYPE
  0               94                224
  1                2                 20
[1] 2 2
[1] FALSE
D73V8, binary
                    cls
clus                  0  1
  18P LOSS MUTATED   37 24
  18P LOSS WILD-TYPE 97 66
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     37   24
  18P LOSS WILD-TYPE   97   66
     clus
vv    18P LOSS MUTATED 18P LOSS WILD-TYPE
  NO                37                 97
  YES               24                 66
[1] 2 2
[1] FALSE
D73V9, binary
                    cls
clus                   0   1
  18P LOSS MUTATED    16  88
  18P LOSS WILD-TYPE  31 231
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     16   88
  18P LOSS WILD-TYPE   31  231
     clus
vv    18P LOSS MUTATED 18P LOSS WILD-TYPE
  NO                16                 31
  YES               88                231
[1] 2 2
[1] FALSE
D73V10, continuous
D73V11, binary
                    cls
clus                   0   1
  18P LOSS MUTATED    40  64
  18P LOSS WILD-TYPE  97 165
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     40   64
  18P LOSS WILD-TYPE   97  165
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  FEMALE               40                 97
  MALE                 64                165
[1] 2 2
[1] FALSE
D73V12, binary
                    cls
clus                   0   1
  18P LOSS MUTATED    92  12
  18P LOSS WILD-TYPE 225  35
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     92   12
  18P LOSS WILD-TYPE  225   35
     clus
vv    18P LOSS MUTATED 18P LOSS WILD-TYPE
  NO                92                225
  YES               12                 35
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18P LOSS MUTATED       0                         0   102
  18P LOSS WILD-TYPE     5                         1   250
D73V13, multiclass
                           clus
vv                          18P LOSS MUTATED 18P LOSS WILD-TYPE
  ASIAN                                    0                  5
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                  102                250
[1] 3 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     2 100
  18P LOSS WILD-TYPE   5 251
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      2  100
  18P LOSS WILD-TYPE    5  251
                        clus
vv                       18P LOSS MUTATED 18P LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  5
  NOT HISPANIC OR LATINO              100                251
[1] 2 2
[1] FALSE

Clustering(74) Variable = 18Q LOSS MUTATION ANALYSIS
D74V1, survival
                    sevent
clus2                 0  1
  18Q LOSS MUTATED   36 39
  18Q LOSS WILD-TYPE 86 84
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                75                170 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                39                 84 
$`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        69.21        76.34       150.61        45.07        64.83 
TCGA-DA-A3F5 TCGA-DA-A95X TCGA-EB-A5SG TCGA-EB-A5UN TCGA-EE-A20C TCGA-EE-A29D 
      225.11        52.90        33.24        52.41        75.55        12.99 
TCGA-EE-A29G TCGA-EE-A29M TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2GD TCGA-EE-A2GE 
       44.28        47.74       346.49       185.19       239.11        12.95 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2MG TCGA-EE-A2MK TCGA-EE-A2MU TCGA-EE-A3AA 
        0.76         0.20        94.19        89.26        53.26       124.31 
TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3J3 TCGA-EE-A3J8 TCGA-EE-A3JH 
      122.73         4.41        54.51        67.89         3.35        19.86 
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-A19S TCGA-ER-A19W TCGA-ER-A3EV TCGA-ER-A42L TCGA-FR-A44A TCGA-FR-A7U8 
       47.18       146.63        15.48        74.47       174.21        26.20 
TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FW-A3TU 
       78.61       130.95       136.27        23.21         5.29        55.59 
TCGA-GN-A268 TCGA-GN-A8LK TCGA-GN-A9SD TCGA-W3-A825 TCGA-W3-AA1V TCGA-WE-A8K1 
       42.48        43.23        59.41         1.97         8.09         1.15 
TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-YG-AA3O 
       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       138.67        53.65        95.51 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A95V TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q 
       58.85        30.44        72.10        14.14        12.30         3.91 
TCGA-EB-A5SH TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A181 
       50.07        18.21        13.15        24.89        62.37        20.38 
TCGA-EE-A182 TCGA-EE-A184 TCGA-EE-A20H TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E 
        0.00        67.50       155.90        75.22        76.14         0.26 
TCGA-EE-A29H TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 
       63.12        27.16        61.12       115.43        30.02        77.98 
TCGA-EE-A2GB TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
       26.14       201.60        68.65        10.62        32.48        18.35 
TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 
       31.00       118.32        71.31        81.99       103.13        15.25 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2ML 
        5.75        23.77       209.79       171.85        63.25       104.78 
TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AC 
      145.45       227.01        25.08       143.93        23.51        64.04 
TCGA-EE-A3AF TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3JB TCGA-ER-A195 TCGA-ER-A197 
        6.28       111.85        45.90       201.80        34.45         1.58 
TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19L TCGA-ER-A19M 
       47.31         4.54        11.47       151.46        99.06        59.84 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
       42.48       120.76        49.71        47.97        22.36         4.70 
TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3PL TCGA-FR-A729 
       16.87        10.95       173.29        68.52        32.05       209.23 
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        42.08        12.92         7.82 
TCGA-FS-A1ZJ TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 
       36.33        35.28         4.47         3.06        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-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 
        6.05         1.91        53.29       117.93        96.92        17.06 
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-RP-A690 TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A828 
        7.23        18.05         0.20         0.33       174.12       120.07 
TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K5 TCGA-WE-A8ZM 
       44.05        79.99       185.13        92.84        59.64        65.42 
TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-AAA0 TCGA-WE-AAA3 
       12.69        21.90        62.89        10.95        31.99        18.31 
TCGA-WE-AAA4 TCGA-Z2-AA3S 
       18.35        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 
             52.90              43.79 
[1] "0.2 - 346.5 (52.9)" "0.0 - 312.1 (43.8)"
[1] "hr=" "1"  
D74V2, survival
                    sevent
clus2                  0   1
  18Q LOSS MUTATED    43  52
  18Q LOSS WILD-TYPE 127 135
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                95                262 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                52                135 
$`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        77.56        76.57       176.55        73.84        53.92 
TCGA-DA-A1IA TCGA-DA-A3F5 TCGA-DA-A95X TCGA-EB-A5SG TCGA-EB-A5UN TCGA-EE-A20B 
       65.92       225.96        61.81        68.25        58.92       133.81 
TCGA-EE-A20C TCGA-EE-A29A TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29M TCGA-EE-A29T 
      151.27        63.35        13.97        72.07        56.84       369.93 
TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE 
       25.87       195.02        17.92        67.43       340.14       173.79 
TCGA-EE-A2GI TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2MG TCGA-EE-A2MK TCGA-EE-A2MQ 
       48.72        13.91        42.77       103.20       180.39        43.23 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AH 
       53.26       124.31       122.73        28.77        54.51       138.81 
TCGA-EE-A3J3 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 
      172.18        34.32        53.19       134.33       152.81        31.40 
TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19H TCGA-ER-A19S TCGA-ER-A19T 
        9.17        98.40        48.89       152.35        49.48         8.88 
TCGA-ER-A19W TCGA-ER-A3EV TCGA-ER-A42L TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A7U8 
      148.18        46.98       149.03       174.21        15.72        27.85 
TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FW-A3TU 
      101.26       133.55       148.80        49.48        27.09        55.59 
TCGA-GN-A268 TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A8LL TCGA-GN-A9SD TCGA-W3-A825 
       62.79        22.13        50.10        21.37        59.41        63.02 
TCGA-W3-AA1V TCGA-WE-A8K1 TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-YG-AA3O 
       42.08        49.05        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-D3-A8GV TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 
       29.06       167.70        54.67         3.65         7.10        15.39 
TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EG TCGA-DA-A1HW 
       22.29        18.44         9.90        25.18        22.95        36.03 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1IB 
      144.89        20.38       207.48        35.93       120.00        40.60 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-DA-A95V TCGA-DA-A95W 
       68.09        33.93        10.49        15.68        72.10        25.15 
TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SH 
       14.14        13.02        13.87        10.36        20.35        54.02 
TCGA-EB-A5UL TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
       29.29         7.04        36.46        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-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E 
       91.56       168.26        13.55        85.08        78.97        63.78 
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-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
       61.28        46.82       115.96        59.64        39.29        86.14 
TCGA-EE-A2GB TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
       59.28       220.24       107.38        54.74        79.66        75.48 
TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 
      102.12       126.81        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-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-A2MP TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AC 
       47.54       248.65       134.40       162.48        71.21        64.04 
TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3JB 
       13.81        41.59       127.20        36.95        64.08       201.80 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A19A 
       27.35        51.35        35.44        13.94        50.76        77.75 
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-A1A1 TCGA-ER-A2NC 
       61.05        44.05       162.08        50.89        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-A3PL TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A729 TCGA-FR-A7U9 
       93.01        33.21        12.95        92.98       220.80        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        46.45        15.45         9.70 
TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZT 
       32.75        47.38        23.93        74.73        11.41        53.16 
TCGA-FS-A1ZU TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 
       26.56        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-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 
       22.92        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        96.92        10.13        64.44 
TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 
       32.48        48.00       121.91        39.35        10.42        48.89 
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-A690 TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A828 TCGA-W3-AA1O 
        0.20         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 
       17.95       101.33        58.98        70.52        63.22        11.80 
TCGA-WE-A8ZX TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YD-A89C TCGA-YD-A9TA 
       35.80        40.41        21.40        24.99         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 
             62.79              46.90 
[1] "8.9 - 369.9 (62.8)" "0.2 - 368.8 (46.9)"
[1] "hr=" "1.2"
D74V3, continuous
                    vv
clus                 I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  18Q LOSS MUTATED             5       3       7        6        9        7
  18Q LOSS WILD-TYPE           8       4      22       12       19       18
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  18Q LOSS MUTATED           1         5         3        13          6
  18Q LOSS WILD-TYPE        13        14        12        27          9
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  18Q LOSS MUTATED            6         14        3
  18Q LOSS WILD-TYPE         27         41       18
D74V4, multiclass
             clus
vv            18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  I OR II NOS                5                  8
  STAGE 0                    3                  4
  STAGE I                    7                 22
  STAGE IA                   6                 12
  STAGE IB                   9                 19
  STAGE II                   7                 18
  STAGE IIA                  1                 13
  STAGE IIB                  5                 14
  STAGE IIC                  3                 12
  STAGE III                 13                 27
  STAGE IIIA                 6                  9
  STAGE IIIB                 6                 27
  STAGE IIIC                14                 41
  STAGE IV                   3                 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 LOSS MUTATED      21 19 18 20
  18Q LOSS WILD-TYPE    43 54 60 50
D74V5, multiclass
       clus
vv      18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  T0+T1               21                 43
  T2                  19                 54
  T3                  18                 60
  T4                  20                 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
  18Q LOSS MUTATED    44  16  12  12
  18Q LOSS WILD-TYPE 133  49  27  33
D74V6, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  N0               44                133
  N1               16                 49
  N2               12                 27
  N3               12                 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"
D74V7, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED    86   4
  18Q LOSS WILD-TYPE 232  18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     86    4
  18Q LOSS WILD-TYPE  232   18
   clus
vv  18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  0               86                232
  1                4                 18
[1] 2 2
[1] FALSE
D74V8, binary
                    cls
clus                  0  1
  18Q LOSS MUTATED   38 20
  18Q LOSS WILD-TYPE 96 70
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     38   20
  18Q LOSS WILD-TYPE   96   70
     clus
vv    18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  NO                38                 96
  YES               20                 70
[1] 2 2
[1] FALSE
D74V9, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED    14  86
  18Q LOSS WILD-TYPE  33 233
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     14   86
  18Q LOSS WILD-TYPE   33  233
     clus
vv    18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  NO                14                 33
  YES               86                233
[1] 2 2
[1] FALSE
D74V10, continuous
D74V11, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED    37  63
  18Q LOSS WILD-TYPE 100 166
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     37   63
  18Q LOSS WILD-TYPE  100  166
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  FEMALE               37                100
  MALE                 63                166
[1] 2 2
[1] FALSE
D74V12, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED    87  13
  18Q LOSS WILD-TYPE 230  34
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     87   13
  18Q LOSS WILD-TYPE  230   34
     clus
vv    18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  NO                87                230
  YES               13                 34
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18Q LOSS MUTATED       0                         0    99
  18Q LOSS WILD-TYPE     5                         1   253
D74V13, multiclass
                           clus
vv                          18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  ASIAN                                    0                  5
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   99                253
[1] 3 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  97
  18Q LOSS WILD-TYPE   5 254
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      2   97
  18Q LOSS WILD-TYPE    5  254
                        clus
vv                       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  5
  NOT HISPANIC OR LATINO               97                254
[1] 2 2
[1] FALSE

Clustering(75) Variable = 19P LOSS MUTATION ANALYSIS
D75V1, survival
                    sevent
clus2                  0   1
  19P LOSS MUTATED    27  23
  19P LOSS WILD-TYPE  95 100
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                50                195 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                23                100 
$`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-DA-A95Y 
       16.90        76.34        95.51        45.07        64.83        14.14 
TCGA-EE-A17X TCGA-EE-A20H TCGA-EE-A29D TCGA-EE-A29H TCGA-EE-A2GM TCGA-EE-A2MG 
       13.15       155.90        12.99        63.12        18.35        94.19 
TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AB TCGA-EE-A3AD TCGA-ER-A19B 
      227.01       143.93        23.51       122.73         4.41        53.29 
TCGA-ER-A19C TCGA-ER-A19Q TCGA-ER-A3EV TCGA-FR-A44A TCGA-FS-A1ZJ TCGA-FS-A1ZQ 
       39.81        49.71        15.48       174.21        36.33       130.95 
TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A4FD TCGA-FW-A3TV TCGA-GF-A4EO TCGA-GN-A262 
       35.28        23.21        80.68        11.54         6.05        53.29 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-W3-A825 TCGA-W3-AA1R TCGA-W3-AA1V 
       42.48         7.59       120.53         1.97        79.99         8.09 
TCGA-WE-A8K1 TCGA-WE-A8ZM 
        1.15        65.42 

$`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        69.21        22.85       138.67        53.65 
TCGA-DA-A1I2 TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A95V TCGA-DA-A95X 
      150.61        58.85        30.44       225.11        72.10        52.90 
TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A6L9 
       12.30         3.91        33.24        50.07        52.41        18.21 
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-A29M TCGA-EE-A29P 
       75.22        76.14         0.26        44.28        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       115.43        30.02        77.98 
TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK 
       26.14       239.11        12.95       201.60        68.65        10.62 
TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
       32.48        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-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MR 
      171.85        63.25        89.26       104.78       145.45        25.08 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J3 
       53.26       124.31        64.04        54.51         6.28        67.89 
TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI 
      111.85        45.90         3.35       201.80        19.86       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-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-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
      120.76        47.18       146.63        47.97        22.36         4.70 
TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3PL TCGA-ER-A42L 
       16.87        10.95       173.29        68.52        32.05        74.47 
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        42.08 
TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZM TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZY 
       12.92         7.82        78.61       136.27         4.47         5.29 
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-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 
       19.30         9.90         1.91       117.93        96.92        17.06 
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-A690 TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A828 
        7.23        18.05         0.20         0.33       174.12       120.07 
TCGA-W3-AA1Q TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K5 TCGA-WE-A8ZN TCGA-WE-A8ZO 
       44.05       185.13        92.84        59.64        12.69        21.90 
TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 
       62.89        10.95        48.39         1.94        31.99        18.31 
TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-Z2-AA3S 
       18.35        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 
            42.265             47.970 
[1] "1.1 - 227.0 (42.3)" "0.0 - 346.5 (48.0)"
[1] "hr=" "1.1"
D75V2, survival
                    sevent
clus2                  0   1
  19P LOSS MUTATED    37  39
  19P LOSS WILD-TYPE 133 148
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                76                281 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                39                148 
$`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-D3-A8GV TCGA-D9-A148 TCGA-D9-A1X3 TCGA-D9-A3Z3 
      152.75       117.17       167.70       151.53        18.12        22.29 
TCGA-D9-A6EA TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I5 TCGA-DA-A1I7 
       25.18        76.57        36.03        20.38       120.00        73.84 
TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A95Y TCGA-EB-A44R TCGA-EB-A5UL TCGA-EE-A17X 
       53.92        65.92        14.14        10.36        29.29        29.82 
TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29D TCGA-EE-A29H TCGA-EE-A29X TCGA-EE-A2A0 
      168.26        13.55        13.97        64.64        17.92        46.82 
TCGA-EE-A2GM TCGA-EE-A2MG TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AB 
       75.48       103.20       248.65       162.48        71.21       122.73 
TCGA-EE-A3AD TCGA-EE-A3J5 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-ER-A19B TCGA-ER-A19C 
       28.77        36.95        53.19        27.35        98.40        48.89 
TCGA-ER-A19Q TCGA-ER-A19T TCGA-ER-A2NH TCGA-ER-A3EV TCGA-FR-A44A TCGA-FR-A69P 
       50.89         8.88        32.05        46.98       174.21        15.72 
TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZQ TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A4FB 
       32.75        47.38       133.55        53.16        49.48        26.73 
TCGA-FS-A4FD TCGA-FW-A3TV TCGA-GF-A4EO TCGA-GN-A262 TCGA-GN-A268 TCGA-GN-A26A 
       80.68        13.51         7.23       139.89        62.79        32.48 
TCGA-GN-A4U3 TCGA-GN-A4U7 TCGA-W3-A825 TCGA-W3-AA1R TCGA-W3-AA1V TCGA-WE-A8JZ 
      121.91        10.42        63.02       111.09        42.08        24.03 
TCGA-WE-A8K1 TCGA-WE-A8ZM TCGA-YD-A9TA TCGA-YG-AA3P 
       49.05       101.33        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        77.56        22.95 
TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1IB TCGA-DA-A1IC 
      144.89       207.48       176.55        35.93        40.60        68.09 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-DA-A95V TCGA-DA-A95W 
       33.93        10.49       225.96        15.68        72.10        25.15 
TCGA-DA-A95X TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH 
       61.81        13.02        13.87        20.35        68.25        54.02 
TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 
       58.92         7.04        36.46        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-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E 
      151.27        91.56        63.35        85.08        78.97        63.78 
TCGA-EE-A29G TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
       72.07         2.60        56.84        18.61        56.42        66.74 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A2A1 
       14.47        61.28       369.93        25.87       195.02       115.96 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD 
       59.64        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 
      173.79       220.24        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-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-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MR 
      180.39       216.66       167.90        47.54        43.23       134.40 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG 
       53.26       124.31        64.04        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-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
       51.35       134.33       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-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
      162.08        49.48       148.18        79.99        43.82        23.34 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3PL 
       20.15        16.37        31.27       247.04        93.01        33.21 
TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 
       12.95       149.03        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        46.45        15.45         9.70 
TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZU 
       23.93       101.26        74.73        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-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        96.92 
TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A26D TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-GN-A4U9 
       10.13        64.44        48.00        39.35        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-QB-AA9O TCGA-RP-A690 TCGA-RP-A693 TCGA-RP-A694 
      297.90         7.23        18.05         0.20         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        17.95        58.98        70.52        63.22        11.80 
TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 
       35.80        49.51        12.16        40.41        21.40        24.99 
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 
            49.115             54.410 
[1] "7.2 - 248.7 (49.1)" "0.2 - 369.9 (54.4)"
[1] "hr=" "1.1"
D75V3, continuous
                    vv
clus                 I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  19P LOSS MUTATED             5       0       7        2        4        5
  19P LOSS WILD-TYPE           8       7      22       16       24       20
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  19P LOSS MUTATED           1         3         3        12          2
  19P LOSS WILD-TYPE        13        16        12        28         13
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  19P LOSS MUTATED           10         12        5
  19P LOSS WILD-TYPE         23         43       16
D75V4, multiclass
             clus
vv            19P LOSS MUTATED 19P LOSS WILD-TYPE
  I OR II NOS                5                  8
  STAGE 0                    0                  7
  STAGE I                    7                 22
  STAGE IA                   2                 16
  STAGE IB                   4                 24
  STAGE II                   5                 20
  STAGE IIA                  1                 13
  STAGE IIB                  3                 16
  STAGE IIC                  3                 12
  STAGE III                 12                 28
  STAGE IIIA                 2                 13
  STAGE IIIB                10                 23
  STAGE IIIC                12                 43
  STAGE IV                   5                 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
  19P LOSS MUTATED      14 17 14 17
  19P LOSS WILD-TYPE    50 56 64 53
D75V5, multiclass
       clus
vv      19P LOSS MUTATED 19P LOSS WILD-TYPE
  T0+T1               14                 50
  T2                  17                 56
  T3                  14                 64
  T4                  17                 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
  19P LOSS MUTATED    34  17  11  12
  19P LOSS WILD-TYPE 143  48  28  33
D75V6, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  N0               34                143
  N1               17                 48
  N2               11                 28
  N3               12                 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"
D75V7, binary
                    cls
clus                   0   1
  19P LOSS MUTATED    67   6
  19P LOSS WILD-TYPE 251  16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED     67    6
  19P LOSS WILD-TYPE  251   16
   clus
vv  19P LOSS MUTATED 19P LOSS WILD-TYPE
  0               67                251
  1                6                 16
[1] 2 2
[1] FALSE
D75V8, binary
                    cls
clus                   0   1
  19P LOSS MUTATED    29  16
  19P LOSS WILD-TYPE 105  74
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED     29   16
  19P LOSS WILD-TYPE  105   74
     clus
vv    19P LOSS MUTATED 19P LOSS WILD-TYPE
  NO                29                105
  YES               16                 74
[1] 2 2
[1] FALSE
D75V9, binary
                    cls
clus                   0   1
  19P LOSS MUTATED     9  68
  19P LOSS WILD-TYPE  38 251
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      9   68
  19P LOSS WILD-TYPE   38  251
     clus
vv    19P LOSS MUTATED 19P LOSS WILD-TYPE
  NO                 9                 38
  YES               68                251
[1] 2 2
[1] FALSE
D75V10, continuous
D75V11, binary
                    cls
clus                   0   1
  19P LOSS MUTATED    33  44
  19P LOSS WILD-TYPE 104 185
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED     33   44
  19P LOSS WILD-TYPE  104  185
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  FEMALE               33                104
  MALE                 44                185
[1] 2 2
[1] FALSE
D75V12, binary
                    cls
clus                   0   1
  19P LOSS MUTATED    61  16
  19P LOSS WILD-TYPE 256  31
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED     61   16
  19P LOSS WILD-TYPE  256   31
     clus
vv    19P LOSS MUTATED 19P LOSS WILD-TYPE
  NO                61                256
  YES               16                 31
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  19P LOSS MUTATED       1                         0    74
  19P LOSS WILD-TYPE     4                         1   278
D75V13, multiclass
                           clus
vv                          19P LOSS MUTATED 19P LOSS WILD-TYPE
  ASIAN                                    1                  4
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   74                278
[1] 3 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  74
  19P LOSS WILD-TYPE   6 277
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      1   74
  19P LOSS WILD-TYPE    6  277
                        clus
vv                       19P LOSS MUTATED 19P LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO               74                277
[1] 2 2
[1] FALSE

Clustering(76) Variable = 19Q LOSS MUTATION ANALYSIS
D76V1, survival
                    sevent
clus2                  0   1
  19Q LOSS MUTATED    28  20
  19Q LOSS WILD-TYPE  94 103
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                48                197 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                20                103 
$`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        76.34        95.51 
TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A95X TCGA-DA-A95Y TCGA-EE-A17X TCGA-EE-A20H 
       45.07        64.83        52.90        14.14        13.15       155.90 
TCGA-EE-A29D TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A2GO TCGA-EE-A2MG TCGA-EE-A2MM 
       12.99        63.12        47.74       118.32        94.19       145.45 
TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AB TCGA-EE-A3AD TCGA-ER-A19B 
      227.01       143.93        23.51       122.73         4.41        53.29 
TCGA-ER-A19C TCGA-ER-A3EV TCGA-FR-A44A TCGA-FS-A1ZJ TCGA-FS-A1ZT TCGA-FS-A1ZW 
       39.81        15.48       174.21        36.33        35.28        23.21 
TCGA-FS-A4FD TCGA-FW-A3TV TCGA-GF-A4EO TCGA-GN-A262 TCGA-GN-A268 TCGA-GN-A26A 
       80.68        11.54         6.05        53.29        42.48         7.59 
TCGA-GN-A4U3 TCGA-W3-A825 TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8ZM 
      120.53         1.97        92.84         1.15        59.64        65.42 

$`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        69.21 
TCGA-D9-A6EG TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1IC TCGA-DA-A3F2 
       22.85       138.67        53.65       150.61        58.85        30.44 
TCGA-DA-A3F5 TCGA-DA-A95V TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5SG TCGA-EB-A5SH 
      225.11        72.10        12.30         3.91        33.24        50.07 
TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 
       52.41        18.21        24.89        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-A29P TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A2 
       27.16        61.12       346.49       185.19       115.43        30.02 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ 
       77.98        26.14       239.11        12.95       201.60        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-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MR 
      209.79       171.85        63.25        89.26       104.78        25.08 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J3 
       53.26       124.31        64.04        54.51         6.28        67.89 
TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI 
      111.85        45.90         3.35       201.80        19.86       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-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        47.18       146.63        47.97        22.36 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3PL 
        4.70        16.87        10.95       173.29        68.52        32.05 
TCGA-ER-A42L TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FS-A1YW 
       74.47       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-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS 
       42.08        12.92         7.82        78.61       130.95       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 
       96.92        17.06        34.49        46.92        43.23        59.41 
TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A690 TCGA-RP-A693 
       85.05       297.01         7.23        18.05         0.20         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-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AA9Y 
       12.69        21.90        62.89        10.95        48.39         1.94 
TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-Z2-AA3S 
       31.99        18.31        18.35        28.21        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              47.18 
[1] "1.1 - 227.0 (46.7)" "0.0 - 346.5 (47.2)"
[1] "hr=" "1.2"
D76V2, survival
                    sevent
clus2                  0   1
  19Q LOSS MUTATED    34  38
  19Q LOSS WILD-TYPE 136 149
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                72                285 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                38                149 
$`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-D3-A8GV TCGA-D9-A148 
      135.75       107.15       152.75       117.17       167.70       151.53 
TCGA-D9-A1X3 TCGA-D9-A3Z3 TCGA-D9-A6EA TCGA-DA-A1HV TCGA-DA-A1I0 TCGA-DA-A1I5 
       18.12        22.29        25.18        76.57        20.38       120.00 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A95X TCGA-DA-A95Y TCGA-EB-A44R 
       73.84        53.92        65.92        61.81        14.14        10.36 
TCGA-EE-A17X TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29D TCGA-EE-A29H TCGA-EE-A29M 
       29.82       168.26        13.55        13.97        64.64        56.84 
TCGA-EE-A29S TCGA-EE-A29X TCGA-EE-A2GO TCGA-EE-A2MG TCGA-EE-A2MM TCGA-EE-A2MP 
       61.28        17.92       126.81       103.20       167.90       248.65 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AG TCGA-EE-A3JA 
      162.48        71.21       122.73        28.77        41.59        53.19 
TCGA-EE-A3JD TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19T TCGA-ER-A2NH TCGA-ER-A3EV 
       27.35        98.40        48.89         8.88        32.05        46.98 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZT TCGA-FS-A1ZW 
      174.21        15.72        32.75        47.38        53.16        49.48 
TCGA-FS-A4F2 TCGA-FS-A4FB TCGA-FS-A4FD TCGA-FW-A3TV TCGA-GF-A4EO TCGA-GN-A262 
       50.14        26.73        80.68        13.51         7.23       139.89 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A4U7 TCGA-W3-A825 
       62.79        32.48        48.00       121.91        10.42        63.02 
TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8ZM TCGA-YD-A9TA TCGA-YG-AA3P 
      105.04        49.05        61.15       101.33        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        77.56        22.95        36.03       144.89 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
      207.48       176.55        35.93        40.60        68.09        33.93 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-DA-A95V TCGA-DA-A95W TCGA-DA-A95Z 
       10.49       225.96        15.68        72.10        25.15        13.02 
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        29.29        58.92 
TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 
        7.04        36.46        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-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G 
       91.56        63.35        85.08        78.97        63.78        72.07 
TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29T 
        2.60        18.61        56.42        66.74        14.47       369.93 
TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 
       25.87       195.02        46.82       115.96        59.64        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       173.79       220.24 
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-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-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML 
      268.73        16.96       204.66        96.23       180.39       216.66 
TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AC 
       47.54        43.23       134.40        53.26       124.31        64.04 
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-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI 
       64.08        34.32       201.80        51.35       134.33       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-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        49.48 
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-A3ES TCGA-ER-A3ET TCGA-ER-A3PL TCGA-ER-A42K TCGA-ER-A42L 
       31.27       247.04        93.01        33.21        12.95       149.03 
TCGA-FR-A3YN TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC 
       92.98       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-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZK TCGA-FS-A1ZM 
       53.52        46.45        15.45         9.70        23.93       101.26 
TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZY 
       74.73       133.55        11.41       148.80        26.56        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-A4FC TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A5DY TCGA-GF-A3OT 
       54.41         0.20        22.92        55.59        19.30         9.90 
TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 
        2.04        15.78       117.93        96.92        10.13        64.44 
TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A8LL TCGA-GN-A9SD 
       39.35        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-A690 TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A828 TCGA-W3-AA1O 
        0.20         0.33         0.69       228.16       121.08         4.01 
TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1V TCGA-W3-AA1W TCGA-WE-A8JZ TCGA-WE-A8K6 
       69.07       111.09        42.08       219.16        24.03        17.95 
TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-A8ZY 
       58.98        70.52        63.22        11.80        35.80        49.51 
TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YD-A89C TCGA-YG-AA3O 
       12.16        40.41        21.40        24.99         6.90        37.94 
TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
       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 
            53.175             51.350 
[1] "7.2 - 248.7 (53.2)" "0.2 - 369.9 (51.4)"
[1] "hr=" "1.1"
D76V3, continuous
                    vv
clus                 I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  19Q LOSS MUTATED             3       0       9        2        6        4
  19Q LOSS WILD-TYPE          10       7      20       16       22       21
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  19Q LOSS MUTATED           1         3         4        10          2
  19Q LOSS WILD-TYPE        13        16        11        30         13
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  19Q LOSS MUTATED            8         10        6
  19Q LOSS WILD-TYPE         25         45       15
D76V4, multiclass
             clus
vv            19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  I OR II NOS                3                 10
  STAGE 0                    0                  7
  STAGE I                    9                 20
  STAGE IA                   2                 16
  STAGE IB                   6                 22
  STAGE II                   4                 21
  STAGE IIA                  1                 13
  STAGE IIB                  3                 16
  STAGE IIC                  4                 11
  STAGE III                 10                 30
  STAGE IIIA                 2                 13
  STAGE IIIB                 8                 25
  STAGE IIIC                10                 45
  STAGE IV                   6                 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
  19Q LOSS MUTATED      12 22 13 15
  19Q LOSS WILD-TYPE    52 51 65 55
D76V5, multiclass
       clus
vv      19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  T0+T1               12                 52
  T2                  22                 51
  T3                  13                 65
  T4                  15                 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 LOSS MUTATED    35  12  12  11
  19Q LOSS WILD-TYPE 142  53  27  34
D76V6, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  N0               35                142
  N1               12                 53
  N2               12                 27
  N3               11                 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"
D76V7, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED    61   7
  19Q LOSS WILD-TYPE 257  15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED     61    7
  19Q LOSS WILD-TYPE  257   15
   clus
vv  19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  0               61                257
  1                7                 15
[1] 2 2
[1] FALSE
D76V8, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED    29  15
  19Q LOSS WILD-TYPE 105  75
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED     29   15
  19Q LOSS WILD-TYPE  105   75
     clus
vv    19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  NO                29                105
  YES               15                 75
[1] 2 2
[1] FALSE
D76V9, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED     8  65
  19Q LOSS WILD-TYPE  39 254
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      8   65
  19Q LOSS WILD-TYPE   39  254
     clus
vv    19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  NO                 8                 39
  YES               65                254
[1] 2 2
[1] FALSE
D76V10, continuous
D76V11, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED    30  43
  19Q LOSS WILD-TYPE 107 186
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED     30   43
  19Q LOSS WILD-TYPE  107  186
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  FEMALE               30                107
  MALE                 43                186
[1] 2 2
[1] FALSE
D76V12, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED    59  14
  19Q LOSS WILD-TYPE 258  33
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED     59   14
  19Q LOSS WILD-TYPE  258   33
     clus
vv    19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  NO                59                258
  YES               14                 33
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  19Q LOSS MUTATED       1                         0    71
  19Q LOSS WILD-TYPE     4                         1   281
D76V13, multiclass
                           clus
vv                          19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  ASIAN                                    1                  4
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   71                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"
D76V14, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED     1  71
  19Q LOSS WILD-TYPE   6 280
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      1   71
  19Q LOSS WILD-TYPE    6  280
                        clus
vv                       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO               71                280
[1] 2 2
[1] FALSE

Clustering(77) Variable = 20P LOSS MUTATION ANALYSIS
D77V1, survival
                    sevent
clus2                  0   1
  20P LOSS MUTATED     9  10
  20P LOSS WILD-TYPE 113 113
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                19                226 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                10                113 
$`20P LOSS MUTATED`
TCGA-D3-A2JC TCGA-D3-A3CF TCGA-D3-A8GK TCGA-DA-A1HV TCGA-DA-A1I1 TCGA-DA-A95Y 
       86.30        16.96       120.00        76.34        53.65        14.14 
TCGA-EE-A29E TCGA-EE-A29G TCGA-ER-A19C TCGA-ER-A19H TCGA-ER-A19W TCGA-ER-A2NG 
        0.26        44.28        39.81       150.12       146.63        10.95 
TCGA-ER-A3PL TCGA-FS-A1ZE TCGA-FS-A4F4 TCGA-GN-A4U3 TCGA-W3-AA1W TCGA-WE-A8K5 
       32.05        42.08        66.67       120.53       185.13        59.64 
TCGA-YG-AA3O 
       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 
       69.21        22.85       138.67       150.61        95.51        45.07 
TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A95V TCGA-DA-A95X 
       64.83        58.85        30.44       225.11        72.10        52.90 
TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A6L9 
       12.30         3.91        33.24        50.07        52.41        18.21 
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-A20C TCGA-EE-A20H TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29H 
       75.55       155.90        75.22        76.14        12.99        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       115.43 
TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
       30.02        77.98        26.14       239.11        12.95       201.60 
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 
       89.26       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        64.04         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-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
      201.80        19.86       152.81        14.56        34.45         1.58 
TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19G 
       47.31         7.82         4.54        53.29        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        47.18 
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        68.52 
TCGA-ER-A3EV TCGA-ER-A42L TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7UA 
       15.48        74.47       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-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM 
      312.07        32.78        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-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TU 
        3.06        30.90       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        96.92        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-A690 TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 
       18.05         0.20         0.33       174.12         1.97       120.07 
TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1V TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8ZM 
       44.05        79.99         8.09        92.84         1.15        65.42 
TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AA9Y 
       12.69        21.90        62.89        10.95        48.39         1.94 
TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-Z2-AA3S 
       31.99        18.31        18.35        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 
             53.65              47.08 
[1] "0.3 - 185.1 (53.6)" "0.0 - 346.5 (47.1)"
[1] "hr=" "1"  
D77V2, survival
                    sevent
clus2                  0   1
  20P LOSS MUTATED    11  14
  20P LOSS WILD-TYPE 159 173
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                25                332 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                14                173 
$`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        76.57 
TCGA-DA-A1I1 TCGA-DA-A95Y TCGA-EE-A29E TCGA-EE-A29G TCGA-ER-A19C TCGA-ER-A19E 
      207.48        14.14        63.78        72.07        48.89        13.02 
TCGA-ER-A19H TCGA-ER-A19W TCGA-ER-A2NG TCGA-ER-A3PL TCGA-FS-A1ZE TCGA-FS-A1ZR 
      152.35       148.18        31.27        33.21        46.45        11.41 
TCGA-FS-A4F4 TCGA-GN-A4U3 TCGA-GN-A4U7 TCGA-W3-AA1W TCGA-WE-A8K5 TCGA-YG-AA3O 
       66.67       121.91        10.42       219.16        61.15        37.94 
TCGA-YG-AA3P 
       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-D3-A8GV TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX 
      117.17       167.70       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-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 
       77.56        22.95        36.03       144.89        20.38       176.55 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB 
       35.93       120.00        73.84        53.92        65.92        40.60 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-DA-A95V 
       68.09        33.93        10.49       225.96        15.68        72.10 
TCGA-DA-A95W TCGA-DA-A95X TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH 
       25.15        61.81        13.02        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        29.29        58.92         7.04        36.46 
TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 
       29.82        27.22         8.65        94.98        33.73        14.70 
TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F 
       26.89        68.15         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-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-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       115.96        59.64        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       173.79       220.24        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-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-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML 
      103.20        16.96       204.66        96.23       180.39       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        64.04        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-A3JB TCGA-EE-A3JD 
       36.95        64.08        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       134.33       152.81        31.40        35.44        13.94 
TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19F 
       50.76         9.17        77.75        98.40        12.59        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-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
       50.89        49.48         8.88        79.99        43.82        23.34 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
       20.15        16.37        32.05       247.04        93.01        46.98 
TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 
       12.95       149.03        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        96.92        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        48.00        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-A690 TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 
        7.23        18.05         0.20         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-AA21 TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN 
      105.04        24.03        49.05        17.95       101.33        58.98 
TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AA9Y 
       70.52        63.22        11.80        35.80        49.51        12.16 
TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YD-A89C TCGA-YD-A9TA TCGA-Z2-A8RT 
       40.41        21.40        24.99         6.90        49.18        27.58 
TCGA-Z2-AA3S TCGA-Z2-AA3V 
       96.99        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 
            61.150             52.255 
[1] "10.4 - 219.2 (61.1)" "0.2 - 369.9 (52.3)" 
[1] "hr=" "1"  
D77V3, continuous
                    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          13       7      28       17       27       21
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  20P LOSS MUTATED           1         1         2         3          1
  20P LOSS WILD-TYPE        13        18        13        37         14
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  20P LOSS MUTATED            2          3        3
  20P LOSS WILD-TYPE         31         52       18
D77V4, multiclass
             clus
vv            20P LOSS MUTATED 20P LOSS WILD-TYPE
  I OR II NOS                0                 13
  STAGE 0                    0                  7
  STAGE I                    1                 28
  STAGE IA                   1                 17
  STAGE IB                   1                 27
  STAGE II                   4                 21
  STAGE IIA                  1                 13
  STAGE IIB                  1                 18
  STAGE IIC                  2                 13
  STAGE III                  3                 37
  STAGE IIIA                 1                 14
  STAGE IIIB                 2                 31
  STAGE IIIC                 3                 52
  STAGE IV                   3                 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
  20P LOSS MUTATED       4  5  7  6
  20P LOSS WILD-TYPE    60 68 71 64
D77V5, multiclass
       clus
vv      20P LOSS MUTATED 20P LOSS WILD-TYPE
  T0+T1                4                 60
  T2                   5                 68
  T3                   7                 71
  T4                   6                 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
  20P LOSS MUTATED    11   2   4   4
  20P LOSS WILD-TYPE 166  63  35  41
D77V6, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  N0               11                166
  N1                2                 63
  N2                4                 35
  N3                4                 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"
D77V7, binary
                    cls
clus                   0   1
  20P LOSS MUTATED    21   3
  20P LOSS WILD-TYPE 297  19
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED     21    3
  20P LOSS WILD-TYPE  297   19
   clus
vv  20P LOSS MUTATED 20P LOSS WILD-TYPE
  0               21                297
  1                3                 19
[1] 2 2
[1] FALSE
D77V8, binary
                    cls
clus                   0   1
  20P LOSS MUTATED    12   6
  20P LOSS WILD-TYPE 122  84
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED     12    6
  20P LOSS WILD-TYPE  122   84
     clus
vv    20P LOSS MUTATED 20P LOSS WILD-TYPE
  NO                12                122
  YES                6                 84
[1] 2 2
[1] FALSE
D77V9, binary
                    cls
clus                   0   1
  20P LOSS MUTATED     3  23
  20P LOSS WILD-TYPE  44 296
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      3   23
  20P LOSS WILD-TYPE   44  296
     clus
vv    20P LOSS MUTATED 20P LOSS WILD-TYPE
  NO                 3                 44
  YES               23                296
[1] 2 2
[1] FALSE
D77V10, continuous
D77V11, binary
                    cls
clus                   0   1
  20P LOSS MUTATED     8  18
  20P LOSS WILD-TYPE 129 211
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      8   18
  20P LOSS WILD-TYPE  129  211
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  FEMALE                8                129
  MALE                 18                211
[1] 2 2
[1] FALSE
D77V12, binary
                    cls
clus                   0   1
  20P LOSS MUTATED    23   3
  20P LOSS WILD-TYPE 294  44
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED     23    3
  20P LOSS WILD-TYPE  294   44
     clus
vv    20P LOSS MUTATED 20P LOSS WILD-TYPE
  NO                23                294
  YES                3                 44
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  20P LOSS MUTATED       0                         0    24
  20P LOSS WILD-TYPE     5                         1   328
D77V13, multiclass
                           clus
vv                          20P LOSS MUTATED 20P LOSS WILD-TYPE
  ASIAN                                    0                  5
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   24                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"
D77V14, binary
                    cls
clus                   0   1
  20P LOSS MUTATED     2  23
  20P LOSS WILD-TYPE   5 328
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      2   23
  20P LOSS WILD-TYPE    5  328
                        clus
vv                       20P LOSS MUTATED 20P LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  5
  NOT HISPANIC OR LATINO               23                328
[1] 2 2
[1] FALSE

Clustering(78) Variable = 20Q LOSS MUTATION ANALYSIS
D78V1, survival
                    sevent
clus2                  0   1
  20Q LOSS MUTATED     2   4
  20Q LOSS WILD-TYPE 120 119
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 6                239 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 4                119 
$`20Q LOSS MUTATED`
TCGA-DA-A1I1 TCGA-EE-A29G TCGA-ER-A19C TCGA-FS-A1ZE TCGA-GN-A4U3 TCGA-WE-A8K5 
       53.65        44.28        39.81        42.08       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        69.21        22.85        76.34 
TCGA-DA-A1HY TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC 
      138.67       150.61        95.51        45.07        64.83        58.85 
TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A95V TCGA-DA-A95X TCGA-DA-A95Y TCGA-DA-A95Z 
       30.44       225.11        72.10        52.90        14.14        12.30 
TCGA-EB-A44Q TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X 
        3.91        33.24        50.07        52.41        18.21        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-A20H TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H 
      155.90        75.22        76.14        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       115.43 
TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
       30.02        77.98        26.14       239.11        12.95       201.60 
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 
       89.26       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        64.04         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-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
      201.80        19.86       152.81        14.56        34.45         1.58 
TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19G 
       47.31         7.82         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-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
       47.18       146.63        47.97        22.36         4.70        16.87 
TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42L 
       10.95       173.29        68.52        15.48        32.05        74.47 
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-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-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-A4U4 TCGA-GN-A4U8 
       96.92        17.06        42.48         7.59        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-A690 TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1Q 
        0.20         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        65.42 
TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AA9Y 
       12.69        21.90        62.89        10.95        48.39         1.94 
TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-Z2-AA3S 
       31.99        18.31        18.35        28.21        91.23 

  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
             39.81               0.00 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
            120.53             346.49 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
            48.965             47.180 
[1] "39.8 - 120.5 (49.0)" "0.0 - 346.5 (47.2)" 
[1] "hr=" "1.5"
D78V2, survival
                    sevent
clus2                  0   1
  20Q LOSS MUTATED     3   5
  20Q LOSS WILD-TYPE 167 182
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 8                349 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 5                182 
$`20Q LOSS MUTATED`
TCGA-DA-A1I1 TCGA-EE-A29G TCGA-ER-A19C TCGA-FS-A1ZE TCGA-GN-A4U3 TCGA-GN-A4U7 
      207.48        72.07        48.89        46.45       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-D3-A8GV TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A1X3 
      167.70       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        77.56 
TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 
       22.95        76.57        36.03       144.89        20.38       176.55 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB 
       35.93       120.00        73.84        53.92        65.92        40.60 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-DA-A95V 
       68.09        33.93        10.49       225.96        15.68        72.10 
TCGA-DA-A95W TCGA-DA-A95X TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A44R 
       25.15        61.81        14.14        13.02        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        29.29        58.92         7.04 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 
       36.46        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       115.96        59.64        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       173.79       220.24 
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 
      180.39       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 
       64.04        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       134.33       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        49.48 
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        93.01        46.98 
TCGA-ER-A3PL TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       33.21        12.95       149.03        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-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-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        96.92 
TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U4 
       10.13        64.44        62.79        32.48        48.00        39.35 
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-A690 
       65.88       368.78       297.90         7.23        18.05         0.20 
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-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ 
       49.05        17.95       101.33        58.98        70.52        63.22 
TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 
       11.80        35.80        49.51        12.16        40.41        21.40 
TCGA-WE-AAA4 TCGA-YD-A89C TCGA-YD-A9TA TCGA-YG-AA3O TCGA-Z2-A8RT TCGA-Z2-AA3S 
       24.99         6.90        49.18        37.94        27.58        96.99 
TCGA-Z2-AA3V 
       15.98 

  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
             10.42               0.20 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
            207.48             369.93 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
             55.02              53.16 
[1] "10.4 - 207.5 (55.0)" "0.2 - 369.9 (53.2)" 
[1] "hr=" "1.2"
D78V3, continuous
                    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          13       7      28       18       28       25
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  20Q LOSS MUTATED           0         1         1         2          1
  20Q LOSS WILD-TYPE        14        18        14        38         14
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  20Q LOSS MUTATED            0          1        2
  20Q LOSS WILD-TYPE         33         54       19
D78V4, multiclass
             clus
vv            20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  I OR II NOS                0                 13
  STAGE 0                    0                  7
  STAGE I                    1                 28
  STAGE IA                   0                 18
  STAGE IB                   0                 28
  STAGE II                   0                 25
  STAGE IIA                  0                 14
  STAGE IIB                  1                 18
  STAGE IIC                  1                 14
  STAGE III                  2                 38
  STAGE IIIA                 1                 14
  STAGE IIIB                 0                 33
  STAGE IIIC                 1                 54
  STAGE IV                   2                 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
  20Q LOSS MUTATED       1  3  1  3
  20Q LOSS WILD-TYPE    63 70 77 67
D78V5, multiclass
       clus
vv      20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  T0+T1                1                 63
  T2                   3                 70
  T3                   1                 77
  T4                   3                 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
  20Q LOSS MUTATED     2   1   2   2
  20Q LOSS WILD-TYPE 175  64  37  43
D78V6, multiclass
    clus
vv   20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  N0                2                175
  N1                1                 64
  N2                2                 37
  N3                2                 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"
D78V7, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     7   2
  20Q LOSS WILD-TYPE 311  20
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      7    2
  20Q LOSS WILD-TYPE  311   20
   clus
vv  20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  0                7                311
  1                2                 20
[1] 2 2
[1] FALSE
D78V8, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     6   1
  20Q LOSS WILD-TYPE 128  89
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      6    1
  20Q LOSS WILD-TYPE  128   89
     clus
vv    20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  NO                 6                128
  YES                1                 89
[1] 2 2
[1] FALSE
D78V9, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     1   8
  20Q LOSS WILD-TYPE  46 311
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      1    8
  20Q LOSS WILD-TYPE   46  311
     clus
vv    20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  NO                 1                 46
  YES                8                311
[1] 2 2
[1] FALSE
D78V10, continuous
D78V11, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     2   7
  20Q LOSS WILD-TYPE 135 222
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      2    7
  20Q LOSS WILD-TYPE  135  222
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  FEMALE                2                135
  MALE                  7                222
[1] 2 2
[1] FALSE
D78V12, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     8   1
  20Q LOSS WILD-TYPE 309  46
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      8    1
  20Q LOSS WILD-TYPE  309   46
     clus
vv    20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  NO                 8                309
  YES                1                 46
[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   344
D78V13, multiclass
                           clus
vv                          20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  ASIAN                                    0                  5
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                    8                344
[1] 3 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   6 343
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      1    8
  20Q LOSS WILD-TYPE    6  343
                        clus
vv                       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO                8                343
[1] 2 2
[1] FALSE

Clustering(79) Variable = 21Q LOSS MUTATION ANALYSIS
D79V1, survival
                    sevent
clus2                  0   1
  21Q LOSS MUTATED    24  19
  21Q LOSS WILD-TYPE  98 104
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                43                202 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                19                104 
$`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-DA-A95V TCGA-DA-A95Z TCGA-EE-A17Y 
       64.83        66.08        11.34        72.10        12.30        24.89 
TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29T TCGA-EE-A29W 
       62.37        20.38        44.28        63.12       346.49       185.19 
TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GO TCGA-EE-A2M6 TCGA-EE-A2MK 
       30.02        77.98        26.14       118.32       103.13        89.26 
TCGA-EE-A2MS TCGA-ER-A197 TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZM TCGA-FS-A1ZT 
      143.93         1.58        42.08         7.82        78.61        35.28 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FW-A5DY TCGA-GN-A262 TCGA-GN-A268 TCGA-GN-A4U3 
        4.47        23.21        19.30        53.29        42.48       120.53 
TCGA-GN-A9SD TCGA-OD-A75X TCGA-QB-AA9O TCGA-W3-AA1R TCGA-WE-A8ZQ TCGA-WE-A8ZY 
       59.41       297.01        18.05        79.99        62.89        48.39 
TCGA-YG-AA3O 
       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 
       69.21        22.85        76.34       138.67        53.65       150.61 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 
       95.51        45.07        64.83        58.85        30.44       225.11 
TCGA-DA-A95X TCGA-DA-A95Y TCGA-EB-A44Q TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN 
       52.90        14.14         3.91        33.24        50.07        52.41 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A182 TCGA-EE-A184 TCGA-EE-A20C TCGA-EE-A20H 
       18.21        13.15         0.00        67.50        75.55       155.90 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29M TCGA-EE-A29P 
       75.22        76.14        12.99         0.26        47.74        27.16 
TCGA-EE-A29Q TCGA-EE-A2A1 TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ 
       61.12       115.43       239.11        12.95       201.60        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-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-A2ML TCGA-EE-A2MM TCGA-EE-A2MP 
       94.19       171.85        63.25       104.78       145.45       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        64.04 
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-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 
        3.35       201.80        19.86       152.81        14.56        34.45 
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-A2NC TCGA-ER-A2ND 
       49.71        47.18       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        68.52        15.48        32.05 
TCGA-ER-A42L TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FR-A8YC 
       74.47       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-A1ZJ TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZY 
       32.78        12.92        36.33       130.95       136.27         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-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A264 
       55.59        11.54         9.90         6.05         1.91       117.93 
TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-GN-A8LK 
       96.92        17.06         7.59        34.49        46.92        43.23 
TCGA-LH-A9QB TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A825 
       85.05         7.23         0.20         0.33       174.12         1.97 
TCGA-W3-A828 TCGA-W3-AA1Q TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 
      120.07        44.05         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-AA9Y 
       59.64        65.42        12.69        21.90        10.95         1.94 
TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-Z2-AA3S 
       31.99        18.31        18.35        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 
            59.410             46.455 
[1] "1.6 - 346.5 (59.4)" "0.0 - 312.1 (46.5)"
[1] "hr=" "1.4"
D79V2, survival
                    sevent
clus2                  0   1
  21Q LOSS MUTATED    34  35
  21Q LOSS WILD-TYPE 136 152
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                69                288 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                35                152 
$`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-DA-A95V TCGA-DA-A95Z 
        7.10         9.90        25.18        20.38        72.10        13.02 
TCGA-EB-A44R TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A20B TCGA-EE-A20I 
       10.36        27.22        94.98        33.73       133.81        13.55 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X 
       72.07        64.64       369.93        25.87       195.02        17.92 
TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GI TCGA-EE-A2GO 
       59.64        86.14        59.28        67.43        48.72       126.81 
TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2MK TCGA-EE-A2MN TCGA-EE-A2MS TCGA-EE-A3AH 
       21.67       129.27       180.39        47.54       162.48       138.81 
TCGA-EE-A3J5 TCGA-EE-A3JA TCGA-ER-A197 TCGA-ER-A19E TCGA-FS-A1ZA TCGA-FS-A1ZE 
       36.95        53.19        13.94        13.02        27.72        46.45 
TCGA-FS-A1ZG TCGA-FS-A1ZM TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FW-A5DY 
        9.70       101.26        53.16        26.56        49.48        19.30 
TCGA-GN-A262 TCGA-GN-A266 TCGA-GN-A268 TCGA-GN-A4U3 TCGA-GN-A4U9 TCGA-GN-A9SD 
      139.89        10.13        62.79       121.91        22.13        59.41 
TCGA-OD-A75X TCGA-QB-AA9O TCGA-RP-A694 TCGA-W3-AA1O TCGA-W3-AA1R TCGA-WE-A8ZQ 
      297.90        18.05         0.69         4.01       111.09        63.22 
TCGA-WE-A8ZY TCGA-YD-A89C TCGA-YG-AA3O 
       49.51         6.90        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-D3-A8GV TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1X3 TCGA-D9-A3Z1 
      167.70       151.53        54.67         3.65        18.12        15.39 
TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW 
       22.29        18.44        77.56        22.95        76.57        36.03 
TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 
      144.89       207.48       176.55        35.93       120.00        73.84 
TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
       53.92        65.92        40.60        68.09        33.93        10.49 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-DA-A95W TCGA-DA-A95X TCGA-DA-A95Y TCGA-EB-A44Q 
      225.96        15.68        25.15        61.81        14.14        13.87 
TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV 
       20.35        68.25        54.02        29.29        58.92         7.04 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 
       36.46        29.82         8.65        14.70        26.89        68.15 
TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29B 
        4.96       151.27        91.56       168.26        63.35        85.08 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N 
       78.97        13.97        63.78         2.60        56.84        18.61 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A2A0 TCGA-EE-A2A1 
       56.42        66.74        14.47        61.28        46.82       115.96 
TCGA-EE-A2A5 TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK 
       39.29       340.14       173.79       220.24       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-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD 
       44.88        94.82        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-A2MM TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MT 
      216.66       167.90       248.65        43.23       134.40        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        64.04        28.77        54.51 
TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 
       13.81        41.59       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       134.33       152.81        31.40 
TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C 
       35.44        50.76         9.17        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        49.48         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        93.01        46.98        33.21 
TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 
       12.95       149.03        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-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZH 
        7.79        48.85       357.37        53.52        15.45        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-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-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 
       22.92        55.59        13.51         9.90         7.23         2.04 
TCGA-GF-A6C9 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A26D 
       15.78       117.93        96.92        64.44        32.48        48.00 
TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A8LK TCGA-GN-A8LL TCGA-HR-A2OG 
       39.35        10.42        48.89        50.10        21.37         0.23 
TCGA-HR-A2OH TCGA-LH-A9QB TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 TCGA-W3-A824 
       65.88       368.78         7.23         0.20         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        17.95       101.33        58.98 
TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 
       70.52        11.80        35.80        12.16        40.41        21.40 
TCGA-WE-AAA4 TCGA-YD-A9TA TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
       24.99        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 
             49.48              53.72 
[1] "0.7 - 369.9 (49.5)" "0.2 - 368.8 (53.7)"
[1] "hr=" "1"  
D79V3, continuous
                    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          10       4      26       13       24       19
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  21Q LOSS MUTATED           2         2         3        10          3
  21Q LOSS WILD-TYPE        12        17        12        30         12
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  21Q LOSS MUTATED            6          9        5
  21Q LOSS WILD-TYPE         27         46       16
D79V4, multiclass
             clus
vv            21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  I OR II NOS                3                 10
  STAGE 0                    3                  4
  STAGE I                    3                 26
  STAGE IA                   5                 13
  STAGE IB                   4                 24
  STAGE II                   6                 19
  STAGE IIA                  2                 12
  STAGE IIB                  2                 17
  STAGE IIC                  3                 12
  STAGE III                 10                 30
  STAGE IIIA                 3                 12
  STAGE IIIB                 6                 27
  STAGE IIIC                 9                 46
  STAGE IV                   5                 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 15
  21Q LOSS WILD-TYPE    54 62 64 55
D79V5, multiclass
       clus
vv      21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  T0+T1               10                 54
  T2                  11                 62
  T3                  14                 64
  T4                  15                 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 LOSS MUTATED    32  15   7   6
  21Q LOSS WILD-TYPE 145  50  32  39
D79V6, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  N0               32                145
  N1               15                 50
  N2                7                 32
  N3                6                 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"
D79V7, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED    60   5
  21Q LOSS WILD-TYPE 258  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     60    5
  21Q LOSS WILD-TYPE  258   17
   clus
vv  21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  0               60                258
  1                5                 17
[1] 2 2
[1] FALSE
D79V8, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED    28  17
  21Q LOSS WILD-TYPE 106  73
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     28   17
  21Q LOSS WILD-TYPE  106   73
     clus
vv    21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  NO                28                106
  YES               17                 73
[1] 2 2
[1] FALSE
D79V9, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED     8  62
  21Q LOSS WILD-TYPE  39 257
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      8   62
  21Q LOSS WILD-TYPE   39  257
     clus
vv    21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  NO                 8                 39
  YES               62                257
[1] 2 2
[1] FALSE
D79V10, continuous
D79V11, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED    28  42
  21Q LOSS WILD-TYPE 109 187
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     28   42
  21Q LOSS WILD-TYPE  109  187
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  FEMALE               28                109
  MALE                 42                187
[1] 2 2
[1] FALSE
D79V12, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED    62   8
  21Q LOSS WILD-TYPE 255  39
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     62    8
  21Q LOSS WILD-TYPE  255   39
     clus
vv    21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  NO                62                255
  YES                8                 39
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  21Q LOSS MUTATED       2                         1    65
  21Q LOSS WILD-TYPE     3                         0   287
D79V13, multiclass
                           clus
vv                          21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  ASIAN                                    2                  3
  BLACK OR AFRICAN AMERICAN                1                  0
  WHITE                                   65                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"
D79V14, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED     1  68
  21Q LOSS WILD-TYPE   6 283
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      1   68
  21Q LOSS WILD-TYPE    6  283
                        clus
vv                       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO               68                283
[1] 2 2
[1] FALSE

Clustering(80) Variable = 22Q LOSS MUTATION ANALYSIS
D80V1, survival
                    sevent
clus2                  0   1
  22Q LOSS MUTATED     9  16
  22Q LOSS WILD-TYPE 113 107
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                25                220 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                16                107 
$`22Q LOSS MUTATED`
TCGA-D3-A1Q3 TCGA-D3-A1Q8 TCGA-D3-A2JB TCGA-D3-A2JL TCGA-DA-A1I2 TCGA-DA-A95X 
       15.72        19.04       168.00       171.58       150.61        52.90 
TCGA-EE-A184 TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A2A6 TCGA-EE-A2GP TCGA-EE-A2MG 
       67.50        76.14         0.26        77.98         0.76        94.19 
TCGA-EE-A2MM TCGA-ER-A19D TCGA-ER-A19H TCGA-ER-A19P TCGA-FS-A1YW TCGA-FS-A1ZJ 
      145.45        11.47       150.12       120.76       171.78        36.33 
TCGA-FS-A1ZY TCGA-FS-A4F0 TCGA-GF-A4EO TCGA-GN-A4U3 TCGA-RP-A693 TCGA-W3-A825 
        5.29        30.90         6.05       120.53         0.33         1.97 
TCGA-WE-A8ZQ 
       62.89 

$`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        69.21 
TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I5 TCGA-DA-A1I7 
       22.85        76.34       138.67        53.65        95.51        45.07 
TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A95V TCGA-DA-A95Y 
       64.83        58.85        30.44       225.11        72.10        14.14 
TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A6L9 
       12.30         3.91        33.24        50.07        52.41        18.21 
TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A20C 
       13.15        24.89        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-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       115.43        30.02 
TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK 
       26.14       239.11        12.95       201.60        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-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-A2MP TCGA-EE-A2MR 
      171.85        63.25        89.26       104.78       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        64.04 
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-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 
        3.35       201.80        19.86       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-A19G TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A19S 
      151.46        99.06        59.84        42.48        49.71        47.18 
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-ER-A42L TCGA-FR-A44A 
      173.29        68.52        15.48        32.05        74.47       174.21 
TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FS-A1YY TCGA-FS-A1Z0 
      209.23        26.20         5.65        10.06        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        42.08        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-A1ZZ TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FD 
       23.21         3.06        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-A268 TCGA-GN-A26A TCGA-GN-A4U4 
      117.93        96.92        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-A690 TCGA-W3-A824 TCGA-W3-A828 TCGA-W3-AA1Q TCGA-W3-AA1R 
       18.05         0.20       174.12       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        65.42 
TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 
       12.69        21.90        10.95        48.39         1.94        31.99 
TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-Z2-AA3S 
       18.31        18.35        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 
             62.89              46.95 
[1] "0.3 - 171.8 (62.9)" "0.0 - 346.5 (47.0)"
[1] "hr=" "1.3"
D80V2, survival
                    sevent
clus2                  0   1
  22Q LOSS MUTATED    13  25
  22Q LOSS WILD-TYPE 157 162
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                38                319 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                25                162 
$`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-DA-A95X TCGA-EB-A44R 
       30.84       161.00        54.67       176.55        61.81        10.36 
TCGA-EE-A184 TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A2A6 TCGA-EE-A2GP TCGA-EE-A2MG 
       68.15        78.97        63.78        86.14        13.91       103.20 
TCGA-EE-A2MM TCGA-EE-A3JA TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19H TCGA-ER-A19P 
      167.90        53.19        12.59        13.02       152.35       162.08 
TCGA-ER-A19T TCGA-FR-A8YD TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1ZJ TCGA-FS-A1ZY 
        8.88        36.26       216.92        48.59        47.38        27.09 
TCGA-FS-A4F0 TCGA-GF-A4EO TCGA-GN-A266 TCGA-GN-A4U3 TCGA-GN-A4U9 TCGA-RP-A693 
       77.82         7.23        10.13       121.91        22.13         0.33 
TCGA-W3-A825 TCGA-WE-A8ZQ 
       63.02        63.22 

$`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-D3-A8GV TCGA-D9-A148 
      152.75        29.06       129.63       117.17       167.70       151.53 
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        77.56        22.95        76.57        36.03 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 
      144.89        20.38       207.48        35.93       120.00        73.84 
TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
       53.92        65.92        40.60        68.09        33.93        10.49 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-DA-A95V TCGA-DA-A95W TCGA-DA-A95Y TCGA-DA-A95Z 
      225.96        15.68        72.10        25.15        14.14        13.02 
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        29.29        58.92 
TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 
        7.04        36.46        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-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29D 
       91.56       168.26        13.55        63.35        85.08        13.97 
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-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-A2GB 
       17.92        46.82       115.96        59.64        39.29        59.28 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       67.43       340.14       173.79       220.24        48.72       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-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-A2MN TCGA-EE-A2MP 
      204.66        96.23       180.39       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        64.04        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-EE-A3JI TCGA-ER-A193 
      201.80        27.35        51.35       134.33       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-A19F TCGA-ER-A19G TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
       48.89        26.37       268.93         6.44       131.51        61.05 
TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
       44.05        50.89        49.48       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-ER-A42K TCGA-ER-A42L TCGA-FR-A3YN 
       93.01        46.98        33.21        12.95       149.03        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        46.45 
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        96.92        64.44        62.79        32.48        48.00 
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-A690 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1Q 
        0.20         0.69       228.16       121.08         4.01        69.07 
TCGA-W3-AA1R TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K1 
      111.09        42.08       219.16       105.04        24.03        49.05 
TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT 
       61.15        17.95       101.33        58.98        70.52        11.80 
TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 
       35.80        49.51        12.16        40.41        21.40        24.99 
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 

  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 
             61.94              50.76 
[1] "0.3 - 216.9 (61.9)" "0.2 - 369.9 (50.8)"
[1] "hr=" "1.3"
D80V3, continuous
                    vv
clus                 I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  22Q LOSS MUTATED             3       1       4        2        7        2
  22Q LOSS WILD-TYPE          10       6      25       16       21       23
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  22Q LOSS MUTATED           1         2         2         2          0
  22Q LOSS WILD-TYPE        13        17        13        38         15
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  22Q LOSS MUTATED            4          2        3
  22Q LOSS WILD-TYPE         29         53       18
D80V4, multiclass
             clus
vv            22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  I OR II NOS                3                 10
  STAGE 0                    1                  6
  STAGE I                    4                 25
  STAGE IA                   2                 16
  STAGE IB                   7                 21
  STAGE II                   2                 23
  STAGE IIA                  1                 13
  STAGE IIB                  2                 17
  STAGE IIC                  2                 13
  STAGE III                  2                 38
  STAGE IIIA                 0                 15
  STAGE IIIB                 4                 29
  STAGE IIIC                 2                 53
  STAGE IV                   3                 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
  22Q LOSS MUTATED       5 12  6  7
  22Q LOSS WILD-TYPE    59 61 72 63
D80V5, multiclass
       clus
vv      22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  T0+T1                5                 59
  T2                  12                 61
  T3                   6                 72
  T4                   7                 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
  22Q LOSS MUTATED    26   5   2   4
  22Q LOSS WILD-TYPE 151  60  37  41
D80V6, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  N0               26                151
  N1                5                 60
  N2                2                 37
  N3                4                 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"
D80V7, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED    35   3
  22Q LOSS WILD-TYPE 283  19
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     35    3
  22Q LOSS WILD-TYPE  283   19
   clus
vv  22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  0               35                283
  1                3                 19
[1] 2 2
[1] FALSE
D80V8, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED    18   6
  22Q LOSS WILD-TYPE 116  84
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     18    6
  22Q LOSS WILD-TYPE  116   84
     clus
vv    22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  NO                18                116
  YES                6                 84
[1] 2 2
[1] FALSE
D80V9, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED     5  34
  22Q LOSS WILD-TYPE  42 285
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      5   34
  22Q LOSS WILD-TYPE   42  285
     clus
vv    22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  NO                 5                 42
  YES               34                285
[1] 2 2
[1] FALSE
D80V10, continuous
D80V11, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED    15  24
  22Q LOSS WILD-TYPE 122 205
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     15   24
  22Q LOSS WILD-TYPE  122  205
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  FEMALE               15                122
  MALE                 24                205
[1] 2 2
[1] FALSE
D80V12, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED    34   5
  22Q LOSS WILD-TYPE 283  42
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     34    5
  22Q LOSS WILD-TYPE  283   42
     clus
vv    22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  NO                34                283
  YES                5                 42
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  22Q LOSS MUTATED       1                         1    36
  22Q LOSS WILD-TYPE     4                         0   316
D80V13, multiclass
                           clus
vv                          22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  ASIAN                                    1                  4
  BLACK OR AFRICAN AMERICAN                1                  0
  WHITE                                   36                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"
D80V14, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED     1  38
  22Q LOSS WILD-TYPE   6 313
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      1   38
  22Q LOSS WILD-TYPE    6  313
                        clus
vv                       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO               38                313
[1] 2 2
[1] FALSE

Clustering(81) Variable = XP LOSS MUTATION ANALYSIS
D81V1, survival
                   sevent
clus2                0  1
  XP LOSS MUTATED   29 41
  XP LOSS WILD-TYPE 93 82
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               70               175 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               41                82 
$`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        95.51 
TCGA-DA-A95X TCGA-EE-A17Y TCGA-EE-A20C TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29H 
       52.90        24.89        75.55        76.14        12.99        63.12 
TCGA-EE-A29Q TCGA-EE-A2A2 TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2MF TCGA-EE-A2MK 
       61.12        30.02         0.20        71.31       209.79        89.26 
TCGA-EE-A2MM TCGA-EE-A2MS TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3J8 TCGA-EE-A3JH 
      145.45       143.93         4.41         6.28         3.35        19.86 
TCGA-ER-A193 TCGA-ER-A19G TCGA-ER-A19L TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A3ET 
       14.56       151.46        99.06         4.70        16.87        68.52 
TCGA-FR-A7U8 TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1ZC TCGA-FS-A1ZF TCGA-FS-A1ZG 
       26.20       171.78        49.74       312.07        12.92         7.82 
TCGA-FS-A1ZJ TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 
       36.33       130.95       136.27         3.06        30.90        66.67 
TCGA-FS-A4F9 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A268 
       13.28        55.59        11.54         1.91        53.29        42.48 
TCGA-GN-A8LK TCGA-LH-A9QB TCGA-OD-A75X TCGA-W3-AA1R TCGA-W3-AA1V TCGA-WE-A8ZM 
       43.23        85.05       297.01        79.99         8.09        65.42 
TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-Z2-AA3S 
       10.95        48.39         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        69.21        22.85 
TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I7 TCGA-DA-A1IA 
       76.34       138.67        53.65       150.61        45.07        64.83 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A95V TCGA-DA-A95Y TCGA-DA-A95Z 
       58.85        30.44       225.11        72.10        14.14        12.30 
TCGA-EB-A44Q TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X 
        3.91        33.24        50.07        52.41        18.21        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 
      115.43        77.98        26.14       239.11        12.95       201.60 
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        64.04        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-A2NG TCGA-ER-A3ES 
       47.18       146.63        47.97        22.36        10.95       173.29 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7UA 
       15.48        32.05        74.47       174.21       209.23         5.65 
TCGA-FR-A8YC TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZD TCGA-FS-A1ZE 
       10.06       195.98         8.35        27.62        32.78        42.08 
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-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GN-A264 TCGA-GN-A265 
       80.68        19.30         9.90         6.05       117.93        96.92 
TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-GN-A9SD 
       17.06         7.59       120.53        34.49        46.92        59.41 
TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A690 TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A825 
        7.23        18.05         0.20         0.33       174.12         1.97 
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-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 
       12.69        21.90        62.89        31.99        18.31        18.35 
TCGA-YG-AA3O 
       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            47.310 
[1] "0.2 - 312.1 (45.1)" "0.0 - 346.5 (47.3)"
[1] "hr=" "1.3"
D81V2, survival
                   sevent
clus2                 0   1
  XP LOSS MUTATED    42  52
  XP LOSS WILD-TYPE 128 135
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               94               263 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               52               135 
$`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-DA-A95X 
       22.29        18.44        36.03       120.00        53.92        61.81 
TCGA-EE-A17Y TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29C 
       27.22         4.96       151.27        91.56        13.55        78.97 
TCGA-EE-A29D TCGA-EE-A29H TCGA-EE-A29Q TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A2 
       13.97        64.64        66.74        25.87        17.92        59.64 
TCGA-EE-A2GC TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2MF TCGA-EE-A2MK TCGA-EE-A2MM 
       67.43        42.77        81.21       268.73       180.39       167.90 
TCGA-EE-A2MS TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J8 TCGA-EE-A3JH 
      162.48        28.77        13.81       138.81        34.32       134.33 
TCGA-ER-A193 TCGA-ER-A19E TCGA-ER-A19G TCGA-ER-A19L TCGA-ER-A2ND TCGA-ER-A2NE 
       31.40        13.02       268.93       131.51        23.34        20.15 
TCGA-ER-A2NF TCGA-ER-A2NH TCGA-ER-A3ET TCGA-FR-A7U8 TCGA-FS-A1YW TCGA-FS-A1YY 
       16.37        32.05        93.01        27.85       216.92       228.59 
TCGA-FS-A1ZC TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZQ 
      357.37        15.45         9.70        32.75        47.38       133.55 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F9 
       11.41       148.80        27.02        77.82        66.67        34.03 
TCGA-FS-A4FB TCGA-FW-A3TU TCGA-FW-A3TV TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 
       26.73        55.59        13.51         2.04        15.78       139.89 
TCGA-GN-A268 TCGA-GN-A8LK TCGA-GN-A8LL TCGA-LH-A9QB TCGA-OD-A75X TCGA-W3-AA1R 
       62.79        50.10        21.37       368.78       297.90       111.09 
TCGA-W3-AA1V TCGA-WE-A8JZ TCGA-WE-A8ZM TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AA9Y 
       42.08        24.03       101.33        11.80        49.51        12.16 
TCGA-YD-A9TA TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S 
       49.18        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-D3-A8GV TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX 
       29.06       117.17       167.70        54.67         3.65         7.10 
TCGA-D9-A3Z1 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV 
       15.39         9.90        25.18        77.56        22.95        76.57 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I7 
      144.89        20.38       207.48       176.55        35.93        73.84 
TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 
       65.92        40.60        68.09        33.93        10.49       225.96 
TCGA-DA-A3F8 TCGA-DA-A95V TCGA-DA-A95W TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q 
       15.68        72.10        25.15        14.14        13.02        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        29.29        58.92 
TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 
        7.04        36.46        29.82         8.65        94.98        33.73 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A20B TCGA-EE-A20H TCGA-EE-A29A 
       14.70        26.89        68.15       133.81       168.26        63.35 
TCGA-EE-A29B TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N 
       85.08        63.78        72.07         2.60        56.84        18.61 
TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A0 
       56.42        14.47        61.28       369.93       195.02        46.82 
TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE 
      115.96        39.29        86.14        59.28       340.14       173.79 
TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
      220.24        48.72       107.38        54.74        79.66        75.48 
TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 
      102.12       126.81        13.91        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-A2MI TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MN 
      103.20        16.96       204.66        96.23       216.66        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-A3AE TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3J4 
      122.73        64.04        54.51        41.59       172.18       127.20 
TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE 
       36.95        64.08        53.19       201.80        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-A19C TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19H TCGA-ER-A19J 
       98.40        48.89        12.59        26.37       152.35         6.44 
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        49.48         8.88 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3EV 
      148.18        79.99        43.82        31.27       247.04        46.98 
TCGA-ER-A3PL TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       33.21        12.95       149.03        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        46.45        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        96.92        10.13        64.44 
TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 
       32.48        48.00       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-A690 TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 
        0.20         0.33         0.69       228.16        63.02       121.08 
TCGA-W3-AA1O TCGA-W3-AA1Q TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8K5 
        4.01        69.07       219.16       105.04        49.05        61.15 
TCGA-WE-A8K6 TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZX TCGA-WE-AAA0 
       17.95        58.98        70.52        63.22        35.80        40.41 
TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YD-A89C TCGA-YG-AA3O TCGA-Z2-AA3V 
       21.40        24.99         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 
            52.01             53.16 
[1] "2.0 - 368.8 (52.0)" "0.2 - 369.9 (53.2)"
[1] "hr=" "1"  
D81V3, continuous
                   vv
clus                I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  XP LOSS MUTATED             5       3       5        2       10        8
  XP LOSS WILD-TYPE           8       4      24       16       18       17
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  XP LOSS MUTATED           2        10         4         6          3
  XP LOSS WILD-TYPE        12         9        11        34         12
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  XP LOSS MUTATED            6         16        7
  XP LOSS WILD-TYPE         27         39       14
D81V4, multiclass
             clus
vv            XP LOSS MUTATED XP LOSS WILD-TYPE
  I OR II NOS               5                 8
  STAGE 0                   3                 4
  STAGE I                   5                24
  STAGE IA                  2                16
  STAGE IB                 10                18
  STAGE II                  8                17
  STAGE IIA                 2                12
  STAGE IIB                10                 9
  STAGE IIC                 4                11
  STAGE III                 6                34
  STAGE IIIA                3                12
  STAGE IIIB                6                27
  STAGE IIIC               16                39
  STAGE IV                  7                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
  XP LOSS MUTATED      15 16 23 20
  XP LOSS WILD-TYPE    49 57 55 50
D81V5, multiclass
       clus
vv      XP LOSS MUTATED XP LOSS WILD-TYPE
  T0+T1              15                49
  T2                 16                57
  T3                 23                55
  T4                 20                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
  XP LOSS MUTATED    49  18   5  12
  XP LOSS WILD-TYPE 128  47  34  33
D81V6, multiclass
    clus
vv   XP LOSS MUTATED XP LOSS WILD-TYPE
  N0              49               128
  N1              18                47
  N2               5                34
  N3              12                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"
D81V7, binary
                   cls
clus                  0   1
  XP LOSS MUTATED    80   8
  XP LOSS WILD-TYPE 238  14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED     80    8
  XP LOSS WILD-TYPE  238   14
   clus
vv  XP LOSS MUTATED XP LOSS WILD-TYPE
  0              80               238
  1               8                14
[1] 2 2
[1] FALSE
D81V8, binary
                   cls
clus                  0   1
  XP LOSS MUTATED    32  26
  XP LOSS WILD-TYPE 102  64
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED     32   26
  XP LOSS WILD-TYPE  102   64
     clus
vv    XP LOSS MUTATED XP LOSS WILD-TYPE
  NO               32               102
  YES              26                64
[1] 2 2
[1] FALSE
D81V9, binary
                   cls
clus                  0   1
  XP LOSS MUTATED     9  88
  XP LOSS WILD-TYPE  38 231
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED      9   88
  XP LOSS WILD-TYPE   38  231
     clus
vv    XP LOSS MUTATED XP LOSS WILD-TYPE
  NO                9                38
  YES              88               231
[1] 2 2
[1] FALSE
D81V10, continuous
D81V11, binary
                   cls
clus                  0   1
  XP LOSS MUTATED    46  51
  XP LOSS WILD-TYPE  91 178
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED     46   51
  XP LOSS WILD-TYPE   91  178
        clus
vv       XP LOSS MUTATED XP LOSS WILD-TYPE
  FEMALE              46                91
  MALE                51               178
[1] 2 2
[1] FALSE
D81V12, binary
                   cls
clus                  0   1
  XP LOSS MUTATED    81  16
  XP LOSS WILD-TYPE 236  31
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED     81   16
  XP LOSS WILD-TYPE  236   31
     clus
vv    XP LOSS MUTATED XP LOSS WILD-TYPE
  NO               81               236
  YES              16                31
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  XP LOSS MUTATED       1                         0    94
  XP LOSS WILD-TYPE     4                         1   258
D81V13, multiclass
                           clus
vv                          XP LOSS MUTATED XP LOSS WILD-TYPE
  ASIAN                                   1                 4
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  94               258
[1] 3 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  92
  XP LOSS WILD-TYPE   5 259
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED      2   92
  XP LOSS WILD-TYPE    5  259
                        clus
vv                       XP LOSS MUTATED XP LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                 5
  NOT HISPANIC OR LATINO              92               259
[1] 2 2
[1] FALSE

Clustering(82) Variable = XQ LOSS MUTATION ANALYSIS
D82V1, survival
                   sevent
clus2                0  1
  XQ LOSS MUTATED   28 37
  XQ LOSS WILD-TYPE 94 86
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               65               180 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               37                86 
$`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-DA-A95X TCGA-EE-A17Y 
       10.78        16.90        18.44        95.51        52.90        24.89 
TCGA-EE-A20C TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29H TCGA-EE-A29Q TCGA-EE-A2A2 
       75.55        76.14        12.99        63.12        61.12        30.02 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2MF TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MS 
        0.20        71.31       209.79        89.26       145.45       143.93 
TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3J8 TCGA-ER-A193 TCGA-ER-A19G TCGA-ER-A19L 
        4.41         6.28         3.35        14.56       151.46        99.06 
TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A3ET TCGA-FR-A7U8 TCGA-FS-A1YW TCGA-FS-A1YY 
       16.87        10.95        68.52        26.20       171.78        49.74 
TCGA-FS-A1ZC TCGA-FS-A1ZF TCGA-FS-A1ZJ TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZZ 
      312.07        12.92        36.33       130.95       136.27         3.06 
TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F9 TCGA-FW-A3TU TCGA-GF-A6C8 TCGA-GN-A262 
       30.90        66.67        13.28        55.59         1.91        53.29 
TCGA-GN-A4U3 TCGA-GN-A8LK TCGA-LH-A9QB TCGA-OD-A75X TCGA-W3-AA1R TCGA-W3-AA1V 
      120.53        43.23        85.05       297.01        79.99         8.09 
TCGA-W3-AA1W TCGA-WE-A8ZM TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-Z2-AA3S 
      185.13        65.42        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 
       69.21        22.85        76.34       138.67        53.65       150.61 
TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A95V 
       45.07        64.83        58.85        30.44       225.11        72.10 
TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN 
       14.14        12.30         3.91        33.24        50.07        52.41 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A184 
       18.21        13.15        62.37        20.38         0.00        67.50 
TCGA-EE-A20H TCGA-EE-A29B TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29M TCGA-EE-A29P 
      155.90        75.22         0.26        44.28        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       115.43        77.98        26.14       239.11 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
       12.95       201.60        68.65        10.62        32.48        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-A2MC TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2ML 
        5.75        23.77        94.19       171.85        63.25       104.78 
TCGA-EE-A2MP TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB 
      227.01        25.08        23.51        53.26       124.31       122.73 
TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3JB 
       64.04        54.51        67.89       111.85        45.90       201.80 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 
       19.86       152.81        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-A19M 
        4.54        53.29        39.81        11.47       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        47.18       146.63        47.97 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A3ES TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42L 
       22.36         4.70       173.29        15.48        32.05        74.47 
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-A1ZG TCGA-FS-A1ZM TCGA-FS-A1ZT 
       27.62        32.78        42.08         7.82        78.61        35.28 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F8 TCGA-FS-A4FD TCGA-FW-A3TV 
        4.47        23.21         5.29       173.19        80.68        11.54 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 
       19.30         9.90         6.05       117.93        96.92        17.06 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-GN-A9SD TCGA-QB-A6FS 
       42.48         7.59        34.49        46.92        59.41         7.23 
TCGA-QB-AA9O TCGA-RP-A690 TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 
       18.05         0.20         0.33       174.12         1.97       120.07 
TCGA-W3-AA1Q TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8ZN TCGA-WE-A8ZO 
       44.05        92.84         1.15        59.64        12.69        21.90 
TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O 
       62.89        10.95        31.99        18.31        18.35        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 
           52.900            45.945 
[1] "0.2 - 312.1 (52.9)" "0.0 - 346.5 (45.9)"
[1] "hr=" "1.1"
D82V2, survival
                   sevent
clus2                 0   1
  XQ LOSS MUTATED    40  49
  XQ LOSS WILD-TYPE 130 138
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               89               268 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               49               138 
$`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-DA-A95X TCGA-EE-A17Y TCGA-EE-A185 
       36.03       120.00        53.92        61.81        27.22         4.96 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29H 
      151.27        91.56        13.55        78.97        13.97        64.64 
TCGA-EE-A29Q TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A2 TCGA-EE-A2GC TCGA-EE-A2GR 
       66.74        25.87        17.92        59.64        67.43        42.77 
TCGA-EE-A2GS TCGA-EE-A2MF TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MS TCGA-EE-A3AD 
       81.21       268.73       180.39       167.90       162.48        28.77 
TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J8 TCGA-ER-A193 TCGA-ER-A19E TCGA-ER-A19G 
       13.81       138.81        34.32        31.40        13.02       268.93 
TCGA-ER-A19L TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ET 
      131.51        20.15        16.37        31.27        32.05        93.01 
TCGA-FR-A7U8 TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1ZA TCGA-FS-A1ZC TCGA-FS-A1ZF 
       27.85       216.92       228.59        27.72       357.37        15.45 
TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZZ 
       32.75        47.38       133.55        11.41       148.80        27.02 
TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FW-A3TU TCGA-GF-A6C8 
       77.82        66.67        34.03        26.73        55.59         2.04 
TCGA-GN-A262 TCGA-GN-A4U3 TCGA-GN-A8LK TCGA-GN-A8LL TCGA-LH-A9QB TCGA-OD-A75X 
      139.89       121.91        50.10        21.37       368.78       297.90 
TCGA-W3-AA1R TCGA-W3-AA1V TCGA-W3-AA1W TCGA-WE-A8JZ TCGA-WE-A8ZM TCGA-WE-A8ZY 
      111.09        42.08       219.16        24.03       101.33        49.51 
TCGA-WE-AA9Y TCGA-YD-A9TA TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S 
       12.16        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-D3-A8GV TCGA-D9-A149 
      161.00       152.75        29.06       117.17       167.70        54.67 
TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC 
        3.65         7.10        15.39         9.90        25.18        77.56 
TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 
       22.95        76.57       144.89        20.38       207.48       176.55 
TCGA-DA-A1I4 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
       35.93        73.84        65.92        40.60        68.09        33.93 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-DA-A95V TCGA-DA-A95W TCGA-DA-A95Y 
       10.49       225.96        15.68        72.10        25.15        14.14 
TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH 
       13.02        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 
       29.29        58.92         7.04        36.46        29.82         8.65 
TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A20B 
       94.98        33.73        14.70        26.89        68.15       133.81 
TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29L 
      168.26        63.35        85.08        63.78        72.07         2.60 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T 
       56.84        18.61        56.42        14.47        61.28       369.93 
TCGA-EE-A29W TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
      195.02        46.82       115.96        39.29        86.14        59.28 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
      340.14       173.79       220.24        48.72       107.38        54.74 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GT 
       79.66        75.48       102.12       126.81        13.91        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-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ 
       47.28       103.27       103.20        16.96       204.66        96.23 
TCGA-EE-A2ML TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MT 
      216.66        47.54       248.65        43.23       134.40        71.21 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3AG 
       53.26       124.31       122.73        64.04        54.51        41.59 
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-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 
       27.35        51.35       134.33       152.81        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-A19F TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P 
       26.37       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        49.48         8.88       148.18        79.99        43.82 
TCGA-ER-A2ND TCGA-ER-A3ES TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-ER-A42L 
       23.34       247.04        46.98        33.21        12.95       149.03 
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        46.45         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        96.92        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        48.00        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-A690 
       59.41         0.23        65.88         7.23        18.05         0.20 
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-AA21 TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZN 
       69.07       105.04        49.05        61.15        17.95        58.98 
TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-AAA0 TCGA-WE-AAA3 
       70.52        63.22        11.80        35.80        40.41        21.40 
TCGA-WE-AAA4 TCGA-YD-A89C TCGA-YG-AA3O TCGA-Z2-AA3V 
       24.99         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 
           53.920            52.255 
[1] "2.0 - 368.8 (53.9)" "0.2 - 369.9 (52.3)"
[1] "hr=" "1.1"
D82V3, continuous
                   vv
clus                I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  XQ LOSS MUTATED             6       3       5        2        9        9
  XQ LOSS WILD-TYPE           7       4      24       16       19       16
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  XQ LOSS MUTATED           2         9         3         6          2
  XQ LOSS WILD-TYPE        12        10        12        34         13
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  XQ LOSS MUTATED            6         15        6
  XQ LOSS WILD-TYPE         27         40       15
D82V4, multiclass
             clus
vv            XQ LOSS MUTATED XQ LOSS WILD-TYPE
  I OR II NOS               6                 7
  STAGE 0                   3                 4
  STAGE I                   5                24
  STAGE IA                  2                16
  STAGE IB                  9                19
  STAGE II                  9                16
  STAGE IIA                 2                12
  STAGE IIB                 9                10
  STAGE IIC                 3                12
  STAGE III                 6                34
  STAGE IIIA                2                13
  STAGE IIIB                6                27
  STAGE IIIC               15                40
  STAGE IV                  6                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
  XQ LOSS MUTATED      13 15 24 18
  XQ LOSS WILD-TYPE    51 58 54 52
D82V5, multiclass
       clus
vv      XQ LOSS MUTATED XQ LOSS WILD-TYPE
  T0+T1              13                51
  T2                 15                58
  T3                 24                54
  T4                 18                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
  XQ LOSS MUTATED    48  17   4  12
  XQ LOSS WILD-TYPE 129  48  35  33
D82V6, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  N0              48               129
  N1              17                48
  N2               4                35
  N3              12                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"
D82V7, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED    78   7
  XQ LOSS WILD-TYPE 240  15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     78    7
  XQ LOSS WILD-TYPE  240   15
   clus
vv  XQ LOSS MUTATED XQ LOSS WILD-TYPE
  0              78               240
  1               7                15
[1] 2 2
[1] FALSE
D82V8, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED    31  25
  XQ LOSS WILD-TYPE 103  65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     31   25
  XQ LOSS WILD-TYPE  103   65
     clus
vv    XQ LOSS MUTATED XQ LOSS WILD-TYPE
  NO               31               103
  YES              25                65
[1] 2 2
[1] FALSE
D82V9, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED     8  85
  XQ LOSS WILD-TYPE  39 234
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      8   85
  XQ LOSS WILD-TYPE   39  234
     clus
vv    XQ LOSS MUTATED XQ LOSS WILD-TYPE
  NO                8                39
  YES              85               234
[1] 2 2
[1] FALSE
D82V10, continuous
D82V11, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED    42  51
  XQ LOSS WILD-TYPE  95 178
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     42   51
  XQ LOSS WILD-TYPE   95  178
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  FEMALE              42                95
  MALE                51               178
[1] 2 2
[1] FALSE
D82V12, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED    76  17
  XQ LOSS WILD-TYPE 241  30
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     76   17
  XQ LOSS WILD-TYPE  241   30
     clus
vv    XQ LOSS MUTATED XQ LOSS WILD-TYPE
  NO               76               241
  YES              17                30
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  XQ LOSS MUTATED       1                         0    90
  XQ LOSS WILD-TYPE     4                         1   262
D82V13, multiclass
                           clus
vv                          XQ LOSS MUTATED XQ LOSS WILD-TYPE
  ASIAN                                   1                 4
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  90               262
[1] 3 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  88
  XQ LOSS WILD-TYPE   5 263
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      2   88
  XQ LOSS WILD-TYPE    5  263
                        clus
vv                       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                 5
  NOT HISPANIC OR LATINO              88               263
[1] 2 2
[1] FALSE
