[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/22507034/SKCM-TM.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/SKCM-TM/22533835/transformed.cor.cli.txt"

nPatients in clinical file=368, in cluster file=367, common to both=367
[1]  82 367
[1] "1P GAIN MUTATION ANALYSIS"
[1] 3
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               93               274 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               93               274 
[1] "1Q GAIN MUTATION ANALYSIS"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              173               194 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              173               194 
[1] "2P GAIN MUTATION ANALYSIS"
[1] 3
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               67               300 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               67               300 
[1] "2Q GAIN MUTATION ANALYSIS"
[1] 3
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               65               302 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               65               302 
[1] "3P GAIN MUTATION ANALYSIS"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               64               303 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               64               303 
[1] "3Q GAIN MUTATION ANALYSIS"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               74               293 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               74               293 
[1] "4P GAIN MUTATION ANALYSIS"
[1] 3
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               57               310 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               57               310 
[1] "4Q GAIN MUTATION ANALYSIS"
[1] 3
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               48               319 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               48               319 
[1] "5P GAIN MUTATION ANALYSIS"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               74               293 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               74               293 
[1] "5Q GAIN MUTATION ANALYSIS"
[1] 3
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               52               315 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               52               315 
[1] "6P GAIN MUTATION ANALYSIS"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
              148               219 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
              148               219 
[1] "6Q GAIN MUTATION ANALYSIS"
[1] 3
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               50               317 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               50               317 
[1] "7P GAIN MUTATION ANALYSIS"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              204               163 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              204               163 
[1] "7Q GAIN MUTATION ANALYSIS"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              199               168 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              199               168 
[1] "8P GAIN MUTATION ANALYSIS"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
              123               244 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
              123               244 
[1] "8Q GAIN MUTATION ANALYSIS"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              172               195 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              172               195 
[1] "9P GAIN MUTATION ANALYSIS"
[1] 3
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               16               351 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               16               351 
[1] "9Q GAIN MUTATION ANALYSIS"
[1] 3
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               20               347 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               20               347 
[1] "10P GAIN MUTATION ANALYSIS"
[1] 3
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                12                355 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                12                355 
[1] "10Q GAIN MUTATION ANALYSIS"
[1] 3
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 3                364 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 3                364 
[1] "11P GAIN MUTATION ANALYSIS"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                34                333 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                34                333 
[1] "11Q GAIN MUTATION ANALYSIS"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                28                339 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                28                339 
[1] "12P GAIN MUTATION ANALYSIS"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                64                303 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                64                303 
[1] "12Q GAIN MUTATION ANALYSIS"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                40                327 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                40                327 
[1] "13Q GAIN MUTATION ANALYSIS"
[1] 3
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                92                275 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                92                275 
[1] "14Q GAIN MUTATION ANALYSIS"
[1] 3
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                42                325 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                42                325 
[1] "15Q GAIN MUTATION ANALYSIS"
[1] 3
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                84                283 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                84                283 
[1] "16P GAIN MUTATION ANALYSIS"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                57                310 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                57                310 
[1] "16Q GAIN MUTATION ANALYSIS"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                45                322 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                45                322 
[1] "17P GAIN MUTATION ANALYSIS"
[1] 3
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                40                327 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                40                327 
[1] "17Q GAIN MUTATION ANALYSIS"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                67                300 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                67                300 
[1] "18P GAIN MUTATION ANALYSIS"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                56                311 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                56                311 
[1] "18Q GAIN MUTATION ANALYSIS"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                45                322 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                45                322 
[1] "19P GAIN MUTATION ANALYSIS"
[1] 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                58                309 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                58                309 
[1] "19Q GAIN MUTATION ANALYSIS"
[1] 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                56                311 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                56                311 
[1] "20P GAIN MUTATION ANALYSIS"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               147                220 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               147                220 
[1] "20Q GAIN MUTATION ANALYSIS"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               180                187 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               180                187 
[1] "21Q GAIN MUTATION ANALYSIS"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                67                300 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                67                300 
[1] "22Q GAIN MUTATION ANALYSIS"
[1] 3
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
               126                241 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
               126                241 
[1] "XP GAIN MUTATION ANALYSIS"
[1] 3
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               42               325 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               42               325 
[1] "XQ GAIN MUTATION ANALYSIS"
[1] 3
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               44               323 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               44               323 
[1] "1P LOSS MUTATION ANALYSIS"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               51               316 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               51               316 
[1] "1Q LOSS MUTATION ANALYSIS"
[1] 3
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               27               340 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               27               340 
[1] "2P LOSS MUTATION ANALYSIS"
[1] 3
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               50               317 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               50               317 
[1] "2Q LOSS MUTATION ANALYSIS"
[1] 3
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               51               316 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               51               316 
[1] "3P LOSS MUTATION ANALYSIS"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               60               307 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               60               307 
[1] "3Q LOSS MUTATION ANALYSIS"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               51               316 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               51               316 
[1] "4P LOSS MUTATION ANALYSIS"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               80               287 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               80               287 
[1] "4Q LOSS MUTATION ANALYSIS"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               85               282 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               85               282 
[1] "5P LOSS MUTATION ANALYSIS"
[1] 3
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               79               288 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               79               288 
[1] "5Q LOSS MUTATION ANALYSIS"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               97               270 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               97               270 
[1] "6P LOSS MUTATION ANALYSIS"
[1] 3
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               70               297 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               70               297 
[1] "6Q LOSS MUTATION ANALYSIS"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
              172               195 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
              172               195 
[1] "7P LOSS MUTATION ANALYSIS"
[1] 3
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               18               349 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               18               349 
[1] "7Q LOSS MUTATION ANALYSIS"
[1] 3
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               17               350 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               17               350 
[1] "8P LOSS MUTATION ANALYSIS"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               66               301 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               66               301 
[1] "8Q LOSS MUTATION ANALYSIS"
[1] 3
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               25               342 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               25               342 
[1] "9P LOSS MUTATION ANALYSIS"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              235               132 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              235               132 
[1] "9Q LOSS MUTATION ANALYSIS"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
              185               182 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
              185               182 
[1] "10P LOSS MUTATION ANALYSIS"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
               204                163 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
               204                163 
[1] "10Q LOSS MUTATION ANALYSIS"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
               224                143 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
               224                143 
[1] "11P LOSS MUTATION ANALYSIS"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
               126                241 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
               126                241 
[1] "11Q LOSS MUTATION ANALYSIS"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
               149                218 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
               149                218 
[1] "12P LOSS MUTATION ANALYSIS"
[1] 3
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                61                306 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                61                306 
[1] "12Q LOSS MUTATION ANALYSIS"
[1] 3
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                68                299 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                68                299 
[1] "13Q LOSS MUTATION ANALYSIS"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                82                285 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                82                285 
[1] "14Q LOSS MUTATION ANALYSIS"
[1] 3
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               112                255 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               112                255 
[1] "15Q LOSS MUTATION ANALYSIS"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                54                313 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                54                313 
[1] "16P LOSS MUTATION ANALYSIS"
[1] 3
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                69                298 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                69                298 
[1] "16Q LOSS MUTATION ANALYSIS"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
               105                262 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
               105                262 
[1] "17P LOSS MUTATION ANALYSIS"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               124                243 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               124                243 
[1] "17Q LOSS MUTATION ANALYSIS"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                62                305 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                62                305 
[1] "18P LOSS MUTATION ANALYSIS"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
               104                263 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
               104                263 
[1] "18Q LOSS MUTATION ANALYSIS"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               100                267 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               100                267 
[1] "19P LOSS MUTATION ANALYSIS"
[1] 3
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                77                290 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                77                290 
[1] "19Q LOSS MUTATION ANALYSIS"
[1] 3
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                73                294 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                73                294 
[1] "20P LOSS MUTATION ANALYSIS"
[1] 3
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                25                342 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                25                342 
[1] "20Q LOSS MUTATION ANALYSIS"
[1] 3
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 9                358 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 9                358 
[1] "21Q LOSS MUTATION ANALYSIS"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                70                297 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                70                297 
[1] "22Q LOSS MUTATION ANALYSIS"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                39                328 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                39                328 
[1] "XP LOSS MUTATION ANALYSIS"
[1] 3
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               96               271 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               96               271 
[1] "XQ LOSS MUTATION ANALYSIS"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               92               275 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               92               275 
[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 367 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=190,	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=164,	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 367 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 81 67 
[1] "table(vv)"
vv
T0+T1    T2    T3    T4 
   64    73    81    67 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
T0 T1 T2 T3 T4 
23 41 73 81 67 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


T0+T1    T2    T3    T4 
   64    73    81    67 
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   31 33
  1P GAIN WILD-TYPE 97 91
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               64               188 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               33                91 
$`1P GAIN MUTATED`
TCGA-D3-A8GI TCGA-EE-A180 TCGA-EE-A2MR TCGA-FR-A729 TCGA-3N-A9WD TCGA-D3-A2J8 
       13.41        31.96       134.40       216.43        12.99        62.86 
TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A3C6 TCGA-D3-A3MR 
       15.75        86.30       171.58        64.83        58.06        90.21 
TCGA-D3-A8GD TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GM TCGA-D3-A8GR TCGA-D9-A3Z1 
       23.61       179.97       120.00        70.62        36.53        15.02 
TCGA-D9-A6EC TCGA-DA-A1I7 TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EE-A17Y TCGA-EE-A181 
       69.21        60.10        14.14        12.30        24.89        20.38 
TCGA-EE-A183 TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29T TCGA-EE-A29W 
       26.24        12.99         0.26        44.28       346.49       185.19 
TCGA-EE-A2A2 TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2M6 
       30.02        18.35        93.63         0.76        71.31       103.13 
TCGA-EE-A2MJ TCGA-EE-A2MM TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3J7 TCGA-ER-A199 
       63.25       145.45        53.26       122.73        45.90         7.82 
TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19Q TCGA-ER-A3ET TCGA-ER-A3PL TCGA-FR-A3YN 
       11.47       184.60        49.71        68.52        32.05         4.50 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A7UA TCGA-FS-A1Z0 TCGA-FS-A1ZQ TCGA-FS-A1ZU 
      174.21         4.14         5.65       195.98       130.95         4.47 
TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A8LK TCGA-W3-A828 TCGA-W3-AA1W 
       17.06         7.59       120.53        43.23       120.07       185.13 
TCGA-WE-A8K1 TCGA-WE-A8ZY TCGA-WE-AAA0 TCGA-YG-AA3O 
       47.54        48.39        37.32        28.21 

$`1P GAIN WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A20H TCGA-EE-A2GD 
        9.76        62.07        38.76        33.24       166.75       269.03 
TCGA-EE-A2GO TCGA-EE-A3JD TCGA-ER-A193 TCGA-FW-A3R5 TCGA-WE-A8K5 TCGA-WE-AAA3 
       52.90        27.35        19.04        36.95        52.73         7.40 
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-A2JB TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JO TCGA-D3-A2JP 
       45.99       168.00       107.61        36.30        66.08        43.53 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MU 
      140.98        40.01        59.70        24.53         9.34        23.67 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T 
      173.85        30.67       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-A8GL 
       42.05        45.70       177.86       124.08        78.21        69.53 
TCGA-D3-A8GP TCGA-D9-A1X3 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6EG TCGA-DA-A1HV 
      135.12        10.78        16.90        18.44        22.85        76.34 
TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1IA TCGA-DA-A1IC 
      138.67        68.68       150.61       110.53        64.83        58.85 
TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-DA-A95V TCGA-DA-A95W TCGA-DA-A95X 
       30.44       225.11         8.71        72.10         0.76        65.03 
TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A182 
        3.91        16.41        52.41        18.21        13.15         0.00 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29H TCGA-EE-A29M 
       75.55        79.20        75.22        76.14        47.41        47.74 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A2A1 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE 
       27.16        61.12       115.43        77.98        26.14        12.95 
TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GR TCGA-EE-A2GU 
      201.60        68.65        10.62        32.48         0.20        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-A2MP TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AA 
       89.26       104.78       227.01       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-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 
        3.35       168.85        19.86       135.98        34.45        10.49 
TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M 
        4.54        53.29        39.81       150.12        99.06        59.84 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
       42.51       120.76        47.18       146.63        73.05        22.36 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3EV 
        4.70        16.87        10.19        28.67       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-A1ZG TCGA-FS-A1ZJ 
       27.62       312.07        32.78        43.92         7.82        36.33 
TCGA-FS-A1ZM TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ 
       78.61       136.27        35.28        23.21         5.29         3.06 
TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TU 
       30.90        66.67       173.19        13.28        80.68        55.59 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 
       11.54        19.30         9.90        18.25         1.91        53.29 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A268 TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-GN-A9SD 
      117.93        96.92        42.48        34.49        46.92        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-AA1Q TCGA-W3-AA1R TCGA-W3-AA1V TCGA-W3-AA21 TCGA-WE-A8ZM 
        1.97        44.05        79.99         8.09        92.84        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        24.99 
TCGA-XV-AB01 TCGA-Z2-AA3S 
        6.61        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 
           47.965            45.845 
[1] "0.3 - 346.5 (48.0)" "0.0 - 312.1 (45.8)"
[1] "hr=" "1"  
D1V2, survival
                   sevent
clus2                 0   1
  1P GAIN MUTATED    41  50
  1P GAIN WILD-TYPE 125 142
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               91               267 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               50               142 
$`1P GAIN MUTATED`
TCGA-D3-A8GI TCGA-EE-A180 TCGA-EE-A29L TCGA-EE-A2MR TCGA-FR-A729 TCGA-3N-A9WD 
       58.52        94.98         2.60       134.40       220.80        12.99 
TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JL TCGA-D3-A2JN 
       65.49       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-A8GJ 
      130.72        58.06       103.59       137.92        23.61       241.38 
TCGA-D3-A8GK TCGA-D3-A8GM TCGA-D3-A8GR TCGA-D9-A1JW TCGA-D9-A3Z1 TCGA-D9-A6E9 
      170.20       107.15       129.63         3.65        15.39         9.90 
TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1I0 TCGA-DA-A1I7 TCGA-DA-A95Y TCGA-DA-A95Z 
       25.18        77.56        20.38        88.87        14.14        13.02 
TCGA-EB-A5UL TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A29D 
       29.29        27.22        33.73        26.89       133.81        13.97 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A2 
       63.78        72.07       369.93       195.02        17.92        59.64 
TCGA-EE-A2GI TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2M6 
       48.72        75.48       102.12        13.91        81.21       129.27 
TCGA-EE-A2MD TCGA-EE-A2MJ TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MU 
       47.28        96.23       167.90        47.54        43.23        53.26 
TCGA-EE-A3AB TCGA-EE-A3AG TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-ER-A199 TCGA-ER-A19D 
      122.73        41.59        64.08        53.19         9.17        12.59 
TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19Q TCGA-ER-A3ET TCGA-ER-A3PL TCGA-ER-A42K 
       26.37       302.07        50.89        93.01        33.21        12.95 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A7UA TCGA-FS-A1YX TCGA-FS-A1Z0 
       92.98       174.21        15.72        38.27        48.59       202.65 
TCGA-FS-A1ZH TCGA-FS-A1ZQ TCGA-FS-A1ZU TCGA-FS-A4F5 TCGA-GF-A6C9 TCGA-GN-A266 
       32.75       133.55        26.56        28.73        15.78        10.13 
TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A8LK TCGA-HR-A2OG TCGA-HR-A2OH 
       64.44        32.48       121.91        50.10         0.23        65.88 
TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1W TCGA-WE-A8K1 TCGA-WE-A8ZY TCGA-WE-AAA0 
      121.08         4.01       219.16        49.05        49.51        40.41 
TCGA-YG-AA3O 
       37.94 

$`1P GAIN WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EB-A5SG TCGA-EB-A5SH 
       27.65        62.07        46.32        13.87        68.25        54.02 
TCGA-EE-A184 TCGA-EE-A20H TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A3JD TCGA-ER-A193 
       68.15       168.26       340.14       126.81        27.35        31.40 
TCGA-ER-A198 TCGA-FS-A1ZF TCGA-FW-A3R5 TCGA-QB-AA9O TCGA-WE-A8K5 TCGA-WE-AAA3 
       50.76        15.45        36.95        18.05        61.15        21.40 
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-A2J9 TCGA-D3-A2JB TCGA-D3-A2JG 
       95.74        43.43       103.10        23.77       168.00       113.52 
TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C7 TCGA-D3-A3CB 
       42.08        12.10        66.08        59.57        46.98       166.52 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MU TCGA-D3-A3MV 
       86.93        60.23        24.53         9.34        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-A5GR TCGA-D3-A5GS 
       63.81        26.89       125.79       135.75       178.32        18.18 
TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GE TCGA-D3-A8GL TCGA-D3-A8GN 
      125.19        30.84        79.59        26.43        89.13       161.00 
TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GS TCGA-D3-A8GV TCGA-D9-A148 TCGA-D9-A149 
      152.75        29.06       117.17       167.70       151.53        54.67 
TCGA-D9-A1JX TCGA-D9-A1X3 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6EG TCGA-DA-A1HV 
        7.10        18.12        22.29        18.44        22.95        76.57 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
       36.03       144.89       222.51       176.55        35.93       135.02 
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-A95X TCGA-EB-A44Q 
      225.96        43.36        72.10        37.35        73.94        13.87 
TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X 
       10.36        20.35        58.92         7.04        36.46        29.82 
TCGA-EE-A17Z TCGA-EE-A182 TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I 
        8.65        14.70         4.96       151.27        91.56        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-A2GE 
      115.96        39.29        86.14        59.28        67.43       173.79 
TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GR TCGA-EE-A2GT 
      220.24       107.38        54.74        79.66        42.77        44.88 
TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2ME 
       94.82        21.67        28.83        19.76        61.51       103.27 
TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML 
      268.73       103.20        16.96       204.66       180.39       216.66 
TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AD 
      248.65       162.48        71.21       124.31        64.04        28.77 
TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 
       54.51        13.81       138.81       172.18       127.20        36.95 
TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 
       34.32       201.80        51.35       134.33       152.81        35.44 
TCGA-ER-A197 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19E TCGA-ER-A19H 
       13.94        77.75        98.40        48.89        13.02       152.35 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19S 
        6.44       131.51        61.05        44.09       162.08        49.48 
TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
        8.88       148.18       105.07        43.82        23.34        20.15 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3EV TCGA-ER-A42L 
       28.83        48.99        41.56       247.04        46.98       149.03 
TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW 
       27.85        18.77        34.82        36.26       104.42       216.92 
TCGA-FS-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-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZK 
      357.37        53.52        46.45         9.70        47.38        23.93 
TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZW 
      101.26        74.73        11.41       148.80        53.16        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-A3TU 
       34.03        26.73        54.41        80.68        17.46        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        19.43         2.04       139.89 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A268 TCGA-GN-A26D TCGA-GN-A4U4 TCGA-GN-A4U7 
      117.93        96.92        62.79        48.00        39.35        10.42 
TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LL TCGA-GN-A9SD TCGA-LH-A9QB TCGA-OD-A75X 
       48.89        22.13        21.37        59.41       368.78       297.90 
TCGA-QB-A6FS TCGA-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-AA1Q TCGA-W3-AA1R TCGA-W3-AA1V TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K6 
       69.07       111.09        42.08       105.04        24.03        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-AA9Y TCGA-WE-AAA4 TCGA-XV-AB01 TCGA-YD-A89C TCGA-YD-A9TA TCGA-YG-AA3P 
       12.16        24.99        13.25         6.90        49.18        14.43 
TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
       27.58        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 
            53.19             51.35 
[1] "0.2 - 369.9 (53.2)" "0.2 - 368.8 (51.4)"
[1] "hr=" "1"  
D1V3, continuous
                   vv
clus                I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  1P GAIN MUTATED          3       4       7        5       10        8
  1P GAIN WILD-TYPE       10       3      22       13       18       18
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  1P GAIN MUTATED           3         2         3        10          9
  1P GAIN WILD-TYPE        11        17        12        29          6
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  1P GAIN MUTATED            6         11        4
  1P GAIN WILD-TYPE         29         43       17
D1V4, multiclass
            clus
vv           1P GAIN MUTATED 1P GAIN WILD-TYPE
  I/II NOS                 3                10
  STAGE 0                  4                 3
  STAGE I                  7                22
  STAGE IA                 5                13
  STAGE IB                10                18
  STAGE II                 8                18
  STAGE IIA                3                11
  STAGE IIB                2                17
  STAGE IIC                3                12
  STAGE III               10                29
  STAGE IIIA               9                 6
  STAGE IIIB               6                29
  STAGE IIIC              11                43
  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      15 18 23 18
  1P GAIN WILD-TYPE    49 55 58 49
D1V5, multiclass
       clus
vv      1P GAIN MUTATED 1P GAIN WILD-TYPE
  T0+T1              15                49
  T2                 18                55
  T3                 23                58
  T4                 18                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
  1P GAIN MUTATED    50  17  10   9
  1P GAIN WILD-TYPE 127  48  29  36
D1V6, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  N0              50               127
  N1              17                48
  N2              10                29
  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"
D1V7, binary
                   cls
clus                  0   1
  1P GAIN MUTATED    83   4
  1P GAIN WILD-TYPE 236  18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     83    4
  1P GAIN WILD-TYPE  236   18
   clus
vv  1P GAIN MUTATED 1P GAIN WILD-TYPE
  0              83               236
  1               4                18
[1] 2 2
[1] FALSE
D1V8, binary
                   cls
clus                 0  1
  1P GAIN MUTATED   41 21
  1P GAIN WILD-TYPE 93 69
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     41   21
  1P GAIN WILD-TYPE   93   69
     clus
vv    1P GAIN MUTATED 1P GAIN WILD-TYPE
  NO               41                93
  YES              21                69
[1] 2 2
[1] FALSE
D1V9, binary
                   cls
clus                  0   1
  1P GAIN MUTATED    11  82
  1P GAIN WILD-TYPE  36 238
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     11   82
  1P GAIN WILD-TYPE   36  238
     clus
vv    1P GAIN MUTATED 1P GAIN WILD-TYPE
  NO               11                36
  YES              82               238
[1] 2 2
[1] FALSE
D1V10, continuous
D1V11, binary
                   cls
clus                  0   1
  1P GAIN MUTATED    33  60
  1P GAIN WILD-TYPE 105 169
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     33   60
  1P GAIN WILD-TYPE  105  169
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  FEMALE              33               105
  MALE                60               169
[1] 2 2
[1] FALSE
D1V12, binary
                   cls
clus                  0   1
  1P GAIN MUTATED    75  18
  1P GAIN WILD-TYPE 244  29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     75   18
  1P GAIN WILD-TYPE  244   29
     clus
vv    1P GAIN MUTATED 1P GAIN WILD-TYPE
  NO               75               244
  YES              18                29
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  1P GAIN MUTATED       1                         0    89
  1P GAIN WILD-TYPE     4                         1   264
D1V13, multiclass
                           clus
vv                          1P GAIN MUTATED 1P GAIN WILD-TYPE
  ASIAN                                   1                 4
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  89               264
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V14, binary
                   cls
clus                  0   1
  1P GAIN MUTATED     2  88
  1P GAIN WILD-TYPE   5 264
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      2   88
  1P GAIN WILD-TYPE    5  264
                        clus
vv                       1P GAIN MUTATED 1P GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 5
  NOT HISPANIC OR LATINO              88               264
[1] 2 2
[1] FALSE

Clustering(2) Variable = 1Q GAIN MUTATION ANALYSIS
D2V1, survival
                   sevent
clus2                0  1
  1Q GAIN MUTATED   61 59
  1Q GAIN WILD-TYPE 67 65
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              120               132 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               59                65 
$`1Q GAIN MUTATED`
TCGA-D3-A2JE TCGA-D3-A8GI TCGA-EE-A180 TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR 
        9.76        13.41        31.96       269.03        52.90       134.40 
TCGA-FR-A729 TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1QB TCGA-D3-A2J8 
      216.43        12.99         8.42        15.72        62.60        62.86 
TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A3C6 TCGA-D3-A3CE 
       15.75        86.30       171.58        64.83        58.06        59.70 
TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A5GL 
        9.34        90.21        23.67        31.76        62.70        42.05 
TCGA-D3-A5GN TCGA-D3-A5GU TCGA-D3-A8GD TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL 
       45.70       124.08        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-A1I1 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC 
       22.85        68.68       110.53        60.10        64.83        58.85 
TCGA-DA-A3F5 TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A5UN TCGA-EE-A17Y TCGA-EE-A181 
      225.11        14.14        12.30        52.41        24.89        20.38 
TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29M TCGA-EE-A29T 
       75.22        12.99         0.26        44.28        47.74       346.49 
TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GE TCGA-EE-A2GH 
      185.19       115.43        30.02        77.98        12.95       201.60 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M7 TCGA-EE-A2MJ 
       18.35        93.63        71.31        81.99        15.25        63.25 
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-A3J7 TCGA-EE-A3JH TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19D TCGA-ER-A19G 
       45.90        19.86        10.49         7.82        11.47       184.60 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A2ND TCGA-ER-A2NF TCGA-ER-A3ET TCGA-ER-A3PL 
      120.76        49.71         4.70        10.19        68.52        32.05 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FS-A1Z0 
        4.50       174.21         4.14         5.65        10.06       195.98 
TCGA-FS-A1Z3 TCGA-FS-A1ZC TCGA-FS-A1ZQ TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZY 
        8.35       312.07       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        47.54 
TCGA-WE-A8ZO TCGA-WE-A8ZY TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-XV-AB01 TCGA-YG-AA3O 
       21.90        48.39        37.32        24.99         6.61        28.21 

$`1Q GAIN WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A20H TCGA-EE-A3JD TCGA-ER-A193 
       62.07        38.76        33.24       166.75        27.35        19.04 
TCGA-FW-A3R5 TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-3N-A9WC TCGA-BF-AAP0 TCGA-D3-A1Q4 
       36.95        52.73         7.40        60.46        14.83        31.89 
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A2J6 
      110.93        49.35       133.25        19.04        76.41        25.64 
TCGA-D3-A2J7 TCGA-D3-A2JB TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JO TCGA-D3-A2JP 
       45.99       168.00       107.61        36.30        66.08        43.53 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51J 
      140.98        40.01        24.53       173.85        30.67       144.46 
TCGA-D3-A51T TCGA-D3-A5GR TCGA-D3-A8GC TCGA-D9-A1X3 TCGA-D9-A4Z6 TCGA-DA-A1HV 
       11.34       177.86        78.21        10.78        18.44        76.34 
TCGA-DA-A1HY TCGA-DA-A1I2 TCGA-DA-A3F2 TCGA-DA-A3F8 TCGA-DA-A95V TCGA-DA-A95W 
      138.67       150.61        30.44         8.71        72.10         0.76 
TCGA-DA-A95X TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A182 
       65.03         3.91        16.41        18.21        13.15         0.00 
TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29H TCGA-EE-A29P 
       26.24        75.55        79.20        76.14        47.41        27.16 
TCGA-EE-A29Q TCGA-EE-A2GB TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GP 
       61.12        26.14        68.65        10.62        32.48         0.76 
TCGA-EE-A2GR TCGA-EE-A2M6 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MG 
        0.20       103.13         5.75        23.77       209.79        94.19 
TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A3AA 
      171.85        89.26       104.78       145.45       227.01       124.31 
TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J8 TCGA-EE-A3JB 
       54.51         6.28        67.89       111.85         3.35       168.85 
TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19H 
      135.98        34.45         4.54        53.29        39.81       150.12 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 
       99.06        59.84        42.51        47.18       146.63        73.05 
TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3EV TCGA-ER-A42L 
       22.36        16.87        28.67       173.29        15.48        74.47 
TCGA-FR-A7U8 TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z4 TCGA-FS-A1ZD TCGA-FS-A1ZE 
       26.20       171.78        49.74        27.62        32.78        43.92 
TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZS TCGA-FS-A1ZW TCGA-FS-A4F0 
        7.82        36.33        78.61       136.27        23.21        30.90 
TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
       66.67       173.19        13.28        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        18.25         1.91        53.29       117.93        96.92 
TCGA-GN-A268 TCGA-OD-A75X TCGA-RP-A690 TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-AA1V 
       42.48       297.01         0.20         0.33       174.12         8.09 
TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-AA9Y TCGA-Z2-AA3S 
       65.42        12.69        62.89        10.95         1.94        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 
           47.230            44.955 
[1] "0.3 - 346.5 (47.2)" "0.0 - 297.0 (45.0)"
[1] "hr=" "1"  
D2V2, survival
                   sevent
clus2                 0   1
  1Q GAIN MUTATED    77  92
  1Q GAIN WILD-TYPE  89 100
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              169               189 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               92               100 
$`1Q GAIN MUTATED`
TCGA-D3-A2JE TCGA-D3-A3ML TCGA-D3-A8GI TCGA-EB-A5SH TCGA-EE-A180 TCGA-EE-A184 
       27.65        13.87        58.52        54.02        94.98        68.15 
TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR TCGA-FR-A729 TCGA-FS-A1ZF 
        2.60       340.14       126.81       134.40       220.80        15.45 
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-A2JL TCGA-D3-A2JN TCGA-D3-A3BZ 
      115.53        86.76        11.87       171.58        66.48       130.72 
TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV 
       58.06        60.23         9.34       103.59        39.75        45.30 
TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GU 
       32.94        63.81       125.79       135.75       137.92       125.19 
TCGA-D3-A8GD TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GP 
       23.61       241.38       170.20        89.13       107.15       152.75 
TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D9-A1JW TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 
       29.06       129.63         3.65        15.39        22.29         9.90 
TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I4 
       25.18        77.56        22.95        20.38       222.51        35.93 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F3 TCGA-DA-A3F5 
      135.02        88.87        65.92        68.09        10.49       225.96 
TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44R TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17Y 
       14.14        13.02        10.36        29.29        58.92        27.22 
TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A20B TCGA-EE-A20I TCGA-EE-A29B TCGA-EE-A29D 
        8.65        33.73       133.81        13.55        85.08        13.97 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29M TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T 
       63.78        72.07        56.84        14.47        61.28       369.93 
TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GE TCGA-EE-A2GH 
      195.02       115.96        59.64        86.14       173.79       220.24 
TCGA-EE-A2GI TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M7 
       48.72        75.48       102.12        81.21        94.82        28.83 
TCGA-EE-A2MD TCGA-EE-A2MJ TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A2MT 
       47.28        96.23        47.54        43.23       162.48        71.21 
TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AG TCGA-EE-A3J7 
       53.26       122.73        64.04        28.77        41.59        64.08 
TCGA-EE-A3JA TCGA-EE-A3JH TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19D TCGA-ER-A19F 
       53.19       134.33        13.94         9.17        12.59        26.37 
TCGA-ER-A19G TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A2ND TCGA-ER-A2NF TCGA-ER-A2NH 
      302.07       162.08        50.89        23.34        28.83        41.56 
TCGA-ER-A3ET TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       93.01        33.21        12.95        92.98       174.21        15.72 
TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FS-A1YX TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1ZA 
       38.27        34.82        48.59       202.65        20.91        27.72 
TCGA-FS-A1ZC TCGA-FS-A1ZH TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZT 
      357.37        32.75        23.93        74.73       133.55        53.16 
TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F5 TCGA-FS-A4FD TCGA-GN-A266 
       26.56        27.09        27.02        28.73        80.68        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-A9SD TCGA-HR-A2OG TCGA-HR-A2OH 
       48.89        22.13        50.10        59.41         0.23        65.88 
TCGA-LH-A9QB TCGA-QB-A6FS TCGA-RP-A694 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O 
      368.78         7.23         0.69        63.02       121.08         4.01 
TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8ZO 
       69.07       111.09       219.16       105.04        49.05        70.52 
TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-XV-AB01 TCGA-YD-A9TA 
       35.80        49.51        40.41        24.99        13.25        49.18 
TCGA-YG-AA3O 
       37.94 

$`1Q GAIN WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A20H TCGA-EE-A3JD TCGA-ER-A193 
       62.07        46.32        68.25       168.26        27.35        31.40 
TCGA-ER-A198 TCGA-FW-A3R5 TCGA-QB-AA9O TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-3N-A9WC 
       50.76        36.95        18.05        61.15        21.40        66.48 
TCGA-BF-AAP0 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       14.93       112.04       112.57        71.80       133.25        28.08 
TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J9 TCGA-D3-A2JB 
       31.59        90.90        43.43       103.10        23.77       168.00 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C7 
      113.52        42.08        12.10        66.08        59.57        46.98 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
      166.52        86.93        24.53       174.84        55.73        56.35 
TCGA-D3-A51J TCGA-D3-A51N TCGA-D3-A51T TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A8GB 
      145.12        22.62        26.89       178.32        18.18        30.84 
TCGA-D3-A8GC TCGA-D3-A8GE TCGA-D3-A8GN TCGA-D3-A8GS TCGA-D3-A8GV TCGA-D9-A148 
       79.59        26.43       161.00       117.17       167.70       151.53 
TCGA-D9-A149 TCGA-D9-A1JX TCGA-D9-A1X3 TCGA-D9-A4Z6 TCGA-DA-A1HV TCGA-DA-A1HW 
       54.67         7.10        18.12        18.44        76.57        36.03 
TCGA-DA-A1HY TCGA-DA-A1I2 TCGA-DA-A1I8 TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-DA-A3F8 
      144.89       176.55        53.92        40.60        33.93        43.36 
TCGA-DA-A95V TCGA-DA-A95W TCGA-DA-A95X TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5VV 
       72.10        37.35        73.94        13.87        20.35         7.04 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20C 
       36.46        29.82        14.70        26.89         4.96       151.27 
TCGA-EE-A20F TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29H TCGA-EE-A29N TCGA-EE-A29P 
       91.56        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-A3JE 
      172.18       127.20        36.95        34.32       201.80        51.35 
TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19E 
      152.81        35.44        77.75        98.40        48.89        13.02 
TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19S 
      152.35         6.44       131.51        61.05        44.09        49.48 
TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NG 
        8.88       148.18       105.07        43.82        20.15        48.99 
TCGA-ER-A3ES TCGA-ER-A3EV TCGA-ER-A42L TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A8YD 
      247.04        46.98       149.03        27.85        18.77        36.26 
TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZB 
      104.42       216.92       228.59        28.08         7.79        48.85 
TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZR 
       53.52        46.45         9.70        47.38       101.26        11.41 
TCGA-FS-A1ZS TCGA-FS-A1ZW TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F8 
      148.80        49.48        77.82        50.14        66.67       174.84 
TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV 
       34.03        26.73        54.41        17.46        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        19.43         2.04        15.78       139.89 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A268 TCGA-GN-A8LL TCGA-OD-A75X TCGA-RP-A690 
      117.93        96.92        62.79        21.37       297.90         0.20 
TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-AA1V TCGA-WE-A8JZ TCGA-WE-A8K6 TCGA-WE-A8ZM 
        0.33       228.16        42.08        24.03        17.95       101.33 
TCGA-WE-A8ZN TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-AA9Y TCGA-YD-A89C TCGA-YG-AA3P 
       58.98        63.22        11.80        12.16         6.90        14.43 
TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
       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 
            53.19             50.76 
[1] "0.2 - 369.9 (53.2)" "0.2 - 297.9 (50.8)"
[1] "hr=" "1"  
D2V3, continuous
                   vv
clus                I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  1Q GAIN MUTATED          4       3      10        9       16       17
  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        19          3
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  1Q GAIN MUTATED           17         22        9
  1Q GAIN WILD-TYPE         18         32       12
D2V4, multiclass
            clus
vv           1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  I/II NOS                 4                 9
  STAGE 0                  3                 4
  STAGE I                 10                19
  STAGE IA                 9                 9
  STAGE IB                16                12
  STAGE II                17                 9
  STAGE IIA                6                 8
  STAGE IIB                8                11
  STAGE IIC                7                 8
  STAGE III               20                19
  STAGE IIIA              12                 3
  STAGE IIIB              17                18
  STAGE IIIC              22                32
  STAGE IV                 9                12
[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      31 35 46 28
  1Q GAIN WILD-TYPE    33 38 35 39
D2V5, multiclass
       clus
vv      1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  T0+T1              31                33
  T2                 35                38
  T3                 46                35
  T4                 28                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 28 24 19
  1Q GAIN WILD-TYPE 92 37 15 26
D2V6, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  N0              85                92
  N1              28                37
  N2              24                15
  N3              19                26
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V7, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED   154   9
  1Q GAIN WILD-TYPE 165  13
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED    154    9
  1Q GAIN WILD-TYPE  165   13
   clus
vv  1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  0             154               165
  1               9                13
[1] 2 2
[1] FALSE
D2V8, binary
                   cls
clus                 0  1
  1Q GAIN MUTATED   69 40
  1Q GAIN WILD-TYPE 65 50
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     69   40
  1Q GAIN WILD-TYPE   65   50
     clus
vv    1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  NO               69                65
  YES              40                50
[1] 2 2
[1] FALSE
D2V9, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED    21 152
  1Q GAIN WILD-TYPE  26 168
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     21  152
  1Q GAIN WILD-TYPE   26  168
     clus
vv    1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  NO               21                26
  YES             152               168
[1] 2 2
[1] FALSE
D2V10, continuous
D2V11, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED    63 110
  1Q GAIN WILD-TYPE  75 119
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     63  110
  1Q GAIN WILD-TYPE   75  119
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  FEMALE              63                75
  MALE               110               119
[1] 2 2
[1] FALSE
D2V12, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED   148  25
  1Q GAIN WILD-TYPE 171  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED    148   25
  1Q GAIN WILD-TYPE  171   22
     clus
vv    1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  NO              148               171
  YES              25                22
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  1Q GAIN MUTATED       2                         0   167
  1Q GAIN WILD-TYPE     3                         1   186
D2V13, multiclass
                           clus
vv                          1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  ASIAN                                   2                 3
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                 167               186
[1] 3 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     5 165
  1Q GAIN WILD-TYPE   2 187
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      5  165
  1Q GAIN WILD-TYPE    2  187
                        clus
vv                       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   5                 2
  NOT HISPANIC OR LATINO             165               187
[1] 2 2
[1] FALSE

Clustering(3) Variable = 2P GAIN MUTATION ANALYSIS
D3V1, survival
                   sevent
clus2                 0   1
  2P GAIN MUTATED    21  22
  2P GAIN WILD-TYPE 107 102
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               43               209 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               22               102 
$`2P GAIN MUTATED`
TCGA-D3-A8GI TCGA-EE-A20H TCGA-EE-A2MR TCGA-D3-A1Q1 TCGA-D3-A1Q6 TCGA-D3-A2JA 
       13.41       166.75       134.40         8.42        49.35        15.75 
TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A5GN TCGA-D3-A8GC 
       64.83        66.08       140.98        40.01        45.70        78.21 
TCGA-DA-A1HY TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A29D TCGA-EE-A29M TCGA-EE-A29Q 
      138.67       225.11         8.71        12.99        47.74        61.12 
TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2M6 
      346.49       185.19       115.43        18.35        93.63       103.13 
TCGA-EE-A2M7 TCGA-EE-A2MU TCGA-EE-A3AE TCGA-EE-A3JB TCGA-EE-A3JI TCGA-ER-A197 
       15.25        53.26        54.51       168.85       135.98        10.49 
TCGA-ER-A19B TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19N TCGA-ER-A2NC TCGA-ER-A42L 
       53.29       184.60       150.12        42.51        22.36        74.47 
TCGA-FR-A3YN TCGA-FS-A1ZD TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-OD-A75X TCGA-W3-A825 
        4.50        32.78        78.61       130.95       297.01         1.97 
TCGA-WE-A8ZY 
       48.39 

$`2P GAIN WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A2GD 
        9.76        62.07        38.76        33.24        31.96       269.03 
TCGA-EE-A2GO TCGA-EE-A3JD TCGA-ER-A193 TCGA-FR-A729 TCGA-FW-A3R5 TCGA-WE-A8K5 
       52.90        27.35        19.04       216.43        36.95        52.73 
TCGA-WE-AAA3 TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
        7.40        60.46        12.99        14.83        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-A2JB TCGA-D3-A2JC TCGA-D3-A2JG TCGA-D3-A2JH 
       45.99        62.86       168.00        86.30       107.61        36.30 
TCGA-D3-A2JL TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO 
      171.58        43.53        58.06        59.70        24.53         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K 
       90.21        23.67       173.85        30.67       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-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-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA 
       76.34        68.68       150.61       110.53        60.10        64.83 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A95V TCGA-DA-A95W TCGA-DA-A95X TCGA-DA-A95Y 
       58.85        30.44        72.10         0.76        65.03        14.14 
TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X 
       12.30         3.91        16.41        52.41        18.21        13.15 
TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A20F 
       24.89        20.38         0.00        26.24        75.55        79.20 
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        47.41        27.16 
TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ 
       30.02        77.98        26.14        12.95       201.60        68.65 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU 
       10.62        32.48         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-A195 TCGA-ER-A199 
      111.85        45.90         3.35        19.86        34.45         7.82 
TCGA-ER-A19A TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19P 
        4.54        39.81        11.47        99.06        59.84       120.76 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2ND TCGA-ER-A2NE 
       49.71        47.18       146.63        73.05         4.70        16.87 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL 
       10.19        28.67       173.29        68.52        15.48        32.05 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FS-A1YW 
      174.21         4.14        26.20         5.65        10.06       171.78 
TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZE 
       49.74       195.98         8.35        27.62       312.07        43.92 
TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW 
        7.82        36.33       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        18.25 
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-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A828 
       85.05         7.23         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        47.54 
TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-AA9Y 
       65.42        12.69        21.90        62.89        10.95         1.94 
TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-XV-AB01 TCGA-YG-AA3O TCGA-Z2-AA3S 
       37.32        24.99         6.61        28.21        91.23 

  2P GAIN MUTATED 2P GAIN WILD-TYPE 
             1.97              0.00 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
           346.49            312.07 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
            61.12             43.23 
[1] "2.0 - 346.5 (61.1)" "0.0 - 312.1 (43.2)"
[1] "hr=" "1.4"
D3V2, survival
                   sevent
clus2                 0   1
  2P GAIN MUTATED    30  35
  2P GAIN WILD-TYPE 136 157
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               65               293 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               35               157 
$`2P GAIN MUTATED`
TCGA-D3-A3ML TCGA-D3-A8GI TCGA-EB-A5SH TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2MR 
       13.87        58.52        54.02       168.26         2.60       134.40 
TCGA-QB-AA9O TCGA-D3-A1Q1 TCGA-D3-A1Q6 TCGA-D3-A1Q9 TCGA-D3-A2JA TCGA-D3-A2JD 
       18.05        16.57        71.80        31.59       115.53        11.87 
TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3MV TCGA-D3-A5GN 
       66.48        66.08       166.52        86.93        45.30       135.75 
TCGA-D3-A8GC TCGA-D3-A8GQ TCGA-D9-A148 TCGA-D9-A6E9 TCGA-DA-A1HY TCGA-DA-A1I8 
       79.59        29.06       151.53         9.90       144.89        53.92 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A29A TCGA-EE-A29D TCGA-EE-A29M TCGA-EE-A29Q 
      225.96        43.36        63.35        13.97        56.84        66.74 
TCGA-EE-A29R TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2GM TCGA-EE-A2GN 
       14.47       369.93       195.02       115.96        75.48       102.12 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MU TCGA-EE-A3AE TCGA-EE-A3AG TCGA-EE-A3JB 
      129.27        28.83        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       302.07       152.35 
TCGA-ER-A19N TCGA-ER-A2NC TCGA-ER-A42L TCGA-FR-A3YN TCGA-FS-A1ZD TCGA-FS-A1ZK 
       44.09        43.82       149.03        92.98        53.52        23.93 
TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A4F5 TCGA-FW-A3I3 TCGA-OD-A75X TCGA-W3-A825 
      101.26       133.55        28.73        17.46       297.90        63.02 
TCGA-W3-AA1O TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-YD-A89C TCGA-YD-A9TA 
        4.01        35.80        49.51         6.90        49.18 

$`2P GAIN WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A184 
       27.65        62.07        46.32        68.25        94.98        68.15 
TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A3JD TCGA-ER-A193 TCGA-ER-A198 TCGA-FR-A729 
      340.14       126.81        27.35        31.40        50.76       220.80 
TCGA-FS-A1ZF TCGA-FW-A3R5 TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-3N-A9WB TCGA-3N-A9WC 
       15.45        36.95        61.15        21.40        17.03        66.48 
TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q7 
       12.99        14.93        16.67       112.04       112.57       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-A2JH TCGA-D3-A2JK 
       23.77       168.00        86.76       113.52        42.08        12.10 
TCGA-D3-A2JL TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CE 
      171.58        59.57       130.72        58.06        46.98        60.23 
TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F 
       24.53         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-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-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM 
       23.61        26.43       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-A149 
      161.00       152.75       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-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I0 
       25.18        77.56        22.95        76.57        36.03        20.38 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA 
      222.51       176.55        35.93       135.02        88.87        65.92 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A95V TCGA-DA-A95W 
       40.60        68.09        33.93        10.49        72.10        37.35 
TCGA-DA-A95X TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH 
       73.94        14.14        13.02        13.87        10.36        20.35 
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-A185 TCGA-EE-A20B 
        8.65        33.73        14.70        26.89         4.96       133.81 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E 
      151.27        91.56        13.55        85.08        78.97        63.78 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29S TCGA-EE-A29V 
       72.07        64.64        18.61        56.42        61.28        25.87 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
       17.92        46.82        59.64        39.29        86.14        59.28 
TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
       67.43       173.79       220.24        48.72       107.38        54.74 
TCGA-EE-A2GL TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU 
       79.66        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-A2MP TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A2MT 
      167.90        47.54       248.65        43.23       162.48        71.21 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AH 
      124.31       122.73        64.04        28.77        13.81       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-A3JE TCGA-EE-A3JH TCGA-ER-A195 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19C 
       51.35       134.33        35.44         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       105.07        23.34 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET 
       20.15        28.83        48.99        41.56       247.04        93.01 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A7U8 
       46.98        33.21        12.95       174.21        15.72        27.85 
TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW 
       18.77        38.27        34.82        36.26       104.42       216.92 
TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 
       48.59       228.59       202.65        20.91        28.08         7.79 
TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZH 
       27.72        48.85       357.37        46.45         9.70        32.75 
TCGA-FS-A1ZJ TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU 
       47.38        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-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3TU 
      174.84        34.03        26.73        54.41        80.68        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        19.43         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-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-A8LL TCGA-GN-A9SD TCGA-HR-A2OG TCGA-HR-A2OH 
       22.13        50.10        21.37        59.41         0.23        65.88 
TCGA-LH-A9QB TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 
      368.78         7.23         0.20         0.33         0.69       228.16 
TCGA-W3-A828 TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 
      121.08        69.07       111.09        42.08       219.16       105.04 
TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO 
       24.03        49.05        17.95       101.33        58.98        70.52 
TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-XV-AB01 
       63.22        11.80        12.16        40.41        24.99        13.25 
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 

  2P GAIN MUTATED 2P GAIN WILD-TYPE 
              2.6               0.2 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
           369.93            368.78 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
            58.52             49.48 
[1] "2.6 - 369.9 (58.5)" "0.2 - 368.8 (49.5)"
[1] "hr=" "1.2"
D3V3, continuous
                   vv
clus                I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  2P GAIN MUTATED          3       2       6        4        6        5
  2P GAIN WILD-TYPE       10       5      23       14       22       21
                   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        31         11
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  2P GAIN MUTATED            5          8        1
  2P GAIN WILD-TYPE         30         46       20
D3V4, multiclass
            clus
vv           2P GAIN MUTATED 2P GAIN WILD-TYPE
  I/II NOS                 3                10
  STAGE 0                  2                 5
  STAGE I                  6                23
  STAGE IA                 4                14
  STAGE IB                 6                22
  STAGE II                 5                21
  STAGE IIA                3                11
  STAGE IIB                1                18
  STAGE IIC                3                12
  STAGE III                8                31
  STAGE IIIA               4                11
  STAGE IIIB               5                30
  STAGE IIIC               8                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 18 12 10
  2P GAIN WILD-TYPE    54 55 69 57
D3V5, multiclass
       clus
vv      2P GAIN MUTATED 2P GAIN WILD-TYPE
  T0+T1              10                54
  T2                 18                55
  T3                 12                69
  T4                 10                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
  2P GAIN MUTATED    36  12   7   6
  2P GAIN WILD-TYPE 141  53  32  39
D3V6, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  N0              36               141
  N1              12                53
  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"
D3V7, binary
                   cls
clus                  0   1
  2P GAIN MUTATED    63   2
  2P GAIN WILD-TYPE 256  20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     63    2
  2P GAIN WILD-TYPE  256   20
   clus
vv  2P GAIN MUTATED 2P GAIN WILD-TYPE
  0              63               256
  1               2                20
[1] 2 2
[1] FALSE
D3V8, binary
                   cls
clus                  0   1
  2P GAIN MUTATED    23  16
  2P GAIN WILD-TYPE 111  74
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     23   16
  2P GAIN WILD-TYPE  111   74
     clus
vv    2P GAIN MUTATED 2P GAIN WILD-TYPE
  NO               23               111
  YES              16                74
[1] 2 2
[1] FALSE
D3V9, binary
                   cls
clus                  0   1
  2P GAIN MUTATED     8  59
  2P GAIN WILD-TYPE  39 261
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      8   59
  2P GAIN WILD-TYPE   39  261
     clus
vv    2P GAIN MUTATED 2P GAIN WILD-TYPE
  NO                8                39
  YES              59               261
[1] 2 2
[1] FALSE
D3V10, continuous
D3V11, binary
                   cls
clus                  0   1
  2P GAIN MUTATED    24  43
  2P GAIN WILD-TYPE 114 186
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     24   43
  2P GAIN WILD-TYPE  114  186
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  FEMALE              24               114
  MALE                43               186
[1] 2 2
[1] FALSE
D3V12, binary
                   cls
clus                  0   1
  2P GAIN MUTATED    57  10
  2P GAIN WILD-TYPE 262  37
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     57   10
  2P GAIN WILD-TYPE  262   37
     clus
vv    2P GAIN MUTATED 2P GAIN WILD-TYPE
  NO               57               262
  YES              10                37
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  2P GAIN MUTATED       0                         0    67
  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                                  67               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  66
  2P GAIN WILD-TYPE   7 286
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      0   66
  2P GAIN WILD-TYPE    7  286
                        clus
vv                       2P GAIN MUTATED 2P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 7
  NOT HISPANIC OR LATINO              66               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 106 105
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               41               211 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               19               105 
$`2Q GAIN MUTATED`
TCGA-D3-A2JE TCGA-D3-A8GI TCGA-EE-A20H TCGA-EE-A2MR TCGA-D3-A1Q1 TCGA-D3-A1Q6 
        9.76        13.41       166.75       134.40         8.42        49.35 
TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A3CB TCGA-D3-A3CC 
       15.75        86.30        64.83        66.08       140.98        40.01 
TCGA-D3-A5GN TCGA-D3-A8GC TCGA-DA-A1HY TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A29M 
       45.70        78.21       138.67       225.11         8.71        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        93.63 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MU TCGA-EE-A3AE TCGA-EE-A3JB TCGA-EE-A3JI 
      103.13        15.25        53.26        54.51       168.85       135.98 
TCGA-ER-A19B TCGA-ER-A19G TCGA-ER-A19N TCGA-ER-A2NC TCGA-ER-A42L TCGA-FR-A3YN 
       53.29       184.60        42.51        22.36        74.47         4.50 
TCGA-FS-A1ZD TCGA-FS-A1ZM TCGA-GN-A9SD TCGA-OD-A75X TCGA-W3-A825 
       32.78        78.61        59.41       297.01         1.97 

$`2Q GAIN WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A2GD TCGA-EE-A2GO 
       62.07        38.76        33.24        31.96       269.03        52.90 
TCGA-EE-A3JD TCGA-ER-A193 TCGA-FR-A729 TCGA-FW-A3R5 TCGA-WE-A8K5 TCGA-WE-AAA3 
       27.35        19.04       216.43        36.95        52.73         7.40 
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-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU 
       58.06        59.70        24.53         9.34        90.21        23.67 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T 
      173.85        30.67       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        68.68 
TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 
      150.61       110.53        60.10        64.83        58.85        30.44 
TCGA-DA-A95V TCGA-DA-A95W TCGA-DA-A95X TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q 
       72.10         0.76        65.03        14.14        12.30         3.91 
TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A181 
       16.41        52.41        18.21        13.15        24.89        20.38 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29C 
        0.00        26.24        75.55        79.20        75.22        76.14 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29P TCGA-EE-A2A2 
       12.99         0.26        44.28        47.41        27.16        30.02 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK 
       77.98        26.14        12.95       201.60        68.65        10.62 
TCGA-EE-A2GL TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M8 
       32.48         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-A2MP TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AA 
      104.78       145.45       227.01       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-A3JH TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 
       45.90         3.35        19.86        34.45        10.49         7.82 
TCGA-ER-A19A TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M 
        4.54        39.81        11.47       150.12        99.06        59.84 
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        73.05         4.70 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
       16.87        10.19        28.67       173.29        68.52        15.48 
TCGA-ER-A3PL TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FR-A8YC 
       32.05       174.21         4.14        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-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT 
       43.92         7.82        36.33       130.95       136.27        35.28 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 
        4.47        23.21         5.29         3.06        30.90        66.67 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
      173.19        13.28        80.68        55.59        11.54        19.30 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        9.90        18.25         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-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 TCGA-W3-A824 
       43.23        85.05         7.23         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-A8K1 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT 
       47.54        65.42        12.69        21.90        62.89        10.95 
TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-XV-AB01 TCGA-YG-AA3O 
       48.39         1.94        37.32        24.99         6.61        28.21 
TCGA-Z2-AA3S 
       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 
            61.12             43.23 
[1] "2.0 - 346.5 (61.1)" "0.0 - 312.1 (43.2)"
[1] "hr=" "1.5"
D4V2, survival
                   sevent
clus2                 0   1
  2Q GAIN MUTATED    31  31
  2Q GAIN WILD-TYPE 135 161
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               62               296 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               31               161 
$`2Q GAIN MUTATED`
TCGA-D3-A2JE TCGA-D3-A3ML TCGA-D3-A8GI TCGA-EB-A5SH TCGA-EE-A20H TCGA-EE-A29L 
       27.65        13.87        58.52        54.02       168.26         2.60 
TCGA-EE-A2MR TCGA-QB-AA9O TCGA-D3-A1Q1 TCGA-D3-A1Q6 TCGA-D3-A1Q9 TCGA-D3-A2JA 
      134.40        18.05        16.57        71.80        31.59       115.53 
TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A3CB TCGA-D3-A3CC 
       86.76        11.87        66.48        66.08       166.52        86.93 
TCGA-D3-A3MV TCGA-D3-A5GN TCGA-D3-A8GC TCGA-D3-A8GQ TCGA-D9-A6E9 TCGA-DA-A1HY 
       45.30       135.75        79.59        29.06         9.90       144.89 
TCGA-DA-A1I8 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A5UL TCGA-EE-A29A TCGA-EE-A29M 
       53.92       225.96        43.36        29.29        63.35        56.84 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2GM 
       66.74        14.47       369.93       195.02       115.96        75.48 
TCGA-EE-A2GN TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MU TCGA-EE-A3AE TCGA-EE-A3AG 
      102.12       129.27        28.83        53.26        54.51        41.59 
TCGA-EE-A3JB TCGA-EE-A3JI TCGA-ER-A19B TCGA-ER-A19E TCGA-ER-A19G TCGA-ER-A19N 
      201.80       152.81        98.40        13.02       302.07        44.09 
TCGA-ER-A2NC TCGA-ER-A42L TCGA-FR-A3YN TCGA-FS-A1ZD TCGA-FS-A1ZM TCGA-FS-A4F5 
       43.82       149.03        92.98        53.52       101.26        28.73 
TCGA-FW-A3I3 TCGA-GN-A9SD TCGA-OD-A75X TCGA-W3-A825 TCGA-W3-AA1O TCGA-WE-A8ZX 
       17.46        59.41       297.90        63.02         4.01        35.80 
TCGA-YD-A89C TCGA-YD-A9TA 
        6.90        49.18 

$`2Q GAIN WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A184 TCGA-EE-A2GD 
       62.07        46.32        68.25        94.98        68.15       340.14 
TCGA-EE-A2GO TCGA-EE-A3JD TCGA-ER-A193 TCGA-ER-A198 TCGA-FR-A729 TCGA-FS-A1ZF 
      126.81        27.35        31.40        50.76       220.80        15.45 
TCGA-FW-A3R5 TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD 
       36.95        61.15        21.40        17.03        66.48        12.99 
TCGA-BF-AAP0 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       14.93        16.67       112.04       112.57       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-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JP 
      168.00       113.52        42.08        12.10       171.58        59.57 
TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO 
      130.72        58.06        46.98        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-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-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I1 
       77.56        22.95        76.57        36.03        20.38       222.51 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IB 
      176.55        35.93       135.02        88.87        65.92        40.60 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A95V TCGA-DA-A95W TCGA-DA-A95X 
       68.09        33.93        10.49        72.10        37.35        73.94 
TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5UN 
       14.14        13.02        13.87        10.36        20.35        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-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F 
       14.70        26.89         4.96       133.81       151.27        91.56 
TCGA-EE-A20I TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G 
       13.55        85.08        78.97        13.97        63.78        72.07 
TCGA-EE-A29H TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29X 
       64.64        18.61        56.42        61.28        25.87        17.92 
TCGA-EE-A2A0 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC 
       46.82        59.64        39.29        86.14        59.28        67.43 
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-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 
       13.91        42.77        81.21        44.88        94.82        21.67 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG 
       19.76        61.51        47.28       103.27       268.73       103.20 
TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-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-A2MS TCGA-EE-A2MT TCGA-EE-A3AA 
       47.54       248.65        43.23       162.48        71.21       124.31 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J3 
      122.73        64.04        28.77        13.81       138.81       172.18 
TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JE 
      127.20        36.95        64.08        34.32        53.19        51.35 
TCGA-EE-A3JH TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19C 
      134.33        35.44        13.94         9.17        77.75        48.89 
TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
       12.59        26.37       152.35         6.44       131.51        61.05 
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       105.07 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES 
       23.34        20.15        28.83        48.99        41.56       247.04 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A44A TCGA-FR-A69P 
       93.01        46.98        33.21        12.95       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-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-A1ZG 
        7.79        27.72        48.85       357.37        46.45         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-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-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-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
       54.41        80.68        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 
       19.43         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-HR-A2OG TCGA-HR-A2OH TCGA-LH-A9QB TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 
        0.23        65.88       368.78         7.23         0.20         0.33 
TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A828 TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1V 
        0.69       228.16       121.08        69.07       111.09        42.08 
TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K6 TCGA-WE-A8ZM 
      219.16       105.04        24.03        49.05        17.95       101.33 
TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AA9Y 
       58.98        70.52        63.22        11.80        49.51        12.16 
TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-XV-AB01 TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-A8RT 
       40.41        24.99        13.25        37.94        14.43        27.58 
TCGA-Z2-AA3S TCGA-Z2-AA3V 
       96.99        15.98 

  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
              2.6               0.2 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
           369.93            368.78 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
           58.965            49.480 
[1] "2.6 - 369.9 (59.0)" "0.2 - 368.8 (49.5)"
[1] "hr=" "1.3"
D4V3, continuous
                   vv
clus                I/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       22
                   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        29         11
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  2Q GAIN MUTATED            4          8        1
  2Q GAIN WILD-TYPE         31         46       20
D4V4, multiclass
            clus
vv           2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  I/II NOS                 3                10
  STAGE 0                  2                 5
  STAGE I                  6                23
  STAGE IA                 5                13
  STAGE IB                 6                22
  STAGE II                 4                22
  STAGE IIA                2                12
  STAGE IIB                1                18
  STAGE IIC                3                12
  STAGE III               10                29
  STAGE IIIA               4                11
  STAGE IIIB               4                31
  STAGE IIIC               8                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
  2Q GAIN MUTATED      12 18 10  8
  2Q GAIN WILD-TYPE    52 55 71 59
D4V5, multiclass
       clus
vv      2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  T0+T1              12                52
  T2                 18                55
  T3                 10                71
  T4                  8                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
  2Q GAIN MUTATED    34  11   8   6
  2Q GAIN WILD-TYPE 143  54  31  39
D4V6, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  N0              34               143
  N1              11                54
  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 257  21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     62    1
  2Q GAIN WILD-TYPE  257   21
   clus
vv  2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  0              62               257
  1               1                21
[1] 2 2
[1] FALSE
D4V8, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED    22  14
  2Q GAIN WILD-TYPE 112  76
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     22   14
  2Q GAIN WILD-TYPE  112   76
     clus
vv    2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  NO               22               112
  YES              14                76
[1] 2 2
[1] FALSE
D4V9, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED     9  56
  2Q GAIN WILD-TYPE  38 264
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      9   56
  2Q GAIN WILD-TYPE   38  264
     clus
vv    2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  NO                9                38
  YES              56               264
[1] 2 2
[1] FALSE
D4V10, continuous
D4V11, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED    26  39
  2Q GAIN WILD-TYPE 112 190
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     26   39
  2Q GAIN WILD-TYPE  112  190
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  FEMALE              26               112
  MALE                39               190
[1] 2 2
[1] FALSE
D4V12, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED    56   9
  2Q GAIN WILD-TYPE 263  38
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     56    9
  2Q GAIN WILD-TYPE  263   38
     clus
vv    2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  NO               56               263
  YES               9                38
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  2Q GAIN MUTATED       0                         0    65
  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                                  65               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  64
  2Q GAIN WILD-TYPE   7 288
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      0   64
  2Q GAIN WILD-TYPE    7  288
                        clus
vv                       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 7
  NOT HISPANIC OR LATINO              64               288
[1] 2 2
[1] FALSE

Clustering(5) Variable = 3P GAIN MUTATION ANALYSIS
D5V1, survival
                   sevent
clus2                 0   1
  3P GAIN MUTATED    24  13
  3P GAIN WILD-TYPE 104 111
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               37               215 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               13               111 
$`3P GAIN MUTATED`
TCGA-D3-A2JF TCGA-D3-A8GI TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A20H TCGA-WE-AAA3 
       62.07        13.41        33.24        31.96       166.75         7.40 
TCGA-D3-A1QA TCGA-D3-A2J8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3MR TCGA-D3-A5GN 
       76.41        62.86       140.98        40.01        90.21        45.70 
TCGA-D3-A5GR TCGA-D3-A8GD TCGA-D3-A8GM TCGA-DA-A1IA TCGA-DA-A3F5 TCGA-DA-A3F8 
      177.86        23.61        70.62        64.83       225.11         8.71 
TCGA-EE-A29M TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2MP 
       47.74       346.49       185.19        93.63         0.76       227.01 
TCGA-EE-A2MU TCGA-EE-A3AE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A19G TCGA-ER-A3ET 
       53.26        54.51        19.86       135.98       184.60        68.52 
TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A7UA TCGA-FS-A1Z0 TCGA-W3-AA1W TCGA-WE-A8K1 
       32.05        74.47         5.65       195.98       185.13        47.54 
TCGA-WE-A8ZY 
       48.39 

$`3P GAIN WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A3C8 TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD 
        9.76        38.76       269.03        52.90       134.40        27.35 
TCGA-ER-A193 TCGA-FR-A729 TCGA-FW-A3R5 TCGA-WE-A8K5 TCGA-3N-A9WC TCGA-3N-A9WD 
       19.04       216.43        36.95        52.73        60.46        12.99 
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-A2J6 TCGA-D3-A2J7 TCGA-D3-A2JA 
      133.25        19.04        62.60        25.64        45.99        15.75 
TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN 
      168.00        86.30       107.61        36.30       171.58        64.83 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO 
       66.08        43.53        58.06        59.70        24.53         9.34 
TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R 
       23.67       173.85        30.67       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        68.68 
TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A95V 
      150.61       110.53        60.10        58.85        30.44        72.10 
TCGA-DA-A95W TCGA-DA-A95X TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5KH 
        0.76        65.03        14.14        12.30         3.91        16.41 
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-A183 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D 
       26.24        75.55        79.20        75.22        76.14        12.99 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A2A1 
        0.26        44.28        47.41        27.16        61.12       115.43 
TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ 
       30.02        77.98        26.14        12.95       201.60        68.65 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU 
       10.62        32.48        18.35         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-A2MS 
      171.85        63.25        89.26       104.78       145.45       143.93 
TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AF 
       23.51       124.31       122.73        64.04         4.41         6.28 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-ER-A195 
       67.89       111.85        45.90         3.35       168.85        34.45 
TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D 
       10.49         7.82         4.54        53.29        39.81        11.47 
TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
      150.12        99.06        59.84        42.51       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        73.05        22.36         4.70        16.87 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3EV TCGA-FR-A3YN TCGA-FR-A44A 
       10.19        28.67       173.29        15.48         4.50       174.21 
TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A8YC TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z3 
        4.14        26.20        10.06       171.78        49.74         8.35 
TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ 
       27.62       312.07        32.78        43.92         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        18.25 
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-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-AA21 
        1.97       120.07        44.05        79.99         8.09        92.84 
TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-AA9Y 
       65.42        12.69        21.90        62.89        10.95         1.94 
TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-XV-AB01 TCGA-YG-AA3O TCGA-Z2-AA3S 
       37.32        24.99         6.61        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 
            62.86             43.23 
[1] "0.8 - 346.5 (62.9)" "0.0 - 312.1 (43.2)"
[1] "hr=" "2.2"
D5V2, survival
                   sevent
clus2                 0   1
  3P GAIN MUTATED    36  26
  3P GAIN WILD-TYPE 130 166
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               62               296 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               26               166 
$`3P GAIN MUTATED`
TCGA-D3-A2JF TCGA-D3-A8GI TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A180 TCGA-EE-A184 
       62.07        58.52        68.25        54.02        94.98        68.15 
TCGA-EE-A20H TCGA-EE-A29L TCGA-WE-AAA3 TCGA-D3-A1QA TCGA-D3-A2J8 TCGA-D3-A3CB 
      168.26         2.60        21.40        90.90        65.49       166.52 
TCGA-D3-A3CC TCGA-D3-A3MR TCGA-D3-A3MV TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A8GD 
       86.93       103.59        45.30       135.75       178.32        23.61 
TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GQ TCGA-DA-A1IA TCGA-DA-A3F3 TCGA-DA-A3F5 
      107.15       161.00        29.06        65.92        10.49       225.96 
TCGA-DA-A3F8 TCGA-EB-A5UL TCGA-EE-A20B TCGA-EE-A29M TCGA-EE-A29R TCGA-EE-A29T 
       43.36        29.29       133.81        56.84        14.47       369.93 
TCGA-EE-A29W TCGA-EE-A2GI TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2M5 TCGA-EE-A2MP 
      195.02        48.72       102.12        13.91        21.67       248.65 
TCGA-EE-A2MU TCGA-EE-A3AE TCGA-EE-A3J5 TCGA-EE-A3JA TCGA-EE-A3JH TCGA-EE-A3JI 
       53.26        54.51        36.95        53.19       134.33       152.81 
TCGA-ER-A19G TCGA-ER-A3ET TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A7UA TCGA-FR-A8YD 
      302.07        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-A8LL 
      202.65        23.93        50.14        15.78        10.13        21.37 
TCGA-HR-A2OG TCGA-HR-A2OH TCGA-W3-AA1W TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K6 
        0.23        65.88       219.16        24.03        49.05        17.95 
TCGA-WE-A8ZY TCGA-Z2-AA3V 
       49.51        15.98 

$`3P GAIN WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR 
       27.65        46.32        13.87       340.14       126.81       134.40 
TCGA-EE-A3JD TCGA-ER-A193 TCGA-ER-A198 TCGA-FR-A729 TCGA-FS-A1ZF TCGA-FW-A3R5 
       27.35        31.40        50.76       220.80        15.45        36.95 
TCGA-QB-AA9O TCGA-WE-A8K5 TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 
       18.05        61.15        17.03        66.48        12.99        14.93 
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.57        16.67       112.04       112.57        71.80       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J9 
       28.08        31.59        95.74        43.43       103.10        23.77 
TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH 
      115.53       168.00        86.76        11.87       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-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MU 
       58.06        46.98        60.23        24.53         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-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       222.51       176.55        35.93       135.02 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A95V 
       88.87        53.92        40.60        68.09        33.93        72.10 
TCGA-DA-A95W TCGA-DA-A95X TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A44R 
       37.35        73.94        14.14        13.02        13.87        10.36 
TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y 
       20.35        58.92         7.04        36.46        29.82        27.22 
TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20C 
        8.65        33.73        14.70        26.89         4.96       151.27 
TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D 
       91.56        13.55        63.35        85.08        78.97        13.97 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
       63.78        72.07        64.64        18.61        56.42        66.74 
TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
       61.28        25.87        17.92        46.82       115.96        59.64 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GH 
       39.29        86.14        59.28        67.43       173.79       220.24 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GR TCGA-EE-A2GS 
      107.38        54.74        79.66        75.48        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-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MQ 
       96.23       180.39       216.66       167.90        47.54        43.23 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
      162.48        71.21       124.31       122.73        64.04        28.77 
TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 
       13.81        41.59       138.81       172.18       127.20        64.08 
TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JE TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 
       34.32       201.80        51.35        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-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P 
      152.35         6.44       131.51        61.05        44.09       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       105.07        43.82 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES 
       23.34        20.15        28.83        48.99        41.56       247.04 
TCGA-ER-A3EV TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A7U8 
       46.98        12.95        92.98       174.21        15.72        27.85 
TCGA-FR-A7U9 TCGA-FR-A8YC TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY 
       18.77        34.82       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-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZM 
       53.52        46.45         9.70        32.75        47.38       101.26 
TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU 
       74.73       133.55        11.41       148.80        53.16        26.56 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 
       49.48        27.09        27.02        77.82        66.67        28.73 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 
      174.84        34.03        26.73        54.41        80.68        17.46 
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        19.43         2.04 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
      139.89       117.93        96.92        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-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 
       50.10        59.41       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-AA21 TCGA-WE-A8ZM TCGA-WE-A8ZN 
       69.07       111.09        42.08       105.04       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-AAA4 TCGA-XV-AB01 TCGA-YD-A89C TCGA-YD-A9TA TCGA-YG-AA3O TCGA-YG-AA3P 
       24.99        13.25         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 
           55.675            49.790 
[1] "0.2 - 369.9 (55.7)" "0.2 - 368.8 (49.8)"
[1] "hr=" "1.6"
D5V3, continuous
                   vv
clus                I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  3P GAIN MUTATED          4       1       6        7        7        5
  3P GAIN WILD-TYPE        9       6      23       11       21       21
                   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        33         14
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  3P GAIN MUTATED            9          5        1
  3P GAIN WILD-TYPE         26         49       20
D5V4, multiclass
            clus
vv           3P GAIN MUTATED 3P GAIN WILD-TYPE
  I/II NOS                 4                 9
  STAGE 0                  1                 6
  STAGE I                  6                23
  STAGE IA                 7                11
  STAGE IB                 7                21
  STAGE II                 5                21
  STAGE IIA                2                12
  STAGE IIB                1                18
  STAGE IIC                4                11
  STAGE III                6                33
  STAGE IIIA               1                14
  STAGE IIIB               9                26
  STAGE IIIC               5                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
  3P GAIN MUTATED      12 17 11 13
  3P GAIN WILD-TYPE    52 56 70 54
D5V5, multiclass
       clus
vv      3P GAIN MUTATED 3P GAIN WILD-TYPE
  T0+T1              12                52
  T2                 17                56
  T3                 11                70
  T4                 13                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
  3P GAIN MUTATED    39  10   5   3
  3P GAIN WILD-TYPE 138  55  34  42
D5V6, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  N0              39               138
  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    59   1
  3P GAIN WILD-TYPE 260  21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     59    1
  3P GAIN WILD-TYPE  260   21
   clus
vv  3P GAIN MUTATED 3P GAIN WILD-TYPE
  0              59               260
  1               1                21
[1] 2 2
[1] FALSE
D5V8, binary
                   cls
clus                  0   1
  3P GAIN MUTATED    24  17
  3P GAIN WILD-TYPE 110  73
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     24   17
  3P GAIN WILD-TYPE  110   73
     clus
vv    3P GAIN MUTATED 3P GAIN WILD-TYPE
  NO               24               110
  YES              17                73
[1] 2 2
[1] FALSE
D5V9, binary
                   cls
clus                  0   1
  3P GAIN MUTATED     5  59
  3P GAIN WILD-TYPE  42 261
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      5   59
  3P GAIN WILD-TYPE   42  261
     clus
vv    3P GAIN MUTATED 3P GAIN WILD-TYPE
  NO                5                42
  YES              59               261
[1] 2 2
[1] FALSE
D5V10, continuous
D5V11, binary
                   cls
clus                  0   1
  3P GAIN MUTATED    27  37
  3P GAIN WILD-TYPE 111 192
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     27   37
  3P GAIN WILD-TYPE  111  192
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  FEMALE              27               111
  MALE                37               192
[1] 2 2
[1] FALSE
D5V12, binary
                   cls
clus                  0   1
  3P GAIN MUTATED    53  11
  3P GAIN WILD-TYPE 266  36
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     53   11
  3P GAIN WILD-TYPE  266   36
     clus
vv    3P GAIN MUTATED 3P GAIN WILD-TYPE
  NO               53               266
  YES              11                36
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3P GAIN MUTATED       0                         0    61
  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                                  61               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  61
  3P GAIN WILD-TYPE   7 291
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      0   61
  3P GAIN WILD-TYPE    7  291
                        clus
vv                       3P GAIN MUTATED 3P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 7
  NOT HISPANIC OR LATINO              61               291
[1] 2 2
[1] FALSE

Clustering(6) Variable = 3Q GAIN MUTATION ANALYSIS
D6V1, survival
                   sevent
clus2                 0   1
  3Q GAIN MUTATED    30  19
  3Q GAIN WILD-TYPE  98 105
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               49               203 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               19               105 
$`3Q GAIN MUTATED`
TCGA-D3-A2JF TCGA-D3-A8GI TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A20H TCGA-WE-AAA3 
       62.07        13.41        33.24        31.96       166.75         7.40 
TCGA-D3-A1QA TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JG TCGA-D3-A2JL TCGA-D3-A2JN 
       76.41        62.86        15.75       107.61       171.58        64.83 
TCGA-D3-A3CB TCGA-D3-A3MR TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A8GD TCGA-D3-A8GM 
      140.98        90.21        45.70       177.86        23.61        70.62 
TCGA-D9-A6EC TCGA-DA-A1IA TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A182 TCGA-EE-A20F 
       69.21        64.83       225.11         8.71         0.00        79.20 
TCGA-EE-A29M TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2M6 
       47.74       346.49       185.19        93.63         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       184.60        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        47.54 
TCGA-WE-A8ZY 
       48.39 

$`3Q GAIN WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A3C8 TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD 
        9.76        38.76       269.03        52.90       134.40        27.35 
TCGA-ER-A193 TCGA-FR-A729 TCGA-FW-A3R5 TCGA-WE-A8K5 TCGA-3N-A9WC TCGA-3N-A9WD 
       19.04       216.43        36.95        52.73        60.46        12.99 
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-A2J6 TCGA-D3-A2J7 TCGA-D3-A2JB 
      133.25        19.04        62.60        25.64        45.99       168.00 
TCGA-D3-A2JC TCGA-D3-A2JH TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CC 
       86.30        36.30        66.08        43.53        58.06        40.01 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F 
       59.70        24.53         9.34        23.67       173.85        30.67 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GU 
      144.46        31.76        62.70        11.34        42.05       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-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IC 
      138.67        68.68       150.61       110.53        60.10        58.85 
TCGA-DA-A3F2 TCGA-DA-A95V TCGA-DA-A95W TCGA-DA-A95X TCGA-DA-A95Y TCGA-DA-A95Z 
       30.44        72.10         0.76        65.03        14.14        12.30 
TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y 
        3.91        16.41        52.41        18.21        13.15        24.89 
TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D 
       20.38        26.24        75.55        75.22        76.14        12.99 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A2A1 
        0.26        44.28        47.41        27.16        61.12       115.43 
TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ 
       30.02        77.98        26.14        12.95       201.60        68.65 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU 
       10.62        32.48        18.35         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-A2MJ TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AB 
       63.25        89.26       145.45       143.93        23.51       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J8 
       64.04         4.41         6.28        67.89       111.85         3.35 
TCGA-EE-A3JB TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A 
      168.85       135.98        34.45        10.49         7.82         4.54 
TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19N 
       53.29        39.81        11.47       150.12        99.06        42.51 
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        73.05        22.36 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3EV TCGA-FR-A3YN 
       16.87        10.19        28.67       173.29        15.48         4.50 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A8YC TCGA-FS-A1YW TCGA-FS-A1YY 
      174.21         4.14        26.20        10.06       171.78        49.74 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG 
        8.35        27.62       312.07        32.78        43.92         7.82 
TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU 
       36.33        78.61       130.95       136.27        35.28         4.47 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 
       23.21         5.29         3.06        30.90        66.67       173.19 
TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
       13.28        80.68        55.59        11.54        19.30         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 
       18.25         1.91        53.29       117.93        96.92        17.06 
TCGA-GN-A268 TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-GN-A8LK TCGA-GN-A9SD 
       42.48       120.53        34.49        46.92        43.23        59.41 
TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-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-AA21 
        1.97       120.07        44.05        79.99         8.09        92.84 
TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-AA9Y 
       65.42        12.69        21.90        62.89        10.95         1.94 
TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-XV-AB01 TCGA-YG-AA3O TCGA-Z2-AA3S 
       37.32        24.99         6.61        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 
            64.83             42.05 
[1] "0.0 - 346.5 (64.8)" "0.2 - 312.1 (42.0)"
[1] "hr=" "1.9"
D6V2, survival
                   sevent
clus2                 0   1
  3Q GAIN MUTATED    41  31
  3Q GAIN WILD-TYPE 125 161
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               72               286 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               31               161 
$`3Q GAIN MUTATED`
TCGA-D3-A2JF TCGA-D3-A8GI TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A184 TCGA-EE-A20H 
       62.07        58.52        68.25        94.98        68.15       168.26 
TCGA-WE-AAA3 TCGA-D3-A1QA TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JG TCGA-D3-A2JL 
       21.40        90.90        65.49       115.53       113.52       171.58 
TCGA-D3-A2JN TCGA-D3-A3CB TCGA-D3-A3MR TCGA-D3-A3MV TCGA-D3-A5GN TCGA-D3-A5GR 
       66.48       166.52       103.59        45.30       135.75       178.32 
TCGA-D3-A8GD TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GQ TCGA-D9-A6EC TCGA-DA-A1IA 
       23.61       107.15       161.00        29.06        77.56        65.92 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A5UL TCGA-EE-A182 TCGA-EE-A20B 
       10.49       225.96        43.36        29.29        14.70       133.81 
TCGA-EE-A20F TCGA-EE-A29M TCGA-EE-A29R TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2GI 
       91.56        56.84        14.47       369.93       195.02        48.72 
TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2ML TCGA-EE-A2MP 
      102.12        13.91        21.67       129.27       216.66       248.65 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AE TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3JA 
       53.26       124.31        54.51        36.95        64.08        53.19 
TCGA-EE-A3JH TCGA-ER-A19G TCGA-ER-A19M TCGA-ER-A2ND TCGA-ER-A3ET TCGA-ER-A3PL 
      134.33       302.07        61.05        23.34        93.01        33.21 
TCGA-ER-A42L TCGA-FR-A7UA TCGA-FR-A8YD TCGA-FS-A1Z0 TCGA-FS-A1ZK TCGA-FS-A4F2 
      149.03        38.27        36.26       202.65        23.93        50.14 
TCGA-GF-A6C9 TCGA-GN-A266 TCGA-GN-A26A TCGA-HR-A2OG TCGA-HR-A2OH TCGA-W3-AA1O 
       15.78        10.13        32.48         0.23        65.88         4.01 
TCGA-W3-AA1W TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K6 TCGA-WE-A8ZY TCGA-Z2-AA3V 
      219.16        24.03        49.05        17.95        49.51        15.98 

$`3Q GAIN WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EB-A5SH TCGA-EE-A29L TCGA-EE-A2GD 
       27.65        46.32        13.87        54.02         2.60       340.14 
TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 TCGA-ER-A198 TCGA-FR-A729 
      126.81       134.40        27.35        31.40        50.76       220.80 
TCGA-FS-A1ZF TCGA-FW-A3R5 TCGA-QB-AA9O TCGA-WE-A8K5 TCGA-3N-A9WB TCGA-3N-A9WC 
       15.45        36.95        18.05        61.15        17.03        66.48 
TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 
       12.99        14.93        16.57        16.67       112.04       112.57 
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-A2J9 TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JH 
      103.10        23.77       168.00        86.76        11.87        42.08 
TCGA-D3-A2JK TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 
       12.10        66.08        59.57       130.72        58.06        46.98 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MU TCGA-D3-A51E 
       86.93        60.23        24.53         9.34        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-A5GS TCGA-D3-A5GU TCGA-D3-A8GB 
       26.89       125.79       137.92        18.18       125.19        30.84 
TCGA-D3-A8GC TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GP 
       79.59        26.43       241.38       170.20        89.13       152.75 
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 
      222.51       176.55        35.93       135.02        88.87        53.92 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A95V TCGA-DA-A95W TCGA-DA-A95X 
       40.60        68.09        33.93        72.10        37.35        73.94 
TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5UN 
       14.14        13.02        13.87        10.36        20.35        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-A183 TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
       26.89         4.96       151.27        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-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-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-A2MM TCGA-EE-A2MN TCGA-EE-A2MQ 
      204.66        96.23       180.39       167.90        47.54        43.23 
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-A3JE TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A 
       51.35       152.81        35.44        13.94         9.17        77.75 
TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19H 
       98.40        48.89        12.59        13.02        26.37       152.35 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S 
        6.44       131.51        44.09       162.08        50.89        49.48 
TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NF 
        8.88       148.18       105.07        43.82        20.15        28.83 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3EV TCGA-ER-A42K TCGA-FR-A3YN 
       48.99        41.56       247.04        46.98        12.95        92.98 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A8YC TCGA-FR-A8YE 
      174.21        15.72        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-A1ZG 
       27.72        48.85       357.37        53.52        46.45         9.70 
TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR 
       32.75        47.38       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-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB 
       77.82        66.67        28.73       174.84        34.03        26.73 
TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
       54.41        80.68        17.46        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        19.43         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-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-AA1Q TCGA-W3-AA1R TCGA-W3-AA1V TCGA-W3-AA21 
       63.02       121.08        69.07       111.09        42.08       105.04 
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-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-XV-AB01 TCGA-YD-A89C TCGA-YD-A9TA 
       12.16        40.41        24.99        13.25         6.90        49.18 
TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S 
       37.94        14.43        27.58        96.99 

  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
             0.23              0.20 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
           369.93            368.78 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
           63.075            49.085 
[1] "0.2 - 369.9 (63.1)" "0.2 - 368.8 (49.1)"
[1] "hr=" "1.6"
D6V3, continuous
                   vv
clus                I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  3Q GAIN MUTATED          5       1       8        7        8        6
  3Q GAIN WILD-TYPE        8       6      21       11       20       20
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  3Q GAIN MUTATED           2         1         2         8          5
  3Q GAIN WILD-TYPE        12        18        13        31         10
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  3Q GAIN MUTATED            9          6        1
  3Q GAIN WILD-TYPE         26         48       20
D6V4, multiclass
            clus
vv           3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  I/II NOS                 5                 8
  STAGE 0                  1                 6
  STAGE I                  8                21
  STAGE IA                 7                11
  STAGE IB                 8                20
  STAGE II                 6                20
  STAGE IIA                2                12
  STAGE IIB                1                18
  STAGE IIC                2                13
  STAGE III                8                31
  STAGE IIIA               5                10
  STAGE IIIB               9                26
  STAGE IIIC               6                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 GAIN MUTATED      17 19 15 10
  3Q GAIN WILD-TYPE    47 54 66 57
D6V5, multiclass
       clus
vv      3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  T0+T1              17                47
  T2                 19                54
  T3                 15                66
  T4                 10                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
  3Q GAIN MUTATED    42  16   7   3
  3Q GAIN WILD-TYPE 135  49  32  42
D6V6, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  N0              42               135
  N1              16                49
  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    69   1
  3Q GAIN WILD-TYPE 250  21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     69    1
  3Q GAIN WILD-TYPE  250   21
   clus
vv  3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  0              69               250
  1               1                21
[1] 2 2
[1] FALSE
D6V8, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED    31  15
  3Q GAIN WILD-TYPE 103  75
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     31   15
  3Q GAIN WILD-TYPE  103   75
     clus
vv    3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  NO               31               103
  YES              15                75
[1] 2 2
[1] FALSE
D6V9, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED     8  66
  3Q GAIN WILD-TYPE  39 254
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      8   66
  3Q GAIN WILD-TYPE   39  254
     clus
vv    3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  NO                8                39
  YES              66               254
[1] 2 2
[1] FALSE
D6V10, continuous
D6V11, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED    30  44
  3Q GAIN WILD-TYPE 108 185
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     30   44
  3Q GAIN WILD-TYPE  108  185
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  FEMALE              30               108
  MALE                44               185
[1] 2 2
[1] FALSE
D6V12, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED    63  11
  3Q GAIN WILD-TYPE 256  36
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     63   11
  3Q GAIN WILD-TYPE  256   36
     clus
vv    3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  NO               63               256
  YES              11                36
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3Q GAIN MUTATED       0                         0    71
  3Q GAIN WILD-TYPE     5                         1   282
D6V13, multiclass
                           clus
vv                          3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  ASIAN                                   0                 5
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  71               282
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V14, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED     0  71
  3Q GAIN WILD-TYPE   7 281
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      0   71
  3Q GAIN WILD-TYPE    7  281
                        clus
vv                       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 7
  NOT HISPANIC OR LATINO              71               281
[1] 2 2
[1] FALSE

Clustering(7) Variable = 4P GAIN MUTATION ANALYSIS
D7V1, survival
                   sevent
clus2                 0   1
  4P GAIN MUTATED    21  18
  4P GAIN WILD-TYPE 107 106
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               39               213 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               18               106 
$`4P GAIN MUTATED`
TCGA-D3-A2JE TCGA-3N-A9WC TCGA-D3-A1Q3 TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3MU 
        9.76        60.46        15.72        58.06        59.70        23.67 
TCGA-D3-A5GU TCGA-D3-A8GP TCGA-DA-A1HV TCGA-DA-A1I1 TCGA-DA-A3F5 TCGA-DA-A95V 
      124.08       135.12        76.34        68.68       225.11        72.10 
TCGA-EB-A6L9 TCGA-EE-A20F TCGA-EE-A29G TCGA-EE-A29P TCGA-EE-A2GB TCGA-EE-A2GP 
       18.21        79.20        44.28        27.16        26.14         0.76 
TCGA-EE-A2MJ TCGA-EE-A2MP TCGA-EE-A3AA TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-EE-A3JB 
       63.25       227.01       124.31        67.89        45.90       168.85 
TCGA-ER-A19H TCGA-ER-A3ET TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A8YC TCGA-FS-A1ZJ 
      150.12        68.52        32.05         4.50        10.06        36.33 
TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZU TCGA-GF-A4EO TCGA-GN-A264 TCGA-GN-A268 
       78.61       130.95         4.47        18.25       117.93        42.48 
TCGA-GN-A8LK TCGA-WE-A8ZN TCGA-WE-A8ZQ 
       43.23        12.69        62.89 

$`4P GAIN WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A8GI TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A20H 
       62.07        38.76        13.41        33.24        31.96       166.75 
TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 TCGA-FR-A729 
      269.03        52.90       134.40        27.35        19.04       216.43 
TCGA-FW-A3R5 TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 
       36.95        52.73         7.40        12.99        14.83         8.42 
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA 
       31.89       110.93        49.35       133.25        19.04        76.41 
TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JB 
       62.60        25.64        45.99        62.86        15.75       168.00 
TCGA-D3-A2JC TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
       86.30       107.61        36.30       171.58        64.83        66.08 
TCGA-D3-A2JP TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR 
       43.53       140.98        40.01        24.53         9.34        90.21 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T 
      173.85        30.67       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-A6EC TCGA-D9-A6EG TCGA-DA-A1HY TCGA-DA-A1I2 
       16.90        18.44        69.21        22.85       138.67       150.61 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F8 
      110.53        60.10        64.83        58.85        30.44         8.71 
TCGA-DA-A95W TCGA-DA-A95X TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5KH 
        0.76        65.03        14.14        12.30         3.91        16.41 
TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
       52.41        13.15        24.89        20.38         0.00        26.24 
TCGA-EE-A20C TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H 
       75.55        75.22        76.14        12.99         0.26        47.41 
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-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
       77.98        12.95       201.60        68.65        10.62        32.48 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 
       18.35        93.63         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-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU 
       89.26       104.78       145.45       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-A195 TCGA-ER-A197 TCGA-ER-A199 
        3.35        19.86       135.98        34.45        10.49         7.82 
TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19L 
        4.54        53.29        39.81        11.47       184.60        99.06 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W 
       59.84        42.51       120.76        49.71        47.18       146.63 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
       73.05        22.36         4.70        16.87        10.19        28.67 
TCGA-ER-A3ES TCGA-ER-A3EV TCGA-ER-A42L TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A7U8 
      173.29        15.48        74.47       174.21         4.14        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-A1ZG TCGA-FS-A1ZS TCGA-FS-A1ZT 
      312.07        32.78        43.92         7.82       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-A9SD TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS 
       34.49        46.92        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-AA1V TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8ZM 
       79.99         8.09       185.13        92.84        47.54        65.42 
TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 
       21.90        10.95        48.39         1.94        37.32        24.99 
TCGA-XV-AB01 TCGA-YG-AA3O TCGA-Z2-AA3S 
        6.61        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 
             59.7              45.7 
[1] "0.8 - 227.0 (59.7)" "0.0 - 346.5 (45.7)"
[1] "hr=" "1.1"
D7V2, survival
                   sevent
clus2                 0   1
  4P GAIN MUTATED    26  29
  4P GAIN WILD-TYPE 140 163
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               55               303 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               29               163 
$`4P GAIN MUTATED`
TCGA-D3-A2JE TCGA-EB-A5SH TCGA-EE-A184 TCGA-QB-AA9O TCGA-3N-A9WC TCGA-D3-A1Q3 
       27.65        54.02        68.15        18.05        66.48        16.67 
TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CE TCGA-D3-A3MU TCGA-D3-A5GU TCGA-D3-A8GB 
       58.06        46.98        60.23        39.75       125.19        30.84 
TCGA-D3-A8GP TCGA-D3-A8GS TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-DA-A1HV TCGA-DA-A1I1 
      152.75       117.17         9.90        25.18        76.57       222.51 
TCGA-DA-A1IB TCGA-DA-A3F5 TCGA-DA-A95V TCGA-EB-A6L9 TCGA-EE-A20F TCGA-EE-A29G 
       40.60       225.96        72.10        36.46        91.56        72.07 
TCGA-EE-A29P TCGA-EE-A2GB TCGA-EE-A2GI TCGA-EE-A2GP TCGA-EE-A2MJ TCGA-EE-A2MP 
       56.42        59.28        48.72        13.91        96.23       248.65 
TCGA-EE-A3AA TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-ER-A19H 
      124.31       172.18        64.08        53.19       201.80       152.35 
TCGA-ER-A3ET TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A8YC TCGA-FS-A1YX TCGA-FS-A1ZJ 
       93.01        33.21        92.98        34.82        48.59        47.38 
TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZU TCGA-FS-A4F2 TCGA-FS-A4F5 
       23.93       101.26       133.55        26.56        50.14        28.73 
TCGA-GF-A4EO TCGA-GN-A264 TCGA-GN-A268 TCGA-GN-A26D TCGA-GN-A8LK TCGA-WE-A8ZN 
       19.43       117.93        62.79        48.00        50.10        58.98 
TCGA-WE-A8ZQ 
       63.22 

$`4P GAIN WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-D3-A8GI TCGA-EB-A5SG TCGA-EE-A180 
       62.07        46.32        13.87        58.52        68.25        94.98 
TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD 
      168.26         2.60       340.14       126.81       134.40        27.35 
TCGA-ER-A193 TCGA-ER-A198 TCGA-FR-A729 TCGA-FS-A1ZF TCGA-FW-A3R5 TCGA-WE-A8K5 
       31.40        50.76       220.80        15.45        36.95        61.15 
TCGA-WE-AAA3 TCGA-3N-A9WB TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q4 
       21.40        17.03        12.99        14.93        16.57       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-A2JG TCGA-D3-A2JH TCGA-D3-A2JK 
      168.00        86.76        11.87       113.52        42.08        12.10 
TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3CB 
      171.58        66.48        66.08        59.57       130.72       166.52 
TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MV TCGA-D3-A51E 
       86.93        24.53         9.34       103.59        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-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL 
       79.59        23.61        26.43       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-A6EC TCGA-D9-A6EG TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 
       18.44        77.56        22.95        36.03       144.89        20.38 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA 
      176.55        35.93       135.02        88.87        53.92        65.92 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-DA-A95W TCGA-DA-A95X 
       68.09        33.93        10.49        43.36        37.35        73.94 
TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5UL 
       14.14        13.02        13.87        10.36        20.35        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-A183 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20I 
       14.70        26.89         4.96       133.81       151.27        13.55 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H 
       63.35        85.08        78.97        13.97        63.78        64.64 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T 
       56.84        18.61        66.74        14.47        61.28       369.93 
TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
       25.87       195.02        17.92        46.82       115.96        59.64 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ 
       39.29        86.14        67.43       173.79       220.24       107.38 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GR TCGA-EE-A2GS 
       54.74        79.66        75.48       102.12        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-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MQ 
      204.66       180.39       216.66       167.90        47.54        43.23 
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-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J5 
       54.51        13.81        41.59       138.81       127.20        36.95 
TCGA-EE-A3J8 TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 
       34.32        51.35       134.33       152.81        35.44        13.94 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E 
        9.17        77.75        98.40        48.89        12.59        13.02 
TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
       26.37       302.07         6.44       131.51        61.05        44.09 
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       105.07 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH 
       43.82        23.34        20.15        28.83        48.99        41.56 
TCGA-ER-A3ES TCGA-ER-A3EV TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A44A TCGA-FR-A69P 
      247.04        46.98        12.95       149.03       174.21        15.72 
TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW 
       27.85        18.77        38.27        36.26       104.42       216.92 
TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA 
      228.59       202.65        20.91        28.08         7.79        27.72 
TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZH 
       48.85       357.37        53.52        46.45         9.70        32.75 
TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A1ZY 
       74.73        11.41       148.80        53.16        49.48        27.09 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-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-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
       54.41        80.68        17.46        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-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-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-A8ZM 
      219.16       105.04        24.03        49.05        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-AAA4 TCGA-XV-AB01 TCGA-YD-A89C TCGA-YD-A9TA TCGA-YG-AA3O TCGA-YG-AA3P 
       24.99        13.25         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 
              9.9               0.2 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
           248.65            369.93 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
            58.98             49.48 
[1] "9.9 - 248.7 (59.0)" "0.2 - 369.9 (49.5)"
[1] "hr=" "1.1"
D7V3, continuous
                   vv
clus                I/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       25
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  4P GAIN MUTATED           2         3         6         9          4
  4P GAIN WILD-TYPE        12        16         9        30         11
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  4P GAIN MUTATED            4          6        1
  4P GAIN WILD-TYPE         31         48       20
D7V4, multiclass
            clus
vv           4P GAIN MUTATED 4P GAIN WILD-TYPE
  I/II NOS                 2                11
  STAGE 0                  0                 7
  STAGE I                  7                22
  STAGE IA                 1                17
  STAGE IB                 8                20
  STAGE II                 1                25
  STAGE IIA                2                12
  STAGE IIB                3                16
  STAGE IIC                6                 9
  STAGE III                9                30
  STAGE IIIA               4                11
  STAGE IIIB               4                31
  STAGE IIIC               6                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
  4P GAIN MUTATED      12 16  8 14
  4P GAIN WILD-TYPE    52 57 73 53
D7V5, multiclass
       clus
vv      4P GAIN MUTATED 4P GAIN WILD-TYPE
  T0+T1              12                52
  T2                 16                57
  T3                  8                73
  T4                 14                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
  4P GAIN MUTATED    31   8   8   5
  4P GAIN WILD-TYPE 146  57  31  40
D7V6, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  N0              31               146
  N1               8                57
  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    51   1
  4P GAIN WILD-TYPE 268  21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED     51    1
  4P GAIN WILD-TYPE  268   21
   clus
vv  4P GAIN MUTATED 4P GAIN WILD-TYPE
  0              51               268
  1               1                21
[1] 2 2
[1] FALSE
D7V8, binary
                   cls
clus                  0   1
  4P GAIN MUTATED    21  15
  4P GAIN WILD-TYPE 113  75
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED     21   15
  4P GAIN WILD-TYPE  113   75
     clus
vv    4P GAIN MUTATED 4P GAIN WILD-TYPE
  NO               21               113
  YES              15                75
[1] 2 2
[1] FALSE
D7V9, binary
                   cls
clus                  0   1
  4P GAIN MUTATED     7  50
  4P GAIN WILD-TYPE  40 270
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      7   50
  4P GAIN WILD-TYPE   40  270
     clus
vv    4P GAIN MUTATED 4P GAIN WILD-TYPE
  NO                7                40
  YES              50               270
[1] 2 2
[1] FALSE
D7V10, continuous
D7V11, binary
                   cls
clus                  0   1
  4P GAIN MUTATED    23  34
  4P GAIN WILD-TYPE 115 195
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED     23   34
  4P GAIN WILD-TYPE  115  195
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  FEMALE              23               115
  MALE                34               195
[1] 2 2
[1] FALSE
D7V12, binary
                   cls
clus                  0   1
  4P GAIN MUTATED    51   6
  4P GAIN WILD-TYPE 268  41
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED     51    6
  4P GAIN WILD-TYPE  268   41
     clus
vv    4P GAIN MUTATED 4P GAIN WILD-TYPE
  NO               51               268
  YES               6                41
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  4P GAIN MUTATED       1                         0    54
  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                                  54               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  56
  4P GAIN WILD-TYPE   6 296
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      1   56
  4P GAIN WILD-TYPE    6  296
                        clus
vv                       4P GAIN MUTATED 4P GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 6
  NOT HISPANIC OR LATINO              56               296
[1] 2 2
[1] FALSE

Clustering(8) Variable = 4Q GAIN MUTATION ANALYSIS
D8V1, survival
                   sevent
clus2                 0   1
  4Q GAIN MUTATED    18  18
  4Q GAIN WILD-TYPE 110 106
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               36               216 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               18               106 
$`4Q GAIN MUTATED`
TCGA-D3-A2JE TCGA-EE-A2MR TCGA-D3-A1Q3 TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3MU 
        9.76       134.40        15.72        58.06        59.70        23.67 
TCGA-D3-A5GU TCGA-D3-A8GP TCGA-DA-A1HV TCGA-DA-A1I1 TCGA-DA-A3F5 TCGA-EB-A6L9 
      124.08       135.12        76.34        68.68       225.11        18.21 
TCGA-EE-A20F TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29P TCGA-EE-A2GB TCGA-EE-A2GP 
       79.20        12.99        44.28        27.16        26.14         0.76 
TCGA-EE-A2MJ TCGA-EE-A2MP TCGA-EE-A3AD TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-EE-A3JB 
       63.25       227.01         4.41        67.89        45.90       168.85 
TCGA-ER-A19H TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A8YC TCGA-FS-A1ZM TCGA-FS-A1ZQ 
      150.12        32.05         4.50        10.06        78.61       130.95 
TCGA-FS-A1ZU TCGA-GF-A4EO TCGA-GN-A264 TCGA-GN-A268 TCGA-GN-A9SD TCGA-WE-A8ZQ 
        4.47        18.25       117.93        42.48        59.41        62.89 

$`4Q GAIN WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A8GI TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A20H 
       62.07        38.76        13.41        33.24        31.96       166.75 
TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A3JD TCGA-ER-A193 TCGA-FR-A729 TCGA-FW-A3R5 
      269.03        52.90        27.35        19.04       216.43        36.95 
TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 
       52.73         7.40        60.46        12.99        14.83         8.42 
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA 
       31.89       110.93        49.35       133.25        19.04        76.41 
TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JB 
       62.60        25.64        45.99        62.86        15.75       168.00 
TCGA-D3-A2JC TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
       86.30       107.61        36.30       171.58        64.83        66.08 
TCGA-D3-A2JP TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR 
       43.53       140.98        40.01        24.53         9.34        90.21 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T 
      173.85        30.67       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-A6EC TCGA-D9-A6EG TCGA-DA-A1HY TCGA-DA-A1I2 
       16.90        18.44        69.21        22.85       138.67       150.61 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F8 
      110.53        60.10        64.83        58.85        30.44         8.71 
TCGA-DA-A95V TCGA-DA-A95W TCGA-DA-A95X TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q 
       72.10         0.76        65.03        14.14        12.30         3.91 
TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A182 
       16.41        52.41        13.15        24.89        20.38         0.00 
TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H 
       26.24        75.55        75.22        76.14         0.26        47.41 
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-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
       77.98        12.95       201.60        68.65        10.62        32.48 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 
       18.35        93.63         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-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU 
       89.26       104.78       145.45       143.93        23.51        53.26 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J4 
      124.31       122.73        64.04        54.51         6.28       111.85 
TCGA-EE-A3J8 TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 
        3.35        19.86       135.98        34.45        10.49         7.82 
TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19L 
        4.54        53.29        39.81        11.47       184.60        99.06 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W 
       59.84        42.51       120.76        49.71        47.18       146.63 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
       73.05        22.36         4.70        16.87        10.19        28.67 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A42L TCGA-FR-A44A TCGA-FR-A69P 
      173.29        68.52        15.48        74.47       174.21         4.14 
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-A1ZG TCGA-FS-A1ZJ 
       27.62       312.07        32.78        43.92         7.82        36.33 
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-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-AA1V TCGA-W3-AA1W TCGA-W3-AA21 
      120.07        44.05        79.99         8.09       185.13        92.84 
TCGA-WE-A8K1 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-A8ZY 
       47.54        65.42        12.69        21.90        10.95        48.39 
TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-XV-AB01 TCGA-YG-AA3O TCGA-Z2-AA3S 
        1.94        37.32        24.99         6.61        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 
           58.735            45.845 
[1] "0.8 - 227.0 (58.7)" "0.0 - 346.5 (45.8)"
[1] "hr=" "1"  
D8V2, survival
                   sevent
clus2                 0   1
  4Q GAIN MUTATED    20  26
  4Q GAIN WILD-TYPE 146 166
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               46               312 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               26               166 
$`4Q GAIN MUTATED`
TCGA-D3-A2JE TCGA-EB-A5SH TCGA-EE-A184 TCGA-EE-A2MR TCGA-D3-A1Q3 TCGA-D3-A3C6 
       27.65        54.02        68.15       134.40        16.67        58.06 
TCGA-D3-A3CE TCGA-D3-A3MU TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GP TCGA-D3-A8GS 
       60.23        39.75       125.19        30.84       152.75       117.17 
TCGA-D9-A6EA TCGA-DA-A1HV TCGA-DA-A1I1 TCGA-DA-A1IB TCGA-DA-A3F5 TCGA-EB-A6L9 
       25.18        76.57       222.51        40.60       225.96        36.46 
TCGA-EE-A20F TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29P TCGA-EE-A2GB TCGA-EE-A2GP 
       91.56        13.97        72.07        56.42        59.28        13.91 
TCGA-EE-A2MJ TCGA-EE-A2MP TCGA-EE-A3AD TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-EE-A3JA 
       96.23       248.65        28.77       172.18        64.08        53.19 
TCGA-EE-A3JB TCGA-ER-A19H TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A8YC TCGA-FS-A1YX 
      201.80       152.35        33.21        92.98        34.82        48.59 
TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZU TCGA-FS-A4F5 TCGA-GF-A4EO TCGA-GN-A264 
      101.26       133.55        26.56        28.73        19.43       117.93 
TCGA-GN-A268 TCGA-GN-A26D TCGA-GN-A9SD TCGA-WE-A8ZQ 
       62.79        48.00        59.41        63.22 

$`4Q GAIN WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-D3-A8GI TCGA-EB-A5SG TCGA-EE-A180 
       62.07        46.32        13.87        58.52        68.25        94.98 
TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A3JD TCGA-ER-A193 
      168.26         2.60       340.14       126.81        27.35        31.40 
TCGA-ER-A198 TCGA-FR-A729 TCGA-FS-A1ZF TCGA-FW-A3R5 TCGA-QB-AA9O TCGA-WE-A8K5 
       50.76       220.80        15.45        36.95        18.05        61.15 
TCGA-WE-AAA3 TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 
       21.40        17.03        66.48        12.99        14.93        16.57 
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-A2JG TCGA-D3-A2JH 
      115.53       168.00        86.76        11.87       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-A3C7 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR 
       46.98       166.52        86.93        24.53         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-A8GJ 
      178.32        18.18        79.59        23.61        26.43       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-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-A6EC TCGA-D9-A6EG 
       15.39        22.29        18.44         9.90        77.56        22.95 
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       135.02 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
       88.87        53.92        65.92        68.09        33.93        10.49 
TCGA-DA-A3F8 TCGA-DA-A95V TCGA-DA-A95W TCGA-DA-A95X TCGA-DA-A95Y TCGA-DA-A95Z 
       43.36        72.10        37.35        73.94        14.14        13.02 
TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV 
       13.87        10.36        20.35        29.29        58.92         7.04 
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-A20B TCGA-EE-A20C TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
        4.96       133.81       151.27        13.55        63.35        85.08 
TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29Q 
       78.97        63.78        64.64        56.84        18.61        66.74 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X 
       14.47        61.28       369.93        25.87       195.02        17.92 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GC 
       46.82       115.96        59.64        39.29        86.14        67.43 
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-A2GN TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU 
       75.48       102.12        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-A2MS TCGA-EE-A2MT 
      216.66       167.90        47.54        43.23       162.48        71.21 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3AF 
       53.26       124.31       122.73        64.04        54.51        13.81 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J8 TCGA-EE-A3JE 
       41.59       138.81       127.20        36.95        34.32        51.35 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A 
      134.33       152.81        35.44        13.94         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       302.07 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
        6.44       131.51        61.05        44.09       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       105.07        43.82        23.34 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET 
       20.15        28.83        48.99        41.56       247.04        93.01 
TCGA-ER-A3EV TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A7U8 
       46.98        12.95       149.03       174.21        15.72        27.85 
TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YY 
       18.77        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-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ 
      357.37        53.52        46.45         9.70        32.75        47.38 
TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZW 
       23.93        74.73        11.41       148.80        53.16        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-A3TU 
       34.03        26.73        54.41        80.68        17.46        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-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 
       96.92        10.13        64.44        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-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-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-AAA4 TCGA-XV-AB01 TCGA-YD-A89C 
       49.51        12.16        40.41        24.99        13.25         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 
            13.91              0.20 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
           248.65            369.93 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
           59.820            49.495 
[1] "13.9 - 248.7 (59.8)" "0.2 - 369.9 (49.5)" 
[1] "hr=" "1.1"
D8V3, continuous
                   vv
clus                I/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       26
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  4Q GAIN MUTATED           1         2         4         8          2
  4Q GAIN WILD-TYPE        13        17        11        31         13
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  4Q GAIN MUTATED            4          6        1
  4Q GAIN WILD-TYPE         31         48       20
D8V4, multiclass
            clus
vv           4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  I/II NOS                 2                11
  STAGE 0                  0                 7
  STAGE I                  7                22
  STAGE IA                 1                17
  STAGE IB                 7                21
  STAGE II                 0                26
  STAGE IIA                1                13
  STAGE IIB                2                17
  STAGE IIC                4                11
  STAGE III                8                31
  STAGE IIIA               2                13
  STAGE IIIB               4                31
  STAGE IIIC               6                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
  4Q GAIN MUTATED      10 15  7 10
  4Q GAIN WILD-TYPE    54 58 74 57
D8V5, multiclass
       clus
vv      4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  T0+T1              10                54
  T2                 15                58
  T3                  7                74
  T4                 10                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 GAIN MUTATED    27   7   7   4
  4Q GAIN WILD-TYPE 150  58  32  41
D8V6, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  N0              27               150
  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    44   1
  4Q GAIN WILD-TYPE 275  21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED     44    1
  4Q GAIN WILD-TYPE  275   21
   clus
vv  4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  0              44               275
  1               1                21
[1] 2 2
[1] FALSE
D8V8, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED    18  13
  4Q GAIN WILD-TYPE 116  77
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED     18   13
  4Q GAIN WILD-TYPE  116   77
     clus
vv    4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  NO               18               116
  YES              13                77
[1] 2 2
[1] FALSE
D8V9, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     5  43
  4Q GAIN WILD-TYPE  42 277
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      5   43
  4Q GAIN WILD-TYPE   42  277
     clus
vv    4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  NO                5                42
  YES              43               277
[1] 2 2
[1] FALSE
D8V10, continuous
D8V11, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED    18  30
  4Q GAIN WILD-TYPE 120 199
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED     18   30
  4Q GAIN WILD-TYPE  120  199
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  FEMALE              18               120
  MALE                30               199
[1] 2 2
[1] FALSE
D8V12, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED    42   6
  4Q GAIN WILD-TYPE 277  41
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED     42    6
  4Q GAIN WILD-TYPE  277   41
     clus
vv    4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  NO               42               277
  YES               6                41
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  4Q GAIN MUTATED       1                         0    46
  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                                  46               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  47
  4Q GAIN WILD-TYPE   6 305
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      1   47
  4Q GAIN WILD-TYPE    6  305
                        clus
vv                       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 6
  NOT HISPANIC OR LATINO              47               305
[1] 2 2
[1] FALSE

Clustering(9) Variable = 5P GAIN MUTATION ANALYSIS
D9V1, survival
                   sevent
clus2                 0   1
  5P GAIN MUTATED    24  23
  5P GAIN WILD-TYPE 104 101
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               47               205 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               23               101 
$`5P GAIN MUTATED`
TCGA-D3-A2JF TCGA-D3-A8GI TCGA-EE-A180 TCGA-EE-A20H TCGA-D3-A1Q3 TCGA-D3-A1Q5 
       62.07        13.41        31.96       166.75        15.72       110.93 
TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A5GN 
       64.83        43.53        58.06        23.67       173.85        45.70 
TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D3-A8GM TCGA-D9-A6EC TCGA-DA-A95V TCGA-EE-A181 
      177.86       124.08        70.62        69.21        72.10        20.38 
TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2GM TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MP 
      346.49       185.19        18.35       103.13        15.25       227.01 
TCGA-EE-A2MS TCGA-EE-A3AA TCGA-EE-A3AE TCGA-EE-A3J3 TCGA-EE-A3JI TCGA-ER-A19B 
      143.93       124.31        54.51        67.89       135.98        53.29 
TCGA-ER-A19C TCGA-ER-A19G TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A2ND 
       39.81       184.60        59.84        42.51       120.76         4.70 
TCGA-ER-A3PL TCGA-FR-A44A TCGA-FR-A8YC TCGA-FS-A1ZE TCGA-FS-A1ZQ TCGA-FW-A3TU 
       32.05       174.21        10.06        43.92       130.95        55.59 
TCGA-GF-A4EO TCGA-GN-A265 TCGA-W3-AA1V TCGA-WE-A8ZQ TCGA-XV-AB01 
       18.25        96.92         8.09        62.89         6.61 

$`5P GAIN WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR 
        9.76        38.76        33.24       269.03        52.90       134.40 
TCGA-EE-A3JD TCGA-ER-A193 TCGA-FR-A729 TCGA-FW-A3R5 TCGA-WE-A8K5 TCGA-WE-AAA3 
       27.35        19.04       216.43        36.95        52.73         7.40 
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-A2JG TCGA-D3-A2JH 
       62.86        15.75       168.00        86.30       107.61        36.30 
TCGA-D3-A2JL TCGA-D3-A2JO TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF 
      171.58        66.08       140.98        40.01        59.70        24.53 
TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R 
        9.34        90.21        30.67       144.46        31.76        62.70 
TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GJ TCGA-D3-A8GK 
       11.34        42.05        78.21        23.61       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-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 
       18.44        22.85        76.34       138.67        68.68       150.61 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 
      110.53        60.10        64.83        58.85        30.44       225.11 
TCGA-DA-A3F8 TCGA-DA-A95W TCGA-DA-A95X TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q 
        8.71         0.76        65.03        14.14        12.30         3.91 
TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A182 
       16.41        52.41        18.21        13.15        24.89         0.00 
TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D 
       26.24        75.55        79.20        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        47.41        47.74        27.16        61.12 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH 
      115.43        30.02        77.98        26.14        12.95       201.60 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR 
       68.65        10.62        32.48        93.63         0.76         0.20 
TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MG 
       71.31        81.99         5.75        23.77       209.79        94.19 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MT 
      171.85        63.25        89.26       104.78       145.45        23.51 
TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3J4 
       53.26       122.73        64.04         4.41         6.28       111.85 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH TCGA-ER-A195 TCGA-ER-A197 
       45.90         3.35       168.85        19.86        34.45        10.49 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19D TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19Q 
        7.82         4.54        11.47       150.12        99.06        49.71 
TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NF 
       47.18       146.63        73.05        22.36        16.87        10.19 
TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A42L TCGA-FR-A3YN 
       28.67       173.29        68.52        15.48        74.47         4.50 
TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 
        4.14        26.20         5.65       171.78        49.74       195.98 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZG TCGA-FS-A1ZJ 
        8.35        27.62       312.07        32.78         7.82        36.33 
TCGA-FS-A1ZM TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY 
       78.61       136.27        35.28         4.47        23.21         5.29 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FD 
        3.06        30.90        66.67       173.19        13.28        80.68 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 
       11.54        19.30         9.90         1.91        53.29       117.93 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 
       17.06        42.48         7.59       120.53        34.49        46.92 
TCGA-GN-A8LK TCGA-GN-A9SD TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 
       43.23        59.41        85.05       297.01         7.23         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-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO 
      185.13        92.84        47.54        65.42        12.69        21.90 
TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-YG-AA3O 
       10.95        48.39         1.94        37.32        24.99        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 
            62.07             42.48 
[1] "4.7 - 346.5 (62.1)" "0.0 - 312.1 (42.5)"
[1] "hr=" "1.4"
D9V2, survival
                   sevent
clus2                 0   1
  5P GAIN MUTATED    36  36
  5P GAIN WILD-TYPE 130 156
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               72               286 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               36               156 
$`5P GAIN MUTATED`
TCGA-D3-A2JF TCGA-D3-A8GI TCGA-EE-A180 TCGA-EE-A20H TCGA-QB-AA9O TCGA-3N-A9WB 
       62.07        58.52        94.98       168.26        18.05        17.03 
TCGA-D3-A1Q3 TCGA-D3-A1Q5 TCGA-D3-A2JK TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3C6 
       16.67       112.57        12.10        66.48        59.57        58.06 
TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51N TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS 
       39.75       174.84        22.62       135.75       178.32        18.18 
TCGA-D3-A5GU TCGA-D3-A8GM TCGA-D9-A148 TCGA-D9-A1JW TCGA-D9-A6E9 TCGA-D9-A6EA 
      125.19       107.15       151.53         3.65         9.90        25.18 
TCGA-D9-A6EC TCGA-DA-A95V TCGA-EB-A44R TCGA-EE-A181 TCGA-EE-A20B TCGA-EE-A29T 
       77.56        72.10        10.36        33.73       133.81       369.93 
TCGA-EE-A29W TCGA-EE-A2A0 TCGA-EE-A2GM TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MP 
      195.02        46.82        75.48       129.27        28.83       248.65 
TCGA-EE-A2MS TCGA-EE-A3AA TCGA-EE-A3AE TCGA-EE-A3J3 TCGA-EE-A3JA TCGA-EE-A3JI 
      162.48       124.31        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       302.07        61.05        44.09       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        17.46        55.59        19.43        96.92        22.13 
TCGA-W3-AA1O TCGA-W3-AA1V TCGA-WE-A8ZQ TCGA-XV-AB01 TCGA-YG-AA3P TCGA-Z2-A8RT 
        4.01        42.08        63.22        13.25        14.43        27.58 

$`5P GAIN WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A184 
       27.65        46.32        13.87        68.25        54.02        68.15 
TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 
        2.60       340.14       126.81       134.40        27.35        31.40 
TCGA-ER-A198 TCGA-FR-A729 TCGA-FS-A1ZF TCGA-FW-A3R5 TCGA-WE-A8K5 TCGA-WE-AAA3 
       50.76       220.80        15.45        36.95        61.15        21.40 
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-A2JG TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JO TCGA-D3-A3BZ 
       11.87       113.52        42.08       171.58        66.08       130.72 
TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO 
       46.98       166.52        86.93        60.23        24.53         9.34 
TCGA-D3-A3MR TCGA-D3-A3MV TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K 
      103.59        45.30        55.73        56.35       145.12        32.94 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GO TCGA-D3-A8GB TCGA-D3-A8GC 
       63.81        26.89       125.79       137.92        30.84        79.59 
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-A149 
      152.75        29.06       129.63       117.17       167.70        54.67 
TCGA-D9-A1JX TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6EG 
        7.10        18.12        15.39        22.29        18.44        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       222.51       176.55 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB 
       35.93       135.02        88.87        53.92        65.92        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        43.36        37.35 
TCGA-DA-A95X TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UL 
       73.94        14.14        13.02        13.87        20.35        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-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I 
       14.70        26.89         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-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
       64.64        56.84        18.61        56.42        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-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
       86.14        59.28        67.43       173.79       220.24        48.72 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR 
      107.38        54.74        79.66       102.12        13.91        42.77 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M8 TCGA-EE-A2MC 
       81.21        44.88        94.82        21.67        19.76        61.51 
TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
       47.28       103.27       268.73       103.20        16.96       204.66 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MQ 
       96.23       180.39       216.66       167.90        47.54        43.23 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AF 
       71.21        53.26       122.73        64.04        28.77        13.81 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 
       41.59       138.81       127.20        36.95        64.08        34.32 
TCGA-EE-A3JB TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 
      201.80        51.35       134.33        35.44        13.94         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       105.07        43.82 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET 
       20.15        28.83        48.99        41.56       247.04        93.01 
TCGA-ER-A3EV TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A69P TCGA-FR-A7U8 
       46.98        12.95       149.03        92.98        15.72        27.85 
TCGA-FR-A7UA TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 
       38.27       216.92       228.59       202.65        20.91        28.08 
TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZG 
        7.79        27.72        48.85       357.37        53.52         9.70 
TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZS 
       32.75        47.38       101.26        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-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-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GF-A6C9 
       80.68        13.51        19.30         9.90         2.04        15.78 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
      139.89       117.93        10.13        64.44        62.79        32.48 
TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A8LK 
       48.00       121.91        39.35        10.42        48.89        50.10 
TCGA-GN-A8LL TCGA-GN-A9SD TCGA-HR-A2OG TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X 
       21.37        59.41         0.23        65.88       368.78       297.90 
TCGA-QB-A6FS TCGA-RP-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-AA1Q TCGA-W3-AA1R TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8JZ 
      121.08        69.07       111.09       219.16       105.04        24.03 
TCGA-WE-A8K1 TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT 
       49.05        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-A89C 
       35.80        49.51        12.16        40.41        24.99         6.90 
TCGA-YD-A9TA TCGA-YG-AA3O TCGA-Z2-AA3S TCGA-Z2-AA3V 
       49.18        37.94        96.99        15.98 

  5P GAIN MUTATED 5P GAIN WILD-TYPE 
             3.65              0.20 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
           369.93            368.78 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
           55.050            50.825 
[1] "3.6 - 369.9 (55.0)" "0.2 - 368.8 (50.8)"
[1] "hr=" "1.2"
D9V3, continuous
                   vv
clus                I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  5P GAIN MUTATED          4       1       7        5        6        8
  5P GAIN WILD-TYPE        9       6      22       13       22       18
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  5P GAIN MUTATED           2         4         5         5          3
  5P GAIN WILD-TYPE        12        15        10        34         12
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  5P GAIN MUTATED            2          8        5
  5P GAIN WILD-TYPE         33         46       16
D9V4, multiclass
            clus
vv           5P GAIN MUTATED 5P GAIN WILD-TYPE
  I/II NOS                 4                 9
  STAGE 0                  1                 6
  STAGE I                  7                22
  STAGE IA                 5                13
  STAGE IB                 6                22
  STAGE II                 8                18
  STAGE IIA                2                12
  STAGE IIB                4                15
  STAGE IIC                5                10
  STAGE III                5                34
  STAGE IIIA               3                12
  STAGE IIIB               2                33
  STAGE IIIC               8                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
  5P GAIN MUTATED      17 13 18 11
  5P GAIN WILD-TYPE    47 60 63 56
D9V5, multiclass
       clus
vv      5P GAIN MUTATED 5P GAIN WILD-TYPE
  T0+T1              17                47
  T2                 13                60
  T3                 18                63
  T4                 11                56
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  5P GAIN MUTATED    45   6   6  10
  5P GAIN WILD-TYPE 132  59  33  35
D9V6, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  N0              45               132
  N1               6                59
  N2               6                33
  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    64   6
  5P GAIN WILD-TYPE 255  16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     64    6
  5P GAIN WILD-TYPE  255   16
   clus
vv  5P GAIN MUTATED 5P GAIN WILD-TYPE
  0              64               255
  1               6                16
[1] 2 2
[1] FALSE
D9V8, binary
                   cls
clus                  0   1
  5P GAIN MUTATED    31  12
  5P GAIN WILD-TYPE 103  78
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     31   12
  5P GAIN WILD-TYPE  103   78
     clus
vv    5P GAIN MUTATED 5P GAIN WILD-TYPE
  NO               31               103
  YES              12                78
[1] 2 2
[1] FALSE
D9V9, binary
                   cls
clus                  0   1
  5P GAIN MUTATED    10  64
  5P GAIN WILD-TYPE  37 256
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     10   64
  5P GAIN WILD-TYPE   37  256
     clus
vv    5P GAIN MUTATED 5P GAIN WILD-TYPE
  NO               10                37
  YES              64               256
[1] 2 2
[1] FALSE
D9V10, continuous
D9V11, binary
                   cls
clus                  0   1
  5P GAIN MUTATED    30  44
  5P GAIN WILD-TYPE 108 185
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     30   44
  5P GAIN WILD-TYPE  108  185
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  FEMALE              30               108
  MALE                44               185
[1] 2 2
[1] FALSE
D9V12, binary
                   cls
clus                  0   1
  5P GAIN MUTATED    64  10
  5P GAIN WILD-TYPE 255  37
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     64   10
  5P GAIN WILD-TYPE  255   37
     clus
vv    5P GAIN MUTATED 5P GAIN WILD-TYPE
  NO               64               255
  YES              10                37
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  5P GAIN MUTATED       1                         0    71
  5P GAIN WILD-TYPE     4                         1   282
D9V13, multiclass
                           clus
vv                          5P GAIN MUTATED 5P GAIN WILD-TYPE
  ASIAN                                   1                 4
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  71               282
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V14, binary
                   cls
clus                  0   1
  5P GAIN MUTATED     2  72
  5P GAIN WILD-TYPE   5 280
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      2   72
  5P GAIN WILD-TYPE    5  280
                        clus
vv                       5P GAIN MUTATED 5P GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 5
  NOT HISPANIC OR LATINO              72               280
[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 110 110
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               32               220 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               14               110 
$`5Q GAIN MUTATED`
TCGA-D3-A2JF TCGA-EE-A180 TCGA-3N-A9WC TCGA-D3-A1Q3 TCGA-D3-A2JN TCGA-D3-A2JP 
       62.07        31.96        60.46        15.72        64.83        43.53 
TCGA-D3-A3MU TCGA-D3-A51K TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D3-A8GM TCGA-DA-A95V 
       23.67        31.76       177.86       124.08        70.62        72.10 
TCGA-DA-A95Z TCGA-EE-A181 TCGA-EE-A29W TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A3AA 
       12.30        20.38       185.19       227.01       143.93       124.31 
TCGA-EE-A3AE TCGA-EE-A3J3 TCGA-EE-A3JI TCGA-ER-A19C TCGA-ER-A19N TCGA-ER-A19P 
       54.51        67.89       135.98        39.81        42.51       120.76 
TCGA-ER-A2ND TCGA-ER-A3PL TCGA-FR-A8YC TCGA-FS-A1ZD TCGA-FW-A3TU TCGA-GF-A4EO 
        4.70        32.05        10.06        32.78        55.59        18.25 
TCGA-GN-A265 TCGA-WE-A8ZQ 
       96.92        62.89 

$`5Q GAIN WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A3C8 TCGA-D3-A8GI TCGA-EB-A5SG TCGA-EE-A20H TCGA-EE-A2GD 
        9.76        38.76        13.41        33.24       166.75       269.03 
TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 TCGA-FR-A729 TCGA-FW-A3R5 
       52.90       134.40        27.35        19.04       216.43        36.95 
TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q4 
       52.73         7.40        12.99        14.83         8.42        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-A2JG TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JO TCGA-D3-A3C6 TCGA-D3-A3CB 
      107.61        36.30       171.58        66.08        58.06       140.98 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A51E 
       40.01        59.70        24.53         9.34        90.21       173.85 
TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN 
       30.67       144.46        62.70        11.34        42.05        45.70 
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        68.68       150.61       110.53 
TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 
       60.10        64.83        58.85        30.44       225.11         8.71 
TCGA-DA-A95W TCGA-DA-A95X TCGA-DA-A95Y TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN 
        0.76        65.03        14.14         3.91        16.41        52.41 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20C 
       18.21        13.15        24.89         0.00        26.24        75.55 
TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G 
       79.20        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 
       47.41        47.74        27.16        61.12       346.49       115.43 
TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ 
       30.02        77.98        26.14        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        93.63         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-A2MT TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
      145.45        23.51        53.26       122.73        64.04         4.41 
TCGA-EE-A3AF TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH 
        6.28       111.85        45.90         3.35       168.85        19.86 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19D 
       34.45        10.49         7.82         4.54        53.29        11.47 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19Q TCGA-ER-A19S 
      184.60       150.12        99.06        59.84        49.71        47.18 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
      146.63        73.05        22.36        16.87        10.19        28.67 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A 
      173.29        68.52        15.48        74.47         4.50       174.21 
TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 
        4.14        26.20         5.65       171.78        49.74       195.98 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ 
        8.35        27.62       312.07        43.92         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-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GN-A262 
       80.68        11.54        19.30         9.90         1.91        53.29 
TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 
      117.93        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-AA1V TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8ZM 
       79.99         8.09       185.13        92.84        47.54        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        37.32 
TCGA-WE-AAA4 TCGA-XV-AB01 TCGA-YG-AA3O TCGA-Z2-AA3S 
       24.99         6.61        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            45.800 
[1] "4.7 - 227.0 (58.0)" "0.0 - 346.5 (45.8)"
[1] "hr=" "1.3"
D10V2, survival
                   sevent
clus2                 0   1
  5Q GAIN MUTATED    27  24
  5Q GAIN WILD-TYPE 139 168
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               51               307 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               24               168 
$`5Q GAIN MUTATED`
TCGA-D3-A2JF TCGA-EE-A180 TCGA-QB-AA9O TCGA-3N-A9WB TCGA-3N-A9WC TCGA-D3-A1Q3 
       62.07        94.98        18.05        17.03        66.48        16.67 
TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3MU TCGA-D3-A51K TCGA-D3-A5GR TCGA-D3-A5GS 
       66.48        59.57        39.75        32.94       178.32        18.18 
TCGA-D3-A5GU TCGA-D3-A8GM TCGA-D9-A148 TCGA-D9-A1JW TCGA-D9-A6E9 TCGA-DA-A95V 
      125.19       107.15       151.53         3.65         9.90        72.10 
TCGA-DA-A95Z TCGA-EB-A44R TCGA-EE-A181 TCGA-EE-A20B TCGA-EE-A29W TCGA-EE-A2MP 
       13.02        10.36        33.73       133.81       195.02       248.65 
TCGA-EE-A2MS TCGA-EE-A3AA TCGA-EE-A3AE TCGA-EE-A3J3 TCGA-EE-A3JA TCGA-EE-A3JI 
      162.48       124.31        54.51       172.18        53.19       152.81 
TCGA-ER-A19C TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19T TCGA-ER-A2ND TCGA-ER-A3PL 
       48.89        44.09       162.08         8.88        23.34        33.21 
TCGA-FR-A7U9 TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YX TCGA-FS-A1ZD 
       18.77        34.82        36.26       104.42        48.59        53.52 
TCGA-FS-A1ZK TCGA-FS-A4F5 TCGA-FW-A3TU TCGA-GF-A4EO TCGA-GN-A265 TCGA-GN-A4U9 
       23.93        28.73        55.59        19.43        96.92        22.13 
TCGA-WE-A8ZQ TCGA-YG-AA3P TCGA-Z2-A8RT 
       63.22        14.43        27.58 

$`5Q GAIN WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-D3-A8GI TCGA-EB-A5SG TCGA-EB-A5SH 
       27.65        46.32        13.87        58.52        68.25        54.02 
TCGA-EE-A184 TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR 
       68.15       168.26         2.60       340.14       126.81       134.40 
TCGA-EE-A3JD TCGA-ER-A193 TCGA-ER-A198 TCGA-FR-A729 TCGA-FS-A1ZF TCGA-FW-A3R5 
       27.35        31.40        50.76       220.80        15.45        36.95 
TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q4 
       61.15        21.40        12.99        14.93        16.57       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-A2JG TCGA-D3-A2JH TCGA-D3-A2JK 
      168.00        86.76        11.87       113.52        42.08        12.10 
TCGA-D3-A2JL TCGA-D3-A2JO TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CB 
      171.58        66.08       130.72        58.06        46.98       166.52 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MV 
       86.93        60.23        24.53         9.34       103.59        45.30 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51N TCGA-D3-A51R 
      174.84        55.73        56.35       145.12        22.62        63.81 
TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A8GB TCGA-D3-A8GC 
       26.89       125.79       135.75       137.92        30.84        79.59 
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-A149 
      152.75        29.06       129.63       117.17       167.70        54.67 
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-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 
      222.51       176.55        35.93       135.02        88.87        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-A5KH 
       43.36        37.35        73.94        14.14        13.87        20.35 
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-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A20F 
        8.65        14.70        26.89         4.96       151.27        91.56 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
       13.55        63.35        85.08        78.97        13.97        63.78 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
       72.07        64.64        56.84        18.61        56.42        66.74 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A0 
       14.47        61.28       369.93        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-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-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT 
       75.48       102.12        13.91        42.77        81.21        44.88 
TCGA-EE-A2GU TCGA-EE-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-A2MQ 
       96.23       180.39       216.66       167.90        47.54        43.23 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AF 
       71.21        53.26       122.73        64.04        28.77        13.81 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 
       41.59       138.81       127.20        36.95        64.08        34.32 
TCGA-EE-A3JB TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 
      201.80        51.35       134.33        35.44        13.94         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       302.07 
TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19Q TCGA-ER-A19S 
      152.35         6.44       131.51        61.05        50.89        49.48 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
      148.18       105.07        43.82        20.15        28.83        48.99 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A42K TCGA-ER-A42L 
       41.56       247.04        93.01        46.98        12.95       149.03 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FS-A1YW 
       92.98       174.21        15.72        27.85        38.27       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-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ 
       48.85       357.37        46.45         9.70        32.75        47.38 
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-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-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GF-A6C9 
       17.46        13.51        19.30         9.90         2.04        15.78 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
      139.89       117.93        10.13        64.44        62.79        32.48 
TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A8LK 
       48.00       121.91        39.35        10.42        48.89        50.10 
TCGA-GN-A8LL TCGA-GN-A9SD TCGA-HR-A2OG TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X 
       21.37        59.41         0.23        65.88       368.78       297.90 
TCGA-QB-A6FS TCGA-RP-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-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN 
      105.04        24.03        49.05        17.95       101.33        58.98 
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-AAA4 TCGA-XV-AB01 TCGA-YD-A89C TCGA-YD-A9TA TCGA-YG-AA3O TCGA-Z2-AA3S 
       24.99        13.25         6.90        49.18        37.94        96.99 
TCGA-Z2-AA3V 
       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             53.16 
[1] "3.6 - 248.7 (48.9)" "0.2 - 369.9 (53.2)"
[1] "hr=" "1.1"
D10V3, continuous
                   vv
clus                I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  5Q GAIN MUTATED          1       1       4        4        4        4
  5Q GAIN WILD-TYPE       12       6      25       14       24       22
                   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        35         13
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  5Q GAIN MUTATED            2          6        4
  5Q GAIN WILD-TYPE         33         48       17
D10V4, multiclass
            clus
vv           5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  I/II NOS                 1                12
  STAGE 0                  1                 6
  STAGE I                  4                25
  STAGE IA                 4                14
  STAGE IB                 4                24
  STAGE II                 4                22
  STAGE IIA                3                11
  STAGE IIB                4                15
  STAGE IIC                3                12
  STAGE III                4                35
  STAGE IIIA               2                13
  STAGE IIIB               2                33
  STAGE IIIC               6                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
  5Q GAIN MUTATED      13 11 11  7
  5Q GAIN WILD-TYPE    51 62 70 60
D10V5, multiclass
       clus
vv      5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  T0+T1              13                51
  T2                 11                62
  T3                 11                70
  T4                  7                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
  5Q GAIN MUTATED    29   4   5   8
  5Q GAIN WILD-TYPE 148  61  34  37
D10V6, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  N0              29               148
  N1               4                61
  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 276  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     43    5
  5Q GAIN WILD-TYPE  276   17
   clus
vv  5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  0              43               276
  1               5                17
[1] 2 2
[1] FALSE
D10V8, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED    21  11
  5Q GAIN WILD-TYPE 113  79
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     21   11
  5Q GAIN WILD-TYPE  113   79
     clus
vv    5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  NO               21               113
  YES              11                79
[1] 2 2
[1] FALSE
D10V9, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED     8  44
  5Q GAIN WILD-TYPE  39 276
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      8   44
  5Q GAIN WILD-TYPE   39  276
     clus
vv    5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  NO                8                39
  YES              44               276
[1] 2 2
[1] FALSE
D10V10, continuous
D10V11, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED    19  33
  5Q GAIN WILD-TYPE 119 196
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     19   33
  5Q GAIN WILD-TYPE  119  196
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  FEMALE              19               119
  MALE                33               196
[1] 2 2
[1] FALSE
D10V12, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED    45   7
  5Q GAIN WILD-TYPE 274  40
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     45    7
  5Q GAIN WILD-TYPE  274   40
     clus
vv    5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  NO               45               274
  YES               7                40
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  5Q GAIN MUTATED       1                         0    49
  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                                  49               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  49
  5Q GAIN WILD-TYPE   4 303
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      3   49
  5Q GAIN WILD-TYPE    4  303
                        clus
vv                       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                 4
  NOT HISPANIC OR LATINO              49               303
[1] 2 2
[1] FALSE

Clustering(11) Variable = 6P GAIN MUTATION ANALYSIS
D11V1, survival
                   sevent
clus2                0  1
  6P GAIN MUTATED   44 56
  6P GAIN WILD-TYPE 84 68
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
              100               152 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               56                68 
$`6P GAIN MUTATED`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-EB-A5SG TCGA-EE-A20H TCGA-EE-A2GD TCGA-WE-AAA3 
        9.76        62.07        33.24       166.75       269.03         7.40 
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-A2JO TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3MR TCGA-D3-A3MU 
       62.86        66.08        58.06        40.01        90.21        23.67 
TCGA-D3-A51E TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GU TCGA-D3-A8GJ TCGA-D3-A8GL 
      173.85        11.34        45.70       124.08       179.97        69.53 
TCGA-D3-A8GP TCGA-D9-A1X3 TCGA-D9-A4Z6 TCGA-DA-A1HV TCGA-DA-A1I2 TCGA-DA-A1IA 
      135.12        10.78        18.44        76.34       150.61        64.83 
TCGA-DA-A95V TCGA-DA-A95X TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A5KH TCGA-EE-A181 
       72.10        65.03        14.14        12.30        16.41        20.38 
TCGA-EE-A29B TCGA-EE-A29P TCGA-EE-A2GB TCGA-EE-A2GH TCGA-EE-A2GN TCGA-EE-A2GP 
       75.22        27.16        26.14       201.60        93.63         0.76 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2MF TCGA-EE-A2MI TCGA-EE-A2MK 
        0.20        71.31        81.99       209.79       171.85        89.26 
TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AD 
      145.45       227.01       143.93        53.26       124.31         4.41 
TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JI TCGA-ER-A197 
        6.28        67.89        45.90         3.35       135.98        10.49 
TCGA-ER-A199 TCGA-ER-A19C TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
        7.82        39.81        59.84        42.51       120.76        49.71 
TCGA-ER-A19S TCGA-ER-A2NC TCGA-ER-A2NF TCGA-ER-A3ES TCGA-ER-A3EV TCGA-ER-A3PL 
       47.18        22.36        10.19       173.29        15.48        32.05 
TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1ZE TCGA-FS-A1ZJ TCGA-FS-A1ZU TCGA-FS-A1ZW 
      195.98         8.35        43.92        36.33         4.47        23.21 
TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F8 TCGA-FS-A4FD TCGA-GF-A4EO TCGA-GN-A264 
        5.29         3.06       173.19        80.68        18.25       117.93 
TCGA-GN-A26A TCGA-GN-A8LK TCGA-GN-A9SD TCGA-LH-A9QB TCGA-RP-A690 TCGA-W3-AA1Q 
        7.59        43.23        59.41        85.05         0.20        44.05 
TCGA-W3-AA1R TCGA-W3-AA1V TCGA-W3-AA21 TCGA-WE-A8ZM TCGA-WE-A8ZO TCGA-WE-A8ZQ 
       79.99         8.09        92.84        65.42        21.90        62.89 
TCGA-WE-A8ZT TCGA-WE-AAA4 TCGA-XV-AB01 TCGA-YG-AA3O 
       10.95        24.99         6.61        28.21 

$`6P GAIN WILD-TYPE`
TCGA-D3-A3C8 TCGA-D3-A8GI TCGA-EE-A180 TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD 
       38.76        13.41        31.96        52.90       134.40        27.35 
TCGA-ER-A193 TCGA-FR-A729 TCGA-FW-A3R5 TCGA-WE-A8K5 TCGA-3N-A9WD TCGA-BF-AAP0 
       19.04       216.43        36.95        52.73        12.99        14.83 
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q8 TCGA-D3-A2J6 TCGA-D3-A2J7 
       31.89       110.93        49.35        19.04        25.64        45.99 
TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL 
       15.75       168.00        86.30       107.61        36.30       171.58 
TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO 
       64.83        43.53       140.98        59.70        24.53         9.34 
TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A5GL TCGA-D3-A5GR 
       30.67       144.46        31.76        62.70        42.05       177.86 
TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GK TCGA-D3-A8GM TCGA-D3-A8GR TCGA-D9-A3Z1 
       78.21        23.61       120.00        70.62        36.53        15.02 
TCGA-D9-A3Z3 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I5 
       16.90        69.21        22.85       138.67        68.68       110.53 
TCGA-DA-A1I7 TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-DA-A95W 
       60.10        58.85        30.44       225.11         8.71         0.76 
TCGA-EB-A44Q TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A182 
        3.91        52.41        18.21        13.15        24.89         0.00 
TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
       26.24        75.55        79.20        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        47.41        47.74        61.12       346.49       185.19 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GE TCGA-EE-A2GJ TCGA-EE-A2GK 
      115.43        30.02        77.98        12.95        68.65        10.62 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC 
       32.48        18.35       103.13        15.25         5.75        23.77 
TCGA-EE-A2MG TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MT TCGA-EE-A3AB TCGA-EE-A3AC 
       94.19        63.25       104.78        23.51       122.73        64.04 
TCGA-EE-A3AE TCGA-EE-A3J4 TCGA-EE-A3JB TCGA-EE-A3JH TCGA-ER-A195 TCGA-ER-A19A 
       54.51       111.85       168.85        19.86        34.45         4.54 
TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19W 
       53.29        11.47       184.60       150.12        99.06       146.63 
TCGA-ER-A1A1 TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A3ET TCGA-ER-A42L 
       73.05         4.70        16.87        28.67        68.52        74.47 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FR-A8YC 
        4.50       174.21         4.14        26.20         5.65        10.06 
TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZG 
      171.78        49.74        27.62       312.07        32.78         7.82 
TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A4F0 TCGA-FS-A4F4 
       78.61       130.95       136.27        35.28        30.90        66.67 
TCGA-FS-A4F9 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 
       13.28        55.59        11.54        19.30         9.90         1.91 
TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A4U3 TCGA-GN-A4U4 
       53.29        96.92        17.06        42.48       120.53        34.49 
TCGA-GN-A4U8 TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A825 
       46.92       297.01         7.23         0.33       174.12         1.97 
TCGA-W3-A828 TCGA-W3-AA1W TCGA-WE-A8K1 TCGA-WE-A8ZN TCGA-WE-A8ZY TCGA-WE-AA9Y 
      120.07       185.13        47.54        12.69        48.39         1.94 
TCGA-WE-AAA0 TCGA-Z2-AA3S 
       37.32        91.23 

  6P GAIN MUTATED 6P GAIN WILD-TYPE 
              0.2               0.0 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
           269.03            346.49 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
           48.445            45.135 
[1] "0.2 - 269.0 (48.4)" "0.0 - 346.5 (45.1)"
[1] "hr=" "1.3"
D11V2, survival
                   sevent
clus2                 0   1
  6P GAIN MUTATED    59  85
  6P GAIN WILD-TYPE 107 107
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
              144               214 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               85               107 
$`6P GAIN MUTATED`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A184 TCGA-EE-A20H 
       27.65        62.07        68.25        54.02        68.15       168.26 
TCGA-EE-A2GD TCGA-QB-AA9O TCGA-WE-AAA3 TCGA-3N-A9WC TCGA-D3-A1Q1 TCGA-D3-A1Q3 
      340.14        18.05        21.40        66.48        16.57        16.67 
TCGA-D3-A1Q7 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JO 
      133.25        90.90        95.74        65.49        23.77        66.08 
TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51T 
       58.06        86.93       103.59        39.75       174.84        26.89 
TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GU TCGA-D3-A8GJ TCGA-D3-A8GL TCGA-D3-A8GP 
      135.75       137.92       125.19       241.38        89.13       152.75 
TCGA-D3-A8GQ TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1X3 TCGA-D9-A4Z6 
       29.06       151.53        54.67         3.65        18.12        18.44 
TCGA-D9-A6E9 TCGA-DA-A1HV TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1IA TCGA-DA-A3F3 
        9.90        76.57        20.38       176.55        65.92        10.49 
TCGA-DA-A95V TCGA-DA-A95X TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A5KH TCGA-EB-A5UL 
       72.10        73.94        14.14        13.02        20.35        29.29 
TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A29B TCGA-EE-A29P 
        8.65        33.73         4.96       133.81        85.08        56.42 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A2A5 TCGA-EE-A2GB TCGA-EE-A2GH TCGA-EE-A2GN 
       14.47        61.28        39.29        59.28       220.24       102.12 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2ME 
       13.91        42.77        81.21        44.88        94.82       103.27 
TCGA-EE-A2MF TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP 
      268.73       204.66       180.39       167.90        47.54       248.65 
TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AD TCGA-EE-A3AF 
       43.23       162.48        53.26       124.31        28.77        13.81 
TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA 
       41.59       172.18        36.95        64.08        34.32        53.19 
TCGA-EE-A3JI TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19C TCGA-ER-A19E TCGA-ER-A19F 
      152.81        13.94         9.17        48.89        13.02        26.37 
TCGA-ER-A19J TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S 
        6.44        61.05        44.09       162.08        50.89        49.48 
TCGA-ER-A2NC TCGA-ER-A2NF TCGA-ER-A3ES TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A8YD 
       43.82        28.83       247.04        46.98        33.21        36.26 
TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1ZA TCGA-FS-A1ZE TCGA-FS-A1ZJ TCGA-FS-A1ZK 
      202.65        20.91        27.72        46.45        47.38        23.93 
TCGA-FS-A1ZP TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F2 
       74.73        26.56        49.48        27.09        27.02        50.14 
TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-GF-A4EO TCGA-GF-A6C9 
       28.73       174.84        80.68        17.46        19.43        15.78 
TCGA-GN-A264 TCGA-GN-A266 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U9 TCGA-GN-A8LK 
      117.93        10.13        32.48        48.00        22.13        50.10 
TCGA-GN-A8LL TCGA-GN-A9SD TCGA-LH-A9QB TCGA-RP-A690 TCGA-RP-A694 TCGA-W3-AA1Q 
       21.37        59.41       368.78         0.20         0.69        69.07 
TCGA-W3-AA1R TCGA-W3-AA1V TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8ZM TCGA-WE-A8ZO 
      111.09        42.08       105.04        24.03       101.33        70.52 
TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-AAA4 TCGA-XV-AB01 TCGA-YG-AA3O 
       63.22        11.80        35.80        24.99        13.25        37.94 

$`6P GAIN WILD-TYPE`
TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-D3-A8GI TCGA-EE-A180 TCGA-EE-A29L TCGA-EE-A2GO 
       46.32        13.87        58.52        94.98         2.60       126.81 
TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 TCGA-ER-A198 TCGA-FR-A729 TCGA-FS-A1ZF 
      134.40        27.35        31.40        50.76       220.80        15.45 
TCGA-FW-A3R5 TCGA-WE-A8K5 TCGA-3N-A9WB TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q4 
       36.95        61.15        17.03        12.99        14.93       112.04 
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A2J6 TCGA-D3-A2J7 
      112.57        71.80        28.08        31.59        43.43       103.10 
TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH 
      115.53       168.00        86.76        11.87       113.52        42.08 
TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C7 
       12.10       171.58        66.48        59.57       130.72        46.98 
TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MV TCGA-D3-A51F 
      166.52        60.23        24.53         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-A8GK TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D3-A8GV 
      170.20       107.15       161.00       129.63       117.17       167.70 
TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG 
        7.10        15.39        22.29        25.18        77.56        22.95 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 
       36.03       144.89       222.51        35.93       135.02        88.87 
TCGA-DA-A1I8 TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 
       53.92        40.60        68.09        33.93       225.96        43.36 
TCGA-DA-A95W TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 
       37.35        13.87        10.36        58.92         7.04        36.46 
TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A20F 
       29.82        27.22        14.70        26.89       151.27        91.56 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G 
       13.55        63.35        78.97        13.97        63.78        72.07 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29V 
       64.64        56.84        18.61        66.74       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-A2GC TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
       67.43       173.79        48.72       107.38        54.74        79.66 
TCGA-EE-A2GM TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC 
       75.48        21.67       129.27        28.83        19.76        61.51 
TCGA-EE-A2MD TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MT 
       47.28       103.20        16.96        96.23       216.66        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-A3JE TCGA-EE-A3JH TCGA-ER-A195 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19D 
       51.35       134.33        35.44        77.75        98.40        12.59 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 
      302.07       152.35       131.51         8.88       148.18       105.07 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ET TCGA-ER-A42K 
       23.34        20.15        48.99        41.56        93.01        12.95 
TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A7U9 
      149.03        92.98       174.21        15.72        27.85        18.77 
TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY 
       38.27        34.82       104.42       216.92        48.59       228.59 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZG 
       28.08         7.79        48.85       357.37        53.52         9.70 
TCGA-FS-A1ZH TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT 
       32.75       101.26       133.55        11.41       148.80        53.16 
TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FW-A3TU 
       77.82        66.67        34.03        26.73        54.41        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-A267 TCGA-GN-A268 TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 
       64.44        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-A8K1 TCGA-WE-A8K6 
       63.02       121.08         4.01       219.16        49.05        17.95 
TCGA-WE-A8ZN TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-YD-A89C TCGA-YD-A9TA 
       58.98        49.51        12.16        40.41         6.90        49.18 
TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
       14.43        27.58        96.99        15.98 

  6P GAIN MUTATED 6P GAIN WILD-TYPE 
             0.20              0.23 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
           368.78            369.93 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
           49.185            54.625 
[1] "0.2 - 368.8 (49.2)" "0.2 - 369.9 (54.6)"
[1] "hr=" "1.2"
D11V3, continuous
                   vv
clus                I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  6P GAIN MUTATED          1       1      14        5       16       12
  6P GAIN WILD-TYPE       12       6      15       13       12       14
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  6P GAIN MUTATED           5         6        11        14          5
  6P GAIN WILD-TYPE         9        13         4        25         10
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  6P GAIN MUTATED           16         16        8
  6P GAIN WILD-TYPE         19         38       13
D11V4, multiclass
            clus
vv           6P GAIN MUTATED 6P GAIN WILD-TYPE
  I/II NOS                 1                12
  STAGE 0                  1                 6
  STAGE I                 14                15
  STAGE IA                 5                13
  STAGE IB                16                12
  STAGE II                12                14
  STAGE IIA                5                 9
  STAGE IIB                6                13
  STAGE IIC               11                 4
  STAGE III               14                25
  STAGE IIIA               5                10
  STAGE IIIB              16                19
  STAGE IIIC              16                38
  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
  6P GAIN MUTATED      22 35 26 34
  6P GAIN WILD-TYPE    42 38 55 33
D11V5, multiclass
       clus
vv      6P GAIN MUTATED 6P GAIN WILD-TYPE
  T0+T1              22                42
  T2                 35                38
  T3                 26                55
  T4                 34                33
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  6P GAIN MUTATED    75  25  13  16
  6P GAIN WILD-TYPE 102  40  26  29
D11V6, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  N0              75               102
  N1              25                40
  N2              13                26
  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"
D11V7, binary
                   cls
clus                  0   1
  6P GAIN MUTATED   123   9
  6P GAIN WILD-TYPE 196  13
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED    123    9
  6P GAIN WILD-TYPE  196   13
   clus
vv  6P GAIN MUTATED 6P GAIN WILD-TYPE
  0             123               196
  1               9                13
[1] 2 2
[1] FALSE
D11V8, binary
                   cls
clus                 0  1
  6P GAIN MUTATED   50 39
  6P GAIN WILD-TYPE 84 51
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     50   39
  6P GAIN WILD-TYPE   84   51
     clus
vv    6P GAIN MUTATED 6P GAIN WILD-TYPE
  NO               50                84
  YES              39                51
[1] 2 2
[1] FALSE
D11V9, binary
                   cls
clus                  0   1
  6P GAIN MUTATED    22 126
  6P GAIN WILD-TYPE  25 194
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     22  126
  6P GAIN WILD-TYPE   25  194
     clus
vv    6P GAIN MUTATED 6P GAIN WILD-TYPE
  NO               22                25
  YES             126               194
[1] 2 2
[1] FALSE
D11V10, continuous
D11V11, binary
                   cls
clus                  0   1
  6P GAIN MUTATED    61  87
  6P GAIN WILD-TYPE  77 142
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     61   87
  6P GAIN WILD-TYPE   77  142
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  FEMALE              61                77
  MALE                87               142
[1] 2 2
[1] FALSE
D11V12, binary
                   cls
clus                  0   1
  6P GAIN MUTATED   130  17
  6P GAIN WILD-TYPE 189  30
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED    130   17
  6P GAIN WILD-TYPE  189   30
     clus
vv    6P GAIN MUTATED 6P GAIN WILD-TYPE
  NO              130               189
  YES              17                30
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  6P GAIN MUTATED       1                         0   143
  6P GAIN WILD-TYPE     4                         1   210
D11V13, multiclass
                           clus
vv                          6P GAIN MUTATED 6P GAIN WILD-TYPE
  ASIAN                                   1                 4
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                 143               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"
D11V14, binary
                   cls
clus                  0   1
  6P GAIN MUTATED     2 145
  6P GAIN WILD-TYPE   5 207
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      2  145
  6P GAIN WILD-TYPE    5  207
                        clus
vv                       6P GAIN MUTATED 6P GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 5
  NOT HISPANIC OR LATINO             145               207
[1] 2 2
[1] FALSE

Clustering(12) Variable = 6Q GAIN MUTATION ANALYSIS
D12V1, survival
                   sevent
clus2                 0   1
  6Q GAIN MUTATED    10  20
  6Q GAIN WILD-TYPE 118 104
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               30               222 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               20               104 
$`6Q GAIN MUTATED`
TCGA-EE-A20H TCGA-D3-A1Q3 TCGA-D3-A1Q7 TCGA-D3-A3CC TCGA-D3-A51E TCGA-D9-A1X3 
      166.75        15.72       133.25        40.01       173.85        10.78 
TCGA-DA-A95X TCGA-EE-A29B TCGA-EE-A2GS TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A3J3 
       65.03        75.22        71.31       171.85        89.26        67.89 
TCGA-EE-A3J8 TCGA-EE-A3JI TCGA-ER-A197 TCGA-ER-A19C TCGA-ER-A19M TCGA-ER-A19Q 
        3.35       135.98        10.49        39.81        59.84        49.71 
TCGA-ER-A19S TCGA-ER-A2NC TCGA-ER-A3EV TCGA-FS-A1ZW TCGA-FS-A4F8 TCGA-GN-A8LK 
       47.18        22.36        15.48        23.21       173.19        43.23 
TCGA-GN-A9SD TCGA-W3-AA1Q TCGA-W3-AA1V TCGA-W3-AA21 TCGA-WE-A8ZT TCGA-XV-AB01 
       59.41        44.05         8.09        92.84        10.95         6.61 

$`6Q GAIN WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A8GI TCGA-EB-A5SG TCGA-EE-A180 
        9.76        62.07        38.76        13.41        33.24        31.96 
TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 TCGA-FR-A729 
      269.03        52.90       134.40        27.35        19.04       216.43 
TCGA-FW-A3R5 TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 
       36.95        52.73         7.40        60.46        12.99        14.83 
TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q8 TCGA-D3-A1QA 
        8.42        31.89       110.93        49.35        19.04        76.41 
TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JB 
       62.60        25.64        45.99        62.86        15.75       168.00 
TCGA-D3-A2JC TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
       86.30       107.61        36.30       171.58        64.83        66.08 
TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO 
       43.53        58.06       140.98        59.70        24.53         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R 
       90.21        23.67        30.67       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        68.68       150.61       110.53        60.10 
TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-DA-A95V 
       64.83        58.85        30.44       225.11         8.71        72.10 
TCGA-DA-A95W TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN 
        0.76        14.14        12.30         3.91        16.41        52.41 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
       18.21        13.15        24.89        20.38         0.00        26.24 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G 
       75.55        79.20        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 
       47.41        47.74        27.16        61.12       346.49       185.19 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH 
      115.43        30.02        77.98        26.14        12.95       201.60 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP 
       68.65        10.62        32.48        18.35        93.63         0.76 
TCGA-EE-A2GR TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC 
        0.20        81.99       103.13        15.25         5.75        23.77 
TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP 
      209.79        94.19        63.25       104.78       145.45       227.01 
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-A3J4 TCGA-EE-A3J7 TCGA-EE-A3JB 
        4.41        54.51         6.28       111.85        45.90       168.85 
TCGA-EE-A3JH TCGA-ER-A195 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19D 
       19.86        34.45         7.82         4.54        53.29        11.47 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19W 
      184.60       150.12        99.06        42.51       120.76       146.63 
TCGA-ER-A1A1 TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES 
       73.05         4.70        16.87        10.19        28.67       173.29 
TCGA-ER-A3ET TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       68.52        32.05        74.47         4.50       174.21         4.14 
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-A1ZG 
        8.35        27.62       312.07        32.78        43.92         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-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        18.25         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-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS 
      120.53        34.49        46.92        85.05       297.01         7.23 
TCGA-RP-A690 TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1R 
        0.20         0.33       174.12         1.97       120.07        79.99 
TCGA-W3-AA1W TCGA-WE-A8K1 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ 
      185.13        47.54        65.42        12.69        21.90        62.89 
TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-Z2-AA3S 
       48.39         1.94        37.32        24.99        28.21        91.23 

  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
             3.35              0.00 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
           173.85            346.49 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
           48.445            45.945 
[1] "3.4 - 173.8 (48.4)" "0.0 - 346.5 (45.9)"
[1] "hr=" "1.5"
D12V2, survival
                   sevent
clus2                 0   1
  6Q GAIN MUTATED    19  31
  6Q GAIN WILD-TYPE 147 161
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               50               308 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               31               161 
$`6Q GAIN MUTATED`
TCGA-EB-A5SH TCGA-EE-A20H TCGA-QB-AA9O TCGA-D3-A1Q3 TCGA-D3-A1Q7 TCGA-D3-A3CC 
       54.02       168.26        18.05        16.67       133.25        86.93 
TCGA-D3-A51E TCGA-D3-A5GO TCGA-D9-A149 TCGA-D9-A1X3 TCGA-D9-A6E9 TCGA-DA-A1I0 
      174.84       137.92        54.67        18.12         9.90        20.38 
TCGA-DA-A95X TCGA-EE-A20B TCGA-EE-A29B TCGA-EE-A29R TCGA-EE-A2GS TCGA-EE-A2GT 
       73.94       133.81        85.08        14.47        81.21        44.88 
TCGA-EE-A2ME TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2MN TCGA-EE-A3J3 TCGA-EE-A3J5 
      103.27       204.66       180.39        47.54       172.18        36.95 
TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JI TCGA-ER-A197 TCGA-ER-A19C TCGA-ER-A19E 
       34.32        53.19       152.81        13.94        48.89        13.02 
TCGA-ER-A19M TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A2NC TCGA-ER-A3EV TCGA-FS-A1ZA 
       61.05        50.89        49.48        43.82        46.98        27.72 
TCGA-FS-A1ZK TCGA-FS-A1ZW TCGA-FS-A4F2 TCGA-FS-A4F8 TCGA-GF-A6C9 TCGA-GN-A266 
       23.93        49.48        50.14       174.84        15.78        10.13 
TCGA-GN-A8LK TCGA-GN-A9SD TCGA-W3-AA1Q TCGA-W3-AA1V TCGA-W3-AA21 TCGA-WE-A8ZT 
       50.10        59.41        69.07        42.08       105.04        11.80 
TCGA-WE-A8ZX TCGA-XV-AB01 
       35.80        13.25 

$`6Q GAIN WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-D3-A8GI TCGA-EB-A5SG 
       27.65        62.07        46.32        13.87        58.52        68.25 
TCGA-EE-A180 TCGA-EE-A184 TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR 
       94.98        68.15         2.60       340.14       126.81       134.40 
TCGA-EE-A3JD TCGA-ER-A193 TCGA-ER-A198 TCGA-FR-A729 TCGA-FS-A1ZF TCGA-FW-A3R5 
       27.35        31.40        50.76       220.80        15.45        36.95 
TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 
       61.15        21.40        17.03        66.48        12.99        14.93 
TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q8 TCGA-D3-A1Q9 
       16.57       112.04       112.57        71.80        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-A2JG TCGA-D3-A2JH 
      115.53       168.00        86.76        11.87       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-A3CB TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO 
       58.06        46.98       166.52        60.23        24.53         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J 
      103.59        39.75        45.30        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-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-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-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-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6EA 
        3.65         7.10        15.39        22.29        18.44        25.18 
TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I1 
       77.56        22.95        76.57        36.03       144.89       222.51 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA 
      176.55        35.93       135.02        88.87        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        43.36 
TCGA-DA-A95V TCGA-DA-A95W TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A44R 
       72.10        37.35        14.14        13.02        13.87        10.36 
TCGA-EB-A5KH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X 
       20.35        29.29        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-A185 
       27.22         8.65        33.73        14.70        26.89         4.96 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29D 
      151.27        91.56        13.55        63.35        78.97        13.97 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P 
       63.78        72.07        64.64        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-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
       67.43       173.79       220.24        48.72       107.38        54.74 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GU 
       79.66        75.48       102.12        13.91        42.77        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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MM 
      268.73       103.20        16.96        96.23       216.66       167.90 
TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA 
      248.65        43.23       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-A3J4 TCGA-EE-A3J7 TCGA-EE-A3JB TCGA-EE-A3JE TCGA-EE-A3JH 
      138.81       127.20        64.08       201.80        51.35       134.33 
TCGA-ER-A195 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19F 
       35.44         9.17        77.75        98.40        12.59        26.37 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A19P 
      302.07       152.35         6.44       131.51        44.09       162.08 
TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF 
        8.88       148.18       105.07        23.34        20.15        28.83 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3PL TCGA-ER-A42K 
       48.99        41.56       247.04        93.01        33.21        12.95 
TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A7U9 
      149.03        92.98       174.21        15.72        27.85        18.77 
TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-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-A1ZB 
      228.59       202.65        20.91        28.08         7.79        48.85 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ 
      357.37        53.52        46.45         9.70        32.75        47.38 
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-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 
       26.56        27.09        27.02        77.82        66.67        28.73 
TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU 
       34.03        26.73        54.41        80.68        17.46        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        19.43         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-A8LL 
      121.91        39.35        10.42        48.89        22.13        21.37 
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-AA1R TCGA-W3-AA1W TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K6 TCGA-WE-A8ZM 
      111.09       219.16        24.03        49.05        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-AAA4 TCGA-YD-A89C TCGA-YD-A9TA TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-A8RT 
       24.99         6.90        49.18        37.94        14.43        27.58 
TCGA-Z2-AA3S TCGA-Z2-AA3V 
       96.99        15.98 

  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
              9.9               0.2 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
           204.66            369.93 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
            49.79             53.72 
[1] "9.9 - 204.7 (49.8)" "0.2 - 369.9 (53.7)"
[1] "hr=" "1.3"
D12V3, continuous
                   vv
clus                I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  6Q GAIN MUTATED          1       0       7        1        9        5
  6Q GAIN WILD-TYPE       12       7      22       17       19       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        34         13
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  6Q GAIN MUTATED            5          2        2
  6Q GAIN WILD-TYPE         30         52       19
D12V4, multiclass
            clus
vv           6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  I/II NOS                 1                12
  STAGE 0                  0                 7
  STAGE I                  7                22
  STAGE IA                 1                17
  STAGE IB                 9                19
  STAGE II                 5                21
  STAGE IIA                1                13
  STAGE IIB                2                17
  STAGE IIC                3                12
  STAGE III                5                34
  STAGE IIIA               2                13
  STAGE IIIB               5                30
  STAGE IIIC               2                52
  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
  6Q GAIN MUTATED       4 15  8 15
  6Q GAIN WILD-TYPE    60 58 73 52
D12V5, multiclass
       clus
vv      6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  T0+T1               4                60
  T2                 15                58
  T3                  8                73
  T4                 15                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
  6Q GAIN MUTATED    29  10   2   2
  6Q GAIN WILD-TYPE 148  55  37  43
D12V6, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  N0              29               148
  N1              10                55
  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"
D12V7, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED    43   2
  6Q GAIN WILD-TYPE 276  20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED     43    2
  6Q GAIN WILD-TYPE  276   20
   clus
vv  6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  0              43               276
  1               2                20
[1] 2 2
[1] FALSE
D12V8, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED    22  12
  6Q GAIN WILD-TYPE 112  78
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED     22   12
  6Q GAIN WILD-TYPE  112   78
     clus
vv    6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  NO               22               112
  YES              12                78
[1] 2 2
[1] FALSE
D12V9, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED     6  44
  6Q GAIN WILD-TYPE  41 276
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      6   44
  6Q GAIN WILD-TYPE   41  276
     clus
vv    6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  NO                6                41
  YES              44               276
[1] 2 2
[1] FALSE
D12V10, continuous
D12V11, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED    19  31
  6Q GAIN WILD-TYPE 119 198
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED     19   31
  6Q GAIN WILD-TYPE  119  198
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  FEMALE              19               119
  MALE                31               198
[1] 2 2
[1] FALSE
D12V12, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED    44   6
  6Q GAIN WILD-TYPE 275  41
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED     44    6
  6Q GAIN WILD-TYPE  275   41
     clus
vv    6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  NO               44               275
  YES               6                41
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  6Q GAIN MUTATED       0                         0    50
  6Q GAIN WILD-TYPE     5                         1   303
D12V13, multiclass
                           clus
vv                          6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  ASIAN                                   0                 5
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  50               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"
D12V14, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED     0  50
  6Q GAIN WILD-TYPE   7 302
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      0   50
  6Q GAIN WILD-TYPE    7  302
                        clus
vv                       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 7
  NOT HISPANIC OR LATINO              50               302
[1] 2 2
[1] FALSE

Clustering(13) Variable = 7P GAIN MUTATION ANALYSIS
D13V1, survival
                   sevent
clus2                0  1
  7P GAIN MUTATED   75 60
  7P GAIN WILD-TYPE 53 64
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              135               117 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               60                64 
$`7P GAIN MUTATED`
TCGA-D3-A2JE TCGA-D3-A3C8 TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GO TCGA-EE-A2MR 
        9.76        38.76        31.96       166.75        52.90       134.40 
TCGA-FR-A729 TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-3N-A9WC TCGA-BF-AAP0 TCGA-D3-A1Q1 
      216.43        52.73         7.40        60.46        14.83         8.42 
TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A2JA TCGA-D3-A2JC 
       15.72        31.89       110.93        49.35        15.75        86.30 
TCGA-D3-A2JG TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CB 
      107.61       171.58        64.83        43.53        58.06       140.98 
TCGA-D3-A3CC TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51J TCGA-D3-A51R 
       40.01         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       110.53        60.10        64.83        58.85       225.11 
TCGA-DA-A95V TCGA-DA-A95W TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN 
       72.10         0.76        12.30         3.91        16.41        52.41 
TCGA-EB-A6L9 TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
       18.21        24.89        20.38        76.14        12.99         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-A2GJ TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP 
      201.60        68.65        32.48        18.35        93.63         0.76 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MP 
      103.13        15.25        63.25        89.26       145.45       227.01 
TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
      143.93        53.26       124.31         4.41        54.51         6.28 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3JB TCGA-ER-A197 TCGA-ER-A199 
       67.89       111.85        45.90       168.85        10.49         7.82 
TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19P TCGA-ER-A19S 
       53.29        39.81       184.60       150.12       120.76        47.18 
TCGA-ER-A2ND TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A 
        4.70        15.48        32.05        74.47         4.50       174.21 
TCGA-FR-A69P TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZC 
        4.14         5.65        10.06         8.35        27.62       312.07 
TCGA-FS-A1ZD TCGA-FS-A1ZG TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZY TCGA-FS-A1ZZ 
       32.78         7.82        78.61       130.95         5.29         3.06 
TCGA-FS-A4F8 TCGA-FW-A5DY TCGA-GF-A4EO TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 
      173.19        19.30        18.25       117.93        96.92        17.06 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U8 TCGA-GN-A8LK TCGA-GN-A9SD TCGA-QB-A6FS 
       42.48         7.59        46.92        43.23        59.41         7.23 
TCGA-RP-A690 TCGA-W3-AA1R TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8ZM TCGA-WE-A8ZQ 
        0.20        79.99       185.13        92.84        65.42        62.89 
TCGA-WE-AA9Y TCGA-XV-AB01 TCGA-YG-AA3O 
        1.94         6.61        28.21 

$`7P GAIN WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A8GI TCGA-EB-A5SG TCGA-EE-A2GD TCGA-EE-A3JD TCGA-ER-A193 
       62.07        13.41        33.24       269.03        27.35        19.04 
TCGA-FW-A3R5 TCGA-3N-A9WD TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB 
       36.95        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-A51F TCGA-D3-A51K TCGA-D3-A51T 
       59.70        24.53       173.85        30.67        31.76        11.34 
TCGA-D3-A5GL TCGA-D3-A8GJ TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GR TCGA-D9-A1X3 
       42.05       179.97        69.53        70.62        36.53        10.78 
TCGA-D9-A3Z1 TCGA-D9-A4Z6 TCGA-DA-A1I1 TCGA-DA-A3F2 TCGA-DA-A3F8 TCGA-DA-A95X 
       15.02        18.44        68.68        30.44         8.71        65.03 
TCGA-DA-A95Y TCGA-EE-A17X TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A20F 
       14.14        13.15         0.00        26.24        75.55        79.20 
TCGA-EE-A29B TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29Q TCGA-EE-A2A1 
       75.22        44.28        47.41        47.74        61.12       115.43 
TCGA-EE-A2A2 TCGA-EE-A2GK TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M8 
       30.02        10.62         0.20        71.31        81.99         5.75 
TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2ML TCGA-EE-A2MT 
       23.77       209.79        94.19       171.85       104.78        23.51 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3J8 TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 
      122.73        64.04         3.35        19.86       135.98        34.45 
TCGA-ER-A19A TCGA-ER-A19D TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19Q 
        4.54        11.47        99.06        59.84        42.51        49.71 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
      146.63        73.05        22.36        16.87        10.19        28.67 
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-A1ZJ TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW 
       43.92        36.33       136.27        35.28         4.47        23.21 
TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV 
       30.90        66.67        13.28        80.68        55.59        11.54 
TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-LH-A9QB 
        9.90         1.91        53.29       120.53        34.49        85.05 
TCGA-OD-A75X TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1Q 
      297.01         0.33       174.12         1.97       120.07        44.05 
TCGA-W3-AA1V TCGA-WE-A8K1 TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-A8ZY 
        8.09        47.54        12.69        21.90        10.95        48.39 
TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-Z2-AA3S 
       37.32        24.99        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 
            52.73             42.51 
[1] "0.2 - 346.5 (52.7)" "0.0 - 297.0 (42.5)"
[1] "hr=" "1.4"
D13V2, survival
                   sevent
clus2                 0   1
  7P GAIN MUTATED    98 101
  7P GAIN WILD-TYPE  68  91
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              199               159 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              101                91 
$`7P GAIN MUTATED`
TCGA-D3-A2JE TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GO 
       27.65        46.32        13.87        94.98       168.26       126.81 
TCGA-EE-A2MR TCGA-FR-A729 TCGA-QB-AA9O TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-3N-A9WB 
      134.40       220.80        18.05        61.15        21.40        17.03 
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-A1Q9 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JD 
       71.80        31.59        23.77       115.53        86.76        11.87 
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-A3CB TCGA-D3-A3CC TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU 
       46.98       166.52        86.93         9.34       103.59        39.75 
TCGA-D3-A51J TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS 
      145.12        22.62        63.81       135.75       178.32        18.18 
TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GK TCGA-D3-A8GN 
      125.19        30.84        79.59        23.61       170.20       161.00 
TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GS TCGA-D3-A8GV TCGA-D9-A148 TCGA-D9-A149 
      152.75        29.06       117.17       167.70       151.53        54.67 
TCGA-D9-A1JX TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG 
        7.10        22.29         9.90        25.18        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-A1IC TCGA-DA-A3F5 
      135.02        88.87        53.92        65.92        68.09       225.96 
TCGA-DA-A95V TCGA-DA-A95W TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UL 
       72.10        37.35        13.02        13.87        20.35        29.29 
TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A20B TCGA-EE-A29A 
       58.92        36.46        27.22        33.73       133.81        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-A2GP 
       48.72       107.38        79.66        75.48       102.12        13.91 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MH TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2MM 
      129.27        28.83        16.96        96.23       180.39       167.90 
TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AA 
       47.54       248.65        43.23       162.48        53.26       124.31 
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-A3JB TCGA-ER-A197 TCGA-ER-A199 
      127.20        36.95        64.08       201.80        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       302.07       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-A7U9 
       12.95       149.03        92.98       174.21        15.72        18.77 
TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YX TCGA-FS-A1Z3 
       38.27        34.82        36.26       104.42        48.59        20.91 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZG TCGA-FS-A1ZH 
       28.08         7.79       357.37        53.52         9.70        32.75 
TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F2 
      101.26       133.55        11.41        27.09        27.02        50.14 
TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FW-A3I3 TCGA-FW-A5DY TCGA-GF-A4EO TCGA-GF-A6C9 
       28.73       174.84        17.46        19.30        19.43        15.78 
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-A4U7 TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A9SD 
       48.00        10.42        48.89        22.13        50.10        59.41 
TCGA-HR-A2OG TCGA-HR-A2OH TCGA-QB-A6FS TCGA-RP-A690 TCGA-W3-AA1O TCGA-W3-AA1R 
        0.23        65.88         7.23         0.20         4.01       111.09 
TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZQ 
      219.16       105.04        24.03        17.95       101.33        63.22 
TCGA-WE-A8ZX TCGA-WE-AA9Y TCGA-XV-AB01 TCGA-YD-A89C TCGA-YD-A9TA TCGA-YG-AA3O 
       35.80        12.16        13.25         6.90        49.18        37.94 
TCGA-YG-AA3P 
       14.43 

$`7P GAIN WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A8GI TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A184 TCGA-EE-A29L 
       62.07        58.52        68.25        54.02        68.15         2.60 
TCGA-EE-A2GD TCGA-EE-A3JD TCGA-ER-A193 TCGA-ER-A198 TCGA-FS-A1ZF TCGA-FW-A3R5 
      340.14        27.35        31.40        50.76        15.45        36.95 
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-A2JH TCGA-D3-A2JK TCGA-D3-A2JO 
      103.10        65.49       168.00        42.08        12.10        66.08 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
       60.23        24.53        45.30       174.84        55.73        56.35 
TCGA-D3-A51K TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GO TCGA-D3-A8GE TCGA-D3-A8GJ 
       32.94        26.89       125.79       137.92        26.43       241.38 
TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GR TCGA-D9-A1JW TCGA-D9-A1X3 TCGA-D9-A3Z1 
       89.13       107.15       129.63         3.65        18.12        15.39 
TCGA-D9-A4Z6 TCGA-DA-A1I1 TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 
       18.44       222.51        40.60        33.93        10.49        43.36 
TCGA-DA-A95X TCGA-DA-A95Y TCGA-EB-A44R TCGA-EB-A5VV TCGA-EE-A17X TCGA-EE-A17Z 
       73.94        14.14        10.36         7.04        29.82         8.65 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I 
       14.70        26.89         4.96       151.27        91.56        13.55 
TCGA-EE-A29B TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29Q TCGA-EE-A29R 
       85.08        72.07        64.64        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-A2GK TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU 
       67.43        54.74        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-A2MI TCGA-EE-A2ML TCGA-EE-A2MT TCGA-EE-A3AB TCGA-EE-A3AC 
      103.20       204.66       216.66        71.21       122.73        64.04 
TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 
       34.32        53.19        51.35       134.33       152.81        35.44 
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        44.09 
TCGA-ER-A19Q TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NF 
       50.89       148.18       105.07        43.82        20.15        28.83 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-FR-A7U8 TCGA-FS-A1YW 
       48.99        41.56       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-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW 
       23.93        74.73       148.80        53.16        26.56        49.48 
TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD 
       77.82        66.67        34.03        26.73        54.41        80.68 
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 
            50.14             53.16 
[1] "0.2 - 369.9 (50.1)" "0.3 - 368.8 (53.2)"
[1] "hr=" "1.1"
D13V3, continuous
                   vv
clus                I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  7P GAIN MUTATED         11       1      18        9        9       14
  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        13          4
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  7P GAIN MUTATED           21         29       13
  7P GAIN WILD-TYPE         14         25        8
D13V4, multiclass
            clus
vv           7P GAIN MUTATED 7P GAIN WILD-TYPE
  I/II NOS                11                 2
  STAGE 0                  1                 6
  STAGE I                 18                11
  STAGE IA                 9                 9
  STAGE IB                 9                19
  STAGE II                14                12
  STAGE IIA                8                 6
  STAGE IIB                6                13
  STAGE IIC               10                 5
  STAGE III               26                13
  STAGE IIIA              11                 4
  STAGE IIIB              21                14
  STAGE IIIC              29                25
  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 43 39
  7P GAIN WILD-TYPE    24 37 38 28
D13V5, multiclass
       clus
vv      7P GAIN MUTATED 7P GAIN WILD-TYPE
  T0+T1              40                24
  T2                 36                37
  T3                 43                38
  T4                 39                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
  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   174  14
  7P GAIN WILD-TYPE 145   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED    174   14
  7P GAIN WILD-TYPE  145    8
   clus
vv  7P GAIN MUTATED 7P GAIN WILD-TYPE
  0             174               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    31 173
  7P GAIN WILD-TYPE  16 147
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     31  173
  7P GAIN WILD-TYPE   16  147
     clus
vv    7P GAIN MUTATED 7P GAIN WILD-TYPE
  NO               31                16
  YES             173               147
[1] 2 2
[1] FALSE
D13V10, continuous
D13V11, binary
                   cls
clus                  0   1
  7P GAIN MUTATED    83 121
  7P GAIN WILD-TYPE  55 108
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     83  121
  7P GAIN WILD-TYPE   55  108
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  FEMALE              83                55
  MALE               121               108
[1] 2 2
[1] FALSE
D13V12, binary
                   cls
clus                  0   1
  7P GAIN MUTATED   178  25
  7P GAIN WILD-TYPE 141  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED    178   25
  7P GAIN WILD-TYPE  141   22
     clus
vv    7P GAIN MUTATED 7P GAIN WILD-TYPE
  NO              178               141
  YES              25                22
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  7P GAIN MUTATED       4                         0   194
  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                                 194               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     5 193
  7P GAIN WILD-TYPE   2 159
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      5  193
  7P GAIN WILD-TYPE    2  159
                        clus
vv                       7P GAIN MUTATED 7P GAIN WILD-TYPE
  HISPANIC OR LATINO                   5                 2
  NOT HISPANIC OR LATINO             193               159
[1] 2 2
[1] FALSE

Clustering(14) Variable = 7Q GAIN MUTATION ANALYSIS
D14V1, survival
                   sevent
clus2                0  1
  7Q GAIN MUTATED   73 60
  7Q GAIN WILD-TYPE 55 64
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              133               119 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               60                64 
$`7Q GAIN MUTATED`
TCGA-D3-A2JE TCGA-D3-A3C8 TCGA-D3-A8GI TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GO 
        9.76        38.76        13.41        31.96       166.75        52.90 
TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 TCGA-FR-A729 TCGA-WE-A8K5 TCGA-WE-AAA3 
      134.40        27.35        19.04       216.43        52.73         7.40 
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-A2JG TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JP 
       15.75        86.30       107.61       171.58        64.83        43.53 
TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU 
       58.06       140.98        40.01         9.34        90.21        23.67 
TCGA-D3-A51J TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D3-A8GC 
      144.46        62.70        45.70       177.86       124.08        78.21 
TCGA-D3-A8GD TCGA-D3-A8GK TCGA-D3-A8GP TCGA-D9-A3Z3 TCGA-D9-A6EC TCGA-D9-A6EG 
       23.61       120.00       135.12        16.90        69.21        22.85 
TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA 
       76.34       138.67       150.61       110.53        60.10        64.83 
TCGA-DA-A1IC TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-DA-A95W TCGA-DA-A95Y TCGA-DA-A95Z 
       58.85       225.11         8.71         0.76        14.14        12.30 
TCGA-EB-A44Q TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A183 
        3.91        52.41        18.21        24.89        20.38        26.24 
TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29P TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A6 
       76.14         0.26        27.16       346.49       185.19        77.98 
TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GP 
       26.14        12.95       201.60        32.48        18.35         0.76 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MP 
      103.13        15.25        63.25        89.26       145.45       227.01 
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-A197 TCGA-ER-A199 TCGA-ER-A19B 
      111.85        45.90       168.85        10.49         7.82        53.29 
TCGA-ER-A19C TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19P TCGA-ER-A19S TCGA-ER-A2ND 
       39.81       184.60       150.12       120.76        47.18         4.70 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       15.48        32.05        74.47         4.50       174.21         4.14 
TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD 
        5.65        10.06         8.35        27.62       312.07        32.78 
TCGA-FS-A1ZG TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZY TCGA-FS-A1ZZ 
        7.82        78.61       130.95       136.27         5.29         3.06 
TCGA-FS-A4F8 TCGA-FW-A5DY TCGA-GF-A4EO TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 
      173.19        19.30        18.25       117.93        96.92        17.06 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A8LK TCGA-GN-A9SD TCGA-LH-A9QB TCGA-QB-A6FS 
       42.48         7.59        43.23        59.41        85.05         7.23 
TCGA-W3-AA1R TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8ZQ TCGA-WE-AA9Y TCGA-XV-AB01 
       79.99       185.13        92.84        62.89         1.94         6.61 
TCGA-YG-AA3O 
       28.21 

$`7Q GAIN WILD-TYPE`
TCGA-D3-A2JF TCGA-EB-A5SG TCGA-EE-A2GD TCGA-FW-A3R5 TCGA-3N-A9WC TCGA-3N-A9WD 
       62.07        33.24       269.03        36.95        60.46        12.99 
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-A2JH TCGA-D3-A2JO TCGA-D3-A3CE TCGA-D3-A3CF 
       62.86       168.00        36.30        66.08        59.70        24.53 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51K TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A8GJ 
      173.85        30.67        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-A95V TCGA-DA-A95X TCGA-EB-A5KH TCGA-EE-A17X 
       68.68        30.44        72.10        65.03        16.41        13.15 
TCGA-EE-A182 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29G 
        0.00        75.55        79.20        75.22        12.99        44.28 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29Q TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2GJ 
       47.41        47.74        61.12       115.43        30.02        68.65 
TCGA-EE-A2GK TCGA-EE-A2GN TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M8 
       10.62        93.63         0.20        71.31        81.99         5.75 
TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2ML TCGA-EE-A2MT 
       23.77       209.79        94.19       171.85       104.78        23.51 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3J8 TCGA-EE-A3JH TCGA-EE-A3JI 
      122.73        64.04         4.41         3.35        19.86       135.98 
TCGA-ER-A195 TCGA-ER-A19A TCGA-ER-A19D TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
       34.45         4.54        11.47        99.06        59.84        42.51 
TCGA-ER-A19Q TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NF 
       49.71       146.63        73.05        22.36        16.87        10.19 
TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-FR-A7U8 TCGA-FS-A1YW TCGA-FS-A1YY 
       28.67       173.29        68.52        26.20       171.78        49.74 
TCGA-FS-A1Z0 TCGA-FS-A1ZE TCGA-FS-A1ZJ TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW 
      195.98        43.92        36.33        35.28         4.47        23.21 
TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV 
       30.90        66.67        13.28        80.68        55.59        11.54 
TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 
        9.90         1.91        53.29       120.53        34.49        46.92 
TCGA-OD-A75X TCGA-RP-A690 TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 
      297.01         0.20         0.33       174.12         1.97       120.07 
TCGA-W3-AA1Q TCGA-W3-AA1V TCGA-WE-A8K1 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO 
       44.05         8.09        47.54        65.42        12.69        21.90 
TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-Z2-AA3S 
       10.95        48.39        37.32        24.99        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 
            49.35             44.28 
[1] "0.3 - 346.5 (49.4)" "0.0 - 297.0 (44.3)"
[1] "hr=" "1.4"
D14V2, survival
                   sevent
clus2                0  1
  7Q GAIN MUTATED   95 99
  7Q GAIN WILD-TYPE 71 93
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              194               164 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               99                93 
$`7Q GAIN MUTATED`
TCGA-D3-A2JE TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-D3-A8GI TCGA-EE-A180 TCGA-EE-A20H 
       27.65        46.32        13.87        58.52        94.98       168.26 
TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 TCGA-FR-A729 TCGA-FS-A1ZF 
      126.81       134.40        27.35        31.40       220.80        15.45 
TCGA-QB-AA9O TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q3 
       18.05        61.15        21.40        14.93        16.57        16.67 
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A2JA 
      112.04       112.57        71.80        31.59        23.77       115.53 
TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JP 
       86.76        11.87       113.52       171.58        66.48        59.57 
TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3MO 
      130.72        58.06        46.98       166.52        86.93         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-A8GK TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GS TCGA-D3-A8GV 
      170.20       161.00       152.75        29.06       117.17       167.70 
TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JX TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA 
      151.53        54.67         7.10        22.29         9.90        25.18 
TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I2 
       77.56        22.95        76.57        36.03       144.89       176.55 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IC 
       35.93       135.02        88.87        53.92        65.92        68.09 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-DA-A95W TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q 
      225.96        43.36        37.35        14.14        13.02        13.87 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A183 
       29.29        58.92        36.46        27.22        33.73        26.89 
TCGA-EE-A20B TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29N TCGA-EE-A29P 
      133.81        63.35        78.97        63.78        18.61        56.42 
TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A0 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE 
      369.93       195.02        46.82        86.14        59.28       173.79 
TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GP TCGA-EE-A2M6 
      220.24        48.72        79.66        75.48        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-A2MS TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AE TCGA-EE-A3AF 
       43.23       162.48        53.26       124.31        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-A3JB TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19E 
      201.80        13.94         9.17        98.40        48.89        13.02 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19P TCGA-ER-A19S TCGA-ER-A19T 
      302.07       152.35         6.44       162.08        49.48         8.88 
TCGA-ER-A2ND TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A3YN 
       23.34        46.98        33.21        12.95       149.03        92.98 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD 
      174.21        15.72        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-A1ZS TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F2 TCGA-FS-A4F5 TCGA-FS-A4F8 
      148.80        27.09        27.02        50.14        28.73       174.84 
TCGA-FW-A3I3 TCGA-FW-A5DY TCGA-GF-A4EO TCGA-GF-A6C9 TCGA-GN-A264 TCGA-GN-A265 
       17.46        19.30        19.43        15.78       117.93        96.92 
TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U7 
       10.13        64.44        62.79        32.48        48.00        10.42 
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-AA1O TCGA-W3-AA1R TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8JZ 
        7.23         4.01       111.09       219.16       105.04        24.03 
TCGA-WE-A8K6 TCGA-WE-A8ZQ TCGA-WE-A8ZX TCGA-WE-AA9Y TCGA-XV-AB01 TCGA-YD-A89C 
       17.95        63.22        35.80        12.16        13.25         6.90 
TCGA-YG-AA3O TCGA-YG-AA3P 
       37.94        14.43 

$`7Q GAIN WILD-TYPE`
TCGA-D3-A2JF TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A184 TCGA-EE-A29L TCGA-EE-A2GD 
       62.07        68.25        54.02        68.15         2.60       340.14 
TCGA-ER-A198 TCGA-FW-A3R5 TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q7 
       50.76        36.95        17.03        66.48        12.99       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-A2JB TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JO TCGA-D3-A3CE TCGA-D3-A3CF 
      168.00        42.08        12.10        66.08        60.23        24.53 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51T 
      174.84        55.73        56.35        32.94        22.62        26.89 
TCGA-D3-A5GL TCGA-D3-A5GO TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GL TCGA-D3-A8GM 
      125.79       137.92        26.43       241.38        89.13       107.15 
TCGA-D3-A8GR TCGA-D9-A1JW TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A4Z6 TCGA-DA-A1I0 
      129.63         3.65        18.12        15.39        18.44        20.38 
TCGA-DA-A1I1 TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A95V TCGA-DA-A95X 
      222.51        40.60        33.93        10.49        72.10        73.94 
TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5VV TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A182 
       10.36        20.35         7.04        29.82         8.65        14.70 
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-A29M TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
       72.07        64.64        56.84        66.74        14.47        61.28 
TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2GC 
       25.87        17.92       115.96        59.64        39.29        67.43 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GN TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT 
      107.38        54.74       102.12        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-A2MN TCGA-EE-A2MT 
      268.73       103.20       204.66       216.66        47.54        71.21 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JE 
      122.73        64.04        28.77        34.32        53.19        51.35 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A19A TCGA-ER-A19D TCGA-ER-A19F 
      134.33       152.81        35.44        77.75        12.59        26.37 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A19W TCGA-ER-A1A1 
      131.51        61.05        44.09        50.89       148.18       105.07 
TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES 
       43.82        20.15        28.83        48.99        41.56       247.04 
TCGA-ER-A3ET TCGA-FR-A7U8 TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1ZA 
       93.01        27.85       216.92       228.59       202.65        27.72 
TCGA-FS-A1ZB TCGA-FS-A1ZE TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZT 
       48.85        46.45        47.38        23.93        74.73        53.16 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F9 TCGA-FS-A4FB 
       26.56        49.48        77.82        66.67        34.03        26.73 
TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV TCGA-GF-A3OT TCGA-GF-A6C8 
       54.41        80.68        55.59        13.51         9.90         2.04 
TCGA-GN-A262 TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-GN-A8LL TCGA-OD-A75X 
      139.89       121.91        39.35        48.89        21.37       297.90 
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-AA1V TCGA-WE-A8K1 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO 
       69.07        42.08        49.05       101.33        58.98        70.52 
TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-YD-A9TA TCGA-Z2-A8RT 
       11.80        49.51        40.41        24.99        49.18        27.58 
TCGA-Z2-AA3S TCGA-Z2-AA3V 
       96.99        15.98 

  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
             0.23              0.20 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
           369.93            340.14 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
           51.700            52.255 
[1] "0.2 - 369.9 (51.7)" "0.2 - 340.1 (52.3)"
[1] "hr=" "1.2"
D14V3, continuous
                   vv
clus                I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  7Q GAIN MUTATED         11       2      18        8        9       14
  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        11        25         11
  7Q GAIN WILD-TYPE         8        12         4        14          4
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  7Q GAIN MUTATED           22         28       11
  7Q GAIN WILD-TYPE         13         26       10
D14V4, multiclass
            clus
vv           7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  I/II NOS                11                 2
  STAGE 0                  2                 5
  STAGE I                 18                11
  STAGE IA                 8                10
  STAGE IB                 9                19
  STAGE II                14                12
  STAGE IIA                6                 8
  STAGE IIB                7                12
  STAGE IIC               11                 4
  STAGE III               25                14
  STAGE IIIA              11                 4
  STAGE IIIB              22                13
  STAGE IIIC              28                26
  STAGE IV                11                10
[1] 14  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1 T2 T3 T4
  7Q GAIN MUTATED      36 36 43 39
  7Q GAIN WILD-TYPE    28 37 38 28
D14V5, multiclass
       clus
vv      7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  T0+T1              36                28
  T2                 36                37
  T3                 43                38
  T4                 39                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   94 38 23 26
  7Q GAIN WILD-TYPE 83 27 16 19
D14V6, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  N0              94                83
  N1              38                27
  N2              23                16
  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"
D14V7, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED   174  12
  7Q GAIN WILD-TYPE 145  10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED    174   12
  7Q GAIN WILD-TYPE  145   10
   clus
vv  7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  0             174               145
  1              12                10
[1] 2 2
[1] FALSE
D14V8, binary
                   cls
clus                 0  1
  7Q GAIN MUTATED   76 44
  7Q GAIN WILD-TYPE 58 46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     76   44
  7Q GAIN WILD-TYPE   58   46
     clus
vv    7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  NO               76                58
  YES              44                46
[1] 2 2
[1] FALSE
D14V9, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED    29 170
  7Q GAIN WILD-TYPE  18 150
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     29  170
  7Q GAIN WILD-TYPE   18  150
     clus
vv    7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  NO               29                18
  YES             170               150
[1] 2 2
[1] FALSE
D14V10, continuous
D14V11, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED    83 116
  7Q GAIN WILD-TYPE  55 113
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     83  116
  7Q GAIN WILD-TYPE   55  113
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  FEMALE              83                55
  MALE               116               113
[1] 2 2
[1] FALSE
D14V12, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED   176  23
  7Q GAIN WILD-TYPE 143  24
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED    176   23
  7Q GAIN WILD-TYPE  143   24
     clus
vv    7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  NO              176               143
  YES              23                24
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  7Q GAIN MUTATED       3                         0   190
  7Q GAIN WILD-TYPE     2                         1   163
D14V13, multiclass
                           clus
vv                          7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  ASIAN                                   3                 2
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                 190               163
[1] 3 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     5 188
  7Q GAIN WILD-TYPE   2 164
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      5  188
  7Q GAIN WILD-TYPE    2  164
                        clus
vv                       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   5                 2
  NOT HISPANIC OR LATINO             188               164
[1] 2 2
[1] FALSE

Clustering(15) Variable = 8P GAIN MUTATION ANALYSIS
D15V1, survival
                   sevent
clus2                0  1
  8P GAIN MUTATED   44 43
  8P GAIN WILD-TYPE 84 81
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               87               165 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               43                81 
$`8P GAIN MUTATED`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A8GI TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR 
        9.76        62.07        13.41       269.03        52.90       134.40 
TCGA-FR-A729 TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q6 TCGA-D3-A2J7 TCGA-D3-A2JC 
      216.43        60.46        12.99        49.35        45.99        86.30 
TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3MR 
       64.83        66.08        43.53        40.01        59.70        90.21 
TCGA-D3-A3MU TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D3-A8GP TCGA-D9-A6EC TCGA-D9-A6EG 
       23.67       177.86       124.08       135.12        69.21        22.85 
TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A3F5 TCGA-DA-A95W TCGA-DA-A95Z 
      138.67        68.68       150.61       225.11         0.76        12.30 
TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A29D TCGA-EE-A29G 
        3.91        16.41        24.89        20.38        12.99        44.28 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP 
       12.95       201.60        32.48        18.35        93.63         0.76 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE 
      103.13        15.25         5.75       122.73         4.41        54.51 
TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-ER-A19C TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L 
      111.85        45.90        39.81       184.60       150.12        99.06 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A2NC TCGA-ER-A2NF TCGA-ER-A42L TCGA-FR-A44A 
       59.84        42.51        22.36        10.19        74.47       174.21 
TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FS-A1YW TCGA-FS-A1Z4 TCGA-FS-A1ZD TCGA-FS-A1ZM 
       26.20         5.65       171.78        27.62        32.78        78.61 
TCGA-FS-A1ZQ TCGA-FS-A1ZY TCGA-FS-A4F4 TCGA-FS-A4FD TCGA-FW-A3TV TCGA-GF-A3OT 
      130.95         5.29        66.67        80.68        11.54         9.90 
TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A9SD TCGA-RP-A693 TCGA-W3-A824 
       17.06         7.59       120.53        59.41         0.33       174.12 
TCGA-W3-A825 TCGA-W3-AA1V TCGA-W3-AA21 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZQ 
        1.97         8.09        92.84        65.42        12.69        62.89 
TCGA-WE-A8ZT TCGA-XV-AB01 TCGA-YG-AA3O 
       10.95         6.61        28.21 

$`8P GAIN WILD-TYPE`
TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A3JD TCGA-ER-A193 
       38.76        33.24        31.96       166.75        27.35        19.04 
TCGA-FW-A3R5 TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q3 
       36.95        52.73         7.40        14.83         8.42        15.72 
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB 
       31.89       110.93       133.25        19.04        76.41        62.60 
TCGA-D3-A2J6 TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JG TCGA-D3-A2JH 
       25.64        62.86        15.75       168.00       107.61        36.30 
TCGA-D3-A2JL TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A51E 
      171.58        58.06       140.98        24.53         9.34       173.85 
TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL 
       30.67       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       110.53        60.10        64.83        58.85        30.44 
TCGA-DA-A3F8 TCGA-DA-A95V TCGA-DA-A95X TCGA-DA-A95Y TCGA-EB-A5UN TCGA-EB-A6L9 
        8.71        72.10        65.03        14.14        52.41        18.21 
TCGA-EE-A17X TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29B 
       13.15         0.00        26.24        75.55        79.20        75.22 
TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29Q 
       76.14         0.26        47.41        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-A2GJ TCGA-EE-A2GK TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2MC 
       68.65        10.62         0.20        71.31        81.99        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-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA 
      145.45       227.01       143.93        23.51        53.26       124.31 
TCGA-EE-A3AC TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH 
       64.04         6.28        67.89         3.35       168.85        19.86 
TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B 
      135.98        34.45        10.49         7.82         4.54        53.29 
TCGA-ER-A19D TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 
       11.47       120.76        49.71        47.18       146.63        73.05 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
        4.70        16.87        28.67       173.29        68.52        15.48 
TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A69P TCGA-FR-A8YC TCGA-FS-A1YY TCGA-FS-A1Z0 
       32.05         4.50         4.14        10.06        49.74       195.98 
TCGA-FS-A1Z3 TCGA-FS-A1ZC TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZS 
        8.35       312.07        43.92         7.82        36.33       136.27 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F8 
       35.28         4.47        23.21         3.06        30.90       173.19 
TCGA-FS-A4F9 TCGA-FW-A3TU TCGA-FW-A5DY TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 
       13.28        55.59        19.30        18.25         1.91        53.29 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A268 TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-GN-A8LK 
      117.93        96.92        42.48        34.49        46.92        43.23 
TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 TCGA-W3-A828 TCGA-W3-AA1Q 
       85.05       297.01         7.23         0.20       120.07        44.05 
TCGA-W3-AA1R TCGA-W3-AA1W TCGA-WE-A8K1 TCGA-WE-A8ZO TCGA-WE-A8ZY TCGA-WE-AA9Y 
       79.99       185.13        47.54        21.90        48.39         1.94 
TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-Z2-AA3S 
       37.32        24.99        91.23 

  8P GAIN MUTATED 8P GAIN WILD-TYPE 
             0.33              0.00 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
           269.03            346.49 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
            45.99             46.92 
[1] "0.3 - 269.0 (46.0)" "0.0 - 346.5 (46.9)"
[1] "hr=" "1"  
D15V2, survival
                   sevent
clus2                 0   1
  8P GAIN MUTATED    55  64
  8P GAIN WILD-TYPE 111 128
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
              119               239 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               64               128 
$`8P GAIN MUTATED`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A8GI TCGA-EB-A5SH TCGA-EE-A2GD TCGA-EE-A2GO 
       27.65        62.07        58.52        54.02       340.14       126.81 
TCGA-EE-A2MR TCGA-FR-A729 TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q6 
      134.40       220.80        17.03        66.48        12.99        71.80 
TCGA-D3-A1Q9 TCGA-D3-A2J7 TCGA-D3-A2JC TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP 
       31.59       103.10        86.76        66.48        66.08        59.57 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A5GR 
       86.93        60.23       103.59        39.75        45.30       178.32 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GP TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HW 
       18.18       125.19       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       222.51       176.55        35.93       225.96        37.35 
TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EE-A17Y TCGA-EE-A181 
       13.02        13.87        10.36        20.35        27.22        33.73 
TCGA-EE-A20B TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29R TCGA-EE-A2GE TCGA-EE-A2GH 
      133.81        13.97        72.07        14.47       173.79       220.24 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2M6 TCGA-EE-A2M7 
       79.66        75.48       102.12        13.91       129.27        28.83 
TCGA-EE-A2M8 TCGA-EE-A2MH TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3J4 
       19.76        16.96       122.73        28.77        54.51       127.20 
TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-ER-A19C TCGA-ER-A19G TCGA-ER-A19H 
       36.95        64.08        53.19        48.89       302.07       152.35 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A2NC TCGA-ER-A2NF 
        6.44       131.51        61.05        44.09        43.82        28.83 
TCGA-ER-A42L TCGA-FR-A44A TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YD 
      149.03       174.21        27.85        18.77        38.27        36.26 
TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZD TCGA-FS-A1ZK 
      216.92        48.59        28.08         7.79        53.52        23.93 
TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZY TCGA-FS-A4F2 
      101.26        74.73       133.55        11.41        27.09        50.14 
TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TV TCGA-GF-A3OT 
       66.67        28.73        80.68        17.46        13.51         9.90 
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-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 
       59.41        65.88         0.33         0.69       228.16        63.02 
TCGA-W3-AA1V TCGA-W3-AA21 TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZQ 
       42.08       105.04        17.95       101.33        58.98        63.22 
TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-XV-AB01 TCGA-YG-AA3O TCGA-Z2-AA3V 
       11.80        35.80        13.25        37.94        15.98 

$`8P GAIN WILD-TYPE`
TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A184 TCGA-EE-A20H 
       46.32        13.87        68.25        94.98        68.15       168.26 
TCGA-EE-A29L TCGA-EE-A3JD TCGA-ER-A193 TCGA-ER-A198 TCGA-FS-A1ZF TCGA-FW-A3R5 
        2.60        27.35        31.40        50.76        15.45        36.95 
TCGA-QB-AA9O TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q3 
       18.05        61.15        21.40        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-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JD 
       43.43        65.49        23.77       115.53       168.00        11.87 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A3BZ TCGA-D3-A3C6 
      113.52        42.08        12.10       171.58       130.72        58.06 
TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A51E TCGA-D3-A51F 
       46.98       166.52        24.53         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       135.02        88.87 
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-A5UL TCGA-EB-A5UN 
       43.36        72.10        73.94        14.14        29.29        58.92 
TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A182 TCGA-EE-A183 
        7.04        36.46        29.82         8.65        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-A29E TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P 
       78.97        63.78        64.64        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-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GR TCGA-EE-A2GS 
       67.43        48.72       107.38        54.74        42.77        81.21 
TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME 
       44.88        94.82        21.67        61.51        47.28       103.27 
TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML 
      268.73       103.20       204.66        96.23       180.39       216.66 
TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A2MT 
      167.90        47.54       248.65        43.23       162.48        71.21 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH 
       53.26       124.31        64.04        13.81        41.59       138.81 
TCGA-EE-A3J3 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI 
      172.18        34.32       201.80        51.35       134.33       152.81 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19D 
       35.44        13.94         9.17        77.75        98.40        12.59 
TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T 
       13.02        26.37       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       105.07        23.34        20.15        48.99        41.56 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN 
      247.04        93.01        46.98        33.21        12.95        92.98 
TCGA-FR-A69P TCGA-FR-A8YC TCGA-FR-A8YE TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
       15.72        34.82       104.42       228.59       202.65        20.91 
TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZH 
       27.72        48.85       357.37        46.45         9.70        32.75 
TCGA-FS-A1ZJ TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZZ 
       47.38       148.80        53.16        26.56        49.48        27.02 
TCGA-FS-A4F0 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FW-A3TU 
       77.82       174.84        34.03        26.73        54.41        55.59 
TCGA-FW-A5DY TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 
       19.30        19.43         2.04        15.78       139.89       117.93 
TCGA-GN-A265 TCGA-GN-A268 TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A4U9 
       96.92        62.79        39.35        10.42        48.89        22.13 
TCGA-GN-A8LK TCGA-HR-A2OG TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 
       50.10         0.23       368.78       297.90         7.23         0.20 
TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1W TCGA-WE-A8JZ 
      121.08         4.01        69.07       111.09       219.16        24.03 
TCGA-WE-A8K1 TCGA-WE-A8ZO TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 
       49.05        70.52        49.51        12.16        40.41        24.99 
TCGA-YD-A89C TCGA-YD-A9TA TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S 
        6.90        49.18        14.43        27.58        96.99 

  8P GAIN MUTATED 8P GAIN WILD-TYPE 
             0.33              0.20 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
           340.14            369.93 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
            53.52             50.89 
[1] "0.3 - 340.1 (53.5)" "0.2 - 369.9 (50.9)"
[1] "hr=" "1"  
D15V3, continuous
                   vv
clus                I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  8P GAIN MUTATED          3       1      12        6        7       14
  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        19          7
  8P GAIN WILD-TYPE         9        16         9        20          8
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  8P GAIN MUTATED           13         13        7
  8P GAIN WILD-TYPE         22         41       14
D15V4, multiclass
            clus
vv           8P GAIN MUTATED 8P GAIN WILD-TYPE
  I/II NOS                 3                10
  STAGE 0                  1                 6
  STAGE I                 12                17
  STAGE IA                 6                12
  STAGE IB                 7                21
  STAGE II                14                12
  STAGE IIA                5                 9
  STAGE IIB                3                16
  STAGE IIC                6                 9
  STAGE III               19                20
  STAGE IIIA               7                 8
  STAGE IIIB              13                22
  STAGE IIIC              13                41
  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 30 20
  8P GAIN WILD-TYPE    39 49 51 47
D15V5, multiclass
       clus
vv      8P GAIN MUTATED 8P GAIN WILD-TYPE
  T0+T1              25                39
  T2                 24                49
  T3                 30                51
  T4                 20                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
  8P GAIN MUTATED    56  29  14  10
  8P GAIN WILD-TYPE 121  36  25  35
D15V6, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  N0              56               121
  N1              29                36
  N2              14                25
  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"
D15V7, binary
                   cls
clus                  0   1
  8P GAIN MUTATED   110   7
  8P GAIN WILD-TYPE 209  15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED    110    7
  8P GAIN WILD-TYPE  209   15
   clus
vv  8P GAIN MUTATED 8P GAIN WILD-TYPE
  0             110               209
  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    18 105
  8P GAIN WILD-TYPE  29 215
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     18  105
  8P GAIN WILD-TYPE   29  215
     clus
vv    8P GAIN MUTATED 8P GAIN WILD-TYPE
  NO               18                29
  YES             105               215
[1] 2 2
[1] FALSE
D15V10, continuous
D15V11, binary
                   cls
clus                  0   1
  8P GAIN MUTATED    43  80
  8P GAIN WILD-TYPE  95 149
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     43   80
  8P GAIN WILD-TYPE   95  149
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  FEMALE              43                95
  MALE                80               149
[1] 2 2
[1] FALSE
D15V12, binary
                   cls
clus                  0   1
  8P GAIN MUTATED   108  15
  8P GAIN WILD-TYPE 211  32
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED    108   15
  8P GAIN WILD-TYPE  211   32
     clus
vv    8P GAIN MUTATED 8P GAIN WILD-TYPE
  NO              108               211
  YES              15                32
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  8P GAIN MUTATED       4                         0   115
  8P GAIN WILD-TYPE     1                         1   238
D15V13, multiclass
                           clus
vv                          8P GAIN MUTATED 8P GAIN WILD-TYPE
  ASIAN                                   4                 1
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                 115               238
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V14, binary
                   cls
clus                  0   1
  8P GAIN MUTATED     2 117
  8P GAIN WILD-TYPE   5 235
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      2  117
  8P GAIN WILD-TYPE    5  235
                        clus
vv                       8P GAIN MUTATED 8P GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 5
  NOT HISPANIC OR LATINO             117               235
[1] 2 2
[1] FALSE

Clustering(16) Variable = 8Q GAIN MUTATION ANALYSIS
D16V1, survival
                   sevent
clus2                0  1
  8Q GAIN MUTATED   66 60
  8Q GAIN WILD-TYPE 62 64
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              126               126 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               60                64 
$`8Q GAIN MUTATED`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A8GI TCGA-EB-A5SG TCGA-EE-A2GD TCGA-EE-A2GO 
        9.76        62.07        13.41        33.24       269.03        52.90 
TCGA-EE-A2MR TCGA-FR-A729 TCGA-WE-AAA3 TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 
      134.40       216.43         7.40        60.46        12.99         8.42 
TCGA-D3-A1Q4 TCGA-D3-A1Q6 TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2JA 
       31.89        49.35        62.60        25.64        45.99        15.75 
TCGA-D3-A2JC TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CB 
       86.30        64.83        66.08        43.53        58.06       140.98 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E 
       40.01        59.70         9.34        90.21        23.67       173.85 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D3-A8GJ 
      144.46        31.76        45.70       177.86       124.08       179.97 
TCGA-D3-A8GP TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 
      135.12        69.21        22.85       138.67        68.68       150.61 
TCGA-DA-A3F5 TCGA-DA-A95V TCGA-DA-A95W TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A6L9 
      225.11        72.10         0.76        12.30         3.91        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-A2GE TCGA-EE-A2GH TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP 
       12.95       201.60        32.48        18.35        93.63         0.76 
TCGA-EE-A2GS TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MF TCGA-EE-A3AA 
       71.31       103.13        15.25         5.75       209.79       124.31 
TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 
      122.73         4.41        54.51        67.89       111.85        45.90 
TCGA-ER-A197 TCGA-ER-A19C TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M 
       10.49        39.81       184.60       150.12        99.06        59.84 
TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NF 
       42.51        49.71        47.18        22.36         4.70        10.19 
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-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD 
      171.78        49.74       195.98        27.62       312.07        32.78 
TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZY 
       78.61       130.95       136.27        35.28         4.47         5.29 
TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4FD TCGA-FW-A3TV TCGA-GF-A3OT TCGA-GN-A265 
       66.67       173.19        80.68        11.54         9.90        96.92 
TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A9SD TCGA-OD-A75X TCGA-QB-A6FS 
       17.06         7.59       120.53        59.41       297.01         7.23 
TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-AA1V TCGA-W3-AA21 TCGA-WE-A8ZM 
        0.33       174.12         1.97         8.09        92.84        65.42 
TCGA-WE-A8ZN TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-XV-AB01 TCGA-YG-AA3O TCGA-Z2-AA3S 
       12.69        62.89        10.95         6.61        28.21        91.23 

$`8Q GAIN WILD-TYPE`
TCGA-D3-A3C8 TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A3JD TCGA-ER-A193 TCGA-FW-A3R5 
       38.76        31.96       166.75        27.35        19.04        36.95 
TCGA-WE-A8K5 TCGA-BF-AAP0 TCGA-D3-A1Q3 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       52.73        14.83        15.72       110.93       133.25        19.04 
TCGA-D3-A1QA TCGA-D3-A2J8 TCGA-D3-A2JB TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL 
       76.41        62.86       168.00       107.61        36.30       171.58 
TCGA-D3-A3CF TCGA-D3-A51F TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A8GC 
       24.53        30.67        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       110.53        60.10 
TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F8 TCGA-DA-A95X TCGA-DA-A95Y 
       64.83        58.85        30.44         8.71        65.03        14.14 
TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20C 
       16.41        52.41        13.15         0.00        26.24        75.55 
TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P 
       79.20        75.22        12.99        47.41        47.74        27.16 
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-A2GJ TCGA-EE-A2GK TCGA-EE-A2GR TCGA-EE-A2GU TCGA-EE-A2MC TCGA-EE-A2MG 
       68.65        10.62         0.20        81.99        23.77        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-A195 TCGA-ER-A199 TCGA-ER-A19A 
      168.85        19.86       135.98        34.45         7.82         4.54 
TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19P TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NE 
       53.29        11.47       120.76       146.63        73.05        16.87 
TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A69P TCGA-FR-A8YC 
       28.67       173.29        32.05         4.50         4.14        10.06 
TCGA-FS-A1Z3 TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZW TCGA-FS-A1ZZ 
        8.35        43.92         7.82        36.33        23.21         3.06 
TCGA-FS-A4F0 TCGA-FS-A4F9 TCGA-FW-A3TU TCGA-FW-A5DY TCGA-GF-A4EO TCGA-GF-A6C8 
       30.90        13.28        55.59        19.30        18.25         1.91 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A268 TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-GN-A8LK 
       53.29       117.93        42.48        34.49        46.92        43.23 
TCGA-LH-A9QB TCGA-RP-A690 TCGA-W3-A828 TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1W 
       85.05         0.20       120.07        44.05        79.99       185.13 
TCGA-WE-A8K1 TCGA-WE-A8ZO TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 
       47.54        21.90        48.39         1.94        37.32        24.99 

  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
             0.26              0.00 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
           346.49            227.01 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
           51.320            42.265 
[1] "0.3 - 346.5 (51.3)" "0.0 - 227.0 (42.3)"
[1] "hr=" "1.4"
D16V2, survival
                   sevent
clus2                 0   1
  8Q GAIN MUTATED    79  89
  8Q GAIN WILD-TYPE  87 103
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              168               190 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               89               103 
$`8Q GAIN MUTATED`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A3ML TCGA-D3-A8GI TCGA-EB-A5SG TCGA-EB-A5SH 
       27.65        62.07        13.87        58.52        68.25        54.02 
TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR TCGA-FR-A729 TCGA-QB-AA9O TCGA-WE-AAA3 
      340.14       126.81       134.40       220.80        18.05        21.40 
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-A2JN 
       95.74        43.43       103.10       115.53        86.76        66.48 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE 
       66.08        59.57        58.06       166.52        86.93        60.23 
TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51J 
        9.34       103.59        39.75        45.30       174.84       145.12 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU 
       32.94        22.62       135.75       178.32        18.18       125.19 
TCGA-D3-A8GJ TCGA-D3-A8GP TCGA-D9-A1JW TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HW 
      241.38       152.75         3.65        77.56        22.95        36.03 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A3F3 
      144.89        20.38       222.51       176.55        35.93        10.49 
TCGA-DA-A3F5 TCGA-DA-A95V TCGA-DA-A95W TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A44R 
      225.96        72.10        37.35        13.02        13.87        10.36 
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-A2GE 
       63.78        72.07        14.47       369.93        39.29       173.79 
TCGA-EE-A2GH TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GS 
      220.24        79.66        75.48       102.12        13.91        81.21 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MF TCGA-EE-A2MH TCGA-EE-A2MN 
      129.27        28.83        19.76       268.73        16.96        47.54 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AG TCGA-EE-A3J3 
      124.31       122.73        28.77        54.51        41.59       172.18 
TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-ER-A197 TCGA-ER-A19C 
      127.20        36.95        64.08        53.19        13.94        48.89 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
      302.07       152.35         6.44       131.51        61.05        44.09 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NF 
       50.89        49.48         8.88        43.82        23.34        28.83 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A42L TCGA-FR-A44A TCGA-FR-A7U8 TCGA-FR-A7U9 
       93.01        46.98       149.03       174.21        27.85        18.77 
TCGA-FR-A7UA TCGA-FR-A8YD TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
       38.27        36.26       216.92        48.59       228.59       202.65 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZK TCGA-FS-A1ZM 
       28.08         7.79       357.37        53.52        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-A1ZY TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4FD 
       27.09        50.14        66.67        28.73       174.84        80.68 
TCGA-FW-A3I3 TCGA-FW-A3TV TCGA-GF-A3OT TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 
       17.46        13.51         9.90        96.92        10.13        64.44 
TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A8LL TCGA-GN-A9SD TCGA-HR-A2OH 
       32.48        48.00       121.91        21.37        59.41        65.88 
TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 
      297.90         7.23         0.33         0.69       228.16        63.02 
TCGA-W3-AA1V TCGA-W3-AA21 TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZQ 
       42.08       105.04        17.95       101.33        58.98        63.22 
TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-XV-AB01 TCGA-YG-AA3O TCGA-Z2-AA3S TCGA-Z2-AA3V 
       11.80        35.80        13.25        37.94        96.99        15.98 

$`8Q GAIN WILD-TYPE`
TCGA-D3-A3C8 TCGA-EE-A180 TCGA-EE-A184 TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A3JD 
       46.32        94.98        68.15       168.26         2.60        27.35 
TCGA-ER-A193 TCGA-ER-A198 TCGA-FS-A1ZF TCGA-FW-A3R5 TCGA-WE-A8K5 TCGA-3N-A9WB 
       31.40        50.76        15.45        36.95        61.15        17.03 
TCGA-BF-AAP0 TCGA-D3-A1Q3 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA 
       14.93        16.67       112.57       133.25        28.08        90.90 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH 
       65.49        23.77       168.00        11.87       113.52        42.08 
TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3CF TCGA-D3-A51F 
       12.10       171.58       130.72        46.98        24.53        55.73 
TCGA-D3-A51H TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GO TCGA-D3-A8GB 
       56.35        63.81        26.89       125.79       137.92        30.84 
TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM 
       79.59        23.61        26.43       170.20        89.13       107.15 
TCGA-D3-A8GN TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D3-A8GV TCGA-D9-A148 
      161.00        29.06       129.63       117.17       167.70       151.53 
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-A6EA TCGA-DA-A1HV TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
        9.90        25.18        76.57       135.02        88.87        53.92 
TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F8 TCGA-DA-A95X 
       65.92        40.60        68.09        33.93        43.36        73.94 
TCGA-DA-A95Y TCGA-EB-A5KH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EE-A17X 
       14.14        20.35        29.29        58.92         7.04        29.82 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I 
       14.70        26.89         4.96       151.27        91.56        13.55 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N 
       63.35        85.08        13.97        64.64        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-A2MG TCGA-EE-A2MI 
       21.67        61.51        47.28       103.27       103.20       204.66 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MQ 
       96.23       180.39       216.66       167.90       248.65        43.23 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AC TCGA-EE-A3AF TCGA-EE-A3AH 
      162.48        71.21        53.26        64.04        13.81       138.81 
TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 
       34.32       201.80        51.35       134.33       152.81        35.44 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F 
        9.17        77.75        98.40        12.59        13.02        26.37 
TCGA-ER-A19P TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A2NH 
      162.08       148.18       105.07        20.15        48.99        41.56 
TCGA-ER-A3ES TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A69P TCGA-FR-A8YC 
      247.04        33.21        12.95        92.98        15.72        34.82 
TCGA-FR-A8YE TCGA-FS-A1Z3 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZE TCGA-FS-A1ZG 
      104.42        20.91        27.72        48.85        46.45         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-A3TU TCGA-FW-A5DY TCGA-GF-A4EO TCGA-GF-A6C8 
       26.73        54.41        55.59        19.30        19.43         2.04 
TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A268 TCGA-GN-A4U4 TCGA-GN-A4U7 
       15.78       139.89       117.93        62.79        39.35        10.42 
TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-HR-A2OG TCGA-LH-A9QB TCGA-RP-A690 
       48.89        22.13        50.10         0.23       368.78         0.20 
TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1W TCGA-WE-A8JZ 
      121.08         4.01        69.07       111.09       219.16        24.03 
TCGA-WE-A8K1 TCGA-WE-A8ZO TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 
       49.05        70.52        49.51        12.16        40.41        24.99 
TCGA-YD-A89C TCGA-YD-A9TA TCGA-YG-AA3P TCGA-Z2-A8RT 
        6.90        49.18        14.43        27.58 

  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
             0.33              0.20 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
           369.93            368.78 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
           56.285            49.330 
[1] "0.3 - 369.9 (56.3)" "0.2 - 368.8 (49.3)"
[1] "hr=" "1.2"
D16V3, continuous
                   vv
clus                I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  8Q GAIN MUTATED          6       1      17        7       12       15
  8Q GAIN WILD-TYPE        7       6      12       11       16       11
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  8Q GAIN MUTATED           6         5         8        25         10
  8Q GAIN WILD-TYPE         8        14         7        14          5
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  8Q GAIN MUTATED           17         19       10
  8Q GAIN WILD-TYPE         18         35       11
D16V4, multiclass
            clus
vv           8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  I/II NOS                 6                 7
  STAGE 0                  1                 6
  STAGE I                 17                12
  STAGE IA                 7                11
  STAGE IB                12                16
  STAGE II                15                11
  STAGE IIA                6                 8
  STAGE IIB                5                14
  STAGE IIC                8                 7
  STAGE III               25                14
  STAGE IIIA              10                 5
  STAGE IIIB              17                18
  STAGE IIIC              19                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 37 35 28
  8Q GAIN WILD-TYPE    27 36 46 39
D16V5, multiclass
       clus
vv      8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  T0+T1              37                27
  T2                 37                36
  T3                 35                46
  T4                 28                39
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  8Q GAIN MUTATED   79 34 23 18
  8Q GAIN WILD-TYPE 98 31 16 27
D16V6, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  N0              79                98
  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   152  10
  8Q GAIN WILD-TYPE 167  12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED    152   10
  8Q GAIN WILD-TYPE  167   12
   clus
vv  8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  0             152               167
  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    28 144
  8Q GAIN WILD-TYPE  19 176
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     28  144
  8Q GAIN WILD-TYPE   19  176
     clus
vv    8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  NO               28                19
  YES             144               176
[1] 2 2
[1] FALSE
D16V10, continuous
D16V11, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED    64 108
  8Q GAIN WILD-TYPE  74 121
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     64  108
  8Q GAIN WILD-TYPE   74  121
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  FEMALE              64                74
  MALE               108               121
[1] 2 2
[1] FALSE
D16V12, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED   153  19
  8Q GAIN WILD-TYPE 166  28
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED    153   19
  8Q GAIN WILD-TYPE  166   28
     clus
vv    8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  NO              153               166
  YES              19                28
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  8Q GAIN MUTATED       4                         0   164
  8Q GAIN WILD-TYPE     1                         1   189
D16V13, multiclass
                           clus
vv                          8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  ASIAN                                   4                 1
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                 164               189
[1] 3 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     3 165
  8Q GAIN WILD-TYPE   4 187
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      3  165
  8Q GAIN WILD-TYPE    4  187
                        clus
vv                       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                 4
  NOT HISPANIC OR LATINO             165               187
[1] 2 2
[1] FALSE

Clustering(17) Variable = 9P GAIN MUTATION ANALYSIS
D17V1, survival
                   sevent
clus2                 0   1
  9P GAIN MUTATED     4   7
  9P GAIN WILD-TYPE 124 117
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               11               241 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                7               117 
$`9P GAIN MUTATED`
TCGA-D3-A1QA TCGA-D3-A2JA TCGA-D3-A5GN TCGA-D3-A8GM TCGA-ER-A19G TCGA-ER-A2NC 
       76.41        15.75        45.70        70.62       184.60        22.36 
TCGA-ER-A2NF TCGA-ER-A3ET TCGA-FS-A1Z0 TCGA-FS-A1ZJ TCGA-FS-A4F8 
       10.19        68.52       195.98        36.33       173.19 

$`9P GAIN WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A8GI TCGA-EB-A5SG TCGA-EE-A180 
        9.76        62.07        38.76        13.41        33.24        31.96 
TCGA-EE-A20H TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 
      166.75       269.03        52.90       134.40        27.35        19.04 
TCGA-FR-A729 TCGA-FW-A3R5 TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-3N-A9WC TCGA-3N-A9WD 
      216.43        36.95        52.73         7.40        60.46        12.99 
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-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 
      133.25        19.04        62.60        25.64        45.99        62.86 
TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN 
      168.00        86.30       107.61        36.30       171.58        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-A3CF TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F 
       24.53         9.34        90.21        23.67       173.85        30.67 
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-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-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 
       69.21        22.85        76.34       138.67        68.68       150.61 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 
      110.53        60.10        64.83        58.85        30.44       225.11 
TCGA-DA-A3F8 TCGA-DA-A95V TCGA-DA-A95W TCGA-DA-A95X TCGA-DA-A95Y TCGA-DA-A95Z 
        8.71        72.10         0.76        65.03        14.14        12.30 
TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y 
        3.91        16.41        52.41        18.21        13.15        24.89 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29B 
       20.38         0.00        26.24        75.55        79.20        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        47.41        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-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK 
       77.98        26.14        12.95       201.60        68.65        10.62 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
       32.48        18.35        93.63         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-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB 
      227.01       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-A195 
       45.90         3.35       168.85        19.86       135.98        34.45 
TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D 
       10.49         7.82         4.54        53.29        39.81        11.47 
TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
      150.12        99.06        59.84        42.51       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        73.05         4.70        16.87        28.67 
TCGA-ER-A3ES TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A 
      173.29        15.48        32.05        74.47         4.50       174.21 
TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FS-A1YW TCGA-FS-A1YY 
        4.14        26.20         5.65        10.06       171.78        49.74 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG 
        8.35        27.62       312.07        32.78        43.92         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        18.25         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-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT 
       47.54        65.42        12.69        21.90        62.89        10.95 
TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-XV-AB01 TCGA-YG-AA3O 
       48.39         1.94        37.32        24.99         6.61        28.21 
TCGA-Z2-AA3S 
       91.23 

  9P GAIN MUTATED 9P GAIN WILD-TYPE 
            10.19              0.00 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
           195.98            346.49 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
            68.52             45.99 
[1] "10.2 - 196.0 (68.5)" "0.0 - 346.5 (46.0)" 
[1] "hr=" "1"  
D17V2, survival
                   sevent
clus2                 0   1
  9P GAIN MUTATED     6  10
  9P GAIN WILD-TYPE 160 182
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               16               342 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               10               182 
$`9P GAIN MUTATED`
TCGA-EB-A5SH TCGA-EE-A184 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A2JA TCGA-D3-A5GN 
       54.02        68.15        31.59        90.90       115.53       135.75 
TCGA-D3-A5GS TCGA-D3-A8GM TCGA-EE-A2M5 TCGA-ER-A19G TCGA-ER-A2NC TCGA-ER-A2NF 
       18.18       107.15        21.67       302.07        43.82        28.83 
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-D3-A2JE TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-D3-A8GI TCGA-EB-A5SG 
       27.65        62.07        46.32        13.87        58.52        68.25 
TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR 
       94.98       168.26         2.60       340.14       126.81       134.40 
TCGA-EE-A3JD TCGA-ER-A193 TCGA-ER-A198 TCGA-FR-A729 TCGA-FS-A1ZF TCGA-FW-A3R5 
       27.35        31.40        50.76       220.80        15.45        36.95 
TCGA-QB-AA9O TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD 
       18.05        61.15        21.40        17.03        66.48        12.99 
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-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 
      133.25        28.08        95.74        43.43       103.10        65.49 
TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH 
       23.77       168.00        86.76        11.87       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-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF 
       58.06        46.98       166.52        86.93        60.23        24.53 
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-A5GO TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GC 
      125.79       137.92       178.32       125.19        30.84        79.59 
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-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       222.51       176.55        35.93 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
      135.02        88.87        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        43.36        72.10        37.35 
TCGA-DA-A95X TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH 
       73.94        14.14        13.02        13.87        10.36        20.35 
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-A185 TCGA-EE-A20B 
        8.65        33.73        14.70        26.89         4.96       133.81 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C 
      151.27        91.56        13.55        63.35        85.08        78.97 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N 
       13.97        63.78        72.07        64.64        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-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
       86.14        59.28        67.43       173.79       220.24        48.72 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP 
      107.38        54.74        79.66        75.48       102.12        13.91 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 
       42.77        81.21        44.88        94.82       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-A2MS TCGA-EE-A2MT TCGA-EE-A2MU 
       47.54       248.65        43.23       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-A3JB TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI 
       34.32        53.19       201.80        51.35       134.33       152.81 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C 
       35.44        13.94         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        44.09       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       105.07        23.34        20.15        48.99        41.56 
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-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-A1YX TCGA-FS-A1YY TCGA-FS-A1Z3 
       36.26       104.42       216.92        48.59       228.59        20.91 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD 
       28.08         7.79        27.72        48.85       357.37        53.52 
TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP 
       46.45         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-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-A3TU 
       34.03        26.73        54.41        80.68        17.46        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        19.43         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-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-A8LL TCGA-GN-A9SD TCGA-HR-A2OG TCGA-HR-A2OH 
       22.13        50.10        21.37        59.41         0.23        65.88 
TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-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-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K6 
       42.08       219.16       105.04        24.03        49.05        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-XV-AB01 TCGA-YD-A89C 
       49.51        12.16        40.41        24.99        13.25         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 

  9P GAIN MUTATED 9P GAIN WILD-TYPE 
            18.18              0.20 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
           302.07            369.93 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
           79.525            50.825 
[1] "18.2 - 302.1 (79.5)" "0.2 - 369.9 (50.8)" 
[1] "hr=" "1.1"
D17V3, continuous
                   vv
clus                I/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       26
                   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        38         13
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  9P GAIN MUTATED            2          0        1
  9P GAIN WILD-TYPE         33         54       20
D17V4, multiclass
            clus
vv           9P GAIN MUTATED 9P GAIN WILD-TYPE
  I/II NOS                 0                13
  STAGE 0                  0                 7
  STAGE I                  4                25
  STAGE IA                 1                17
  STAGE IB                 3                25
  STAGE II                 0                26
  STAGE IIA                0                14
  STAGE IIB                1                18
  STAGE IIC                0                15
  STAGE III                1                38
  STAGE IIIA               2                13
  STAGE IIIB               2                33
  STAGE IIIC               0                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  3  2
  9P GAIN WILD-TYPE    60 67 78 65
D17V5, multiclass
       clus
vv      9P GAIN MUTATED 9P GAIN WILD-TYPE
  T0+T1               4                60
  T2                  6                67
  T3                  3                78
  T4                  2                65
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  9P GAIN MUTATED    11   3   1   1
  9P GAIN WILD-TYPE 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 304  21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED     15    1
  9P GAIN WILD-TYPE  304   21
   clus
vv  9P GAIN MUTATED 9P GAIN WILD-TYPE
  0              15               304
  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  47 304
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      0   16
  9P GAIN WILD-TYPE   47  304
     clus
vv    9P GAIN MUTATED 9P GAIN WILD-TYPE
  NO                0                47
  YES              16               304
[1] 2 2
[1] FALSE
D17V10, continuous
D17V11, binary
                   cls
clus                  0   1
  9P GAIN MUTATED     6  10
  9P GAIN WILD-TYPE 132 219
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      6   10
  9P GAIN WILD-TYPE  132  219
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  FEMALE               6               132
  MALE                10               219
[1] 2 2
[1] FALSE
D17V12, binary
                   cls
clus                  0   1
  9P GAIN MUTATED    13   3
  9P GAIN WILD-TYPE 306  44
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED     13    3
  9P GAIN WILD-TYPE  306   44
     clus
vv    9P GAIN MUTATED 9P GAIN WILD-TYPE
  NO               13               306
  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   337
D17V13, multiclass
                           clus
vv                          9P GAIN MUTATED 9P GAIN WILD-TYPE
  ASIAN                                   0                 5
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  16               337
[1] 3 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   7 336
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      0   16
  9P GAIN WILD-TYPE    7  336
                        clus
vv                       9P GAIN MUTATED 9P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 7
  NOT HISPANIC OR LATINO              16               336
[1] 2 2
[1] FALSE

Clustering(18) Variable = 9Q GAIN MUTATION ANALYSIS
D18V1, survival
                   sevent
clus2                 0   1
  9Q GAIN MUTATED     4   8
  9Q GAIN WILD-TYPE 124 116
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               12               240 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                8               116 
$`9Q GAIN MUTATED`
TCGA-D3-A2JB TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A8GM TCGA-EE-A3J3 TCGA-ER-A19G 
      168.00        45.70       177.86        70.62        67.89       184.60 
TCGA-ER-A2NC TCGA-ER-A2NF TCGA-FR-A44A TCGA-FS-A1Z0 TCGA-FS-A1ZJ TCGA-FS-A4F8 
       22.36        10.19       174.21       195.98        36.33       173.19 

$`9Q GAIN WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A8GI TCGA-EB-A5SG TCGA-EE-A180 
        9.76        62.07        38.76        13.41        33.24        31.96 
TCGA-EE-A20H TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 
      166.75       269.03        52.90       134.40        27.35        19.04 
TCGA-FR-A729 TCGA-FW-A3R5 TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-3N-A9WC TCGA-3N-A9WD 
      216.43        36.95        52.73         7.40        60.46        12.99 
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-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-A2JG TCGA-D3-A2JH TCGA-D3-A2JL 
       62.86        15.75        86.30       107.61        36.30       171.58 
TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CC 
       64.83        66.08        43.53        58.06       140.98        40.01 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E 
       59.70        24.53         9.34        90.21        23.67       173.85 
TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL 
       30.67       144.46        31.76        62.70        11.34        42.05 
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-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 
       69.21        22.85        76.34       138.67        68.68       150.61 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 
      110.53        60.10        64.83        58.85        30.44       225.11 
TCGA-DA-A3F8 TCGA-DA-A95V TCGA-DA-A95W TCGA-DA-A95X TCGA-DA-A95Y TCGA-DA-A95Z 
        8.71        72.10         0.76        65.03        14.14        12.30 
TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y 
        3.91        16.41        52.41        18.21        13.15        24.89 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29B 
       20.38         0.00        26.24        75.55        79.20        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        47.41        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-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK 
       77.98        26.14        12.95       201.60        68.65        10.62 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
       32.48        18.35        93.63         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-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB 
      227.01       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-A195 TCGA-ER-A197 
        3.35       168.85        19.86       135.98        34.45        10.49 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19H 
        7.82         4.54        53.29        39.81        11.47       150.12 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S 
       99.06        59.84        42.51       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        73.05         4.70        16.87        28.67       173.29 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A69P 
       68.52        15.48        32.05        74.47         4.50         4.14 
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-A1ZG TCGA-FS-A1ZM 
       27.62       312.07        32.78        43.92         7.82        78.61 
TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY 
      130.95       136.27        35.28         4.47        23.21         5.29 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TU 
        3.06        30.90        66.67        13.28        80.68        55.59 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 
       11.54        19.30         9.90        18.25         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-A8LK TCGA-GN-A9SD TCGA-LH-A9QB TCGA-OD-A75X 
       34.49        46.92        43.23        59.41        85.05       297.01 
TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 
        7.23         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        47.54 
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-XV-AB01 TCGA-YG-AA3O TCGA-Z2-AA3S 
        1.94        37.32        24.99         6.61        28.21        91.23 

  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
            10.19              0.00 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
           195.98            346.49 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
           119.31             45.09 
[1] "10.2 - 196.0 (119.3)" "0.0 - 346.5 (45.1)"  
[1] "hr=" "1.3"
D18V2, survival
                   sevent
clus2                 0   1
  9Q GAIN MUTATED     6  14
  9Q GAIN WILD-TYPE 160 178
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               20               338 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               14               178 
$`9Q GAIN MUTATED`
TCGA-D3-A3ML TCGA-EE-A184 TCGA-D3-A1Q9 TCGA-D3-A2JB TCGA-D3-A5GN TCGA-D3-A5GR 
       13.87        68.15        31.59       168.00       135.75       178.32 
TCGA-D3-A5GS TCGA-D3-A8GM TCGA-EE-A2M5 TCGA-EE-A2MD TCGA-EE-A3J3 TCGA-ER-A19G 
       18.18       107.15        21.67        47.28       172.18       302.07 
TCGA-ER-A2NC TCGA-ER-A2NF TCGA-FR-A44A TCGA-FS-A1YX TCGA-FS-A1Z0 TCGA-FS-A1ZJ 
       43.82        28.83       174.21        48.59       202.65        47.38 
TCGA-FS-A4F8 TCGA-YD-A9TA 
      174.84        49.18 

$`9Q GAIN WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A8GI TCGA-EB-A5SG TCGA-EB-A5SH 
       27.65        62.07        46.32        58.52        68.25        54.02 
TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR 
       94.98       168.26         2.60       340.14       126.81       134.40 
TCGA-EE-A3JD TCGA-ER-A193 TCGA-ER-A198 TCGA-FR-A729 TCGA-FS-A1ZF TCGA-FW-A3R5 
       27.35        31.40        50.76       220.80        15.45        36.95 
TCGA-QB-AA9O TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD 
       18.05        61.15        21.40        17.03        66.48        12.99 
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-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
      133.25        28.08        90.90        95.74        43.43       103.10 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG 
       65.49        23.77       115.53        86.76        11.87       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-A3CB TCGA-D3-A3CC TCGA-D3-A3CE 
      130.72        58.06        46.98       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-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-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       222.51       176.55        35.93 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
      135.02        88.87        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        43.36        72.10        37.35 
TCGA-DA-A95X TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH 
       73.94        14.14        13.02        13.87        10.36        20.35 
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-A185 TCGA-EE-A20B 
        8.65        33.73        14.70        26.89         4.96       133.81 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C 
      151.27        91.56        13.55        63.35        85.08        78.97 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N 
       13.97        63.78        72.07        64.64        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-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
       86.14        59.28        67.43       173.79       220.24        48.72 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP 
      107.38        54.74        79.66        75.48       102.12        13.91 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 
       42.77        81.21        44.88        94.82       129.27        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-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-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA 
      248.65        43.23       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-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA 
      138.81       127.20        36.95        64.08        34.32        53.19 
TCGA-EE-A3JB TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 
      201.80        51.35       134.33       152.81        35.44        13.94 
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        44.09 
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       105.07 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET 
       23.34        20.15        48.99        41.56       247.04        93.01 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A69P 
       46.98        33.21        12.95       149.03        92.98        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-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZH 
       48.85       357.37        53.52        46.45         9.70        32.75 
TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS 
       23.93       101.26        74.73       133.55        11.41       148.80 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 
       53.16        26.56        49.48        27.09        27.02        77.82 
TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC 
       50.14        66.67        28.73        34.03        26.73        54.41 
TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
       80.68        17.46        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 
       19.43         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-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-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO 
       24.03        49.05        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-AAA4 TCGA-XV-AB01 TCGA-YD-A89C TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-A8RT 
       24.99        13.25         6.90        37.94        14.43        27.58 
TCGA-Z2-AA3S TCGA-Z2-AA3V 
       96.99        15.98 

  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
            13.87              0.20 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
           302.07            369.93 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
           58.665            52.255 
[1] "13.9 - 302.1 (58.7)" "0.2 - 369.9 (52.3)" 
[1] "hr=" "1.1"
D18V3, continuous
                   vv
clus                I/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       24
                   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        38         14
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  9Q GAIN MUTATED            2          0        1
  9Q GAIN WILD-TYPE         33         54       20
D18V4, multiclass
            clus
vv           9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  I/II NOS                 0                13
  STAGE 0                  1                 6
  STAGE I                  5                24
  STAGE IA                 1                17
  STAGE IB                 3                25
  STAGE II                 2                24
  STAGE IIA                0                14
  STAGE IIB                1                18
  STAGE IIC                0                15
  STAGE III                1                38
  STAGE IIIA               1                14
  STAGE IIIB               2                33
  STAGE IIIC               0                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
  9Q GAIN MUTATED       5  6  5  1
  9Q GAIN WILD-TYPE    59 67 76 66
D18V5, multiclass
       clus
vv      9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  T0+T1               5                59
  T2                  6                67
  T3                  5                76
  T4                  1                66
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  9Q GAIN MUTATED    14   2   2   1
  9Q GAIN WILD-TYPE 163  63  37  44
D18V6, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  N0              14               163
  N1               2                63
  N2               2                37
  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"
D18V7, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED    18   1
  9Q GAIN WILD-TYPE 301  21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     18    1
  9Q GAIN WILD-TYPE  301   21
   clus
vv  9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  0              18               301
  1               1                21
[1] 2 2
[1] FALSE
D18V8, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED    10   4
  9Q GAIN WILD-TYPE 124  86
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     10    4
  9Q GAIN WILD-TYPE  124   86
     clus
vv    9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  NO               10               124
  YES               4                86
[1] 2 2
[1] FALSE
D18V9, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED     0  20
  9Q GAIN WILD-TYPE  47 300
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      0   20
  9Q GAIN WILD-TYPE   47  300
     clus
vv    9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  NO                0                47
  YES              20               300
[1] 2 2
[1] FALSE
D18V10, continuous
D18V11, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED     8  12
  9Q GAIN WILD-TYPE 130 217
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      8   12
  9Q GAIN WILD-TYPE  130  217
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  FEMALE               8               130
  MALE                12               217
[1] 2 2
[1] FALSE
D18V12, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED    17   3
  9Q GAIN WILD-TYPE 302  44
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     17    3
  9Q GAIN WILD-TYPE  302   44
     clus
vv    9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  NO               17               302
  YES               3                44
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  9Q GAIN MUTATED       0                         1    19
  9Q GAIN WILD-TYPE     5                         0   334
D18V13, multiclass
                           clus
vv                          9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  ASIAN                                   0                 5
  BLACK OR AFRICAN AMERICAN               1                 0
  WHITE                                  19               334
[1] 3 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  20
  9Q GAIN WILD-TYPE   7 332
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      0   20
  9Q GAIN WILD-TYPE    7  332
                        clus
vv                       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 7
  NOT HISPANIC OR LATINO              20               332
[1] 2 2
[1] FALSE

Clustering(19) Variable = 10P GAIN MUTATION ANALYSIS
D19V1, survival
                    sevent
clus2                  0   1
  10P GAIN MUTATED     3   5
  10P GAIN WILD-TYPE 125 119
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 8                244 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 5                119 
$`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 
       39.81        59.84 

$`10P GAIN WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A8GI TCGA-EB-A5SG TCGA-EE-A180 
        9.76        62.07        38.76        13.41        33.24        31.96 
TCGA-EE-A20H TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 
      166.75       269.03        52.90       134.40        27.35        19.04 
TCGA-FR-A729 TCGA-FW-A3R5 TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-3N-A9WC TCGA-3N-A9WD 
      216.43        36.95        52.73         7.40        60.46        12.99 
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-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-A2JG TCGA-D3-A2JH 
       62.86        15.75       168.00        86.30       107.61        36.30 
TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3CB TCGA-D3-A3CC 
      171.58        64.83        66.08        43.53       140.98        40.01 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F 
       59.70        24.53         9.34        23.67       173.85        30.67 
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-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-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       69.53       135.12        36.53        10.78        15.02        16.90 
TCGA-D9-A4Z6 TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 
       18.44        22.85        76.34        68.68       150.61       110.53 
TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 
       60.10        64.83        58.85        30.44       225.11         8.71 
TCGA-DA-A95V TCGA-DA-A95W TCGA-DA-A95X TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q 
       72.10         0.76        65.03        14.14        12.30         3.91 
TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A181 
       16.41        52.41        18.21        13.15        24.89        20.38 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29C 
        0.00        26.24        75.55        79.20        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        47.41        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-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-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 
       93.63         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-A2MS 
       63.25        89.26       104.78       145.45       227.01       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-A195 TCGA-ER-A197 TCGA-ER-A199 
      168.85        19.86       135.98        34.45        10.49         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       184.60       150.12        99.06 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 
       42.51       120.76        49.71        47.18       146.63        73.05 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES 
       22.36         4.70        16.87        10.19        28.67       173.29 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A 
       68.52        15.48        32.05        74.47         4.50       174.21 
TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FS-A1YW TCGA-FS-A1YY 
        4.14        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        43.92 
TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT 
        7.82        36.33        78.61       130.95       136.27        35.28 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 
        4.47        23.21         5.29         3.06        30.90        66.67 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
      173.19        13.28        80.68        55.59        11.54        19.30 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        9.90        18.25         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-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-A8ZM TCGA-WE-A8ZN 
        8.09       185.13        92.84        47.54        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        37.32 
TCGA-WE-AAA4 TCGA-XV-AB01 TCGA-YG-AA3O TCGA-Z2-AA3S 
       24.99         6.61        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 
            64.525             45.800 
[1] "13.0 - 138.7 (64.5)" "0.0 - 346.5 (45.8)" 
[1] "hr=" "1.2"
D19V2, survival
                    sevent
clus2                  0   1
  10P GAIN MUTATED     6   6
  10P GAIN WILD-TYPE 160 186
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                12                346 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 6                186 
$`10P GAIN MUTATED`
TCGA-QB-AA9O TCGA-D3-A3C6 TCGA-D3-A3MR TCGA-D3-A51N TCGA-D3-A8GM TCGA-D9-A6EC 
       18.05        58.06       103.59        22.62       107.15        77.56 
TCGA-DA-A1HY TCGA-EE-A29D TCGA-ER-A19C TCGA-ER-A19M TCGA-FW-A3I3 TCGA-GF-A6C9 
      144.89        13.97        48.89        61.05        17.46        15.78 

$`10P GAIN WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-D3-A8GI TCGA-EB-A5SG 
       27.65        62.07        46.32        13.87        58.52        68.25 
TCGA-EB-A5SH TCGA-EE-A180 TCGA-EE-A184 TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GD 
       54.02        94.98        68.15       168.26         2.60       340.14 
TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 TCGA-ER-A198 TCGA-FR-A729 
      126.81       134.40        27.35        31.40        50.76       220.80 
TCGA-FS-A1ZF TCGA-FW-A3R5 TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-3N-A9WB TCGA-3N-A9WC 
       15.45        36.95        61.15        21.40        17.03        66.48 
TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 
       12.99        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-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-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-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3CB 
       66.48        66.08        59.57       130.72        46.98       166.52 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MU TCGA-D3-A3MV 
       86.93        60.23        24.53         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-A8GJ 
      125.19        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-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-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 
       22.95        76.57        36.03        20.38       222.51       176.55 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB 
       35.93       135.02        88.87        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        43.36        72.10 
TCGA-DA-A95W TCGA-DA-A95X TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A44R 
       37.35        73.94        14.14        13.02        13.87        10.36 
TCGA-EB-A5KH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X 
       20.35        29.29        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-A185 
       27.22         8.65        33.73        14.70        26.89         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-A29M TCGA-EE-A29N 
       78.97        63.78        72.07        64.64        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-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
       86.14        59.28        67.43       173.79       220.24        48.72 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP 
      107.38        54.74        79.66        75.48       102.12        13.91 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-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-A2MS TCGA-EE-A2MT 
      167.90        47.54       248.65        43.23       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-A3J5 
       13.81        41.59       138.81       172.18       127.20        36.95 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JE TCGA-EE-A3JH 
       64.08        34.32        53.19       201.80        51.35       134.33 
TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B 
      152.81        35.44        13.94         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       302.07       152.35         6.44 
TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T 
      131.51        44.09       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       105.07        43.82        23.34        20.15        28.83 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL 
       48.99        41.56       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-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW 
       18.77        38.27        34.82        36.26       104.42       216.92 
TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 
       48.59       228.59       202.65        20.91        28.08         7.79 
TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG 
       27.72        48.85       357.37        53.52        46.45         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-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-A4F5 TCGA-FS-A4F8 
       27.02        77.82        50.14        66.67        28.73       174.84 
TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV 
       34.03        26.73        54.41        80.68        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        19.43         2.04       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-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-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-AAA4 TCGA-XV-AB01 TCGA-YD-A89C TCGA-YD-A9TA TCGA-YG-AA3O 
       40.41        24.99        13.25         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 

  10P GAIN MUTATED 10P GAIN WILD-TYPE 
             13.97               0.20 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
            144.89             369.93 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
            53.475             52.255 
[1] "14.0 - 144.9 (53.5)" "0.2 - 369.9 (52.3)" 
[1] "hr=" "1.2"
D19V3, continuous
                    vv
clus                 I/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       26
                    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        37         14
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  10P GAIN MUTATED            1          2        2
  10P GAIN WILD-TYPE         34         52       19
D19V4, multiclass
            clus
vv           10P GAIN MUTATED 10P GAIN WILD-TYPE
  I/II NOS                  0                 13
  STAGE 0                   0                  7
  STAGE I                   1                 28
  STAGE IA                  0                 18
  STAGE IB                  2                 26
  STAGE II                  0                 26
  STAGE IIA                 0                 14
  STAGE IIB                 1                 18
  STAGE IIC                 0                 15
  STAGE III                 2                 37
  STAGE IIIA                1                 14
  STAGE IIIB                1                 34
  STAGE IIIC                2                 52
  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  0
  10P GAIN WILD-TYPE    62 69 78 67
D19V5, multiclass
       clus
vv      10P GAIN MUTATED 10P GAIN WILD-TYPE
  T0+T1                2                 62
  T2                   4                 69
  T3                   3                 78
  T4                   0                 67
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  10P GAIN MUTATED     4   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 310  20
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      9    2
  10P GAIN WILD-TYPE  310   20
   clus
vv  10P GAIN MUTATED 10P GAIN WILD-TYPE
  0                9                310
  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  42 313
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      5    7
  10P GAIN WILD-TYPE   42  313
     clus
vv    10P GAIN MUTATED 10P GAIN WILD-TYPE
  NO                 5                 42
  YES                7                313
[1] 2 2
[1] FALSE
D19V10, continuous
D19V11, binary
                    cls
clus                   0   1
  10P GAIN MUTATED     3   9
  10P GAIN WILD-TYPE 135 220
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      3    9
  10P GAIN WILD-TYPE  135  220
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  FEMALE                3                135
  MALE                  9                220
[1] 2 2
[1] FALSE
D19V12, binary
                    cls
clus                   0   1
  10P GAIN MUTATED    10   2
  10P GAIN WILD-TYPE 309  45
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED     10    2
  10P GAIN WILD-TYPE  309   45
     clus
vv    10P GAIN MUTATED 10P GAIN WILD-TYPE
  NO                10                309
  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   341
D19V13, multiclass
                           clus
vv                          10P GAIN MUTATED 10P GAIN WILD-TYPE
  ASIAN                                    0                  5
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   12                341
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V14, binary
                    cls
clus                   0   1
  10P GAIN MUTATED     0  12
  10P GAIN WILD-TYPE   7 340
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      0   12
  10P GAIN WILD-TYPE    7  340
                        clus
vv                       10P GAIN MUTATED 10P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  7
  NOT HISPANIC OR LATINO               12                340
[1] 2 2
[1] FALSE

Clustering(20) Variable = 10Q GAIN MUTATION ANALYSIS
D20V1, survival
                    sevent
clus2                  0   1
  10Q GAIN MUTATED     1   1
  10Q GAIN WILD-TYPE 127 123
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 2                250 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 1                123 
$`10Q GAIN MUTATED`
TCGA-DA-A1HY TCGA-ER-A3ET 
      138.67        68.52 

$`10Q GAIN WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A8GI TCGA-EB-A5SG TCGA-EE-A180 
        9.76        62.07        38.76        13.41        33.24        31.96 
TCGA-EE-A20H TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 
      166.75       269.03        52.90       134.40        27.35        19.04 
TCGA-FR-A729 TCGA-FW-A3R5 TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-3N-A9WC TCGA-3N-A9WD 
      216.43        36.95        52.73         7.40        60.46        12.99 
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-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-A2JG TCGA-D3-A2JH 
       62.86        15.75       168.00        86.30       107.61        36.30 
TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CB 
      171.58        64.83        66.08        43.53        58.06       140.98 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU 
       40.01        59.70        24.53         9.34        90.21        23.67 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T 
      173.85        30.67       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-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA 
       76.34        68.68       150.61       110.53        60.10        64.83 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-DA-A95V TCGA-DA-A95W 
       58.85        30.44       225.11         8.71        72.10         0.76 
TCGA-DA-A95X TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN 
       65.03        14.14        12.30         3.91        16.41        52.41 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
       18.21        13.15        24.89        20.38         0.00        26.24 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
       75.55        79.20        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        47.41        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-A2GE 
      185.19       115.43        30.02        77.98        26.14        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        93.63 
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-A2MS TCGA-EE-A2MT 
       89.26       104.78       145.45       227.01       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-A3JB 
        6.28        67.89       111.85        45.90         3.35       168.85 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A 
       19.86       135.98        34.45        10.49         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       184.60       150.12        99.06 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W 
       59.84        42.51       120.76        49.71        47.18       146.63 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
       73.05        22.36         4.70        16.87        10.19        28.67 
TCGA-ER-A3ES TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A 
      173.29        15.48        32.05        74.47         4.50       174.21 
TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FS-A1YW TCGA-FS-A1YY 
        4.14        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        43.92 
TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT 
        7.82        36.33        78.61       130.95       136.27        35.28 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 
        4.47        23.21         5.29         3.06        30.90        66.67 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
      173.19        13.28        80.68        55.59        11.54        19.30 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        9.90        18.25         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-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-A8ZM TCGA-WE-A8ZN 
        8.09       185.13        92.84        47.54        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        37.32 
TCGA-WE-AAA4 TCGA-XV-AB01 TCGA-YG-AA3O TCGA-Z2-AA3S 
       24.99         6.61        28.21        91.23 

  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
             68.52               0.00 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
            138.67             346.49 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
           103.595             45.945 
[1] "68.5 - 138.7 (103.6)" "0.0 - 346.5 (45.9)"  
[1] "Remove cluster labels:" "10Q GAIN MUTATED"      
D20V2, survival
                    sevent
clus2                  0   1
  10Q GAIN MUTATED     1   2
  10Q GAIN WILD-TYPE 165 190
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 3                355 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 2                190 
$`10Q GAIN MUTATED`
TCGA-QB-AA9O TCGA-DA-A1HY TCGA-ER-A3ET 
       18.05       144.89        93.01 

$`10Q GAIN WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-D3-A8GI TCGA-EB-A5SG 
       27.65        62.07        46.32        13.87        58.52        68.25 
TCGA-EB-A5SH TCGA-EE-A180 TCGA-EE-A184 TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GD 
       54.02        94.98        68.15       168.26         2.60       340.14 
TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 TCGA-ER-A198 TCGA-FR-A729 
      126.81       134.40        27.35        31.40        50.76       220.80 
TCGA-FS-A1ZF TCGA-FW-A3R5 TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-3N-A9WB TCGA-3N-A9WC 
       15.45        36.95        61.15        21.40        17.03        66.48 
TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 
       12.99        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-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-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-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-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR 
      166.52        86.93        60.23        24.53         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-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM 
       23.61        26.43       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-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-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 
       76.57        36.03        20.38       222.51       176.55        35.93 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
      135.02        88.87        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        43.36        72.10        37.35 
TCGA-DA-A95X TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH 
       73.94        14.14        13.02        13.87        10.36        20.35 
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-A185 TCGA-EE-A20B 
        8.65        33.73        14.70        26.89         4.96       133.81 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C 
      151.27        91.56        13.55        63.35        85.08        78.97 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N 
       13.97        63.78        72.07        64.64        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-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
       86.14        59.28        67.43       173.79       220.24        48.72 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP 
      107.38        54.74        79.66        75.48       102.12        13.91 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-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-A2MS TCGA-EE-A2MT 
      167.90        47.54       248.65        43.23       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-A3J5 
       13.81        41.59       138.81       172.18       127.20        36.95 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JE TCGA-EE-A3JH 
       64.08        34.32        53.19       201.80        51.35       134.33 
TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B 
      152.81        35.44        13.94         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       302.07       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        44.09       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       105.07        43.82        23.34 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3EV 
       20.15        28.83        48.99        41.56       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-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-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP 
        9.70        32.75        47.38        23.93       101.26        74.73 
TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW 
      133.55        11.41       148.80        53.16        26.56        49.48 
TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 
       27.09        27.02        77.82        50.14        66.67        28.73 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 
      174.84        34.03        26.73        54.41        80.68        17.46 
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        19.43         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-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-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-AAA4 TCGA-XV-AB01 
       35.80        49.51        12.16        40.41        24.99        13.25 
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 

  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 
             93.01              51.35 
[1] "18.1 - 144.9 (93.0)" "0.2 - 369.9 (51.4)" 
[1] "hr=" "1.1"
D20V3, continuous
                    vv
clus                 I/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       26
                    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        38         14
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  10Q GAIN MUTATED            0          1        0
  10Q GAIN WILD-TYPE         35         53       21
D20V4, multiclass
            clus
vv           10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  I/II NOS                  0                 13
  STAGE 0                   0                  7
  STAGE I                   0                 29
  STAGE IA                  0                 18
  STAGE IB                  0                 28
  STAGE II                  0                 26
  STAGE IIA                 0                 14
  STAGE IIB                 0                 19
  STAGE IIC                 0                 15
  STAGE III                 1                 38
  STAGE IIIA                1                 14
  STAGE IIIB                0                 35
  STAGE IIIC                1                 53
  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 80 67
D20V5, multiclass
[1] "Remove cluster labels:" "10Q GAIN MUTATED"      
clus
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 2                283 
        TCGA-D3-A2JF         TCGA-D3-A3ML         TCGA-D3-A8GI 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EB-A5SH         TCGA-EE-A180         TCGA-EE-A184 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EE-A20H         TCGA-EE-A29L         TCGA-EE-A2GD 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EE-A2GO         TCGA-EE-A2MR         TCGA-ER-A193 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-FR-A3YO         TCGA-FR-A729         TCGA-FS-A1ZF 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-WE-A8K5         TCGA-WE-AAA3         TCGA-3N-A9WB 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-3N-A9WC         TCGA-3N-A9WD         TCGA-BF-AAP0 
"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-A1Q8 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A1QA         TCGA-D3-A1QB 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A2J7         TCGA-D3-A2J8 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D3-A2J9         TCGA-D3-A2JA         TCGA-D3-A2JC 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-A2JG         TCGA-D3-A2JH 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A2JN         TCGA-D3-A2JP 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D3-A3BZ         TCGA-D3-A3C6         TCGA-D3-A3C7 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D3-A3CB         TCGA-D3-A3CC         TCGA-D3-A3CE 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D3-A3CF         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-A8GJ         TCGA-D3-A8GK 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D3-A8GL         TCGA-D3-A8GM         TCGA-D3-A8GO 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D3-A8GP         TCGA-D3-A8GQ         TCGA-D3-A8GS 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D9-A1JW         TCGA-D9-A1X3         TCGA-D9-A3Z1 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D9-A3Z3         TCGA-D9-A4Z6         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-A1HV         TCGA-DA-A1HW         TCGA-DA-A1I0 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DA-A1I1         TCGA-DA-A1I2         TCGA-DA-A1I4 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DA-A1IA         TCGA-DA-A1IB         TCGA-DA-A1IC 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DA-A3F2         TCGA-DA-A3F3         TCGA-DA-A3F5 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-DA-A95V         TCGA-DA-A95X 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DA-A95Y         TCGA-EB-A5KH         TCGA-EB-A5UN 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EB-A5VV         TCGA-EE-A17X         TCGA-EE-A17Y 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A182 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20B         TCGA-EE-A20F 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EE-A29A         TCGA-EE-A29B         TCGA-EE-A29C 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29G 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EE-A29H         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-A2GE         TCGA-EE-A2GH         TCGA-EE-A2GI 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EE-A2GJ         TCGA-EE-A2GK         TCGA-EE-A2GL 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EE-A2GM         TCGA-EE-A2GN         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-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-A197         TCGA-ER-A199 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-ER-A19C         TCGA-ER-A19D         TCGA-ER-A19E 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-ER-A19M         TCGA-ER-A19O         TCGA-ER-A19T 
"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-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-A1ZG 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZH         TCGA-FS-A1ZJ         TCGA-FS-A1ZK 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZM         TCGA-FS-A1ZP         TCGA-FS-A1ZR 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZS         TCGA-FS-A1ZT         TCGA-FS-A1ZU 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZW         TCGA-FS-A1ZY         TCGA-FS-A1ZZ 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-FS-A4F0         TCGA-FS-A4F2         TCGA-FS-A4F4 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-FS-A4F5         TCGA-FS-A4F8         TCGA-FS-A4F9 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-FS-A4FB         TCGA-FS-A4FC         TCGA-FS-A4FD 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-FW-A3TV         TCGA-FW-A5DY         TCGA-GF-A3OT 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-GF-A4EO         TCGA-GF-A6C8         TCGA-GN-A267 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26A         TCGA-GN-A26D 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-GN-A4U3         TCGA-GN-A4U4         TCGA-GN-A4U7 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-GN-A4U9         TCGA-GN-A8LK         TCGA-GN-A8LL 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-GN-A9SD         TCGA-HR-A2OH         TCGA-QB-A6FS 
"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-AA1R         TCGA-W3-AA1V         TCGA-W3-AA1W 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-W3-AA21         TCGA-WE-A8JZ         TCGA-WE-A8K1 
"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-XV-AB01         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 316  22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      3    0
  10Q GAIN WILD-TYPE  316   22
   clus
vv  10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  0                3                316
  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  46 318
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      1    2
  10Q GAIN WILD-TYPE   46  318
     clus
vv    10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  NO                 1                 46
  YES                2                318
[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-D3-A2JF         TCGA-D3-A3ML         TCGA-D3-A51G 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D3-A8GI         TCGA-EB-A5SH         TCGA-EE-A180 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EE-A184         TCGA-EE-A20H         TCGA-EE-A29L 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EE-A2GD         TCGA-EE-A2GO         TCGA-EE-A2MR 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-ER-A198         TCGA-FR-A729         TCGA-FS-A1ZF 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-WE-A8K5         TCGA-WE-AAA3         TCGA-3N-A9WB 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-3N-A9WC         TCGA-3N-A9WD         TCGA-D3-A1Q1 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q3         TCGA-D3-A1Q4         TCGA-D3-A1Q6 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q9         TCGA-D3-A1QA 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A2J7         TCGA-D3-A2J8 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D3-A2J9         TCGA-D3-A2JA         TCGA-D3-A2JD 
"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-A3BZ         TCGA-D3-A3C6         TCGA-D3-A3CB 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D3-A3CC         TCGA-D3-A3CF         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-A51K         TCGA-D3-A51R 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D3-A51T         TCGA-D3-A5GL         TCGA-D3-A5GN 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D3-A5GO         TCGA-D3-A5GR         TCGA-D3-A5GS 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D3-A5GU         TCGA-D3-A8GB         TCGA-D3-A8GD 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D3-A8GJ         TCGA-D3-A8GK         TCGA-D3-A8GL 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D3-A8GM         TCGA-D3-A8GO         TCGA-D3-A8GP 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D3-A8GQ         TCGA-D3-A8GR         TCGA-D3-A8GS 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D9-A1X3         TCGA-D9-A3Z1         TCGA-D9-A3Z3 
"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-A1HW         TCGA-DA-A1I0 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DA-A1I4         TCGA-DA-A1I5         TCGA-DA-A1I8 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DA-A1IA         TCGA-DA-A1IB         TCGA-DA-A1IC 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DA-A3F2         TCGA-DA-A3F5         TCGA-DA-A3F8 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DA-A95V         TCGA-DA-A95X         TCGA-DA-A95Y 
"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-A181         TCGA-EE-A182         TCGA-EE-A185 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         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-A29M         TCGA-EE-A29P         TCGA-EE-A29Q 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29V 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EE-A29W         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-A2GE         TCGA-EE-A2GH         TCGA-EE-A2GI 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EE-A2GJ         TCGA-EE-A2GK         TCGA-EE-A2GL 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EE-A2GM         TCGA-EE-A2GN         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-A2MS         TCGA-EE-A2MT 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EE-A2MU         TCGA-EE-A3AE         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-A197         TCGA-ER-A199 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-ER-A19C         TCGA-ER-A19D         TCGA-ER-A19E 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-ER-A19F         TCGA-ER-A19G         TCGA-ER-A19H 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-ER-A19M         TCGA-ER-A19Q         TCGA-ER-A19T 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-ER-A19W         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-A44A 
"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-A1ZG         TCGA-FS-A1ZH         TCGA-FS-A1ZJ 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZK         TCGA-FS-A1ZM         TCGA-FS-A1ZP 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A1ZS         TCGA-FS-A1ZT 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZU         TCGA-FS-A1ZW         TCGA-FS-A1ZY 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZZ         TCGA-FS-A4F0         TCGA-FS-A4F2 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-FS-A4F4         TCGA-FS-A4F5         TCGA-FS-A4F8 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-FS-A4F9         TCGA-FS-A4FB         TCGA-FS-A4FC 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-FS-A4FD         TCGA-FW-A3TV         TCGA-GF-A6C8 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A264         TCGA-GN-A267 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26A         TCGA-GN-A26D 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-GN-A4U3         TCGA-GN-A4U4         TCGA-GN-A4U7 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-GN-A4U9         TCGA-GN-A8LK         TCGA-GN-A8LL 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-GN-A9SD         TCGA-HR-A2OH         TCGA-W3-A824 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-W3-A825         TCGA-W3-A828         TCGA-W3-AA1V 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-W3-AA1W         TCGA-W3-AA21         TCGA-WE-A8JZ 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-WE-A8K1         TCGA-WE-A8ZN         TCGA-WE-A8ZO 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-WE-A8ZQ         TCGA-WE-A8ZT         TCGA-WE-A8ZY 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-WE-AA9Y         TCGA-WE-AAA0         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 137 227
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      1    2
  10Q GAIN WILD-TYPE  137  227
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  FEMALE                1                137
  MALE                  2                227
[1] 2 2
[1] FALSE
D20V12, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED     2   1
  10Q GAIN WILD-TYPE 317  46
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      2    1
  10Q GAIN WILD-TYPE  317   46
     clus
vv    10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  NO                 2                317
  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   350
D20V13, multiclass
                           clus
vv                          10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  ASIAN                                    0                  5
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                    3                350
[1] 3 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   7 349
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      0    3
  10Q GAIN WILD-TYPE    7  349
                        clus
vv                       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  7
  NOT HISPANIC OR LATINO                3                349
[1] 2 2
[1] FALSE

Clustering(21) Variable = 11P GAIN MUTATION ANALYSIS
D21V1, survival
                    sevent
clus2                  0   1
  11P GAIN MUTATED    12  10
  11P GAIN WILD-TYPE 116 114
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                22                230 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                10                114 
$`11P GAIN MUTATED`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-EE-A180 TCGA-D3-A2JC TCGA-D3-A2JP TCGA-D3-A3CB 
        9.76        62.07        31.96        86.30        43.53       140.98 
TCGA-D3-A3CE TCGA-D9-A6EC TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2GB TCGA-EE-A2GH 
       59.70        69.21       346.49       185.19        26.14       201.60 
TCGA-EE-A2GP TCGA-EE-A2MC TCGA-EE-A3JB TCGA-EE-A3JI TCGA-ER-A19N TCGA-FS-A1ZD 
        0.76        23.77       168.85       135.98        42.51        32.78 
TCGA-FS-A1ZS TCGA-GN-A268 TCGA-W3-A825 TCGA-WE-A8ZQ 
      136.27        42.48         1.97        62.89 

$`11P GAIN WILD-TYPE`
TCGA-D3-A3C8 TCGA-D3-A8GI TCGA-EB-A5SG TCGA-EE-A20H TCGA-EE-A2GD TCGA-EE-A2GO 
       38.76        13.41        33.24       166.75       269.03        52.90 
TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 TCGA-FR-A729 TCGA-FW-A3R5 TCGA-WE-A8K5 
      134.40        27.35        19.04       216.43        36.95        52.73 
TCGA-WE-AAA3 TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q3 
        7.40        60.46        12.99        14.83         8.42        15.72 
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA 
       31.89       110.93        49.35       133.25        19.04        76.41 
TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JB 
       62.60        25.64        45.99        62.86        15.75       168.00 
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-A3CC TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E 
       40.01        24.53         9.34        90.21        23.67       173.85 
TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL 
       30.67       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-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC 
       68.68       150.61       110.53        60.10        64.83        58.85 
TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-DA-A95V TCGA-DA-A95W TCGA-DA-A95X 
       30.44       225.11         8.71        72.10         0.76        65.03 
TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A6L9 
       14.14        12.30         3.91        16.41        52.41        18.21 
TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20C 
       13.15        24.89        20.38         0.00        26.24        75.55 
TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G 
       79.20        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 
       47.41        47.74        27.16        61.12       115.43        30.02 
TCGA-EE-A2A6 TCGA-EE-A2GE TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
       77.98        12.95        68.65        10.62        32.48        18.35 
TCGA-EE-A2GN TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 
       93.63         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-A2MS TCGA-EE-A2MT TCGA-EE-A2MU 
      104.78       145.45       227.01       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-A3JH TCGA-ER-A195 
       67.89       111.85        45.90         3.35        19.86        34.45 
TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D 
       10.49         7.82         4.54        53.29        39.81        11.47 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19P TCGA-ER-A19Q 
      184.60       150.12        99.06        59.84       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        73.05        22.36         4.70        16.87 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL 
       10.19        28.67       173.29        68.52        15.48        32.05 
TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A7UA 
       74.47         4.50       174.21         4.14        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-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ 
      312.07        43.92         7.82        36.33        78.61       130.95 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 
       35.28         4.47        23.21         5.29         3.06        30.90 
TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV 
       66.67       173.19        13.28        80.68        55.59        11.54 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 
       19.30         9.90        18.25         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-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-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO 
      185.13        92.84        47.54        65.42        12.69        21.90 
TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-XV-AB01 
       10.95        48.39         1.94        37.32        24.99         6.61 
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 
            60.885             45.945 
[1] "0.8 - 346.5 (60.9)" "0.0 - 312.1 (45.9)"
[1] "hr=" "1.5"
D21V2, survival
                    sevent
clus2                  0   1
  11P GAIN MUTATED    14  18
  11P GAIN WILD-TYPE 152 174
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                32                326 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                18                174 
$`11P GAIN MUTATED`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-EE-A180 TCGA-D3-A2JC TCGA-D3-A2JP TCGA-D3-A3CB 
       27.65        62.07        94.98        86.76        59.57       166.52 
TCGA-D3-A3CE TCGA-D9-A6EC TCGA-DA-A3F3 TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2GB 
       60.23        77.56        10.49       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-A1ZD TCGA-FS-A1ZS TCGA-FS-A4F2 
       44.09        12.95        48.59        53.52       148.80        50.14 
TCGA-GN-A266 TCGA-GN-A268 TCGA-GN-A26D TCGA-GN-A8LL TCGA-W3-A825 TCGA-WE-A8K6 
       10.13        62.79        48.00        21.37        63.02        17.95 
TCGA-WE-A8ZQ TCGA-WE-A8ZX 
       63.22        35.80 

$`11P GAIN WILD-TYPE`
TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-D3-A8GI TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A184 
       46.32        13.87        58.52        68.25        54.02        68.15 
TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD 
      168.26         2.60       340.14       126.81       134.40        27.35 
TCGA-ER-A193 TCGA-ER-A198 TCGA-FR-A729 TCGA-FS-A1ZF TCGA-FW-A3R5 TCGA-QB-AA9O 
       31.40        50.76       220.80        15.45        36.95        18.05 
TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 
       61.15        21.40        17.03        66.48        12.99        14.93 
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.57        16.67       112.04       112.57        71.80       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-A2JD TCGA-D3-A2JG 
       65.49        23.77       115.53       168.00        11.87       113.52 
TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A3BZ 
       42.08        12.10       171.58        66.48        66.08       130.72 
TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR 
       58.06        46.98        86.93        24.53         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-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM 
       23.61        26.43       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-A1X3 TCGA-D9-A3Z1 
      151.53        54.67         3.65         7.10        18.12        15.39 
TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EG TCGA-DA-A1HV 
       22.29        18.44         9.90        25.18        22.95        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       222.51       176.55        35.93 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
      135.02        88.87        53.92        65.92        40.60        68.09 
TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-DA-A95V TCGA-DA-A95W TCGA-DA-A95X 
       33.93       225.96        43.36        72.10        37.35        73.94 
TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5UL 
       14.14        13.02        13.87        10.36        20.35        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-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-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D 
       91.56        13.55        63.35        85.08        78.97        13.97 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P 
       63.78        72.07        64.64        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-A2GE 
      115.96        59.64        39.29        86.14        67.43       173.79 
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-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-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA 
      248.65        43.23       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-A3JE TCGA-EE-A3JH TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 
       53.19        51.35       134.33        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-A19P 
      302.07       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       105.07        43.82 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES 
       23.34        20.15        28.83        48.99        41.56       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-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD 
       15.72        27.85        18.77        38.27        34.82        36.26 
TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 
      104.42       216.92       228.59       202.65        20.91        28.08 
TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZE TCGA-FS-A1ZG 
        7.79        27.72        48.85       357.37        46.45         9.70 
TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ 
       32.75        47.38        23.93       101.26        74.73       133.55 
TCGA-FS-A1ZR TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ 
       11.41        53.16        26.56        49.48        27.09        27.02 
TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB 
       77.82        66.67        28.73       174.84        34.03        26.73 
TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
       54.41        80.68        17.46        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        19.43         2.04        15.78       139.89       117.93 
TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 
       96.92        64.44        32.48       121.91        39.35        10.42 
TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A9SD TCGA-HR-A2OG TCGA-HR-A2OH 
       48.89        22.13        50.10        59.41         0.23        65.88 
TCGA-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-AA1O TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1V 
      228.16       121.08         4.01        69.07       111.09        42.08 
TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8ZM TCGA-WE-A8ZN 
      219.16       105.04        24.03        49.05       101.33        58.98 
TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 
       70.52        11.80        49.51        12.16        40.41        24.99 
TCGA-XV-AB01 TCGA-YD-A89C TCGA-YD-A9TA TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-A8RT 
       13.25         6.90        49.18        37.94        14.43        27.58 
TCGA-Z2-AA3S TCGA-Z2-AA3V 
       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 
             59.90              50.43 
[1] "10.1 - 369.9 (59.9)" "0.2 - 368.8 (50.4)" 
[1] "hr=" "1.1"
D21V3, continuous
                    vv
clus                 I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  11P GAIN MUTATED          3       1       6        1        0        1
  11P GAIN WILD-TYPE       10       6      23       17       28       25
                    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        35         14
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  11P GAIN MUTATED            5          3        0
  11P GAIN WILD-TYPE         30         51       21
D21V4, multiclass
            clus
vv           11P GAIN MUTATED 11P GAIN WILD-TYPE
  I/II NOS                  3                 10
  STAGE 0                   1                  6
  STAGE I                   6                 23
  STAGE IA                  1                 17
  STAGE IB                  0                 28
  STAGE II                  1                 25
  STAGE IIA                 2                 12
  STAGE IIB                 1                 18
  STAGE IIC                 3                 12
  STAGE III                 4                 35
  STAGE IIIA                1                 14
  STAGE IIIB                5                 30
  STAGE IIIC                3                 51
  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  4  7
  11P GAIN WILD-TYPE    59 64 77 60
D21V5, multiclass
       clus
vv      11P GAIN MUTATED 11P GAIN WILD-TYPE
  T0+T1                5                 59
  T2                   9                 64
  T3                   4                 77
  T4                   7                 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
  11P GAIN MUTATED    18   7   2   3
  11P GAIN WILD-TYPE 159  58  37  42
D21V6, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  N0               18                159
  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    31   0
  11P GAIN WILD-TYPE 288  22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED     31    0
  11P GAIN WILD-TYPE  288   22
   clus
vv  11P GAIN MUTATED 11P GAIN WILD-TYPE
  0               31                288
  1                0                 22
[1] 2 2
[1] FALSE
D21V8, binary
                    cls
clus                   0   1
  11P GAIN MUTATED     9   7
  11P GAIN WILD-TYPE 125  83
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      9    7
  11P GAIN WILD-TYPE  125   83
     clus
vv    11P GAIN MUTATED 11P GAIN WILD-TYPE
  NO                 9                125
  YES                7                 83
[1] 2 2
[1] FALSE
D21V9, binary
                    cls
clus                   0   1
  11P GAIN MUTATED     7  27
  11P GAIN WILD-TYPE  40 293
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      7   27
  11P GAIN WILD-TYPE   40  293
     clus
vv    11P GAIN MUTATED 11P GAIN WILD-TYPE
  NO                 7                 40
  YES               27                293
[1] 2 2
[1] FALSE
D21V10, continuous
D21V11, binary
                    cls
clus                   0   1
  11P GAIN MUTATED    13  21
  11P GAIN WILD-TYPE 125 208
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED     13   21
  11P GAIN WILD-TYPE  125  208
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  FEMALE               13                125
  MALE                 21                208
[1] 2 2
[1] FALSE
D21V12, binary
                    cls
clus                   0   1
  11P GAIN MUTATED    26   8
  11P GAIN WILD-TYPE 293  39
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED     26    8
  11P GAIN WILD-TYPE  293   39
     clus
vv    11P GAIN MUTATED 11P GAIN WILD-TYPE
  NO                26                293
  YES                8                 39
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  11P GAIN MUTATED       0                         0    33
  11P GAIN WILD-TYPE     5                         1   320
D21V13, multiclass
                           clus
vv                          11P GAIN MUTATED 11P GAIN WILD-TYPE
  ASIAN                                    0                  5
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   33                320
[1] 3 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  34
  11P GAIN WILD-TYPE   7 318
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      0   34
  11P GAIN WILD-TYPE    7  318
                        clus
vv                       11P GAIN MUTATED 11P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  7
  NOT HISPANIC OR LATINO               34                318
[1] 2 2
[1] FALSE

Clustering(22) Variable = 11Q GAIN MUTATION ANALYSIS
D22V1, survival
                    sevent
clus2                  0   1
  11Q GAIN MUTATED    12   7
  11Q GAIN WILD-TYPE 116 117
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                19                233 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 7                117 
$`11Q GAIN MUTATED`
TCGA-D3-A2JF TCGA-FR-A729 TCGA-D3-A2JC TCGA-D3-A2JP TCGA-D3-A3CB TCGA-D3-A3CE 
       62.07       216.43        86.30        43.53       140.98        59.70 
TCGA-D9-A6EC TCGA-EE-A29W TCGA-EE-A2GH TCGA-EE-A2GP TCGA-EE-A2MC TCGA-EE-A3JB 
       69.21       185.19       201.60         0.76        23.77       168.85 
TCGA-EE-A3JI TCGA-ER-A19N TCGA-FS-A1ZD TCGA-FS-A1ZS TCGA-GF-A4EO TCGA-GN-A268 
      135.98        42.51        32.78       136.27        18.25        42.48 
TCGA-WE-A8ZQ 
       62.89 

$`11Q GAIN WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A3C8 TCGA-D3-A8GI TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A20H 
        9.76        38.76        13.41        33.24        31.96       166.75 
TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 TCGA-FW-A3R5 
      269.03        52.90       134.40        27.35        19.04        36.95 
TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 
       52.73         7.40        60.46        12.99        14.83         8.42 
TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       15.72        31.89       110.93        49.35       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-A2JG TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
      168.00       107.61        36.30       171.58        64.83        66.08 
TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU 
       58.06        40.01        24.53         9.34        90.21        23.67 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T 
      173.85        30.67       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        68.68       150.61       110.53        60.10        64.83 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-DA-A95V TCGA-DA-A95W 
       58.85        30.44       225.11         8.71        72.10         0.76 
TCGA-DA-A95X TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN 
       65.03        14.14        12.30         3.91        16.41        52.41 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
       18.21        13.15        24.89        20.38         0.00        26.24 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
       75.55        79.20        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        47.41        47.74        27.16        61.12       346.49 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GJ 
      115.43        30.02        77.98        26.14        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        93.63         0.20        71.31 
TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MF TCGA-EE-A2MG 
       81.99       103.13        15.25         5.75       209.79        94.19 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP 
      171.85        63.25        89.26       104.78       145.45       227.01 
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-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A 
        3.35        19.86        34.45        10.49         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       184.60       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        73.05 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES 
       22.36         4.70        16.87        10.19        28.67       173.29 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A 
       68.52        15.48        32.05        74.47         4.50       174.21 
TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FS-A1YW TCGA-FS-A1YY 
        4.14        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-A1ZG 
      195.98         8.35        27.62       312.07        43.92         7.82 
TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW 
       36.33        78.61       130.95        35.28         4.47        23.21 
TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 
        5.29         3.06        30.90        66.67       173.19        13.28 
TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 
       80.68        55.59        11.54        19.30         9.90         1.91 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A4U3 
       53.29       117.93        96.92        17.06         7.59       120.53 
TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-GN-A8LK TCGA-GN-A9SD TCGA-LH-A9QB TCGA-OD-A75X 
       34.49        46.92        43.23        59.41        85.05       297.01 
TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 
        7.23         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        47.54 
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-AAA4 TCGA-XV-AB01 TCGA-YG-AA3O TCGA-Z2-AA3S 
       37.32        24.99         6.61        28.21        91.23 

  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
              0.76               0.00 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
            216.43             346.49 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
             62.89              45.70 
[1] "0.8 - 216.4 (62.9)" "0.0 - 346.5 (45.7)"
[1] "hr=" "1.9"
D22V2, survival
                    sevent
clus2                  0   1
  11Q GAIN MUTATED    14  12
  11Q GAIN WILD-TYPE 152 180
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                26                332 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                12                180 
$`11Q GAIN MUTATED`
TCGA-D3-A2JF TCGA-FR-A729 TCGA-D3-A2JC TCGA-D3-A2JP TCGA-D3-A3CB TCGA-D3-A3CE 
       62.07       220.80        86.76        59.57       166.52        60.23 
TCGA-D9-A6EC TCGA-DA-A3F3 TCGA-EE-A29W TCGA-EE-A2GH TCGA-EE-A2GP TCGA-EE-A2M5 
       77.56        10.49       195.02       220.24        13.91        21.67 
TCGA-EE-A2MC TCGA-EE-A3JB TCGA-EE-A3JI TCGA-ER-A19N TCGA-ER-A42K TCGA-FS-A1YX 
       61.51       201.80       152.81        44.09        12.95        48.59 
TCGA-FS-A1ZD TCGA-FS-A1ZS TCGA-FS-A4F2 TCGA-GF-A4EO TCGA-GN-A268 TCGA-WE-A8K6 
       53.52       148.80        50.14        19.43        62.79        17.95 
TCGA-WE-A8ZQ TCGA-WE-A8ZX 
       63.22        35.80 

$`11Q GAIN WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-D3-A8GI TCGA-EB-A5SG TCGA-EB-A5SH 
       27.65        46.32        13.87        58.52        68.25        54.02 
TCGA-EE-A180 TCGA-EE-A184 TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2GO 
       94.98        68.15       168.26         2.60       340.14       126.81 
TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 TCGA-ER-A198 TCGA-FS-A1ZF TCGA-FW-A3R5 
      134.40        27.35        31.40        50.76        15.45        36.95 
TCGA-QB-AA9O TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD 
       18.05        61.15        21.40        17.03        66.48        12.99 
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-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-A2JD 
      103.10        65.49        23.77       115.53       168.00        11.87 
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-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3MO 
      130.72        58.06        46.98        86.93        24.53         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-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL 
       79.59        23.61        26.43       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       222.51       176.55 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB 
       35.93       135.02        88.87        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        43.36        72.10        37.35 
TCGA-DA-A95X TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH 
       73.94        14.14        13.02        13.87        10.36        20.35 
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-A185 TCGA-EE-A20B 
        8.65        33.73        14.70        26.89         4.96       133.81 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C 
      151.27        91.56        13.55        63.35        85.08        78.97 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N 
       13.97        63.78        72.07        64.64        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-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-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-A2MD TCGA-EE-A2ME 
       94.82       129.27        28.83        19.76        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-A2MS 
      216.66       167.90        47.54       248.65        43.23       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-A3JE TCGA-EE-A3JH 
       36.95        64.08        34.32        53.19        51.35       134.33 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C 
       35.44        13.94         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       302.07       152.35         6.44 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T 
      131.51        61.05       162.08        50.89        49.48         8.88 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF 
      148.18       105.07        43.82        23.34        20.15        28.83 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL 
       48.99        41.56       247.04        93.01        46.98        33.21 
TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A7U9 
      149.03        92.98       174.21        15.72        27.85        18.77 
TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YY 
       38.27        34.82        36.26       104.42       216.92       228.59 
TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB 
      202.65        20.91        28.08         7.79        27.72        48.85 
TCGA-FS-A1ZC TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK 
      357.37        46.45         9.70        32.75        47.38        23.93 
TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZT TCGA-FS-A1ZU 
      101.26        74.73       133.55        11.41        53.16        26.56 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 
       49.48        27.09        27.02        77.82        66.67        28.73 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 
      174.84        34.03        26.73        54.41        80.68        17.46 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GF-A6C9 
       55.59        13.51        19.30         9.90         2.04        15.78 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A26A 
      139.89       117.93        96.92        10.13        64.44        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-A8ZM TCGA-WE-A8ZN 
      219.16       105.04        24.03        49.05       101.33        58.98 
TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 
       70.52        11.80        49.51        12.16        40.41        24.99 
TCGA-XV-AB01 TCGA-YD-A89C TCGA-YD-A9TA TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-A8RT 
       13.25         6.90        49.18        37.94        14.43        27.58 
TCGA-Z2-AA3S TCGA-Z2-AA3V 
       96.99        15.98 

  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
             10.49               0.20 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
            220.80             369.93 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
             60.87              50.43 
[1] "10.5 - 220.8 (60.9)" "0.2 - 369.9 (50.4)" 
[1] "hr=" "1.3"
D22V3, continuous
                    vv
clus                 I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  11Q GAIN MUTATED          3       1       7        1        0        0
  11Q GAIN WILD-TYPE       10       6      22       17       28       26
                    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        36         14
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  11Q GAIN MUTATED            4          3        0
  11Q GAIN WILD-TYPE         31         51       21
D22V4, multiclass
            clus
vv           11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  I/II NOS                  3                 10
  STAGE 0                   1                  6
  STAGE I                   7                 22
  STAGE IA                  1                 17
  STAGE IB                  0                 28
  STAGE II                  0                 26
  STAGE IIA                 2                 12
  STAGE IIB                 1                 18
  STAGE IIC                 1                 14
  STAGE III                 3                 36
  STAGE IIIA                1                 14
  STAGE IIIB                4                 31
  STAGE IIIC                3                 51
  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  3  4
  11Q GAIN WILD-TYPE    57 65 78 63
D22V5, multiclass
       clus
vv      11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  T0+T1                7                 57
  T2                   8                 65
  T3                   3                 78
  T4                   4                 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
  11Q GAIN MUTATED    16   6   2   3
  11Q GAIN WILD-TYPE 161  59  37  42
D22V6, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  N0               16                161
  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    27   0
  11Q GAIN WILD-TYPE 292  22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED     27    0
  11Q GAIN WILD-TYPE  292   22
   clus
vv  11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  0               27                292
  1                0                 22
[1] 2 2
[1] FALSE
D22V8, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED     9   4
  11Q GAIN WILD-TYPE 125  86
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      9    4
  11Q GAIN WILD-TYPE  125   86
     clus
vv    11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  NO                 9                125
  YES                4                 86
[1] 2 2
[1] FALSE
D22V9, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED     7  21
  11Q GAIN WILD-TYPE  40 299
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      7   21
  11Q GAIN WILD-TYPE   40  299
     clus
vv    11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  NO                 7                 40
  YES               21                299
[1] 2 2
[1] FALSE
D22V10, continuous
D22V11, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED    10  18
  11Q GAIN WILD-TYPE 128 211
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED     10   18
  11Q GAIN WILD-TYPE  128  211
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  FEMALE               10                128
  MALE                 18                211
[1] 2 2
[1] FALSE
D22V12, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED    21   7
  11Q GAIN WILD-TYPE 298  40
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED     21    7
  11Q GAIN WILD-TYPE  298   40
     clus
vv    11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  NO                21                298
  YES                7                 40
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  11Q GAIN MUTATED       0                         0    27
  11Q GAIN WILD-TYPE     5                         1   326
D22V13, multiclass
                           clus
vv                          11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  ASIAN                                    0                  5
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   27                326
[1] 3 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  28
  11Q GAIN WILD-TYPE   7 324
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      0   28
  11Q GAIN WILD-TYPE    7  324
                        clus
vv                       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  7
  NOT HISPANIC OR LATINO               28                324
[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 110  93
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                49                203 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                31                 93 
$`12P GAIN MUTATED`
TCGA-EE-A180 TCGA-EE-A20H TCGA-FR-A729 TCGA-D3-A1Q1 TCGA-D3-A1Q6 TCGA-D3-A2JN 
       31.96       166.75       216.43         8.42        49.35        64.83 
TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A5GN TCGA-D3-A5GU 
       58.06        40.01        59.70        24.53        45.70       124.08 
TCGA-D3-A8GC TCGA-D3-A8GL TCGA-D9-A6EC TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A3F5 
       78.21        69.53        69.21        60.10        64.83       225.11 
TCGA-DA-A95V TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EE-A17Y TCGA-EE-A29D 
       72.10        12.30         3.91        16.41        24.89        12.99 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GH TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A3AA 
       77.98        26.14       201.60        81.99       103.13       124.31 
TCGA-EE-A3AD TCGA-EE-A3JI TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19L TCGA-ER-A19M 
        4.41       135.98        53.29        39.81        99.06        59.84 
TCGA-ER-A3ET TCGA-ER-A3PL TCGA-FS-A1ZM TCGA-FS-A1ZU TCGA-GN-A267 TCGA-GN-A26A 
       68.52        32.05        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-D3-A2JE TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A8GI TCGA-EB-A5SG TCGA-EE-A2GD 
        9.76        62.07        38.76        13.41        33.24       269.03 
TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 TCGA-FW-A3R5 TCGA-WE-A8K5 
       52.90       134.40        27.35        19.04        36.95        52.73 
TCGA-WE-AAA3 TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
        7.40        60.46        12.99        14.83        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-A2JG 
       45.99        62.86        15.75       168.00        86.30       107.61 
TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3CB TCGA-D3-A3MO 
       36.30       171.58        66.08        43.53       140.98         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K 
       90.21        23.67       173.85        30.67       144.46        31.76 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GR TCGA-D3-A8GD TCGA-D3-A8GJ 
       62.70        11.34        42.05       177.86        23.61       179.97 
TCGA-D3-A8GK TCGA-D3-A8GM TCGA-D3-A8GP TCGA-D3-A8GR TCGA-D9-A1X3 TCGA-D9-A3Z1 
      120.00        70.62       135.12        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        68.68 
TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F8 TCGA-DA-A95W 
      150.61       110.53        58.85        30.44         8.71         0.76 
TCGA-DA-A95X TCGA-DA-A95Y TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A181 
       65.03        14.14        52.41        18.21        13.15        20.38 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29C 
        0.00        26.24        75.55        79.20        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        47.41        47.74        27.16        61.12 
TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2GE TCGA-EE-A2GJ 
      346.49       185.19       115.43        30.02        12.95        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        93.63         0.76         0.20 
TCGA-EE-A2GS TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MG 
       71.31        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-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AE 
      143.93        23.51        53.26       122.73        64.04        54.51 
TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB 
        6.28        67.89       111.85        45.90         3.35       168.85 
TCGA-EE-A3JH TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19D 
       19.86        34.45        10.49         7.82         4.54        11.47 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S 
      184.60       150.12        42.51       120.76        49.71        47.18 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF 
      146.63        73.05        22.36         4.70        16.87        10.19 
TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3EV TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A 
       28.67       173.29        15.48        74.47         4.50       174.21 
TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FS-A1YW TCGA-FS-A1YY 
        4.14        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        43.92 
TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZW 
        7.82        36.33       130.95       136.27        35.28        23.21 
TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 
        5.29         3.06        30.90        66.67       173.19        13.28 
TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
       80.68        55.59        11.54        19.30         9.90        18.25 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A268 TCGA-GN-A4U3 
        1.91        53.29       117.93        96.92        42.48       120.53 
TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-GN-A9SD TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS 
       34.49        46.92        59.41        85.05       297.01         7.23 
TCGA-RP-A690 TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A828 TCGA-W3-AA1V TCGA-WE-A8K1 
        0.20         0.33       174.12       120.07         8.09        47.54 
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-XV-AB01 TCGA-Z2-AA3S 
        1.94        37.32        24.99         6.61        91.23 

  12P GAIN MUTATED 12P GAIN WILD-TYPE 
              1.97               0.00 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
            225.11             346.49 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
             59.70              43.92 
[1] "2.0 - 225.1 (59.7)" "0.0 - 346.5 (43.9)"
[1] "hr=" "1.3"
D23V2, survival
                    sevent
clus2                  0   1
  12P GAIN MUTATED    24  40
  12P GAIN WILD-TYPE 142 152
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                64                294 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                40                152 
$`12P GAIN MUTATED`
TCGA-EE-A180 TCGA-EE-A20H TCGA-FR-A729 TCGA-QB-AA9O TCGA-D3-A1Q1 TCGA-D3-A1Q6 
       94.98       168.26       220.80        18.05        16.57        71.80 
TCGA-D3-A1Q9 TCGA-D3-A2JN TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF 
       31.59        66.48        58.06        86.93        60.23        24.53 
TCGA-D3-A3MV TCGA-D3-A5GN TCGA-D3-A5GU TCGA-D3-A8GC TCGA-D3-A8GL TCGA-D3-A8GV 
       45.30       135.75       125.19        79.59        89.13       167.70 
TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-DA-A1HW TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A3F5 
        9.90        77.56        36.03        88.87        65.92       225.96 
TCGA-DA-A95V TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UL TCGA-EE-A17Y 
       72.10        13.02        13.87        20.35        29.29        27.22 
TCGA-EE-A29D TCGA-EE-A29X TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GH 
       13.97        17.92        39.29        86.14        59.28       220.24 
TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A3AA TCGA-EE-A3AD TCGA-EE-A3J5 
       94.82        21.67       129.27       124.31        28.77        36.95 
TCGA-EE-A3JE TCGA-EE-A3JI TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19J TCGA-ER-A19L 
       51.35       152.81        98.40        48.89         6.44       131.51 
TCGA-ER-A19M TCGA-ER-A3ET TCGA-ER-A3PL TCGA-FS-A1ZM TCGA-FS-A1ZU TCGA-GN-A267 
       61.05        93.01        33.21       101.26        26.56        64.44 
TCGA-GN-A26A TCGA-GN-A8LK TCGA-W3-A825 TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1W 
       32.48        50.10        63.02        69.07       111.09       219.16 
TCGA-W3-AA21 TCGA-WE-A8ZX TCGA-YG-AA3O TCGA-YG-AA3P 
      105.04        35.80        37.94        14.43 

$`12P GAIN WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-D3-A8GI TCGA-EB-A5SG 
       27.65        62.07        46.32        13.87        58.52        68.25 
TCGA-EB-A5SH TCGA-EE-A184 TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR 
       54.02        68.15         2.60       340.14       126.81       134.40 
TCGA-EE-A3JD TCGA-ER-A193 TCGA-ER-A198 TCGA-FS-A1ZF TCGA-FW-A3R5 TCGA-WE-A8K5 
       27.35        31.40        50.76        15.45        36.95        61.15 
TCGA-WE-AAA3 TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q3 
       21.40        17.03        66.48        12.99        14.93        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-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL 
       86.76        11.87       113.52        42.08        12.10       171.58 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3MO 
       66.08        59.57       130.72        46.98       166.52         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-A8GB TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GJ 
      178.32        18.18        30.84        23.61        26.43       241.38 
TCGA-D3-A8GK TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR 
      170.20       107.15       161.00       152.75        29.06       129.63 
TCGA-D3-A8GS TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A1X3 
      117.17       151.53        54.67         3.65         7.10        18.12 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6EA TCGA-D9-A6EG TCGA-DA-A1HV 
       15.39        22.29        18.44        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       222.51       176.55        35.93       135.02 
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        43.36 
TCGA-DA-A95W TCGA-DA-A95X TCGA-DA-A95Y TCGA-EB-A44R TCGA-EB-A5UN TCGA-EB-A5VV 
       37.35        73.94        14.14        10.36        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-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-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M 
       85.08        78.97        63.78        72.07        64.64        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-A2GC 
       25.87       195.02        46.82       115.96        59.64        67.43 
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-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2M7 
      102.12        13.91        42.77        81.21        44.88        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-A2MS TCGA-EE-A2MT TCGA-EE-A2MU 
       47.54       248.65        43.23       162.48        71.21        53.26 
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-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB 
      172.18       127.20        64.08        34.32        53.19       201.80 
TCGA-EE-A3JH TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19D 
      134.33        35.44        13.94         9.17        77.75        12.59 
TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19N TCGA-ER-A19P 
       13.02        26.37       302.07       152.35        44.09       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       105.07        43.82 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES 
       23.34        20.15        28.83        48.99        41.56       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-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-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZQ 
        9.70        32.75        47.38        23.93        74.73       133.55 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-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-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 
       77.82        50.14        66.67        28.73       174.84        34.03 
TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV 
       26.73        54.41        80.68        17.46        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        19.43         2.04        15.78       139.89 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A268 TCGA-GN-A26D TCGA-GN-A4U3 
      117.93        96.92        10.13        62.79        48.00       121.91 
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-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-A828 TCGA-W3-AA1O TCGA-W3-AA1V 
        0.33         0.69       228.16       121.08         4.01        42.08 
TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO 
       24.03        49.05        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-AAA4 
       63.22        11.80        49.51        12.16        40.41        24.99 
TCGA-XV-AB01 TCGA-YD-A89C TCGA-YD-A9TA TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
       13.25         6.90        49.18        27.58        96.99        15.98 

  12P GAIN MUTATED 12P GAIN WILD-TYPE 
              6.44               0.20 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
            225.96             369.93 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
            62.035             49.495 
[1] "6.4 - 226.0 (62.0)" "0.2 - 369.9 (49.5)"
[1] "hr=" "1.2"
D23V3, continuous
                    vv
clus                 I/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       23
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  12P GAIN MUTATED           0         1         3        11          5
  12P GAIN WILD-TYPE        14        18        12        28         10
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  12P GAIN MUTATED           10          6        3
  12P GAIN WILD-TYPE         25         48       18
D23V4, multiclass
            clus
vv           12P GAIN MUTATED 12P GAIN WILD-TYPE
  I/II NOS                  1                 12
  STAGE 0                   0                  7
  STAGE I                  10                 19
  STAGE IA                  2                 16
  STAGE IB                  6                 22
  STAGE II                  3                 23
  STAGE IIA                 0                 14
  STAGE IIB                 1                 18
  STAGE IIC                 3                 12
  STAGE III                11                 28
  STAGE IIIA                5                 10
  STAGE IIIB               10                 25
  STAGE IIIC                6                 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
  12P GAIN MUTATED      16 15 11 10
  12P GAIN WILD-TYPE    48 58 70 57
D23V5, multiclass
       clus
vv      12P GAIN MUTATED 12P GAIN WILD-TYPE
  T0+T1               16                 48
  T2                  15                 58
  T3                  11                 70
  T4                  10                 57
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  12P GAIN MUTATED    28  21   5   6
  12P GAIN WILD-TYPE 149  44  34  39
D23V6, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  N0               28                149
  N1               21                 44
  N2                5                 34
  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"
D23V7, binary
                    cls
clus                   0   1
  12P GAIN MUTATED    57   3
  12P GAIN WILD-TYPE 262  19
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     57    3
  12P GAIN WILD-TYPE  262   19
   clus
vv  12P GAIN MUTATED 12P GAIN WILD-TYPE
  0               57                262
  1                3                 19
[1] 2 2
[1] FALSE
D23V8, binary
                    cls
clus                   0   1
  12P GAIN MUTATED    26  12
  12P GAIN WILD-TYPE 108  78
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     26   12
  12P GAIN WILD-TYPE  108   78
     clus
vv    12P GAIN MUTATED 12P GAIN WILD-TYPE
  NO                26                108
  YES               12                 78
[1] 2 2
[1] FALSE
D23V9, binary
                    cls
clus                   0   1
  12P GAIN MUTATED    11  53
  12P GAIN WILD-TYPE  36 267
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     11   53
  12P GAIN WILD-TYPE   36  267
     clus
vv    12P GAIN MUTATED 12P GAIN WILD-TYPE
  NO                11                 36
  YES               53                267
[1] 2 2
[1] FALSE
D23V10, continuous
D23V11, binary
                    cls
clus                   0   1
  12P GAIN MUTATED    21  43
  12P GAIN WILD-TYPE 117 186
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     21   43
  12P GAIN WILD-TYPE  117  186
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  FEMALE               21                117
  MALE                 43                186
[1] 2 2
[1] FALSE
D23V12, binary
                    cls
clus                   0   1
  12P GAIN MUTATED    56   8
  12P GAIN WILD-TYPE 263  39
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     56    8
  12P GAIN WILD-TYPE  263   39
     clus
vv    12P GAIN MUTATED 12P GAIN WILD-TYPE
  NO                56                263
  YES                8                 39
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  12P GAIN MUTATED       3                         0    59
  12P GAIN WILD-TYPE     2                         1   294
D23V13, multiclass
                           clus
vv                          12P GAIN MUTATED 12P GAIN WILD-TYPE
  ASIAN                                    3                  2
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   59                294
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V14, binary
                    cls
clus                   0   1
  12P GAIN MUTATED     2  61
  12P GAIN WILD-TYPE   5 291
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      2   61
  12P GAIN WILD-TYPE    5  291
                        clus
vv                       12P GAIN MUTATED 12P GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  5
  NOT HISPANIC OR LATINO               61                291
[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 117 106
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                29                223 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                18                106 
$`12Q GAIN MUTATED`
TCGA-EE-A180 TCGA-FR-A729 TCGA-D3-A1Q6 TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A3C6 
       31.96       216.43        49.35        64.83        66.08        58.06 
TCGA-D3-A3CF TCGA-D3-A5GN TCGA-D3-A5GU TCGA-D3-A8GL TCGA-DA-A3F5 TCGA-DA-A95V 
       24.53        45.70       124.08        69.53       225.11        72.10 
TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EE-A17Y TCGA-EE-A29D TCGA-EE-A2A6 TCGA-EE-A2GB 
       12.30         3.91        24.89        12.99        77.98        26.14 
TCGA-EE-A2GH TCGA-EE-A3JI TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19L TCGA-FS-A1ZM 
      201.60       135.98        53.29        39.81        99.06        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-D3-A2JE TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A8GI TCGA-EB-A5SG TCGA-EE-A20H 
        9.76        62.07        38.76        13.41        33.24       166.75 
TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 TCGA-FW-A3R5 
      269.03        52.90       134.40        27.35        19.04        36.95 
TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 
       52.73         7.40        60.46        12.99        14.83         8.42 
TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA 
       15.72        31.89       110.93       133.25        19.04        76.41 
TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JB 
       62.60        25.64        45.99        62.86        15.75       168.00 
TCGA-D3-A2JC TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JP TCGA-D3-A3CB 
       86.30       107.61        36.30       171.58        43.53       140.98 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E 
       40.01        59.70         9.34        90.21        23.67       173.85 
TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL 
       30.67       144.46        31.76        62.70        11.34        42.05 
TCGA-D3-A5GR TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GM 
      177.86        78.21        23.61       179.97       120.00        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        68.68       150.61 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F8 
      110.53        60.10        64.83        58.85        30.44         8.71 
TCGA-DA-A95W TCGA-DA-A95X TCGA-DA-A95Y TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A6L9 
        0.76        65.03        14.14        16.41        52.41        18.21 
TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A20F 
       13.15        20.38         0.00        26.24        75.55        79.20 
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        47.41        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-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        93.63 
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-A2MS TCGA-EE-A2MT 
       89.26       104.78       145.45       227.01       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-A3JB 
        6.28        67.89       111.85        45.90         3.35       168.85 
TCGA-EE-A3JH TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19D 
       19.86        34.45        10.49         7.82         4.54        11.47 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
      184.60       150.12        59.84        42.51       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        73.05        22.36         4.70        16.87 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL 
       10.19        28.67       173.29        68.52        15.48        32.05 
TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A7UA 
       74.47         4.50       174.21         4.14        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-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZQ 
      312.07        32.78        43.92         7.82        36.33       130.95 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ 
      136.27        35.28         4.47        23.21         5.29         3.06 
TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TU 
       30.90        66.67       173.19        13.28        80.68        55.59 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 
       11.54        19.30         9.90        18.25         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-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-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-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ 
       92.84        47.54        65.42        12.69        21.90        62.89 
TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-XV-AB01 
       10.95        48.39         1.94        37.32        24.99         6.61 
TCGA-Z2-AA3S 
       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 
             49.35              45.99 
[1] "2.0 - 225.1 (49.4)" "0.0 - 346.5 (46.0)"
[1] "hr=" "1.3"
D24V2, survival
                    sevent
clus2                  0   1
  12Q GAIN MUTATED    15  25
  12Q GAIN WILD-TYPE 151 167
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                40                318 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                25                167 
$`12Q GAIN MUTATED`
TCGA-EE-A180 TCGA-FR-A729 TCGA-QB-AA9O TCGA-D3-A1Q6 TCGA-D3-A1Q9 TCGA-D3-A2JN 
       94.98       220.80        18.05        71.80        31.59        66.48 
TCGA-D3-A2JO TCGA-D3-A3C6 TCGA-D3-A3CF TCGA-D3-A5GN TCGA-D3-A5GS TCGA-D3-A5GU 
       66.08        58.06        24.53       135.75        18.18       125.19 
TCGA-D3-A8GL TCGA-D3-A8GV TCGA-DA-A1HW TCGA-DA-A3F5 TCGA-DA-A95V TCGA-DA-A95Z 
       89.13       167.70        36.03       225.96        72.10        13.02 
TCGA-EB-A44Q TCGA-EB-A5UL TCGA-EE-A17Y TCGA-EE-A29D TCGA-EE-A2A6 TCGA-EE-A2GB 
       13.87        29.29        27.22        13.97        86.14        59.28 
TCGA-EE-A2GH TCGA-EE-A2M5 TCGA-EE-A3J5 TCGA-EE-A3JE TCGA-EE-A3JI TCGA-ER-A19B 
      220.24        21.67        36.95        51.35       152.81        98.40 
TCGA-ER-A19C TCGA-ER-A19L TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-GN-A267 TCGA-GN-A26A 
       48.89       131.51        23.93       101.26        64.44        32.48 
TCGA-GN-A8LK TCGA-W3-A825 TCGA-WE-A8ZX TCGA-YG-AA3O 
       50.10        63.02        35.80        37.94 

$`12Q GAIN WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-D3-A8GI TCGA-EB-A5SG 
       27.65        62.07        46.32        13.87        58.52        68.25 
TCGA-EB-A5SH TCGA-EE-A184 TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2GO 
       54.02        68.15       168.26         2.60       340.14       126.81 
TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 TCGA-ER-A198 TCGA-FS-A1ZF TCGA-FW-A3R5 
      134.40        27.35        31.40        50.76        15.45        36.95 
TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 
       61.15        21.40        17.03        66.48        12.99        14.93 
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       16.57        16.67       112.04       112.57       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-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH 
      115.53       168.00        86.76        11.87       113.52        42.08 
TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3CB 
       12.10       171.58        59.57       130.72        46.98       166.52 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV 
       86.93        60.23         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-A5GO TCGA-D3-A5GR TCGA-D3-A8GB 
       63.81        26.89       125.79       137.92       178.32        30.84 
TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GM 
       79.59        23.61        26.43       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-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-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
      144.89        20.38       222.51       176.55        35.93       135.02 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
       88.87        53.92        65.92        40.60        68.09        33.93 
TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-DA-A95W TCGA-DA-A95X TCGA-DA-A95Y TCGA-EB-A44R 
       10.49        43.36        37.35        73.94        14.14        10.36 
TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Z 
       20.35        58.92         7.04        36.46        29.82         8.65 
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-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-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
       72.07        64.64        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-A2GC TCGA-EE-A2GE 
       46.82       115.96        59.64        39.29        67.43       173.79 
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-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-A2MP TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A2MT 
      167.90        47.54       248.65        43.23       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-A3JH TCGA-ER-A195 TCGA-ER-A197 
       34.32        53.19       201.80       134.33        35.44        13.94 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G 
        9.17        77.75        12.59        13.02        26.37       302.07 
TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
      152.35         6.44        61.05        44.09       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       105.07        43.82        23.34 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET 
       20.15        28.83        48.99        41.56       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-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-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZP TCGA-FS-A1ZQ 
       46.45         9.70        32.75        47.38        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-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 
       27.02        77.82        50.14        66.67        28.73       174.84 
TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU 
       34.03        26.73        54.41        80.68        17.46        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        19.43         2.04        15.78 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A268 TCGA-GN-A26D 
      139.89       117.93        96.92        10.13        62.79        48.00 
TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LL 
      121.91        39.35        10.42        48.89        22.13        21.37 
TCGA-GN-A9SD TCGA-HR-A2OG TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS 
       59.41         0.23        65.88       368.78       297.90         7.23 
TCGA-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-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-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-XV-AB01 
       11.80        49.51        12.16        40.41        24.99        13.25 
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 
            58.670             50.825 
[1] "13.0 - 226.0 (58.7)" "0.2 - 369.9 (50.8)" 
[1] "hr=" "1.2"
D24V3, continuous
                    vv
clus                 I/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       24
                    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        33         13
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  12Q GAIN MUTATED            7          5        2
  12Q GAIN WILD-TYPE         28         49       19
D24V4, multiclass
            clus
vv           12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  I/II NOS                  1                 12
  STAGE 0                   0                  7
  STAGE I                   7                 22
  STAGE IA                  1                 17
  STAGE IB                  3                 25
  STAGE II                  2                 24
  STAGE IIA                 0                 14
  STAGE IIB                 0                 19
  STAGE IIC                 1                 14
  STAGE III                 6                 33
  STAGE IIIA                2                 13
  STAGE IIIB                7                 28
  STAGE IIIC                5                 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
  12Q GAIN MUTATED       9  8  5  8
  12Q GAIN WILD-TYPE    55 65 76 59
D24V5, multiclass
       clus
vv      12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  T0+T1                9                 55
  T2                   8                 65
  T3                   5                 76
  T4                   8                 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
  12Q GAIN MUTATED    16  14   2   4
  12Q GAIN WILD-TYPE 161  51  37  41
D24V6, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  N0               16                161
  N1               14                 51
  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"
D24V7, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED    34   2
  12Q GAIN WILD-TYPE 285  20
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     34    2
  12Q GAIN WILD-TYPE  285   20
   clus
vv  12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  0               34                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     4  36
  12Q GAIN WILD-TYPE  43 284
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      4   36
  12Q GAIN WILD-TYPE   43  284
     clus
vv    12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  NO                 4                 43
  YES               36                284
[1] 2 2
[1] FALSE
D24V10, continuous
D24V11, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED    11  29
  12Q GAIN WILD-TYPE 127 200
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     11   29
  12Q GAIN WILD-TYPE  127  200
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  FEMALE               11                127
  MALE                 29                200
[1] 2 2
[1] FALSE
D24V12, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED    35   5
  12Q GAIN WILD-TYPE 284  42
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     35    5
  12Q GAIN WILD-TYPE  284   42
     clus
vv    12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  NO                35                284
  YES                5                 42
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  12Q GAIN MUTATED       2                         0    37
  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                                   37                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  38
  12Q GAIN WILD-TYPE   6 314
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      1   38
  12Q GAIN WILD-TYPE    6  314
                        clus
vv                       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO               38                314
[1] 2 2
[1] FALSE

Clustering(25) Variable = 13Q GAIN MUTATION ANALYSIS
D25V1, survival
                    sevent
clus2                  0   1
  13Q GAIN MUTATED    22  44
  13Q GAIN WILD-TYPE 106  80
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                66                186 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                44                 80 
$`13Q GAIN MUTATED`
TCGA-D3-A2JF TCGA-D3-A8GI TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A20H TCGA-FR-A729 
       62.07        13.41        33.24        31.96       166.75       216.43 
TCGA-WE-AAA3 TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q6 TCGA-D3-A3C6 
        7.40        12.99         8.42        15.72        49.35        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-DA-A95W TCGA-EE-A17Y TCGA-EE-A29B TCGA-EE-A29G TCGA-EE-A29P 
       60.10         0.76        24.89        75.22        44.28        27.16 
TCGA-EE-A2GB TCGA-EE-A2GH TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2M7 
       26.14       201.60        18.35        93.63         0.76        15.25 
TCGA-EE-A2MF TCGA-EE-A2MP TCGA-EE-A3AA TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J7 
      209.79       227.01       124.31         6.28        67.89        45.90 
TCGA-EE-A3JI TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19L 
      135.98        10.49         7.82        39.81        11.47        99.06 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A2NC TCGA-ER-A3PL TCGA-FR-A69P 
       59.84        42.51       120.76        22.36        32.05         4.14 
TCGA-FR-A8YC TCGA-FS-A1YW TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZE 
       10.06       171.78       195.98         8.35        27.62        43.92 
TCGA-FS-A1ZQ TCGA-FS-A1ZT TCGA-FS-A1ZY TCGA-FS-A4FD TCGA-FW-A3TU TCGA-GN-A265 
      130.95        35.28         5.29        80.68        55.59        96.92 
TCGA-GN-A267 TCGA-GN-A268 TCGA-OD-A75X TCGA-W3-A824 TCGA-W3-A825 TCGA-XV-AB01 
       17.06        42.48       297.01       174.12         1.97         6.61 

$`13Q GAIN WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A3C8 TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD 
        9.76        38.76       269.03        52.90       134.40        27.35 
TCGA-ER-A193 TCGA-FW-A3R5 TCGA-WE-A8K5 TCGA-3N-A9WC TCGA-BF-AAP0 TCGA-D3-A1Q4 
       19.04        36.95        52.73        60.46        14.83        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-A2JG 
       45.99        62.86        15.75       168.00        86.30       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-A3CF TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F 
       24.53         9.34        90.21        23.67       173.85        30.67 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR 
      144.46        31.76        62.70        42.05        45.70       177.86 
TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GP TCGA-D3-A8GR 
       78.21        23.61       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        68.68       150.61       110.53        64.83 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-DA-A95V TCGA-DA-A95X 
       58.85        30.44       225.11         8.71        72.10        65.03 
TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A6L9 
       14.14        12.30         3.91        16.41        52.41        18.21 
TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A20F 
       13.15        20.38         0.00        26.24        75.55        79.20 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29Q 
       76.14        12.99         0.26        47.41        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-A2GR TCGA-EE-A2GS TCGA-EE-A2GU 
       68.65        10.62        32.48         0.20        71.31        81.99 
TCGA-EE-A2M6 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ 
      103.13         5.75        23.77        94.19       171.85        63.25 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU 
       89.26       104.78       145.45       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-A195 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19G 
      168.85        19.86        34.45         4.54        53.29       184.60 
TCGA-ER-A19H TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2ND 
      150.12        49.71        47.18       146.63        73.05         4.70 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
       16.87        10.19        28.67       173.29        68.52        15.48 
TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FS-A1YY 
       74.47         4.50       174.21        26.20         5.65        49.74 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZS 
      312.07        32.78         7.82        36.33        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        18.25         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-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT 
       47.54        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        37.32        24.99        28.21        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 
            42.495             47.640 
[1] "0.8 - 297.0 (42.5)" "0.0 - 346.5 (47.6)"
[1] "hr=" "1.5"
D25V2, survival
                    sevent
clus2                  0   1
  13Q GAIN MUTATED    32  55
  13Q GAIN WILD-TYPE 134 137
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                87                271 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                55                137 
$`13Q GAIN MUTATED`
TCGA-D3-A2JF TCGA-D3-A8GI TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A20H TCGA-FR-A729 
       62.07        58.52        68.25        94.98       168.26       220.80 
TCGA-QB-AA9O TCGA-WE-AAA3 TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q6 
       18.05        21.40        12.99        16.57        16.67        71.80 
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-A8GL TCGA-D3-A8GM TCGA-DA-A1I7 TCGA-DA-A3F3 TCGA-DA-A95W TCGA-EB-A44R 
       89.13       107.15        88.87        10.49        37.35        10.36 
TCGA-EB-A5UL TCGA-EE-A17Y TCGA-EE-A20B TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29G 
       29.29        27.22       133.81        63.35        85.08        72.07 
TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A2A5 TCGA-EE-A2GB TCGA-EE-A2GH TCGA-EE-A2GM 
       56.42        14.47        39.29        59.28       220.24        75.48 
TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2M7 TCGA-EE-A2MF TCGA-EE-A2MP TCGA-EE-A3AA 
      102.12        13.91        28.83       268.73       248.65       124.31 
TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-EE-A3JI TCGA-ER-A197 
       13.81       172.18        64.08        53.19       152.81        13.94 
TCGA-ER-A199 TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19L TCGA-ER-A19M 
        9.17        48.89        12.59        13.02       131.51        61.05 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A2NC TCGA-ER-A3PL TCGA-FR-A69P TCGA-FR-A8YC 
       44.09       162.08        43.82        33.21        15.72        34.82 
TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 
      216.92        48.59       202.65        20.91        28.08         7.79 
TCGA-FS-A1ZE TCGA-FS-A1ZQ TCGA-FS-A1ZT TCGA-FS-A1ZY TCGA-FS-A4F2 TCGA-FS-A4FD 
       46.45       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-W3-A824 TCGA-W3-A825 TCGA-WE-A8K6 TCGA-WE-A8ZX TCGA-XV-AB01 
      297.90       228.16        63.02        17.95        35.80        13.25 
TCGA-YD-A89C TCGA-YD-A9TA TCGA-Z2-A8RT 
        6.90        49.18        27.58 

$`13Q GAIN WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EB-A5SH TCGA-EE-A184 TCGA-EE-A29L 
       27.65        46.32        13.87        54.02        68.15         2.60 
TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 TCGA-ER-A198 
      340.14       126.81       134.40        27.35        31.40        50.76 
TCGA-FS-A1ZF TCGA-FW-A3R5 TCGA-WE-A8K5 TCGA-3N-A9WB TCGA-3N-A9WC TCGA-BF-AAP0 
       15.45        36.95        61.15        17.03        66.48        14.93 
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA 
      112.04       112.57       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-A2JG TCGA-D3-A2JH TCGA-D3-A2JK 
      168.00        86.76        11.87       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-A3CB TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV 
      166.52        24.53         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-A5GL TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A8GB 
       63.81       125.79       135.75       178.32        18.18        30.84 
TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GN 
       79.59        23.61        26.43       241.38       170.20       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       222.51       176.55        35.93 
TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
      135.02        53.92        65.92        40.60        68.09        33.93 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-DA-A95V TCGA-DA-A95X TCGA-DA-A95Y TCGA-DA-A95Z 
      225.96        43.36        72.10        73.94        14.14        13.02 
TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X 
       13.87        20.35        58.92         7.04        36.46        29.82 
TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20C 
        8.65        33.73        14.70        26.89         4.96       151.27 
TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H 
       91.56        13.55        78.97        13.97        63.78        64.64 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V 
       56.84        18.61        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-A2A6 
      195.02        17.92        46.82       115.96        59.64        86.14 
TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
       67.43       173.79        48.72       107.38        54.74        79.66 
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-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-A2MQ TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC 
       43.23       162.48        71.21        53.26       122.73        64.04 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J5 
       28.77        54.51        41.59       138.81       127.20        36.95 
TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A195 TCGA-ER-A19A 
       34.32       201.80        51.35       134.33        35.44        77.75 
TCGA-ER-A19B TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19Q 
       98.40        26.37       302.07       152.35         6.44        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       105.07        23.34        20.15 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
       28.83        48.99        41.56       247.04        93.01        46.98 
TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A7U8 TCGA-FR-A7U9 
       12.95       149.03        92.98       174.21        27.85        18.77 
TCGA-FR-A7UA TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YY TCGA-FS-A1ZA TCGA-FS-A1ZB 
       38.27        36.26       104.42       228.59        27.72        48.85 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK 
      357.37        53.52         9.70        32.75        47.38        23.93 
TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZW 
      101.26        74.73        11.41       148.80        26.56        49.48 
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-FW-A3I3 TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
       26.73        54.41        17.46        13.51        19.30         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A266 
       19.43         2.04        15.78       139.89       117.93        10.13 
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-A8LK TCGA-GN-A8LL TCGA-GN-A9SD TCGA-HR-A2OH TCGA-LH-A9QB TCGA-QB-A6FS 
       50.10        21.37        59.41        65.88       368.78         7.23 
TCGA-RP-A690 TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1Q 
        0.20         0.33         0.69       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-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZY 
      101.33        58.98        70.52        63.22        11.80        49.51 
TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-AA3S 
       12.16        40.41        24.99        37.94        14.43        96.99 
TCGA-Z2-AA3V 
       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 
             55.59              50.76 
[1] "0.2 - 297.9 (55.6)" "0.2 - 369.9 (50.8)"
[1] "hr=" "1.2"
D25V3, continuous
                    vv
clus                 I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  13Q GAIN MUTATED          3       1      11        4       10        5
  13Q GAIN WILD-TYPE       10       6      18       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        33         11
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  13Q GAIN MUTATED           11         11        3
  13Q GAIN WILD-TYPE         24         43       18
D25V4, multiclass
            clus
vv           13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  I/II NOS                  3                 10
  STAGE 0                   1                  6
  STAGE I                  11                 18
  STAGE IA                  4                 14
  STAGE IB                 10                 18
  STAGE II                  5                 21
  STAGE IIA                 1                 13
  STAGE IIB                 6                 13
  STAGE IIC                 6                  9
  STAGE III                 6                 33
  STAGE IIIA                4                 11
  STAGE IIIB               11                 24
  STAGE IIIC               11                 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      14 25 13 18
  13Q GAIN WILD-TYPE    50 48 68 49
D25V5, multiclass
       clus
vv      13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  T0+T1               14                 50
  T2                  25                 48
  T3                  13                 68
  T4                  18                 49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  13Q GAIN MUTATED    48  18   6   7
  13Q GAIN WILD-TYPE 129  47  33  38
D25V6, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  N0               48                129
  N1               18                 47
  N2                6                 33
  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"
D25V7, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED    80   3
  13Q GAIN WILD-TYPE 239  19
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED     80    3
  13Q GAIN WILD-TYPE  239   19
   clus
vv  13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  0               80                239
  1                3                 19
[1] 2 2
[1] FALSE
D25V8, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED    28  24
  13Q GAIN WILD-TYPE 106  66
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED     28   24
  13Q GAIN WILD-TYPE  106   66
     clus
vv    13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  NO                28                106
  YES               24                 66
[1] 2 2
[1] FALSE
D25V9, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED    12  80
  13Q GAIN WILD-TYPE  35 240
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED     12   80
  13Q GAIN WILD-TYPE   35  240
     clus
vv    13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  NO                12                 35
  YES               80                240
[1] 2 2
[1] FALSE
D25V10, continuous
D25V11, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED    35  57
  13Q GAIN WILD-TYPE 103 172
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED     35   57
  13Q GAIN WILD-TYPE  103  172
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  FEMALE               35                103
  MALE                 57                172
[1] 2 2
[1] FALSE
D25V12, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED    82  10
  13Q GAIN WILD-TYPE 237  37
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED     82   10
  13Q GAIN WILD-TYPE  237   37
     clus
vv    13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  NO                82                237
  YES               10                 37
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  13Q GAIN MUTATED       2                         0    89
  13Q GAIN WILD-TYPE     3                         1   264
D25V13, multiclass
                           clus
vv                          13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  ASIAN                                    2                  3
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   89                264
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V14, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED     1  87
  13Q GAIN WILD-TYPE   6 265
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      1   87
  13Q GAIN WILD-TYPE    6  265
                        clus
vv                       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO               87                265
[1] 2 2
[1] FALSE

Clustering(26) Variable = 14Q GAIN MUTATION ANALYSIS
D26V1, survival
                    sevent
clus2                  0   1
  14Q GAIN MUTATED    17  14
  14Q GAIN WILD-TYPE 111 110
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                31                221 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                14                110 
$`14Q GAIN MUTATED`
TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GO TCGA-FR-A729 TCGA-WE-AAA3 TCGA-D3-A2JA 
       31.96       166.75        52.90       216.43         7.40        15.75 
TCGA-D3-A2JL TCGA-D3-A3C6 TCGA-D3-A8GK TCGA-D3-A8GM TCGA-DA-A1I2 TCGA-DA-A1I7 
      171.58        58.06       120.00        70.62       150.61        60.10 
TCGA-EE-A29D TCGA-EE-A29M TCGA-EE-A2GH TCGA-EE-A2GM TCGA-EE-A2MJ TCGA-EE-A2MU 
       12.99        47.74       201.60        18.35        63.25        53.26 
TCGA-EE-A3AE TCGA-EE-A3JH TCGA-ER-A19C TCGA-ER-A19L TCGA-ER-A19M TCGA-FR-A69P 
       54.51        19.86        39.81        99.06        59.84         4.14 
TCGA-FR-A8YC TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-GN-A265 TCGA-GN-A9SD TCGA-W3-A828 
       10.06        23.21         5.29        96.92        59.41       120.07 
TCGA-XV-AB01 
        6.61 

$`14Q GAIN WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A8GI TCGA-EB-A5SG TCGA-EE-A2GD 
        9.76        62.07        38.76        13.41        33.24       269.03 
TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 TCGA-FW-A3R5 TCGA-WE-A8K5 TCGA-3N-A9WC 
      134.40        27.35        19.04        36.95        52.73        60.46 
TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 
       12.99        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-A2JC TCGA-D3-A2JG TCGA-D3-A2JH 
       45.99        62.86       168.00        86.30       107.61        36.30 
TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE 
       64.83        66.08        43.53       140.98        40.01        59.70 
TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F 
       24.53         9.34        90.21        23.67       173.85        30.67 
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-A5GU TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GJ TCGA-D3-A8GL 
      177.86       124.08        78.21        23.61       179.97        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-A1I5 
       69.21        22.85        76.34       138.67        68.68       110.53 
TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-DA-A95V 
       64.83        58.85        30.44       225.11         8.71        72.10 
TCGA-DA-A95W TCGA-DA-A95X TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5KH 
        0.76        65.03        14.14        12.30         3.91        16.41 
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-A183 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E 
       26.24        75.55        79.20        75.22        76.14         0.26 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W 
       44.28        47.41        27.16        61.12       346.49       185.19 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GJ 
      115.43        30.02        77.98        26.14        12.95        68.65 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
       10.62        32.48        93.63         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-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP 
       94.19       171.85        89.26       104.78       145.45       227.01 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
      143.93        23.51       124.31       122.73        64.04         4.41 
TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB 
        6.28        67.89       111.85        45.90         3.35       168.85 
TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B 
      135.98        34.45        10.49         7.82         4.54        53.29 
TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
       11.47       184.60       150.12        42.51       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        73.05        22.36         4.70        16.87 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL 
       10.19        28.67       173.29        68.52        15.48        32.05 
TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FS-A1YW 
       74.47         4.50       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-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS 
       43.92         7.82        36.33        78.61       130.95       136.27 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 
       35.28         4.47         3.06        30.90        66.67       173.19 
TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
       13.28        80.68        55.59        11.54        19.30         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 
       18.25         1.91        53.29       117.93        17.06        42.48 
TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-GN-A8LK TCGA-LH-A9QB 
        7.59       120.53        34.49        46.92        43.23        85.05 
TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A825 
      297.01         7.23         0.20         0.33       174.12         1.97 
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        47.54 
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        37.32        24.99        28.21        91.23 

  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
              4.14               0.00 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
            216.43             346.49 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
             54.51              44.28 
[1] "4.1 - 216.4 (54.5)" "0.0 - 346.5 (44.3)"
[1] "hr=" "1.1"
D26V2, survival
                    sevent
clus2                  0   1
  14Q GAIN MUTATED    19  22
  14Q GAIN WILD-TYPE 147 170
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                41                317 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                22                170 
$`14Q GAIN MUTATED`
TCGA-EB-A5SH TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GO TCGA-FR-A729 
       54.02        94.98       168.26         2.60       126.81       220.80 
TCGA-QB-AA9O TCGA-WE-AAA3 TCGA-D3-A1Q9 TCGA-D3-A2JA TCGA-D3-A2JL TCGA-D3-A3C6 
       18.05        21.40        31.59       115.53       171.58        58.06 
TCGA-D3-A8GK TCGA-D3-A8GM TCGA-D9-A6E9 TCGA-DA-A1I2 TCGA-DA-A1I7 TCGA-EE-A29D 
      170.20       107.15         9.90       176.55        88.87        13.97 
TCGA-EE-A29M TCGA-EE-A2GH TCGA-EE-A2GM TCGA-EE-A2M5 TCGA-EE-A2MJ TCGA-EE-A2MU 
       56.84       220.24        75.48        21.67        96.23        53.26 
TCGA-EE-A3AE TCGA-EE-A3JH TCGA-ER-A19C TCGA-ER-A19L TCGA-ER-A19M TCGA-FR-A69P 
       54.51       134.33        48.89       131.51        61.05        15.72 
TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FS-A1ZP TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-GN-A265 
       34.82        36.26        74.73        49.48        27.09        96.92 
TCGA-GN-A26D TCGA-GN-A9SD TCGA-W3-A828 TCGA-W3-AA1O TCGA-XV-AB01 
       48.00        59.41       121.08         4.01        13.25 

$`14Q GAIN WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-D3-A8GI TCGA-EB-A5SG 
       27.65        62.07        46.32        13.87        58.52        68.25 
TCGA-EE-A184 TCGA-EE-A2GD TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 TCGA-ER-A198 
       68.15       340.14       134.40        27.35        31.40        50.76 
TCGA-FS-A1ZF TCGA-FW-A3R5 TCGA-WE-A8K5 TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD 
       15.45        36.95        61.15        17.03        66.48        12.99 
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-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
      133.25        28.08        90.90        95.74        43.43       103.10 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG 
       65.49        23.77       168.00        86.76        11.87       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-A3C7 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO 
       46.98       166.52        86.93        60.23        24.53         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-A8GJ TCGA-D3-A8GL TCGA-D3-A8GN 
       79.59        23.61        26.43       241.38        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-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-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-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I8 
      144.89        20.38       222.51        35.93       135.02        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 
       43.36        72.10        37.35        73.94        14.14        13.02 
TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV 
       13.87        10.36        20.35        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-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I 
       26.89         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-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-A2GE TCGA-EE-A2GI 
       39.29        86.14        59.28        67.43       173.79        48.72 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR 
      107.38        54.74        79.66       102.12        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-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP 
      204.66       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-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-A3JE 
       36.95        64.08        34.32        53.19       201.80        51.35 
TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B 
      152.81        35.44        13.94         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       302.07       152.35         6.44 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W 
       44.09       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 
      105.07        43.82        23.34        20.15        28.83        48.99 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K 
       41.56       247.04        93.01        46.98        33.21        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-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-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM 
       46.45         9.70        32.75        47.38        23.93       101.26 
TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZZ 
      133.55        11.41       148.80        53.16        26.56        27.02 
TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 
       77.82        50.14        66.67        28.73       174.84        34.03 
TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV 
       26.73        54.41        80.68        17.46        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        19.43         2.04        15.78       139.89 
TCGA-GN-A264 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 
      117.93        10.13        64.44        62.79        32.48       121.91 
TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A8LL 
       39.35        10.42        48.89        22.13        50.10        21.37 
TCGA-HR-A2OG TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-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-AA1Q TCGA-W3-AA1R 
        0.33         0.69       228.16        63.02        69.07       111.09 
TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K6 
       42.08       219.16       105.04        24.03        49.05        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 
             58.06              50.10 
[1] "2.6 - 220.8 (58.1)" "0.2 - 369.9 (50.1)"
[1] "hr=" "1.1"
D26V3, continuous
                    vv
clus                 I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  14Q GAIN MUTATED          1       1       5        3        4        4
  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        34         13
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  14Q GAIN MUTATED            3          5        0
  14Q GAIN WILD-TYPE         32         49       21
D26V4, multiclass
            clus
vv           14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  I/II NOS                  1                 12
  STAGE 0                   1                  6
  STAGE I                   5                 24
  STAGE IA                  3                 15
  STAGE IB                  4                 24
  STAGE II                  4                 22
  STAGE IIA                 1                 13
  STAGE IIB                 3                 16
  STAGE IIC                 3                 12
  STAGE III                 5                 34
  STAGE IIIA                2                 13
  STAGE IIIB                3                 32
  STAGE IIIC                5                 49
  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 10 10
  14Q GAIN WILD-TYPE    59 63 71 57
D26V5, multiclass
       clus
vv      14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  T0+T1                5                 59
  T2                  10                 63
  T3                  10                 71
  T4                  10                 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
  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    38   0
  14Q GAIN WILD-TYPE 281  22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED     38    0
  14Q GAIN WILD-TYPE  281   22
   clus
vv  14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  0               38                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  37
  14Q GAIN WILD-TYPE  42 283
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      5   37
  14Q GAIN WILD-TYPE   42  283
     clus
vv    14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  NO                 5                 42
  YES               37                283
[1] 2 2
[1] FALSE
D26V10, continuous
D26V11, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED    15  27
  14Q GAIN WILD-TYPE 123 202
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED     15   27
  14Q GAIN WILD-TYPE  123  202
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  FEMALE               15                123
  MALE                 27                202
[1] 2 2
[1] FALSE
D26V12, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED    39   3
  14Q GAIN WILD-TYPE 280  44
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED     39    3
  14Q GAIN WILD-TYPE  280   44
     clus
vv    14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  NO                39                280
  YES                3                 44
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  14Q GAIN MUTATED       0                         0    42
  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                                   42                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  42
  14Q GAIN WILD-TYPE   7 310
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      0   42
  14Q GAIN WILD-TYPE    7  310
                        clus
vv                       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  7
  NOT HISPANIC OR LATINO               42                310
[1] 2 2
[1] FALSE

Clustering(27) Variable = 15Q GAIN MUTATION ANALYSIS
D27V1, survival
                    sevent
clus2                  0   1
  15Q GAIN MUTATED    28  29
  15Q GAIN WILD-TYPE 100  95
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                57                195 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                29                 95 
$`15Q GAIN MUTATED`
TCGA-D3-A2JF TCGA-D3-A8GI TCGA-EE-A20H TCGA-EE-A2GO TCGA-EE-A2MR TCGA-ER-A193 
       62.07        13.41       166.75        52.90       134.40        19.04 
TCGA-FR-A729 TCGA-D3-A1Q5 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JL TCGA-D3-A2JN 
      216.43       110.93        15.75        86.30       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        60.10 
TCGA-DA-A3F5 TCGA-EE-A17Y TCGA-EE-A29D TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 
      225.11        24.89        12.99       346.49       185.19       115.43 
TCGA-EE-A2GM TCGA-EE-A2GP TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MJ TCGA-EE-A2MP 
       18.35         0.76       103.13        15.25        63.25       227.01 
TCGA-EE-A2MS TCGA-EE-A3AA TCGA-EE-A3AE TCGA-EE-A3J3 TCGA-EE-A3JH TCGA-EE-A3JI 
      143.93       124.31        54.51        67.89        19.86       135.98 
TCGA-ER-A19C TCGA-ER-A19M TCGA-ER-A19P TCGA-ER-A19S TCGA-ER-A42L TCGA-FR-A44A 
       39.81        59.84       120.76        47.18        74.47       174.21 
TCGA-FR-A69P TCGA-FR-A8YC TCGA-FS-A1Z3 TCGA-FS-A1ZD TCGA-FS-A1ZY TCGA-FS-A4FD 
        4.14        10.06         8.35        32.78         5.29        80.68 
TCGA-GF-A4EO TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A9SD TCGA-W3-A825 TCGA-W3-A828 
       18.25       117.93        17.06        59.41         1.97       120.07 
TCGA-WE-A8ZM TCGA-WE-A8ZQ TCGA-XV-AB01 
       65.42        62.89         6.61 

$`15Q GAIN WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A2GD TCGA-EE-A3JD 
        9.76        38.76        33.24        31.96       269.03        27.35 
TCGA-FW-A3R5 TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 
       36.95        52.73         7.40        60.46        12.99        14.83 
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
        8.42        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-A2JH TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CC 
      107.61        36.30        66.08        43.53        58.06        40.01 
TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F 
       24.53         9.34        90.21        23.67       173.85        30.67 
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-A5GU TCGA-D3-A8GC TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GP 
      177.86       124.08        78.21       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-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 
       22.85        76.34       138.67        68.68       150.61       110.53 
TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F8 TCGA-DA-A95V TCGA-DA-A95W 
       64.83        58.85        30.44         8.71        72.10         0.76 
TCGA-DA-A95X TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN 
       65.03        14.14        12.30         3.91        16.41        52.41 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20C 
       18.21        13.15        20.38         0.00        26.24        75.55 
TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H 
       79.20        75.22        76.14         0.26        44.28        47.41 
TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB 
       47.74        27.16        61.12        30.02        77.98        26.14 
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        93.63 
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-A2MT 
       94.19       171.85        89.26       104.78       145.45        23.51 
TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3J4 
       53.26       122.73        64.04         4.41         6.28       111.85 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 
       45.90         3.35       168.85        34.45        10.49         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       184.60       150.12        99.06 
TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
       42.51        49.71       146.63        73.05        22.36         4.70 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
       16.87        10.19        28.67       173.29        68.52        15.48 
TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FS-A1YW TCGA-FS-A1YY 
       32.05         4.50        26.20         5.65       171.78        49.74 
TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ 
      195.98        27.62       312.07        43.92         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-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FW-A3TU 
        3.06        30.90        66.67       173.19        13.28        55.59 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A265 
       11.54        19.30         9.90         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-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-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        47.54 
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        37.32 
TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-Z2-AA3S 
       24.99        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 
             62.89              42.51 
[1] "0.8 - 346.5 (62.9)" "0.0 - 312.1 (42.5)"
[1] "hr=" "1.3"
D27V2, survival
                    sevent
clus2                  0   1
  15Q GAIN MUTATED    39  42
  15Q GAIN WILD-TYPE 127 150
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                81                277 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                42                150 
$`15Q GAIN MUTATED`
TCGA-D3-A2JF TCGA-D3-A8GI TCGA-EE-A20H TCGA-EE-A2GO TCGA-EE-A2MR TCGA-ER-A193 
       62.07        58.52       168.26       126.81       134.40        31.40 
TCGA-FR-A729 TCGA-D3-A1Q5 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JC 
      220.80       112.57        31.59        23.77       115.53        86.76 
TCGA-D3-A2JD TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3MV 
       11.87       171.58        66.48       166.52        60.23        45.30 
TCGA-D3-A8GD TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GQ TCGA-D9-A149 TCGA-D9-A6EA 
       23.61        89.13       107.15        29.06        54.67        25.18 
TCGA-DA-A1HW TCGA-DA-A1I7 TCGA-DA-A3F5 TCGA-EE-A17Y TCGA-EE-A20B TCGA-EE-A29D 
       36.03        88.87       225.96        27.22       133.81        13.97 
TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2GI TCGA-EE-A2GM 
      369.93       195.02        17.92       115.96        48.72        75.48 
TCGA-EE-A2GP TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MJ TCGA-EE-A2MN TCGA-EE-A2MP 
       13.91       129.27        28.83        96.23        47.54       248.65 
TCGA-EE-A2MS TCGA-EE-A3AA TCGA-EE-A3AE TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3J5 
      162.48       124.31        54.51        41.59       172.18        36.95 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A19C TCGA-ER-A19M TCGA-ER-A19P TCGA-ER-A19S 
      134.33       152.81        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-A7U9 
        8.88        12.95       149.03       174.21        15.72        18.77 
TCGA-FR-A8YC TCGA-FS-A1Z3 TCGA-FS-A1ZD TCGA-FS-A1ZY TCGA-FS-A4F2 TCGA-FS-A4FD 
       34.82        20.91        53.52        27.09        50.14        80.68 
TCGA-GF-A4EO TCGA-GF-A6C9 TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A9SD TCGA-HR-A2OG 
       19.43        15.78       117.93        64.44        59.41         0.23 
TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZQ 
       63.02       121.08         4.01        17.95       101.33        63.22 
TCGA-WE-A8ZX TCGA-XV-AB01 TCGA-YD-A9TA 
       35.80        13.25        49.18 

$`15Q GAIN WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A180 
       27.65        46.32        13.87        68.25        54.02        94.98 
TCGA-EE-A184 TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A3JD TCGA-ER-A198 TCGA-FS-A1ZF 
       68.15         2.60       340.14        27.35        50.76        15.45 
TCGA-FW-A3R5 TCGA-QB-AA9O TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-3N-A9WB TCGA-3N-A9WC 
       36.95        18.05        61.15        21.40        17.03        66.48 
TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q6 
       12.99        14.93        16.57        16.67       112.04        71.80 
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
      133.25        28.08        90.90        95.74        43.43       103.10 
TCGA-D3-A2J8 TCGA-D3-A2JB TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JO 
       65.49       168.00       113.52        42.08        12.10        66.08 
TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CC TCGA-D3-A3CF 
       59.57       130.72        58.06        46.98        86.93        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-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-A8GE TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GN TCGA-D3-A8GP 
       79.59        26.43       241.38       170.20       161.00       152.75 
TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D3-A8GV TCGA-D9-A148 TCGA-D9-A1JW TCGA-D9-A1JX 
      129.63       117.17       167.70       151.53         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-A1I1 TCGA-DA-A1I2 
       22.95        76.57       144.89        20.38       222.51       176.55 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
       35.93       135.02        53.92        65.92        40.60        68.09 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-DA-A95V TCGA-DA-A95W TCGA-DA-A95X 
       33.93        10.49        43.36        72.10        37.35        73.94 
TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5UL 
       14.14        13.02        13.87        10.36        20.35        29.29 
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-A185 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I 
       14.70        26.89         4.96       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-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
       56.84        18.61        56.42        66.74        14.47        61.28 
TCGA-EE-A29V TCGA-EE-A2A0 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
       25.87        46.82        59.64        39.29        86.14        59.28 
TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
       67.43       173.79       220.24       107.38        54.74        79.66 
TCGA-EE-A2GN TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 
      102.12        42.77        81.21        44.88        94.82        21.67 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG 
       19.76        61.51        47.28       103.27       268.73       103.20 
TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MQ 
       16.96       204.66       180.39       216.66       167.90        43.23 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AF 
       71.21        53.26       122.73        64.04        28.77        13.81 
TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB 
      138.81       127.20        64.08        34.32        53.19       201.80 
TCGA-EE-A3JE TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B 
       51.35        35.44        13.94         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       302.07       152.35         6.44 
TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
      131.51        44.09        50.89       148.18       105.07        43.82 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES 
       23.34        20.15        28.83        48.99        41.56       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-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP 
        9.70        32.75        47.38        23.93       101.26        74.73 
TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW 
      133.55        11.41       148.80        53.16        26.56        49.48 
TCGA-FS-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-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
       26.73        54.41        17.46        55.59        13.51        19.30 
TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A268 
        9.90         2.04       139.89        96.92        10.13        62.79 
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-A8LL TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X 
       22.13        50.10        21.37        65.88       368.78       297.90 
TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-AA1Q 
        7.23         0.20         0.33         0.69       228.16        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-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 
       58.98        70.52        11.80        49.51        12.16        40.41 
TCGA-WE-AAA4 TCGA-YD-A89C TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S 
       24.99         6.90        37.94        14.43        27.58        96.99 
TCGA-Z2-AA3V 
       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 
             59.41              49.51 
[1] "0.2 - 369.9 (59.4)" "0.2 - 368.8 (49.5)"
[1] "hr=" "1.2"
D27V3, continuous
                    vv
clus                 I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  15Q GAIN MUTATED          6       1       9        5        5       10
  15Q GAIN WILD-TYPE        7       6      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        31         13
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  15Q GAIN MUTATED           11         10        2
  15Q GAIN WILD-TYPE         24         44       19
D27V4, multiclass
            clus
vv           15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  I/II NOS                  6                  7
  STAGE 0                   1                  6
  STAGE I                   9                 20
  STAGE IA                  5                 13
  STAGE IB                  5                 23
  STAGE II                 10                 16
  STAGE IIA                 2                 12
  STAGE IIB                 4                 15
  STAGE IIC                 2                 13
  STAGE III                 8                 31
  STAGE IIIA                2                 13
  STAGE IIIB               11                 24
  STAGE IIIC               10                 44
  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
  15Q GAIN MUTATED      16 19 18 13
  15Q GAIN WILD-TYPE    48 54 63 54
D27V5, multiclass
       clus
vv      15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  T0+T1               16                 48
  T2                  19                 54
  T3                  18                 63
  T4                  13                 54
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  15Q GAIN MUTATED    44  15   7   9
  15Q GAIN WILD-TYPE 133  50  32  36
D27V6, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  N0               44                133
  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   2
  15Q GAIN WILD-TYPE 243  20
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED     76    2
  15Q GAIN WILD-TYPE  243   20
   clus
vv  15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  0               76                243
  1                2                 20
[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  71
  15Q GAIN WILD-TYPE  34 249
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED     13   71
  15Q GAIN WILD-TYPE   34  249
     clus
vv    15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  NO                13                 34
  YES               71                249
[1] 2 2
[1] FALSE
D27V10, continuous
D27V11, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED    31  53
  15Q GAIN WILD-TYPE 107 176
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED     31   53
  15Q GAIN WILD-TYPE  107  176
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  FEMALE               31                107
  MALE                 53                176
[1] 2 2
[1] FALSE
D27V12, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED    71  13
  15Q GAIN WILD-TYPE 248  34
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED     71   13
  15Q GAIN WILD-TYPE  248   34
     clus
vv    15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  NO                71                248
  YES               13                 34
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  15Q GAIN MUTATED       1                         0    81
  15Q GAIN WILD-TYPE     4                         1   272
D27V13, multiclass
                           clus
vv                          15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  ASIAN                                    1                  4
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   81                272
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V14, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED     1  81
  15Q GAIN WILD-TYPE   6 271
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      1   81
  15Q GAIN WILD-TYPE    6  271
                        clus
vv                       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO               81                271
[1] 2 2
[1] FALSE

Clustering(28) Variable = 16P GAIN MUTATION ANALYSIS
D28V1, survival
                    sevent
clus2                  0   1
  16P GAIN MUTATED    20  22
  16P GAIN WILD-TYPE 108 102
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                42                210 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                22                102 
$`16P GAIN MUTATED`
TCGA-D3-A2JE TCGA-D3-A8GI TCGA-EE-A20H TCGA-FR-A729 TCGA-WE-AAA3 TCGA-D3-A1Q6 
        9.76        13.41       166.75       216.43         7.40        49.35 
TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A5GR TCGA-D3-A8GJ TCGA-D3-A8GP TCGA-D3-A8GR 
       58.06        59.70       177.86       179.97       135.12        36.53 
TCGA-DA-A95V TCGA-DA-A95Z TCGA-EE-A17Y TCGA-EE-A29P TCGA-EE-A2A1 TCGA-EE-A2GB 
       72.10        12.30        24.89        27.16       115.43        26.14 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MP TCGA-EE-A3AE 
       18.35        93.63       103.13        15.25       227.01        54.51 
TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19M 
       67.89        45.90        53.29        39.81        11.47        59.84 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A69P TCGA-FS-A1ZY 
       42.51       120.76        32.05        74.47         4.14         5.29 
TCGA-FS-A4F4 TCGA-FS-A4FD TCGA-GF-A4EO TCGA-GN-A9SD TCGA-W3-AA1V TCGA-XV-AB01 
       66.67        80.68        18.25        59.41         8.09         6.61 

$`16P GAIN WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A2GD TCGA-EE-A2GO 
       62.07        38.76        33.24        31.96       269.03        52.90 
TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 TCGA-FW-A3R5 TCGA-WE-A8K5 TCGA-3N-A9WC 
      134.40        27.35        19.04        36.95        52.73        60.46 
TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 
       12.99        14.83         8.42        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-A2JG TCGA-D3-A2JH 
       62.86        15.75       168.00        86.30       107.61        36.30 
TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3CB TCGA-D3-A3CC 
      171.58        64.83        66.08        43.53       140.98        40.01 
TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F 
       24.53         9.34        90.21        23.67       173.85        30.67 
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-A8GK TCGA-D3-A8GL TCGA-D3-A8GM 
      124.08        78.21        23.61       120.00        69.53        70.62 
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        68.68       150.61       110.53        60.10 
TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-DA-A95W 
       64.83        58.85        30.44       225.11         8.71         0.76 
TCGA-DA-A95X TCGA-DA-A95Y TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A6L9 
       65.03        14.14         3.91        16.41        52.41        18.21 
TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A20F 
       13.15        20.38         0.00        26.24        75.55        79.20 
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        47.41 
TCGA-EE-A29M TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A2 TCGA-EE-A2A6 
       47.74        61.12       346.49       185.19        30.02        77.98 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GP 
       12.95       201.60        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-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM 
       94.19       171.85        63.25        89.26       104.78       145.45 
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-A3AF TCGA-EE-A3J4 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH 
        4.41         6.28       111.85         3.35       168.85        19.86 
TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19G 
      135.98        34.45        10.49         7.82         4.54       184.60 
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        73.05 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES 
       22.36         4.70        16.87        10.19        28.67       173.29 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A7U8 TCGA-FR-A7UA 
       68.52        15.48         4.50       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-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM 
      312.07        32.78        43.92         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-A4F8 TCGA-FS-A4F9 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
       30.90       173.19        13.28        55.59        11.54        19.30 
TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 
        9.90         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-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-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT 
       47.54        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        37.32        24.99        28.21        91.23 

  16P GAIN MUTATED 16P GAIN WILD-TYPE 
              4.14               0.00 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
            227.01             346.49 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
            51.320             45.845 
[1] "4.1 - 227.0 (51.3)" "0.0 - 346.5 (45.8)"
[1] "hr=" "1.1"
D28V2, survival
                    sevent
clus2                  0   1
  16P GAIN MUTATED    26  28
  16P GAIN WILD-TYPE 140 164
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                54                304 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                28                164 
$`16P GAIN MUTATED`
TCGA-D3-A2JE TCGA-D3-A8GI TCGA-EE-A20H TCGA-FR-A729 TCGA-WE-AAA3 TCGA-D3-A1Q6 
       27.65        58.52       168.26       220.80        21.40        71.80 
TCGA-D3-A1Q9 TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A5GR TCGA-D3-A8GJ TCGA-D3-A8GP 
       31.59        58.06        60.23       178.32       241.38       152.75 
TCGA-D3-A8GR TCGA-D3-A8GS TCGA-DA-A95V TCGA-DA-A95Z TCGA-EE-A17Y TCGA-EE-A20B 
      129.63       117.17        72.10        13.02        27.22       133.81 
TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-EE-A2GB TCGA-EE-A2GI 
       56.42        14.47       115.96        39.29        59.28        48.72 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MP TCGA-EE-A3AE 
       75.48       102.12       129.27        28.83       248.65        54.51 
TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19M 
      172.18        64.08        98.40        48.89        12.59        61.05 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A69P TCGA-FS-A1YX 
       44.09       162.08        33.21       149.03        15.72        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        19.43 
TCGA-GN-A9SD TCGA-HR-A2OG TCGA-W3-AA1V TCGA-WE-A8K6 TCGA-XV-AB01 TCGA-Z2-AA3V 
       59.41         0.23        42.08        17.95        13.25        15.98 

$`16P GAIN WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A180 
       62.07        46.32        13.87        68.25        54.02        94.98 
TCGA-EE-A184 TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD 
       68.15         2.60       340.14       126.81       134.40        27.35 
TCGA-ER-A193 TCGA-ER-A198 TCGA-FS-A1ZF TCGA-FW-A3R5 TCGA-QB-AA9O TCGA-WE-A8K5 
       31.40        50.76        15.45        36.95        18.05        61.15 
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-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-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3CB 
       66.48        66.08        59.57       130.72        46.98       166.52 
TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV 
       86.93        24.53         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-A5GS 
       63.81        26.89       125.79       135.75       137.92        18.18 
TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GK 
      125.19        30.84        79.59        23.61        26.43       170.20 
TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GQ TCGA-D3-A8GV TCGA-D9-A148 
       89.13       107.15       161.00        29.06       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       222.51       176.55        35.93 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
      135.02        88.87        53.92        65.92        40.60        68.09 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-DA-A95W TCGA-DA-A95X 
       33.93        10.49       225.96        43.36        37.35        73.94 
TCGA-DA-A95Y TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5UL TCGA-EB-A5UN 
       14.14        13.87        10.36        20.35        29.29        58.92 
TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 
        7.04        36.46        29.82         8.65        33.73        14.70 
TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29A 
       26.89         4.96       151.27        91.56        13.55        63.35 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H 
       85.08        78.97        13.97        63.78        72.07        64.64 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V 
       56.84        18.61        66.74        61.28       369.93        25.87 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GC 
      195.02        17.92        46.82        59.64        86.14        67.43 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GP 
      173.79       220.24       107.38        54.74        79.66        13.91 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M8 
       42.77        81.21        44.88        94.82        21.67        19.76 
TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH 
       61.51        47.28       103.27       268.73       103.20        16.96 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN 
      204.66        96.23       180.39       216.66       167.90        47.54 
TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB 
       43.23       162.48        71.21        53.26       124.31       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J4 
       64.04        28.77        13.81        41.59       138.81       127.20 
TCGA-EE-A3J5 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JE TCGA-EE-A3JH 
       36.95        34.32        53.19       201.80        51.35       134.33 
TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19E 
      152.81        35.44        13.94         9.17        77.75        13.02 
TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19Q 
       26.37       302.07       152.35         6.44       131.51        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       105.07        43.82        23.34 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET 
       20.15        28.83        48.99        41.56       247.04        93.01 
TCGA-ER-A3EV TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A7U8 TCGA-FR-A7U9 
       46.98        12.95        92.98       174.21        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-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ 
      357.37        53.52        46.45         9.70        32.75        47.38 
TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT 
       23.93       101.26       133.55        11.41       148.80        53.16 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F8 
       26.56        49.48        27.02        77.82        50.14       174.84 
TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV 
       34.03        26.73        54.41        17.46        55.59        13.51 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 
       19.30         9.90         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-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 
       21.37        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-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 
       37.94        14.43        27.58        96.99 

  16P GAIN MUTATED 16P GAIN WILD-TYPE 
              0.23               0.20 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
            248.65             369.93 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
             58.90              50.12 
[1] "0.2 - 248.7 (58.9)" "0.2 - 369.9 (50.1)"
[1] "hr=" "1.1"
D28V3, continuous
                    vv
clus                 I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  16P GAIN MUTATED          2       2       8        5        7        8
  16P GAIN WILD-TYPE       11       5      21       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        35         15
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  16P GAIN MUTATED            4          6        2
  16P GAIN WILD-TYPE         31         48       19
D28V4, multiclass
            clus
vv           16P GAIN MUTATED 16P GAIN WILD-TYPE
  I/II NOS                  2                 11
  STAGE 0                   2                  5
  STAGE I                   8                 21
  STAGE IA                  5                 13
  STAGE IB                  7                 21
  STAGE II                  8                 18
  STAGE IIA                 1                 13
  STAGE IIB                 1                 18
  STAGE IIC                 3                 12
  STAGE III                 4                 35
  STAGE IIIA                0                 15
  STAGE IIIB                4                 31
  STAGE IIIC                6                 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 17 12  6
  16P GAIN WILD-TYPE    53 56 69 61
D28V5, multiclass
       clus
vv      16P GAIN MUTATED 16P GAIN WILD-TYPE
  T0+T1               11                 53
  T2                  17                 56
  T3                  12                 69
  T4                   6                 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
  16P GAIN MUTATED    38   7   3   4
  16P GAIN WILD-TYPE 139  58  36  41
D28V6, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  N0               38                139
  N1                7                 58
  N2                3                 36
  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"
D28V7, binary
                    cls
clus                   0   1
  16P GAIN MUTATED    51   2
  16P GAIN WILD-TYPE 268  20
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     51    2
  16P GAIN WILD-TYPE  268   20
   clus
vv  16P GAIN MUTATED 16P GAIN WILD-TYPE
  0               51                268
  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     5  52
  16P GAIN WILD-TYPE  42 268
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      5   52
  16P GAIN WILD-TYPE   42  268
     clus
vv    16P GAIN MUTATED 16P GAIN WILD-TYPE
  NO                 5                 42
  YES               52                268
[1] 2 2
[1] FALSE
D28V10, continuous
D28V11, binary
                    cls
clus                   0   1
  16P GAIN MUTATED    25  32
  16P GAIN WILD-TYPE 113 197
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     25   32
  16P GAIN WILD-TYPE  113  197
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  FEMALE               25                113
  MALE                 32                197
[1] 2 2
[1] FALSE
D28V12, binary
                    cls
clus                   0   1
  16P GAIN MUTATED    51   6
  16P GAIN WILD-TYPE 268  41
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     51    6
  16P GAIN WILD-TYPE  268   41
     clus
vv    16P GAIN MUTATED 16P GAIN WILD-TYPE
  NO                51                268
  YES                6                 41
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16P GAIN MUTATED       1                         0    55
  16P GAIN WILD-TYPE     4                         1   298
D28V13, multiclass
                           clus
vv                          16P GAIN MUTATED 16P GAIN WILD-TYPE
  ASIAN                                    1                  4
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   55                298
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V14, binary
                    cls
clus                   0   1
  16P GAIN MUTATED     1  53
  16P GAIN WILD-TYPE   6 299
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      1   53
  16P GAIN WILD-TYPE    6  299
                        clus
vv                       16P GAIN MUTATED 16P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO               53                299
[1] 2 2
[1] FALSE

Clustering(29) Variable = 16Q GAIN MUTATION ANALYSIS
D29V1, survival
                    sevent
clus2                  0   1
  16Q GAIN MUTATED    15  18
  16Q GAIN WILD-TYPE 113 106
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                33                219 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                18                106 
$`16Q GAIN MUTATED`
TCGA-D3-A2JE TCGA-EE-A20H TCGA-FR-A729 TCGA-D3-A1Q6 TCGA-D3-A3C6 TCGA-D3-A3CE 
        9.76       166.75       216.43        49.35        58.06        59.70 
TCGA-D3-A5GR TCGA-D3-A8GP TCGA-D3-A8GR TCGA-DA-A95Z TCGA-EE-A17Y TCGA-EE-A2A1 
      177.86       135.12        36.53        12.30        24.89       115.43 
TCGA-EE-A2GB TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MP 
       26.14        18.35        93.63       103.13        15.25       227.01 
TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19M TCGA-ER-A19P 
       67.89        45.90        39.81        11.47        59.84       120.76 
TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A69P TCGA-FS-A1ZY TCGA-FS-A4F4 TCGA-GF-A4EO 
       32.05        74.47         4.14         5.29        66.67        18.25 
TCGA-GN-A9SD TCGA-W3-AA1V TCGA-XV-AB01 
       59.41         8.09         6.61 

$`16Q GAIN WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A8GI TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A2GD 
       62.07        38.76        13.41        33.24        31.96       269.03 
TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 TCGA-FW-A3R5 TCGA-WE-A8K5 
       52.90       134.40        27.35        19.04        36.95        52.73 
TCGA-WE-AAA3 TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q3 
        7.40        60.46        12.99        14.83         8.42        15.72 
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB 
       31.89       110.93       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-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-A3CB TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU 
      140.98        40.01        24.53         9.34        90.21        23.67 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T 
      173.85        30.67       144.46        31.76        62.70        11.34 
TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GU TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GJ 
       42.05        45.70       124.08        78.21        23.61       179.97 
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        68.68 
TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 
      150.61       110.53        60.10        64.83        58.85        30.44 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-DA-A95V TCGA-DA-A95W TCGA-DA-A95X TCGA-DA-A95Y 
      225.11         8.71        72.10         0.76        65.03        14.14 
TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A181 
        3.91        16.41        52.41        18.21        13.15        20.38 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29C 
        0.00        26.24        75.55        79.20        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        47.41        47.74        27.16 
TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GE 
       61.12       346.49       185.19        30.02        77.98        12.95 
TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GP TCGA-EE-A2GR 
      201.60        68.65        10.62        32.48         0.76         0.20 
TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MG 
       71.31        81.99         5.75        23.77       209.79        94.19 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MS 
      171.85        63.25        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-A3AD 
       23.51        53.26       124.31       122.73        64.04         4.41 
TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J4 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH 
       54.51         6.28       111.85         3.35       168.85        19.86 
TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B 
      135.98        34.45        10.49         7.82         4.54        53.29 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A19S 
      184.60       150.12        99.06        42.51        49.71        47.18 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF 
      146.63        73.05        22.36         4.70        16.87        10.19 
TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-FR-A3YN TCGA-FR-A44A 
       28.67       173.29        68.52        15.48         4.50       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-A1ZG 
        8.35        27.62       312.07        32.78        43.92         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-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FD 
       23.21         3.06        30.90       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-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-AA1R TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8ZM TCGA-WE-A8ZN 
       79.99       185.13        92.84        47.54        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        37.32 
TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-Z2-AA3S 
       24.99        28.21        91.23 

  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
              4.14               0.00 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
            227.01             346.49 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
             49.35              45.99 
[1] "4.1 - 227.0 (49.4)" "0.0 - 346.5 (46.0)"
[1] "hr=" "1.1"
D29V2, survival
                    sevent
clus2                  0   1
  16Q GAIN MUTATED    20  21
  16Q GAIN WILD-TYPE 146 171
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                41                317 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                21                171 
$`16Q GAIN MUTATED`
TCGA-D3-A2JE TCGA-EE-A20H TCGA-FR-A729 TCGA-D3-A1Q6 TCGA-D3-A1Q9 TCGA-D3-A3C6 
       27.65       168.26       220.80        71.80        31.59        58.06 
TCGA-D3-A3CE TCGA-D3-A5GR TCGA-D3-A8GP TCGA-D3-A8GR TCGA-DA-A95Z TCGA-EE-A17Y 
       60.23       178.32       152.75       129.63        13.02        27.22 
TCGA-EE-A20B TCGA-EE-A29R TCGA-EE-A2A1 TCGA-EE-A2GB TCGA-EE-A2GI TCGA-EE-A2GM 
      133.81        14.47       115.96        59.28        48.72        75.48 
TCGA-EE-A2GN TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MP TCGA-EE-A3J3 TCGA-EE-A3J7 
      102.12       129.27        28.83       248.65       172.18        64.08 
TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19M TCGA-ER-A19P TCGA-ER-A3PL TCGA-ER-A42L 
       48.89        12.59        61.05       162.08        33.21       149.03 
TCGA-FR-A69P TCGA-FS-A1YX TCGA-FS-A1ZY TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-GF-A4EO 
       15.72        48.59        27.09        66.67        28.73        19.43 
TCGA-GN-A9SD TCGA-HR-A2OG TCGA-W3-AA1V TCGA-WE-A8K6 TCGA-XV-AB01 
       59.41         0.23        42.08        17.95        13.25 

$`16Q GAIN WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-D3-A8GI TCGA-EB-A5SG TCGA-EB-A5SH 
       62.07        46.32        13.87        58.52        68.25        54.02 
TCGA-EE-A180 TCGA-EE-A184 TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR 
       94.98        68.15         2.60       340.14       126.81       134.40 
TCGA-EE-A3JD TCGA-ER-A193 TCGA-ER-A198 TCGA-FS-A1ZF TCGA-FW-A3R5 TCGA-QB-AA9O 
       27.35        31.40        50.76        15.45        36.95        18.05 
TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 
       61.15        21.40        17.03        66.48        12.99        14.93 
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       16.57        16.67       112.04       112.57       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-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH 
      115.53       168.00        86.76        11.87       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-A3C7 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR 
       46.98       166.52        86.93        24.53         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-A5GS TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GD 
      137.92        18.18       125.19        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-A8GS TCGA-D3-A8GV TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW 
       29.06       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       222.51       176.55        35.93       135.02        88.87 
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-A95X TCGA-DA-A95Y 
      225.96        43.36        72.10        37.35        73.94        14.14 
TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV 
       13.87        10.36        20.35        29.29        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-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-A29M 
       78.97        13.97        63.78        72.07        64.64        56.84 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V 
       18.61        56.42        66.74        61.28       369.93        25.87 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
      195.02        17.92        46.82        59.64        39.29        86.14 
TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
       67.43       173.79       220.24       107.38        54.74        79.66 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 
       13.91        42.77        81.21        44.88        94.82        21.67 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG 
       19.76        61.51        47.28       103.27       268.73       103.20 
TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-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-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-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-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB 
      138.81       127.20        36.95        34.32        53.19       201.80 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 
       51.35       134.33       152.81        35.44        13.94         9.17 
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       302.07       152.35 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T 
        6.44       131.51        44.09        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       105.07        43.82        23.34        20.15        28.83 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A42K 
       48.99        41.56       247.04        93.01        46.98        12.95 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC 
       92.98       174.21        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-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD 
       28.08         7.79        27.72        48.85       357.37        53.52 
TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM 
       46.45         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-A4F2 TCGA-FS-A4F8 TCGA-FS-A4F9 
       49.48        27.02        77.82        50.14       174.84        34.03 
TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV 
       26.73        54.41        80.68        17.46        55.59        13.51 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 
       19.30         9.90         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-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 
       21.37        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-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 

  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
              0.23               0.20 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
            248.65             369.93 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
             59.28              50.89 
[1] "0.2 - 248.7 (59.3)" "0.2 - 369.9 (50.9)"
[1] "hr=" "1.1"
D29V3, continuous
                    vv
clus                 I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  16Q GAIN MUTATED          2       2       7        2        6        6
  16Q GAIN WILD-TYPE       11       5      22       16       22       20
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  16Q GAIN MUTATED           1         1         1         4          0
  16Q GAIN WILD-TYPE        13        18        14        35         15
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  16Q GAIN MUTATED            5          4        2
  16Q GAIN WILD-TYPE         30         50       19
D29V4, multiclass
            clus
vv           16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  I/II NOS                  2                 11
  STAGE 0                   2                  5
  STAGE I                   7                 22
  STAGE IA                  2                 16
  STAGE IB                  6                 22
  STAGE II                  6                 20
  STAGE IIA                 1                 13
  STAGE IIB                 1                 18
  STAGE IIC                 1                 14
  STAGE III                 4                 35
  STAGE IIIA                0                 15
  STAGE IIIB                5                 30
  STAGE IIIC                4                 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
  16Q GAIN MUTATED       7 15 11  3
  16Q GAIN WILD-TYPE    57 58 70 64
D29V5, multiclass
       clus
vv      16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  T0+T1                7                 57
  T2                  15                 58
  T3                  11                 70
  T4                   3                 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
  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    41   2
  16Q GAIN WILD-TYPE 278  20
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     41    2
  16Q GAIN WILD-TYPE  278   20
   clus
vv  16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  0               41                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  41
  16Q GAIN WILD-TYPE  43 279
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      4   41
  16Q GAIN WILD-TYPE   43  279
     clus
vv    16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  NO                 4                 43
  YES               41                279
[1] 2 2
[1] FALSE
D29V10, continuous
D29V11, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED    20  25
  16Q GAIN WILD-TYPE 118 204
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     20   25
  16Q GAIN WILD-TYPE  118  204
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  FEMALE               20                118
  MALE                 25                204
[1] 2 2
[1] FALSE
D29V12, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED    40   5
  16Q GAIN WILD-TYPE 279  42
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     40    5
  16Q GAIN WILD-TYPE  279   42
     clus
vv    16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  NO                40                279
  YES                5                 42
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16Q GAIN MUTATED       1                         0    43
  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                                   43                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  41
  16Q GAIN WILD-TYPE   6 311
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      1   41
  16Q GAIN WILD-TYPE    6  311
                        clus
vv                       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO               41                311
[1] 2 2
[1] FALSE

Clustering(30) Variable = 17P GAIN MUTATION ANALYSIS
D30V1, survival
                    sevent
clus2                  0   1
  17P GAIN MUTATED    15  14
  17P GAIN WILD-TYPE 113 110
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                29                223 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                14                110 
$`17P GAIN MUTATED`
TCGA-D3-A2JE TCGA-D3-A1Q1 TCGA-D3-A2JC TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A5GU 
        9.76         8.42        86.30        58.06        59.70       124.08 
TCGA-D3-A8GM TCGA-D3-A8GP TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1I7 TCGA-DA-A1IA 
       70.62       135.12        69.21        76.34        60.10        64.83 
TCGA-EE-A17Y TCGA-EE-A182 TCGA-EE-A20F TCGA-EE-A29D TCGA-EE-A29P TCGA-EE-A2A6 
       24.89         0.00        79.20        12.99        27.16        77.98 
TCGA-EE-A2GH TCGA-EE-A2GM TCGA-EE-A2M7 TCGA-EE-A3AE TCGA-ER-A2ND TCGA-ER-A3PL 
      201.60        18.35        15.25        54.51         4.70        32.05 
TCGA-FS-A1ZD TCGA-FS-A1ZM TCGA-FS-A1ZS TCGA-GN-A9SD TCGA-W3-A825 
       32.78        78.61       136.27        59.41         1.97 

$`17P GAIN WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A8GI TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A20H 
       62.07        38.76        13.41        33.24        31.96       166.75 
TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 TCGA-FR-A729 
      269.03        52.90       134.40        27.35        19.04       216.43 
TCGA-FW-A3R5 TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 
       36.95        52.73         7.40        60.46        12.99        14.83 
TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       15.72        31.89       110.93        49.35       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-A2JG TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
      168.00       107.61        36.30       171.58        64.83        66.08 
TCGA-D3-A2JP TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR 
       43.53       140.98        40.01        24.53         9.34        90.21 
TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R 
       23.67       173.85        30.67       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-A8GR TCGA-D9-A1X3 TCGA-D9-A3Z1 
      179.97       120.00        69.53        36.53        10.78        15.02 
TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6EG TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 
       16.90        18.44        22.85       138.67        68.68       150.61 
TCGA-DA-A1I5 TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-DA-A95V 
      110.53        58.85        30.44       225.11         8.71        72.10 
TCGA-DA-A95W TCGA-DA-A95X TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5KH 
        0.76        65.03        14.14        12.30         3.91        16.41 
TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A20C 
       52.41        18.21        13.15        20.38        26.24        75.55 
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        47.41        47.74 
TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2GB 
       61.12       346.49       185.19       115.43        30.02        26.14 
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        93.63         0.76 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M8 TCGA-EE-A2MC 
        0.20        71.31        81.99       103.13         5.75        23.77 
TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML 
      209.79        94.19       171.85        63.25        89.26       104.78 
TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA 
      145.45       227.01       143.93        23.51        53.26       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-A3JH TCGA-EE-A3JI TCGA-ER-A195 
       45.90         3.35       168.85        19.86       135.98        34.45 
TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D 
       10.49         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 
      184.60       150.12        99.06        59.84        42.51       120.76 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE 
       49.71        47.18       146.63        73.05        22.36        16.87 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A42L 
       10.19        28.67       173.29        68.52        15.48        74.47 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FR-A8YC 
        4.50       174.21         4.14        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-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZQ TCGA-FS-A1ZT TCGA-FS-A1ZU 
       43.92         7.82        36.33       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 
       18.25         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-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-A828 TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 
      120.07        44.05        79.99         8.09       185.13        92.84 
TCGA-WE-A8K1 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT 
       47.54        65.42        12.69        21.90        62.89        10.95 
TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-XV-AB01 TCGA-YG-AA3O 
       48.39         1.94        37.32        24.99         6.61        28.21 
TCGA-Z2-AA3S 
       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 
             59.41              45.70 
[1] "0.0 - 201.6 (59.4)" "0.2 - 346.5 (45.7)"
[1] "hr=" "1.1"
D30V2, survival
                    sevent
clus2                  0   1
  17P GAIN MUTATED    18  21
  17P GAIN WILD-TYPE 148 171
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                39                319 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                21                171 
$`17P GAIN MUTATED`
TCGA-D3-A2JE TCGA-D3-A1Q1 TCGA-D3-A1Q9 TCGA-D3-A2JC TCGA-D3-A3BZ TCGA-D3-A3C6 
       27.65        16.57        31.59        86.76       130.72        58.06 
TCGA-D3-A3CE TCGA-D3-A3MV TCGA-D3-A5GU TCGA-D3-A8GM TCGA-D3-A8GP TCGA-D9-A6EC 
       60.23        45.30       125.19       107.15       152.75        77.56 
TCGA-DA-A1HV TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-EE-A17Y TCGA-EE-A182 TCGA-EE-A20F 
       76.57        88.87        65.92        27.22        14.70        91.56 
TCGA-EE-A29D TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A2A6 TCGA-EE-A2GH 
       13.97        18.61        56.42        14.47        86.14       220.24 
TCGA-EE-A2GM TCGA-EE-A2M7 TCGA-EE-A3AE TCGA-EE-A3AG TCGA-EE-A3JA TCGA-ER-A19T 
       75.48        28.83        54.51        41.59        53.19         8.88 
TCGA-ER-A2ND TCGA-ER-A3PL TCGA-FS-A1ZD TCGA-FS-A1ZM TCGA-FS-A1ZS TCGA-GN-A26D 
       23.34        33.21        53.52       101.26       148.80        48.00 
TCGA-GN-A9SD TCGA-W3-A825 TCGA-W3-AA1O 
       59.41        63.02         4.01 

$`17P GAIN WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-D3-A8GI TCGA-EB-A5SG TCGA-EB-A5SH 
       62.07        46.32        13.87        58.52        68.25        54.02 
TCGA-EE-A180 TCGA-EE-A184 TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2GO 
       94.98        68.15       168.26         2.60       340.14       126.81 
TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 TCGA-ER-A198 TCGA-FR-A729 TCGA-FS-A1ZF 
      134.40        27.35        31.40        50.76       220.80        15.45 
TCGA-FW-A3R5 TCGA-QB-AA9O TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-3N-A9WB TCGA-3N-A9WC 
       36.95        18.05        61.15        21.40        17.03        66.48 
TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 
       12.99        14.93        16.67       112.04       112.57        71.80 
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
      133.25        28.08        90.90        95.74        43.43       103.10 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JD TCGA-D3-A2JG 
       65.49        23.77       115.53       168.00        11.87       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-A3C7 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR 
       46.98       166.52        86.93        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-A5GN TCGA-D3-A5GO 
       22.62        63.81        26.89       125.79       135.75       137.92 
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-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GN TCGA-D3-A8GQ TCGA-D3-A8GR 
      241.38       170.20        89.13       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-A6EA 
       18.12        15.39        22.29        18.44         9.90        25.18 
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       222.51       176.55 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
       35.93       135.02        53.92        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        43.36        72.10        37.35        73.94 
TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5UL 
       14.14        13.02        13.87        10.36        20.35        29.29 
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-A183 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20I TCGA-EE-A29A 
       26.89         4.96       133.81       151.27        13.55        63.35 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M 
       85.08        78.97        63.78        72.07        64.64        56.84 
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-A2GB TCGA-EE-A2GC 
       46.82       115.96        59.64        39.29        59.28        67.43 
TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN 
      173.79        48.72       107.38        54.74        79.66       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-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF 
      129.27        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-A2MS TCGA-EE-A2MT 
      167.90        47.54       248.65        43.23       162.48        71.21 
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        28.77        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-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 
      201.80        51.35       134.33       152.81        35.44        13.94 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E 
        9.17        77.75        98.40        48.89        12.59        13.02 
TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
       26.37       302.07       152.35         6.44       131.51        61.05 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 
       44.09       162.08        50.89        49.48       148.18       105.07 
TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES 
       43.82        20.15        28.83        48.99        41.56       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-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-A1ZE 
       28.08         7.79        27.72        48.85       357.37        46.45 
TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZQ 
        9.70        32.75        47.38        23.93        74.73       133.55 
TCGA-FS-A1ZR TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ 
       11.41        53.16        26.56        49.48        27.09        27.02 
TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 
       77.82        50.14        66.67        28.73       174.84        34.03 
TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV 
       26.73        54.41        80.68        17.46        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        19.43         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-RP-A690 TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A828 TCGA-W3-AA1Q 
        0.20         0.33         0.69       228.16       121.08        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-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-AAA4 TCGA-XV-AB01 
       35.80        49.51        12.16        40.41        24.99        13.25 
TCGA-YD-A89C TCGA-YD-A9TA TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S 
        6.90        49.18        37.94        14.43        27.58        96.99 
TCGA-Z2-AA3V 
       15.98 

  17P GAIN MUTATED 17P GAIN WILD-TYPE 
              4.01               0.20 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
            220.24             369.93 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
             56.42              50.14 
[1] "4.0 - 220.2 (56.4)" "0.2 - 369.9 (50.1)"
[1] "hr=" "1.1"
D30V3, continuous
                    vv
clus                 I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  17P GAIN MUTATED          2       0       3        3        3        2
  17P GAIN WILD-TYPE       11       7      26       15       25       24
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  17P GAIN MUTATED           1         2         3         6          1
  17P GAIN WILD-TYPE        13        17        12        33         14
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  17P GAIN MUTATED            6          6        2
  17P GAIN WILD-TYPE         29         48       19
D30V4, multiclass
            clus
vv           17P GAIN MUTATED 17P GAIN WILD-TYPE
  I/II NOS                  2                 11
  STAGE 0                   0                  7
  STAGE I                   3                 26
  STAGE IA                  3                 15
  STAGE IB                  3                 25
  STAGE II                  2                 24
  STAGE IIA                 1                 13
  STAGE IIB                 2                 17
  STAGE IIC                 3                 12
  STAGE III                 6                 33
  STAGE IIIA                1                 14
  STAGE IIIB                6                 29
  STAGE IIIC                6                 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
  17P GAIN MUTATED      12  9  8  7
  17P GAIN WILD-TYPE    52 64 73 60
D30V5, multiclass
       clus
vv      17P GAIN MUTATED 17P GAIN WILD-TYPE
  T0+T1               12                 52
  T2                   9                 64
  T3                   8                 73
  T4                   7                 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
  17P GAIN MUTATED    19   7   9   4
  17P GAIN WILD-TYPE 158  58  30  41
D30V6, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  N0               19                158
  N1                7                 58
  N2                9                 30
  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    37   2
  17P GAIN WILD-TYPE 282  20
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED     37    2
  17P GAIN WILD-TYPE  282   20
   clus
vv  17P GAIN MUTATED 17P GAIN WILD-TYPE
  0               37                282
  1                2                 20
[1] 2 2
[1] FALSE
D30V8, binary
                    cls
clus                   0   1
  17P GAIN MUTATED    12  12
  17P GAIN WILD-TYPE 122  78
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED     12   12
  17P GAIN WILD-TYPE  122   78
     clus
vv    17P GAIN MUTATED 17P GAIN WILD-TYPE
  NO                12                122
  YES               12                 78
[1] 2 2
[1] FALSE
D30V9, binary
                    cls
clus                   0   1
  17P GAIN MUTATED     6  34
  17P GAIN WILD-TYPE  41 286
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      6   34
  17P GAIN WILD-TYPE   41  286
     clus
vv    17P GAIN MUTATED 17P GAIN WILD-TYPE
  NO                 6                 41
  YES               34                286
[1] 2 2
[1] FALSE
D30V10, continuous
D30V11, binary
                    cls
clus                   0   1
  17P GAIN MUTATED    18  22
  17P GAIN WILD-TYPE 120 207
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED     18   22
  17P GAIN WILD-TYPE  120  207
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  FEMALE               18                120
  MALE                 22                207
[1] 2 2
[1] FALSE
D30V12, binary
                    cls
clus                   0   1
  17P GAIN MUTATED    35   5
  17P GAIN WILD-TYPE 284  42
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED     35    5
  17P GAIN WILD-TYPE  284   42
     clus
vv    17P GAIN MUTATED 17P GAIN WILD-TYPE
  NO                35                284
  YES                5                 42
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  17P GAIN MUTATED       1                         0    39
  17P GAIN WILD-TYPE     4                         1   314
D30V13, multiclass
                           clus
vv                          17P GAIN MUTATED 17P GAIN WILD-TYPE
  ASIAN                                    1                  4
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   39                314
[1] 3 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  38
  17P GAIN WILD-TYPE   6 314
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      1   38
  17P GAIN WILD-TYPE    6  314
                        clus
vv                       17P GAIN MUTATED 17P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO               38                314
[1] 2 2
[1] FALSE

Clustering(31) Variable = 17Q GAIN MUTATION ANALYSIS
D31V1, survival
                    sevent
clus2                  0   1
  17Q GAIN MUTATED    23  20
  17Q GAIN WILD-TYPE 105 104
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                43                209 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                20                104 
$`17Q GAIN MUTATED`
TCGA-D3-A2JE TCGA-EE-A2MR TCGA-WE-AAA3 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1QA 
        9.76       134.40         7.40         8.42        15.72        76.41 
TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JL TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A8GM 
      168.00        86.30       171.58        58.06        59.70        70.62 
TCGA-D3-A8GP TCGA-DA-A1HV TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-EE-A17Y 
      135.12        76.34        60.10        64.83        58.85        24.89 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A20F TCGA-EE-A29D TCGA-EE-A29P TCGA-EE-A2A6 
       20.38         0.00        79.20        12.99        27.16        77.98 
TCGA-EE-A2GH TCGA-EE-A2GM TCGA-EE-A2M7 TCGA-EE-A2MS TCGA-EE-A3AC TCGA-EE-A3AE 
      201.60        18.35        15.25       143.93        64.04        54.51 
TCGA-ER-A2NC TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FS-A1ZD TCGA-FS-A1ZM TCGA-FS-A1ZS 
       22.36        32.05         4.50        32.78        78.61       136.27 
TCGA-FS-A1ZU TCGA-GN-A265 TCGA-GN-A268 TCGA-GN-A9SD TCGA-QB-A6FS TCGA-W3-A825 
        4.47        96.92        42.48        59.41         7.23         1.97 
TCGA-WE-A8K1 
       47.54 

$`17Q GAIN WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A8GI TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A20H 
       62.07        38.76        13.41        33.24        31.96       166.75 
TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A3JD TCGA-ER-A193 TCGA-FR-A729 TCGA-FW-A3R5 
      269.03        52.90        27.35        19.04       216.43        36.95 
TCGA-WE-A8K5 TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q4 TCGA-D3-A1Q5 
       52.73        60.46        12.99        14.83        31.89       110.93 
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-A2JG TCGA-D3-A2JH TCGA-D3-A2JN TCGA-D3-A2JO 
       62.86        15.75       107.61        36.30        64.83        66.08 
TCGA-D3-A2JP TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR 
       43.53       140.98        40.01        24.53         9.34        90.21 
TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R 
       23.67       173.85        30.67       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-A8GR TCGA-D9-A1X3 
       23.61       179.97       120.00        69.53        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-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 
       68.68       150.61       110.53        30.44       225.11         8.71 
TCGA-DA-A95V TCGA-DA-A95W TCGA-DA-A95X TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q 
       72.10         0.76        65.03        14.14        12.30         3.91 
TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A183 TCGA-EE-A20C 
       16.41        52.41        18.21        13.15        26.24        75.55 
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        47.41        47.74 
TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2GB 
       61.12       346.49       185.19       115.43        30.02        26.14 
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        93.63         0.76 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M8 TCGA-EE-A2MC 
        0.20        71.31        81.99       103.13         5.75        23.77 
TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML 
      209.79        94.19       171.85        63.25        89.26       104.78 
TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB 
      145.45       227.01        23.51        53.26       124.31       122.73 
TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 
        4.41         6.28        67.89       111.85        45.90         3.35 
TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 
      168.85        19.86       135.98        34.45        10.49         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       184.60       150.12 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S 
       99.06        59.84        42.51       120.76        49.71        47.18 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
      146.63        73.05         4.70        16.87        10.19        28.67 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A42L TCGA-FR-A44A TCGA-FR-A69P 
      173.29        68.52        15.48        74.47       174.21         4.14 
TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 
       26.20         5.65        10.06       171.78        49.74       195.98 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ 
        8.35        27.62       312.07        43.92         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        18.25         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-RP-A690 TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A828 
       85.05       297.01         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-A8ZM 
       44.05        79.99         8.09       185.13        92.84        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-XV-AB01 TCGA-YG-AA3O TCGA-Z2-AA3S 
       37.32        24.99         6.61        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 
             58.06              45.70 
[1] "0.0 - 201.6 (58.1)" "0.2 - 346.5 (45.7)"
[1] "hr=" "1"  
D31V2, survival
                    sevent
clus2                  0   1
  17Q GAIN MUTATED    34  32
  17Q GAIN WILD-TYPE 132 160
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                66                292 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                32                160 
$`17Q GAIN MUTATED`
TCGA-D3-A2JE TCGA-EE-A184 TCGA-EE-A29L TCGA-EE-A2MR TCGA-WE-AAA3 TCGA-D3-A1Q1 
       27.65        68.15         2.60       134.40        21.40        16.57 
TCGA-D3-A1Q3 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JL 
       16.67        31.59        90.90       168.00        86.76       171.58 
TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3MV TCGA-D3-A5GS TCGA-D3-A8GM 
      130.72        58.06        60.23        45.30        18.18       107.15 
TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D9-A148 TCGA-D9-A1JW TCGA-D9-A6E9 TCGA-DA-A1HV 
      161.00       152.75       151.53         3.65         9.90        76.57 
TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A182 
       88.87        65.92        68.09        27.22        33.73        14.70 
TCGA-EE-A185 TCGA-EE-A20F TCGA-EE-A29D TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29R 
        4.96        91.56        13.97        18.61        56.42        14.47 
TCGA-EE-A2A6 TCGA-EE-A2GC TCGA-EE-A2GH TCGA-EE-A2GM TCGA-EE-A2M7 TCGA-EE-A2MD 
       86.14        67.43       220.24        75.48        28.83        47.28 
TCGA-EE-A2MS TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3J5 TCGA-EE-A3JA TCGA-ER-A19T 
      162.48        64.04        54.51        36.95        53.19         8.88 
TCGA-ER-A2NC TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FS-A1YX TCGA-FS-A1ZD TCGA-FS-A1ZM 
       43.82        33.21        92.98        48.59        53.52       101.26 
TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-GN-A265 TCGA-GN-A268 TCGA-GN-A26D TCGA-GN-A9SD 
      148.80        26.56        96.92        62.79        48.00        59.41 
TCGA-QB-A6FS TCGA-RP-A694 TCGA-W3-A825 TCGA-W3-AA1O TCGA-WE-A8JZ TCGA-WE-A8K1 
        7.23         0.69        63.02         4.01        24.03        49.05 

$`17Q GAIN WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-D3-A8GI TCGA-EB-A5SG TCGA-EB-A5SH 
       62.07        46.32        13.87        58.52        68.25        54.02 
TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A3JD TCGA-ER-A193 
       94.98       168.26       340.14       126.81        27.35        31.40 
TCGA-ER-A198 TCGA-FR-A729 TCGA-FS-A1ZF TCGA-FW-A3R5 TCGA-QB-AA9O TCGA-WE-A8K5 
       50.76       220.80        15.45        36.95        18.05        61.15 
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-A2JG TCGA-D3-A2JH 
       65.49        23.77       115.53        11.87       113.52        42.08 
TCGA-D3-A2JK TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C7 TCGA-D3-A3CB 
       12.10        66.48        66.08        59.57        46.98       166.52 
TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E 
       86.93        24.53         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-A5GU 
       26.89       125.79       135.75       137.92       178.32       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-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D3-A8GV TCGA-D9-A149 
       89.13        29.06       129.63       117.17       167.70        54.67 
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-A6EC TCGA-D9-A6EG TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 
       77.56        22.95        36.03       144.89        20.38       222.51 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A1IB TCGA-DA-A3F2 
      176.55        35.93       135.02        53.92        40.60        33.93 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-DA-A95V TCGA-DA-A95W TCGA-DA-A95X 
       10.49       225.96        43.36        72.10        37.35        73.94 
TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5UL 
       14.14        13.02        13.87        10.36        20.35        29.29 
TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A183 
       58.92         7.04        36.46        29.82         8.65        26.89 
TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C 
      133.81       151.27        13.55        63.35        85.08        78.97 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29Q TCGA-EE-A29S 
       63.78        72.07        64.64        56.84        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-A2GB TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GJ 
       59.64        39.29        59.28       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-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M8 TCGA-EE-A2MC 
       44.88        94.82        21.67       129.27        19.76        61.51 
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-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AF 
       71.21        53.26       124.31       122.73        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-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 
      201.80        51.35       134.33       152.81        35.44        13.94 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E 
        9.17        77.75        98.40        48.89        12.59        13.02 
TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
       26.37       302.07       152.35         6.44       131.51        61.05 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 
       44.09       162.08        50.89        49.48       148.18       105.07 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES 
       23.34        20.15        28.83        48.99        41.56       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-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-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZH 
       27.72        48.85       357.37        46.45         9.70        32.75 
TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZT 
       47.38        23.93        74.73       133.55        11.41        53.16 
TCGA-FS-A1ZW TCGA-FS-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 
       17.46        55.59        13.51        19.30         9.90        19.43 
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-RP-A690 TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A828 TCGA-W3-AA1Q TCGA-W3-AA1R 
        0.20         0.33       228.16       121.08        69.07       111.09 
TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN 
       42.08       219.16       105.04        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-AAA4 TCGA-XV-AB01 TCGA-YD-A89C TCGA-YD-A9TA TCGA-YG-AA3O 
       40.41        24.99        13.25         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 

  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 
            54.015             50.825 
[1] "0.7 - 220.2 (54.0)" "0.2 - 369.9 (50.8)"
[1] "hr=" "1"  
D31V3, continuous
                    vv
clus                 I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  17Q GAIN MUTATED          4       1       5        3        6        5
  17Q GAIN WILD-TYPE        9       6      24       15       22       21
                    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        32         14
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  17Q GAIN MUTATED            8         10        4
  17Q GAIN WILD-TYPE         27         44       17
D31V4, multiclass
            clus
vv           17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  I/II NOS                  4                  9
  STAGE 0                   1                  6
  STAGE I                   5                 24
  STAGE IA                  3                 15
  STAGE IB                  6                 22
  STAGE II                  5                 21
  STAGE IIA                 1                 13
  STAGE IIB                 4                 15
  STAGE IIC                 5                 10
  STAGE III                 7                 32
  STAGE IIIA                1                 14
  STAGE IIIB                8                 27
  STAGE IIIC               10                 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
  17Q GAIN MUTATED      13 15 14 15
  17Q GAIN WILD-TYPE    51 58 67 52
D31V5, multiclass
       clus
vv      17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  T0+T1               13                 51
  T2                  15                 58
  T3                  14                 67
  T4                  15                 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
  17Q GAIN MUTATED    34  10  12   8
  17Q GAIN WILD-TYPE 143  55  27  37
D31V6, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  N0               34                143
  N1               10                 55
  N2               12                 27
  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"
D31V7, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED    60   5
  17Q GAIN WILD-TYPE 259  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     60    5
  17Q GAIN WILD-TYPE  259   17
   clus
vv  17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  0               60                259
  1                5                 17
[1] 2 2
[1] FALSE
D31V8, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED    23  21
  17Q GAIN WILD-TYPE 111  69
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     23   21
  17Q GAIN WILD-TYPE  111   69
     clus
vv    17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  NO                23                111
  YES               21                 69
[1] 2 2
[1] FALSE
D31V9, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED    10  57
  17Q GAIN WILD-TYPE  37 263
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     10   57
  17Q GAIN WILD-TYPE   37  263
     clus
vv    17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  NO                10                 37
  YES               57                263
[1] 2 2
[1] FALSE
D31V10, continuous
D31V11, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED    27  40
  17Q GAIN WILD-TYPE 111 189
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     27   40
  17Q GAIN WILD-TYPE  111  189
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  FEMALE               27                111
  MALE                 40                189
[1] 2 2
[1] FALSE
D31V12, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED    60   7
  17Q GAIN WILD-TYPE 259  40
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     60    7
  17Q GAIN WILD-TYPE  259   40
     clus
vv    17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  NO                60                259
  YES                7                 40
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  17Q GAIN MUTATED       1                         1    64
  17Q GAIN WILD-TYPE     4                         0   289
D31V13, multiclass
                           clus
vv                          17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  ASIAN                                    1                  4
  BLACK OR AFRICAN AMERICAN                1                  0
  WHITE                                   64                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"
D31V14, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED     1  64
  17Q GAIN WILD-TYPE   6 288
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      1   64
  17Q GAIN WILD-TYPE    6  288
                        clus
vv                       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO               64                288
[1] 2 2
[1] FALSE

Clustering(32) Variable = 18P GAIN MUTATION ANALYSIS
D32V1, survival
                    sevent
clus2                  0   1
  18P GAIN MUTATED    23  15
  18P GAIN WILD-TYPE 105 109
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                38                214 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                15                109 
$`18P GAIN MUTATED`
TCGA-D3-A2JE TCGA-EE-A180 TCGA-FR-A729 TCGA-WE-AAA3 TCGA-D3-A1Q5 TCGA-D3-A1QA 
        9.76        31.96       216.43         7.40       110.93        76.41 
TCGA-D3-A2JN TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A51E TCGA-D3-A51K TCGA-D3-A8GP 
       64.83        40.01        59.70       173.85        31.76       135.12 
TCGA-D9-A6EC TCGA-DA-A1I1 TCGA-DA-A95V TCGA-DA-A95X TCGA-EB-A6L9 TCGA-EE-A181 
       69.21        68.68        72.10        65.03        18.21        20.38 
TCGA-EE-A29E TCGA-EE-A29P TCGA-EE-A2GB TCGA-EE-A2GH TCGA-EE-A2GM TCGA-EE-A2MP 
        0.26        27.16        26.14       201.60        18.35       227.01 
TCGA-ER-A197 TCGA-ER-A19W TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FS-A1Z0 
       10.49       146.63        15.48        32.05         4.50       195.98 
TCGA-FS-A1ZC TCGA-FS-A1ZJ TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-GF-A4EO TCGA-GN-A267 
      312.07        36.33        35.28         4.47        18.25        17.06 
TCGA-GN-A26A TCGA-XV-AB01 
        7.59         6.61 

$`18P GAIN WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A8GI TCGA-EB-A5SG TCGA-EE-A20H TCGA-EE-A2GD 
       62.07        38.76        13.41        33.24       166.75       269.03 
TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 TCGA-FW-A3R5 TCGA-WE-A8K5 
       52.90       134.40        27.35        19.04        36.95        52.73 
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-A2JG TCGA-D3-A2JH 
       62.86        15.75       168.00        86.30       107.61        36.30 
TCGA-D3-A2JL TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CF 
      171.58        66.08        43.53        58.06       140.98        24.53 
TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51R 
        9.34        90.21        23.67        30.67       144.46        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-A8GR 
       23.61       179.97       120.00        69.53        70.62        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-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC 
      138.67       150.61       110.53        60.10        64.83        58.85 
TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-DA-A95W TCGA-DA-A95Y TCGA-DA-A95Z 
       30.44       225.11         8.71         0.76        14.14        12.30 
TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A182 
        3.91        16.41        52.41        13.15        24.89         0.00 
TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D 
       26.24        75.55        79.20        75.22        76.14        12.99 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W 
       44.28        47.41        47.74        61.12       346.49       185.19 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GE TCGA-EE-A2GJ TCGA-EE-A2GK 
      115.43        30.02        77.98        12.95        68.65        10.62 
TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU 
       32.48        93.63         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-A2MS 
      171.85        63.25        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-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-A195 TCGA-ER-A199 TCGA-ER-A19A 
      168.85        19.86       135.98        34.45         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       184.60       150.12        99.06 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A1A1 
       59.84        42.51       120.76        49.71        47.18        73.05 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES 
       22.36         4.70        16.87        10.19        28.67       173.29 
TCGA-ER-A3ET TCGA-ER-A42L TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A7UA 
       68.52        74.47       174.21         4.14        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-A1ZG TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZW 
       43.92         7.82        78.61       130.95       136.27        23.21 
TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 
        5.29         3.06        30.90        66.67       173.19        13.28 
TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 
       80.68        55.59        11.54        19.30         9.90         1.91 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A268 TCGA-GN-A4U3 TCGA-GN-A4U4 
       53.29       117.93        96.92        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-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        47.54        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 
       37.32        24.99        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 
            33.665             47.475 
[1] "0.3 - 312.1 (33.7)" "0.0 - 346.5 (47.5)"
[1] "hr=" "1.5"
D32V2, survival
                    sevent
clus2                  0   1
  18P GAIN MUTATED    29  26
  18P GAIN WILD-TYPE 137 166
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                55                303 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                26                166 
$`18P GAIN MUTATED`
TCGA-D3-A2JE TCGA-EE-A180 TCGA-EE-A29L TCGA-FR-A729 TCGA-WE-AAA3 TCGA-D3-A1Q5 
       27.65        94.98         2.60       220.80        21.40       112.57 
TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A2J9 TCGA-D3-A2JN TCGA-D3-A3CC TCGA-D3-A3CE 
       31.59        90.90        23.77        66.48        86.93        60.23 
TCGA-D3-A51E TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A8GP TCGA-D9-A6EA TCGA-D9-A6EC 
      174.84        32.94        22.62       152.75        25.18        77.56 
TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A95V TCGA-DA-A95X TCGA-EB-A5UL 
       36.03        20.38       222.51        72.10        73.94        29.29 
TCGA-EB-A6L9 TCGA-EE-A181 TCGA-EE-A29E TCGA-EE-A29P TCGA-EE-A2GB TCGA-EE-A2GH 
       36.46        33.73        63.78        56.42        59.28       220.24 
TCGA-EE-A2GM TCGA-EE-A2M5 TCGA-EE-A2MP TCGA-EE-A3J5 TCGA-ER-A197 TCGA-ER-A19W 
       75.48        21.67       248.65        36.95        13.94       148.18 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FS-A1YX TCGA-FS-A1Z0 TCGA-FS-A1ZC 
       46.98        33.21        92.98        48.59       202.65       357.37 
TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A4F2 TCGA-GF-A4EO 
       47.38        23.93        53.16        26.56        50.14        19.43 
TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A26D TCGA-HR-A2OG TCGA-WE-A8K6 TCGA-XV-AB01 
       64.44        32.48        48.00         0.23        17.95        13.25 
TCGA-YD-A9TA 
       49.18 

$`18P GAIN WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-D3-A8GI TCGA-EB-A5SG TCGA-EB-A5SH 
       62.07        46.32        13.87        58.52        68.25        54.02 
TCGA-EE-A184 TCGA-EE-A20H TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD 
       68.15       168.26       340.14       126.81       134.40        27.35 
TCGA-ER-A193 TCGA-ER-A198 TCGA-FS-A1ZF TCGA-FW-A3R5 TCGA-QB-AA9O TCGA-WE-A8K5 
       31.40        50.76        15.45        36.95        18.05        61.15 
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-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JO TCGA-D3-A2JP 
      113.52        42.08        12.10       171.58        66.08        59.57 
TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CF TCGA-D3-A3MO 
      130.72        58.06        46.98       166.52        24.53         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J 
      103.59        39.75        45.30        55.73        56.35       145.12 
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-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-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
       22.95        76.57       144.89       176.55        35.93       135.02 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
       88.87        53.92        65.92        40.60        68.09        33.93 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-DA-A95W TCGA-DA-A95Y TCGA-DA-A95Z 
       10.49       225.96        43.36        37.35        14.14        13.02 
TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EE-A17X 
       13.87        10.36        20.35        58.92         7.04        29.82 
TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B 
       27.22         8.65        14.70        26.89         4.96       133.81 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C 
      151.27        91.56        13.55        63.35        85.08        78.97 
TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29Q 
       13.97        72.07        64.64        56.84        18.61        66.74 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X 
       14.47        61.28       369.93        25.87       195.02        17.92 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GC 
       46.82       115.96        59.64        39.29        86.14        67.43 
TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN 
      173.79        48.72       107.38        54.74        79.66       102.12 
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-A2MS TCGA-EE-A2MT TCGA-EE-A2MU 
      167.90        47.54        43.23       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-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 
       53.19       201.80        51.35       134.33       152.81        35.44 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E 
        9.17        77.75        98.40        48.89        12.59        13.02 
TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
       26.37       302.07       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-A1A1 
       44.09       162.08        50.89        49.48         8.88       105.07 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH 
       43.82        23.34        20.15        28.83        48.99        41.56 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A44A TCGA-FR-A69P 
      247.04        93.01        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-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZM 
       48.85        53.52        46.45         9.70        32.75       101.26 
TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZW TCGA-FS-A1ZY 
       74.73       133.55        11.41       148.80        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-A3TU TCGA-FW-A3TV 
       26.73        54.41        80.68        17.46        55.59        13.51 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 
       19.30         9.90         2.04        15.78       139.89       117.93 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A268 TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 
       96.92        10.13        62.79       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-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8ZM 
       42.08       219.16       105.04        24.03        49.05       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 
             48.59              53.52 
[1] "0.2 - 357.4 (48.6)" "0.2 - 369.9 (53.5)"
[1] "hr=" "1.2"
D32V3, continuous
                    vv
clus                 I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  18P GAIN MUTATED          4       0       6        1        3        3
  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        30         12
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  18P GAIN MUTATED            7          7        3
  18P GAIN WILD-TYPE         28         47       18
D32V4, multiclass
            clus
vv           18P GAIN MUTATED 18P GAIN WILD-TYPE
  I/II NOS                  4                  9
  STAGE 0                   0                  7
  STAGE I                   6                 23
  STAGE IA                  1                 17
  STAGE IB                  3                 25
  STAGE II                  3                 23
  STAGE IIA                 0                 14
  STAGE IIB                 0                 19
  STAGE IIC                 7                  8
  STAGE III                 9                 30
  STAGE IIIA                3                 12
  STAGE IIIB                7                 28
  STAGE IIIC                7                 47
  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  6 19
  18P GAIN WILD-TYPE    56 61 75 48
D32V5, multiclass
       clus
vv      18P GAIN MUTATED 18P GAIN WILD-TYPE
  T0+T1                8                 56
  T2                  12                 61
  T3                   6                 75
  T4                  19                 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
  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    48   3
  18P GAIN WILD-TYPE 271  19
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED     48    3
  18P GAIN WILD-TYPE  271   19
   clus
vv  18P GAIN MUTATED 18P GAIN WILD-TYPE
  0               48                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  51
  18P GAIN WILD-TYPE  42 269
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      5   51
  18P GAIN WILD-TYPE   42  269
     clus
vv    18P GAIN MUTATED 18P GAIN WILD-TYPE
  NO                 5                 42
  YES               51                269
[1] 2 2
[1] FALSE
D32V10, continuous
D32V11, binary
                    cls
clus                   0   1
  18P GAIN MUTATED    26  30
  18P GAIN WILD-TYPE 112 199
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED     26   30
  18P GAIN WILD-TYPE  112  199
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  FEMALE               26                112
  MALE                 30                199
[1] 2 2
[1] FALSE
D32V12, binary
                    cls
clus                   0   1
  18P GAIN MUTATED    52   4
  18P GAIN WILD-TYPE 267  43
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED     52    4
  18P GAIN WILD-TYPE  267   43
     clus
vv    18P GAIN MUTATED 18P GAIN WILD-TYPE
  NO                52                267
  YES                4                 43
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18P GAIN MUTATED       1                         0    54
  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                                   54                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  54
  18P GAIN WILD-TYPE   6 298
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      1   54
  18P GAIN WILD-TYPE    6  298
                        clus
vv                       18P GAIN MUTATED 18P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO               54                298
[1] 2 2
[1] FALSE

Clustering(33) Variable = 18Q GAIN MUTATION ANALYSIS
D33V1, survival
                    sevent
clus2                  0   1
  18Q GAIN MUTATED    19  10
  18Q GAIN WILD-TYPE 109 114
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                29                223 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                10                114 
$`18Q GAIN MUTATED`
TCGA-D3-A2JE TCGA-EE-A180 TCGA-FR-A729 TCGA-WE-AAA3 TCGA-D3-A1Q5 TCGA-D3-A1QA 
        9.76        31.96       216.43         7.40       110.93        76.41 
TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3CC TCGA-D3-A51E TCGA-D3-A51K TCGA-D3-A8GP 
       64.83        43.53        40.01       173.85        31.76       135.12 
TCGA-DA-A1I1 TCGA-EE-A29P TCGA-EE-A2GB TCGA-EE-A2GH TCGA-EE-A2GM TCGA-EE-A2MP 
       68.68        27.16        26.14       201.60        18.35       227.01 
TCGA-ER-A197 TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FS-A1Z0 TCGA-FS-A1ZC TCGA-FS-A1ZT 
       10.49        32.05         4.50       195.98       312.07        35.28 
TCGA-FS-A1ZU TCGA-GF-A4EO TCGA-GN-A267 TCGA-GN-A26A TCGA-XV-AB01 
        4.47        18.25        17.06         7.59         6.61 

$`18Q GAIN WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A8GI TCGA-EB-A5SG TCGA-EE-A20H TCGA-EE-A2GD 
       62.07        38.76        13.41        33.24       166.75       269.03 
TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 TCGA-FW-A3R5 TCGA-WE-A8K5 
       52.90       134.40        27.35        19.04        36.95        52.73 
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-A2JG TCGA-D3-A2JH 
       62.86        15.75       168.00        86.30       107.61        36.30 
TCGA-D3-A2JL TCGA-D3-A2JO TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3CF 
      171.58        66.08        58.06       140.98        59.70        24.53 
TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51R 
        9.34        90.21        23.67        30.67       144.46        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-A8GR 
       23.61       179.97       120.00        69.53        70.62        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-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA 
       76.34       138.67       150.61       110.53        60.10        64.83 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-DA-A95V TCGA-DA-A95W 
       58.85        30.44       225.11         8.71        72.10         0.76 
TCGA-DA-A95X TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN 
       65.03        14.14        12.30         3.91        16.41        52.41 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
       18.21        13.15        24.89        20.38         0.00        26.24 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
       75.55        79.20        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        47.41        47.74        61.12       346.49       185.19 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GE TCGA-EE-A2GJ TCGA-EE-A2GK 
      115.43        30.02        77.98        12.95        68.65        10.62 
TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU 
       32.48        93.63         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-A2MS 
      171.85        63.25        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-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-A195 TCGA-ER-A199 TCGA-ER-A19A 
      168.85        19.86       135.98        34.45         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       184.60       150.12        99.06 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W 
       59.84        42.51       120.76        49.71        47.18       146.63 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
       73.05        22.36         4.70        16.87        10.19        28.67 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A42L TCGA-FR-A44A TCGA-FR-A69P 
      173.29        68.52        15.48        74.47       174.21         4.14 
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-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM 
       27.62        32.78        43.92         7.82        36.33        78.61 
TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 
      130.95       136.27        23.21         5.29         3.06        30.90 
TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV 
       66.67       173.19        13.28        80.68        55.59        11.54 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
       19.30         9.90         1.91        53.29       117.93        96.92 
TCGA-GN-A268 TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-GN-A8LK TCGA-GN-A9SD 
       42.48       120.53        34.49        46.92        43.23        59.41 
TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-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-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ 
       92.84        47.54        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        37.32        24.99        28.21 
TCGA-Z2-AA3S 
       91.23 

  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
              4.47               0.00 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
            312.07             346.49 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             32.05              47.54 
[1] "4.5 - 312.1 (32.0)" "0.0 - 346.5 (47.5)"
[1] "hr=" "1.8"
D33V2, survival
                    sevent
clus2                  0   1
  18Q GAIN MUTATED    25  18
  18Q GAIN WILD-TYPE 141 174
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                43                315 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                18                174 
$`18Q GAIN MUTATED`
TCGA-D3-A2JE TCGA-EE-A180 TCGA-EE-A29L TCGA-FR-A729 TCGA-WE-AAA3 TCGA-D3-A1Q5 
       27.65        94.98         2.60       220.80        21.40       112.57 
TCGA-D3-A1QA TCGA-D3-A2J9 TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3CC TCGA-D3-A51E 
       90.90        23.77        66.48        59.57        86.93       174.84 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A8GP TCGA-D9-A6EA TCGA-DA-A1HW TCGA-DA-A1I1 
       32.94        22.62       152.75        25.18        36.03       222.51 
TCGA-EB-A5UL TCGA-EE-A29P TCGA-EE-A2GB TCGA-EE-A2GH TCGA-EE-A2GM TCGA-EE-A2M5 
       29.29        56.42        59.28       220.24        75.48        21.67 
TCGA-EE-A2MP TCGA-EE-A3J5 TCGA-ER-A197 TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FS-A1YX 
      248.65        36.95        13.94        33.21        92.98        48.59 
TCGA-FS-A1Z0 TCGA-FS-A1ZC TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A4F2 TCGA-GF-A4EO 
      202.65       357.37        53.16        26.56        50.14        19.43 
TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A26D TCGA-HR-A2OG TCGA-WE-A8JZ TCGA-WE-A8K6 
       64.44        32.48        48.00         0.23        24.03        17.95 
TCGA-XV-AB01 
       13.25 

$`18Q GAIN WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-D3-A8GI TCGA-EB-A5SG TCGA-EB-A5SH 
       62.07        46.32        13.87        58.52        68.25        54.02 
TCGA-EE-A184 TCGA-EE-A20H TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD 
       68.15       168.26       340.14       126.81       134.40        27.35 
TCGA-ER-A193 TCGA-ER-A198 TCGA-FS-A1ZF TCGA-FW-A3R5 TCGA-QB-AA9O TCGA-WE-A8K5 
       31.40        50.76        15.45        36.95        18.05        61.15 
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-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JO 
       11.87       113.52        42.08        12.10       171.58        66.08 
TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3CF 
      130.72        58.06        46.98       166.52        60.23        24.53 
TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51F TCGA-D3-A51H 
        9.34       103.59        39.75        45.30        55.73        56.35 
TCGA-D3-A51J TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO 
      145.12        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-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-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I0 
        9.90        77.56        22.95        76.57       144.89        20.38 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA 
      176.55        35.93       135.02        88.87        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        43.36 
TCGA-DA-A95V TCGA-DA-A95W TCGA-DA-A95X TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q 
       72.10        37.35        73.94        14.14        13.02        13.87 
TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X 
       10.36        20.35        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-A185 
       27.22         8.65        33.73        14.70        26.89         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-A29M 
       78.97        13.97        63.78        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-A2GE TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
       86.14        67.43       173.79        48.72       107.38        54.74 
TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT 
       79.66       102.12        13.91        42.77        81.21        44.88 
TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD 
       94.82       129.27        28.83        19.76        61.51        47.28 
TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ 
      103.27       268.73       103.20        16.96       204.66        96.23 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MS 
      180.39       216.66       167.90        47.54        43.23       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-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JE TCGA-EE-A3JH 
       64.08        34.32        53.19       201.80        51.35       134.33 
TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C 
      152.81        35.44         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       302.07       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        44.09       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       105.07        43.82        23.34        20.15 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
       28.83        48.99        41.56       247.04        93.01        46.98 
TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A7U9 
       12.95       149.03       174.21        15.72        27.85        18.77 
TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YY 
       38.27        34.82        36.26       104.42       216.92       228.59 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZD 
       20.91        28.08         7.79        27.72        48.85        53.52 
TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM 
       46.45         9.70        32.75        47.38        23.93       101.26 
TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZW TCGA-FS-A1ZY 
       74.73       133.55        11.41       148.80        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-A3TU TCGA-FW-A3TV 
       26.73        54.41        80.68        17.46        55.59        13.51 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 
       19.30         9.90         2.04        15.78       139.89       117.93 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A268 TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 
       96.92        10.13        62.79       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-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8ZM TCGA-WE-A8ZN 
       42.08       219.16       105.04        49.05       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 
             48.59              53.26 
[1] "0.2 - 357.4 (48.6)" "0.2 - 369.9 (53.3)"
[1] "hr=" "1.4"
D33V3, continuous
                    vv
clus                 I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  18Q GAIN MUTATED          4       1       5        1        2        1
  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        32         13
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  18Q GAIN MUTATED            6          7        2
  18Q GAIN WILD-TYPE         29         47       19
D33V4, multiclass
            clus
vv           18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  I/II NOS                  4                  9
  STAGE 0                   1                  6
  STAGE I                   5                 24
  STAGE IA                  1                 17
  STAGE IB                  2                 26
  STAGE II                  1                 25
  STAGE IIA                 0                 14
  STAGE IIB                 0                 19
  STAGE IIC                 6                  9
  STAGE III                 7                 32
  STAGE IIIA                2                 13
  STAGE IIIB                6                 29
  STAGE IIIC                7                 47
  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  3 15
  18Q GAIN WILD-TYPE    56 63 78 52
D33V5, multiclass
       clus
vv      18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  T0+T1                8                 56
  T2                  10                 63
  T3                   3                 78
  T4                  15                 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
  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    41   2
  18Q GAIN WILD-TYPE 278  20
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED     41    2
  18Q GAIN WILD-TYPE  278   20
   clus
vv  18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  0               41                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  40
  18Q GAIN WILD-TYPE  42 280
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      5   40
  18Q GAIN WILD-TYPE   42  280
     clus
vv    18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  NO                 5                 42
  YES               40                280
[1] 2 2
[1] FALSE
D33V10, continuous
D33V11, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED    21  24
  18Q GAIN WILD-TYPE 117 205
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED     21   24
  18Q GAIN WILD-TYPE  117  205
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  FEMALE               21                117
  MALE                 24                205
[1] 2 2
[1] FALSE
D33V12, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED    42   3
  18Q GAIN WILD-TYPE 277  44
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED     42    3
  18Q GAIN WILD-TYPE  277   44
     clus
vv    18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  NO                42                277
  YES                3                 44
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18Q GAIN MUTATED       0                         0    43
  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                                   43                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  42
  18Q GAIN WILD-TYPE   6 310
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      1   42
  18Q GAIN WILD-TYPE    6  310
                        clus
vv                       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO               42                310
[1] 2 2
[1] FALSE

Clustering(34) Variable = 19P GAIN MUTATION ANALYSIS
D34V1, survival
                    sevent
clus2                  0   1
  19P GAIN MUTATED    22  22
  19P GAIN WILD-TYPE 106 102
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                44                208 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                22                102 
$`19P GAIN MUTATED`
TCGA-D3-A2JE TCGA-D3-A8GI TCGA-EE-A180 TCGA-EE-A2GO TCGA-FR-A729 TCGA-WE-AAA3 
        9.76        13.41        31.96        52.90       216.43         7.40 
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1QB TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JO 
      110.93        49.35        62.60        15.75        86.30        66.08 
TCGA-D3-A2JP TCGA-D3-A5GU TCGA-D9-A6EC TCGA-DA-A95V TCGA-DA-A95Z TCGA-EE-A17Y 
       43.53       124.08        69.21        72.10        12.30        24.89 
TCGA-EE-A29E TCGA-EE-A29P TCGA-EE-A2GH TCGA-EE-A2GS TCGA-EE-A2M6 TCGA-EE-A2M7 
        0.26        27.16       201.60        71.31       103.13        15.25 
TCGA-EE-A2MM TCGA-EE-A3JI TCGA-ER-A199 TCGA-ER-A2ND TCGA-ER-A2NG TCGA-ER-A3PL 
      145.45       135.98         7.82         4.70        28.67        32.05 
TCGA-FS-A1Z3 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZM TCGA-FS-A1ZS TCGA-FS-A1ZU 
        8.35       312.07        32.78        78.61       136.27         4.47 
TCGA-FS-A1ZY TCGA-GN-A267 TCGA-W3-AA21 TCGA-WE-A8ZQ TCGA-WE-A8ZY TCGA-WE-AA9Y 
        5.29        17.06        92.84        62.89        48.39         1.94 
TCGA-XV-AB01 TCGA-YG-AA3O 
        6.61        28.21 

$`19P GAIN WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A20H TCGA-EE-A2GD TCGA-EE-A2MR 
       62.07        38.76        33.24       166.75       269.03       134.40 
TCGA-EE-A3JD TCGA-ER-A193 TCGA-FW-A3R5 TCGA-WE-A8K5 TCGA-3N-A9WC TCGA-3N-A9WD 
       27.35        19.04        36.95        52.73        60.46        12.99 
TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       14.83         8.42        15.72        31.89       133.25        19.04 
TCGA-D3-A1QA TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JB TCGA-D3-A2JG 
       76.41        25.64        45.99        62.86       168.00       107.61 
TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CC 
       36.30       171.58        64.83        58.06       140.98        40.01 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E 
       59.70        24.53         9.34        90.21        23.67       173.85 
TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL 
       30.67       144.46        31.76        62.70        11.34        42.05 
TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GJ TCGA-D3-A8GK 
       45.70       177.86        78.21        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-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 
       16.90        18.44        22.85        76.34       138.67        68.68 
TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 
      150.61       110.53        60.10        64.83        58.85        30.44 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-DA-A95W TCGA-DA-A95X TCGA-DA-A95Y TCGA-EB-A44Q 
      225.11         8.71         0.76        65.03        14.14         3.91 
TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A182 
       16.41        52.41        18.21        13.15        20.38         0.00 
TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D 
       26.24        75.55        79.20        75.22        76.14        12.99 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W 
       44.28        47.41        47.74        61.12       346.49       185.19 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GJ 
      115.43        30.02        77.98        26.14        12.95        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        93.63         0.76         0.20 
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-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MT 
       63.25        89.26       104.78       227.01       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-A3JB 
        6.28        67.89       111.85        45.90         3.35       168.85 
TCGA-EE-A3JH TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C 
       19.86        34.45        10.49         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       184.60       150.12        99.06        59.84        42.51 
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        73.05        22.36 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A42L 
       16.87        10.19       173.29        68.52        15.48        74.47 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FR-A8YC 
        4.50       174.21         4.14        26.20         5.65        10.06 
TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1ZE TCGA-FS-A1ZG 
      171.78        49.74       195.98        27.62        43.92         7.82 
TCGA-FS-A1ZJ TCGA-FS-A1ZQ TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A1ZZ TCGA-FS-A4F0 
       36.33       130.95        35.28        23.21         3.06        30.90 
TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV 
       66.67       173.19        13.28        80.68        55.59        11.54 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 
       19.30         9.90        18.25         1.91        53.29       117.93 
TCGA-GN-A265 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 
       96.92        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-A825 TCGA-W3-A828 TCGA-W3-AA1Q TCGA-W3-AA1R 
        0.33       174.12         1.97       120.07        44.05        79.99 
TCGA-W3-AA1V TCGA-W3-AA1W TCGA-WE-A8K1 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO 
        8.09       185.13        47.54        65.42        12.69        21.90 
TCGA-WE-A8ZT TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-Z2-AA3S 
       10.95        37.32        24.99        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 
            38.155             47.050 
[1] "0.3 - 312.1 (38.2)" "0.0 - 346.5 (47.0)"
[1] "hr=" "1.1"
D34V2, survival
                    sevent
clus2                  0   1
  19P GAIN MUTATED    29  29
  19P GAIN WILD-TYPE 137 163
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                58                300 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                29                163 
$`19P GAIN MUTATED`
TCGA-D3-A2JE TCGA-D3-A8GI TCGA-EB-A5SH TCGA-EE-A180 TCGA-EE-A29L TCGA-EE-A2GO 
       27.65        58.52        54.02        94.98         2.60       126.81 
TCGA-FR-A729 TCGA-QB-AA9O TCGA-WE-AAA3 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1QB 
      220.80        18.05        21.40       112.57        71.80        95.74 
TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A5GU TCGA-D9-A6E9 
      115.53        86.76        66.08        59.57       125.19         9.90 
TCGA-D9-A6EC TCGA-DA-A95V TCGA-DA-A95Z TCGA-EE-A17Y TCGA-EE-A29E TCGA-EE-A29P 
       77.56        72.10        13.02        27.22        63.78        56.42 
TCGA-EE-A29R TCGA-EE-A2GH TCGA-EE-A2GS TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MM 
       14.47       220.24        81.21       129.27        28.83       167.90 
TCGA-EE-A3JI TCGA-ER-A199 TCGA-ER-A19E TCGA-ER-A2ND TCGA-ER-A2NG TCGA-ER-A3PL 
      152.81         9.17        13.02        23.34        48.99        33.21 
TCGA-FS-A1YX TCGA-FS-A1Z3 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZM TCGA-FS-A1ZS 
       48.59        20.91       357.37        53.52       101.26       148.80 
TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A4F2 TCGA-FS-A4F5 TCGA-FW-A3I3 TCGA-GF-A6C9 
       26.56        27.09        50.14        28.73        17.46        15.78 
TCGA-GN-A266 TCGA-GN-A267 TCGA-HR-A2OG TCGA-W3-AA21 TCGA-WE-A8ZQ TCGA-WE-A8ZX 
       10.13        64.44         0.23       105.04        63.22        35.80 
TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-XV-AB01 TCGA-YG-AA3O 
       49.51        12.16        13.25        37.94 

$`19P GAIN WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EB-A5SG TCGA-EE-A184 TCGA-EE-A20H 
       62.07        46.32        13.87        68.25        68.15       168.26 
TCGA-EE-A2GD TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 TCGA-ER-A198 TCGA-FS-A1ZF 
      340.14       134.40        27.35        31.40        50.76        15.45 
TCGA-FW-A3R5 TCGA-WE-A8K5 TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 
       36.95        61.15        17.03        66.48        12.99        14.93 
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 
       16.57        16.67       112.04       133.25        28.08        31.59 
TCGA-D3-A1QA TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JB 
       90.90        43.43       103.10        65.49        23.77       168.00 
TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       11.87       113.52        42.08        12.10       171.58        66.48 
TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE 
      130.72        58.06        46.98       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-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       26.89       125.79       135.75       137.92       178.32        18.18 
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-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-A6EG 
       18.12        15.39        22.29        18.44        25.18        22.95 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 
       76.57        36.03       144.89        20.38       222.51       176.55 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB 
       35.93       135.02        88.87        53.92        65.92        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        43.36        37.35 
TCGA-DA-A95X TCGA-DA-A95Y TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5UL 
       73.94        14.14        13.87        10.36        20.35        29.29 
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-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F 
       14.70        26.89         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-A29G 
       13.55        63.35        85.08        78.97        13.97        72.07 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29T 
       64.64        56.84        18.61        66.74        61.28       369.93 
TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
       25.87       195.02        17.92        46.82       115.96        59.64 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GI 
       39.29        86.14        59.28        67.43       173.79        48.72 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP 
      107.38        54.74        79.66        75.48       102.12        13.91 
TCGA-EE-A2GR TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M8 TCGA-EE-A2MC 
       42.77        44.88        94.82        21.67        19.76        61.51 
TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
       47.28       103.27       268.73       103.20        16.96       204.66 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ 
       96.23       180.39       216.66        47.54       248.65        43.23 
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-A3JE TCGA-EE-A3JH TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A19A TCGA-ER-A19B 
       51.35       134.33        35.44        13.94        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       302.07       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        44.09       162.08        50.89        49.48 
TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NF 
        8.88       148.18       105.07        43.82        20.15        28.83 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A42K TCGA-ER-A42L 
       41.56       247.04        93.01        46.98        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-A1YY TCGA-FS-A1Z0 
       34.82        36.26       104.42       216.92       228.59       202.65 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZE TCGA-FS-A1ZG 
       28.08         7.79        27.72        48.85        46.45         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-A1ZW TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 
       53.16        49.48        27.02        77.82        66.67       174.84 
TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV 
       34.03        26.73        54.41        80.68        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        19.43         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-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K6 
      111.09        42.08       219.16        24.03        49.05        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 
              0.23               0.20 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
            357.37             369.93 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
            51.830             52.255 
[1] "0.2 - 357.4 (51.8)" "0.2 - 369.9 (52.3)"
[1] "hr=" "1"  
D34V3, continuous
                    vv
clus                 I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  19P GAIN MUTATED          2       0       8        1        4        3
  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        33         11
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  19P GAIN MUTATED            4         11        4
  19P GAIN WILD-TYPE         31         43       17
D34V4, multiclass
            clus
vv           19P GAIN MUTATED 19P GAIN WILD-TYPE
  I/II NOS                  2                 11
  STAGE 0                   0                  7
  STAGE I                   8                 21
  STAGE IA                  1                 17
  STAGE IB                  4                 24
  STAGE II                  3                 23
  STAGE IIA                 3                 11
  STAGE IIB                 1                 18
  STAGE IIC                 4                 11
  STAGE III                 6                 33
  STAGE IIIA                4                 11
  STAGE IIIB                4                 31
  STAGE IIIC               11                 43
  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 13 11
  19P GAIN WILD-TYPE    56 60 68 56
D34V5, multiclass
       clus
vv      19P GAIN MUTATED 19P GAIN WILD-TYPE
  T0+T1                8                 56
  T2                  13                 60
  T3                  13                 68
  T4                  11                 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
  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    49   4
  19P GAIN WILD-TYPE 270  18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     49    4
  19P GAIN WILD-TYPE  270   18
   clus
vv  19P GAIN MUTATED 19P GAIN WILD-TYPE
  0               49                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  48
  19P GAIN WILD-TYPE  37 272
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     10   48
  19P GAIN WILD-TYPE   37  272
     clus
vv    19P GAIN MUTATED 19P GAIN WILD-TYPE
  NO                10                 37
  YES               48                272
[1] 2 2
[1] FALSE
D34V10, continuous
D34V11, binary
                    cls
clus                   0   1
  19P GAIN MUTATED    26  32
  19P GAIN WILD-TYPE 112 197
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     26   32
  19P GAIN WILD-TYPE  112  197
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  FEMALE               26                112
  MALE                 32                197
[1] 2 2
[1] FALSE
D34V12, binary
                    cls
clus                   0   1
  19P GAIN MUTATED    53   5
  19P GAIN WILD-TYPE 266  42
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     53    5
  19P GAIN WILD-TYPE  266   42
     clus
vv    19P GAIN MUTATED 19P GAIN WILD-TYPE
  NO                53                266
  YES                5                 42
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  19P GAIN MUTATED       1                         0    54
  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                                   54                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  55
  19P GAIN WILD-TYPE   6 297
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      1   55
  19P GAIN WILD-TYPE    6  297
                        clus
vv                       19P GAIN MUTATED 19P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO               55                297
[1] 2 2
[1] FALSE

Clustering(35) Variable = 19Q GAIN MUTATION ANALYSIS
D35V1, survival
                    sevent
clus2                  0   1
  19Q GAIN MUTATED    18  25
  19Q GAIN WILD-TYPE 110  99
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                43                209 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                25                 99 
$`19Q GAIN MUTATED`
TCGA-D3-A2JE TCGA-D3-A8GI TCGA-EE-A180 TCGA-EE-A2GD TCGA-WE-AAA3 TCGA-D3-A1Q1 
        9.76        13.41        31.96       269.03         7.40         8.42 
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JO TCGA-D3-A2JP 
      110.93        49.35        15.75        86.30        66.08        43.53 
TCGA-D3-A3CE TCGA-D9-A6EC TCGA-DA-A95V TCGA-DA-A95Z TCGA-EE-A17Y TCGA-EE-A29E 
       59.70        69.21        72.10        12.30        24.89         0.26 
TCGA-EE-A29P TCGA-EE-A29T TCGA-EE-A2GH TCGA-EE-A2GS TCGA-EE-A2M6 TCGA-EE-A2M7 
       27.16       346.49       201.60        71.31       103.13        15.25 
TCGA-EE-A3JI TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A2NG TCGA-ER-A3ET TCGA-ER-A3PL 
      135.98        10.49         7.82        28.67        68.52        32.05 
TCGA-FS-A1Z3 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS 
        8.35       312.07        32.78        78.61       130.95       136.27 
TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-GN-A267 TCGA-WE-A8ZQ TCGA-WE-A8ZY TCGA-WE-AA9Y 
        4.47         5.29        17.06        62.89        48.39         1.94 
TCGA-YG-AA3O 
       28.21 

$`19Q GAIN WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A20H TCGA-EE-A2GO TCGA-EE-A2MR 
       62.07        38.76        33.24       166.75        52.90       134.40 
TCGA-EE-A3JD TCGA-ER-A193 TCGA-FR-A729 TCGA-FW-A3R5 TCGA-WE-A8K5 TCGA-3N-A9WC 
       27.35        19.04       216.43        36.95        52.73        60.46 
TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       12.99        14.83        15.72        31.89       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-A2JH TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A3C6 TCGA-D3-A3CB 
      107.61        36.30       171.58        64.83        58.06       140.98 
TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E 
       40.01        24.53         9.34        90.21        23.67       173.85 
TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL 
       30.67       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-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC 
       68.68       150.61       110.53        60.10        64.83        58.85 
TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-DA-A95W TCGA-DA-A95X TCGA-DA-A95Y 
       30.44       225.11         8.71         0.76        65.03        14.14 
TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A181 
        3.91        16.41        52.41        18.21        13.15        20.38 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29C 
        0.00        26.24        75.55        79.20        75.22        76.14 
TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29Q TCGA-EE-A29W 
       12.99        44.28        47.41        47.74        61.12       185.19 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GJ 
      115.43        30.02        77.98        26.14        12.95        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        93.63         0.76         0.20 
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-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MS 
       63.25        89.26       104.78       145.45       227.01       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-ER-A195 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C 
      168.85        19.86        34.45         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       184.60       150.12        99.06        59.84        42.51 
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        73.05        22.36 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A3ES TCGA-ER-A3EV TCGA-ER-A42L 
        4.70        16.87        10.19       173.29        15.48        74.47 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FR-A8YC 
        4.50       174.21         4.14        26.20         5.65        10.06 
TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1ZE TCGA-FS-A1ZG 
      171.78        49.74       195.98        27.62        43.92         7.82 
TCGA-FS-A1ZJ TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 
       36.33        35.28        23.21         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        18.25         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-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO 
      185.13        92.84        47.54        65.42        12.69        21.90 
TCGA-WE-A8ZT TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-XV-AB01 TCGA-Z2-AA3S 
       10.95        37.32        24.99         6.61        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 
             32.78              47.18 
[1] "0.3 - 346.5 (32.8)" "0.0 - 297.0 (47.2)"
[1] "hr=" "1.1"
D35V2, survival
                    sevent
clus2                  0   1
  19Q GAIN MUTATED    25  31
  19Q GAIN WILD-TYPE 141 161
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                56                302 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                31                161 
$`19Q GAIN MUTATED`
TCGA-D3-A2JE TCGA-D3-A8GI TCGA-EB-A5SH TCGA-EE-A180 TCGA-EE-A29L TCGA-EE-A2GD 
       27.65        58.52        54.02        94.98         2.60       340.14 
TCGA-QB-AA9O TCGA-WE-AAA3 TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A2JA 
       18.05        21.40        16.57       112.57        71.80       115.53 
TCGA-D3-A2JC TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3CE TCGA-D9-A6E9 TCGA-D9-A6EC 
       86.76        66.08        59.57        60.23         9.90        77.56 
TCGA-DA-A95V TCGA-DA-A95Z TCGA-EE-A17Y TCGA-EE-A29E TCGA-EE-A29P TCGA-EE-A29R 
       72.10        13.02        27.22        63.78        56.42        14.47 
TCGA-EE-A29T TCGA-EE-A2GH TCGA-EE-A2GS TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A3JI 
      369.93       220.24        81.21       129.27        28.83       152.81 
TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19E TCGA-ER-A2NG TCGA-ER-A3ET TCGA-ER-A3PL 
       13.94         9.17        13.02        48.99        93.01        33.21 
TCGA-FS-A1YX TCGA-FS-A1Z3 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZM TCGA-FS-A1ZQ 
       48.59        20.91       357.37        53.52       101.26       133.55 
TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A4F5 TCGA-FW-A3I3 TCGA-GF-A6C9 
      148.80        26.56        27.09        28.73        17.46        15.78 
TCGA-GN-A266 TCGA-GN-A267 TCGA-HR-A2OG TCGA-WE-A8ZQ TCGA-WE-A8ZX TCGA-WE-A8ZY 
       10.13        64.44         0.23        63.22        35.80        49.51 
TCGA-WE-AA9Y TCGA-YG-AA3O 
       12.16        37.94 

$`19Q GAIN WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EB-A5SG TCGA-EE-A184 TCGA-EE-A20H 
       62.07        46.32        13.87        68.25        68.15       168.26 
TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 TCGA-ER-A198 TCGA-FR-A729 
      126.81       134.40        27.35        31.40        50.76       220.80 
TCGA-FS-A1ZF TCGA-FW-A3R5 TCGA-WE-A8K5 TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD 
       15.45        36.95        61.15        17.03        66.48        12.99 
TCGA-BF-AAP0 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 
       14.93        16.67       112.04       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-A2JB TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL 
      168.00        11.87       113.52        42.08        12.10       171.58 
TCGA-D3-A2JN TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CC 
       66.48       130.72        58.06        46.98       166.52        86.93 
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-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       222.51 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA 
      176.55        35.93       135.02        88.87        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        43.36 
TCGA-DA-A95W TCGA-DA-A95X TCGA-DA-A95Y TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH 
       37.35        73.94        14.14        13.87        10.36        20.35 
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-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-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D 
       91.56        13.55        63.35        85.08        78.97        13.97 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29S 
       72.07        64.64        56.84        18.61        66.74        61.28 
TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
       25.87       195.02        17.92        46.82       115.96        59.64 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GI 
       39.29        86.14        59.28        67.43       173.79        48.72 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP 
      107.38        54.74        79.66        75.48       102.12        13.91 
TCGA-EE-A2GR TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M8 TCGA-EE-A2MC 
       42.77        44.88        94.82        21.67        19.76        61.51 
TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
       47.28       103.27       268.73       103.20        16.96       204.66 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP 
       96.23       180.39       216.66       167.90        47.54       248.65 
TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB 
       43.23       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-A3JE TCGA-EE-A3JH TCGA-ER-A195 TCGA-ER-A19A TCGA-ER-A19B 
      201.80        51.35       134.33        35.44        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       302.07       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        44.09       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       105.07        43.82        23.34        20.15 
TCGA-ER-A2NF TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3EV TCGA-ER-A42K TCGA-ER-A42L 
       28.83        41.56       247.04        46.98        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-A1YY TCGA-FS-A1Z0 
       34.82        36.26       104.42       216.92       228.59       202.65 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZE TCGA-FS-A1ZG 
       28.08         7.79        27.72        48.85        46.45         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-A1ZW TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F8 
       49.48        27.02        77.82        50.14        66.67       174.84 
TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV 
       34.03        26.73        54.41        80.68        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        19.43         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-A8JZ TCGA-WE-A8K1 
      111.09        42.08       219.16       105.04        24.03        49.05 
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-XV-AB01 TCGA-YD-A89C TCGA-YD-A9TA TCGA-YG-AA3P TCGA-Z2-A8RT 
       24.99        13.25         6.90        49.18        14.43        27.58 
TCGA-Z2-AA3S TCGA-Z2-AA3V 
       96.99        15.98 

  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
              0.23               0.20 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
            369.93             368.78 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
            51.515             52.255 
[1] "0.2 - 369.9 (51.5)" "0.2 - 368.8 (52.3)"
[1] "hr=" "1.1"
D35V3, continuous
                    vv
clus                 I/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       25
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  19Q GAIN MUTATED           3         2         3         6          5
  19Q GAIN WILD-TYPE        11        17        12        33         10
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  19Q GAIN MUTATED            5         11        4
  19Q GAIN WILD-TYPE         30         43       17
D35V4, multiclass
            clus
vv           19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  I/II NOS                  3                 10
  STAGE 0                   0                  7
  STAGE I                   5                 24
  STAGE IA                  1                 17
  STAGE IB                  3                 25
  STAGE II                  1                 25
  STAGE IIA                 3                 11
  STAGE IIB                 2                 17
  STAGE IIC                 3                 12
  STAGE III                 6                 33
  STAGE IIIA                5                 10
  STAGE IIIB                5                 30
  STAGE IIIC               11                 43
  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 12
  19Q GAIN WILD-TYPE    58 62 69 55
D35V5, multiclass
       clus
vv      19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  T0+T1                6                 58
  T2                  11                 62
  T3                  12                 69
  T4                  12                 55
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  19Q GAIN MUTATED    26  12   3   9
  19Q GAIN WILD-TYPE 151  53  36  36
D35V6, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  N0               26                151
  N1               12                 53
  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    47   4
  19Q GAIN WILD-TYPE 272  18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     47    4
  19Q GAIN WILD-TYPE  272   18
   clus
vv  19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  0               47                272
  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  37 274
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     10   46
  19Q GAIN WILD-TYPE   37  274
     clus
vv    19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  NO                10                 37
  YES               46                274
[1] 2 2
[1] FALSE
D35V10, continuous
D35V11, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED    25  31
  19Q GAIN WILD-TYPE 113 198
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     25   31
  19Q GAIN WILD-TYPE  113  198
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  FEMALE               25                113
  MALE                 31                198
[1] 2 2
[1] FALSE
D35V12, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED    48   8
  19Q GAIN WILD-TYPE 271  39
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     48    8
  19Q GAIN WILD-TYPE  271   39
     clus
vv    19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  NO                48                271
  YES                8                 39
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  19Q GAIN MUTATED       1                         0    52
  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                                   52                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  53
  19Q GAIN WILD-TYPE   6 299
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      1   53
  19Q GAIN WILD-TYPE    6  299
                        clus
vv                       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO               53                299
[1] 2 2
[1] FALSE

Clustering(36) Variable = 20P GAIN MUTATION ANALYSIS
D36V1, survival
                    sevent
clus2                 0  1
  20P GAIN MUTATED   50 52
  20P GAIN WILD-TYPE 78 72
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               102                150 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                52                 72 
$`20P GAIN MUTATED`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A8GI TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GO 
        9.76        62.07        13.41        31.96       166.75        52.90 
TCGA-FR-A729 TCGA-WE-AAA3 TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q5 
      216.43         7.40        12.99        14.83         8.42       110.93 
TCGA-D3-A2JA TCGA-D3-A2JH TCGA-D3-A2JN TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CE 
       15.75        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        60.10       225.11        72.10        12.30 
TCGA-EB-A6L9 TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A29D TCGA-EE-A29T TCGA-EE-A29W 
       18.21        24.89        20.38        12.99       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-A2GP TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 
       93.63         0.76        81.99       103.13        15.25         5.75 
TCGA-EE-A2MP TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AE TCGA-EE-A3J3 
      227.01        53.26       124.31       122.73        54.51        67.89 
TCGA-EE-A3J7 TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A199 TCGA-ER-A19B 
       45.90       168.85        19.86       135.98         7.82        53.29 
TCGA-ER-A19G TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19P TCGA-ER-A2NC TCGA-ER-A2ND 
      184.60        99.06        59.84       120.76        22.36         4.70 
TCGA-ER-A3EV TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1Z0 TCGA-FS-A1Z4 
       15.48         4.50       174.21         4.14       195.98        27.62 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ 
      312.07        32.78         7.82        36.33        78.61       130.95 
TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A4F8 TCGA-FS-A4FD TCGA-GN-A264 
      136.27         4.47         5.29       173.19        80.68       117.93 
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-W3-A825 TCGA-W3-AA21 TCGA-WE-A8ZQ TCGA-WE-A8ZY TCGA-XV-AB01 
        7.23         1.97        92.84        62.89        48.39         6.61 

$`20P GAIN WILD-TYPE`
TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A2GD TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 
       38.76        33.24       269.03       134.40        27.35        19.04 
TCGA-FW-A3R5 TCGA-WE-A8K5 TCGA-3N-A9WC TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q6 
       36.95        52.73        60.46        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-A2JB TCGA-D3-A2JC TCGA-D3-A2JG TCGA-D3-A2JL TCGA-D3-A2JO 
       62.86       168.00        86.30       107.61       171.58        66.08 
TCGA-D3-A2JP TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MU TCGA-D3-A51E 
       43.53        40.01        24.53         9.34        23.67       173.85 
TCGA-D3-A51F TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL 
       30.67        11.34        42.05       179.97       120.00        69.53 
TCGA-D3-A8GR TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A4Z6 TCGA-D9-A6EG TCGA-DA-A1HV 
       36.53        10.78        15.02        18.44        22.85        76.34 
TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I5 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 
      138.67        68.68       110.53        64.83        58.85        30.44 
TCGA-DA-A3F8 TCGA-DA-A95W TCGA-DA-A95X TCGA-DA-A95Y TCGA-EB-A44Q TCGA-EB-A5KH 
        8.71         0.76        65.03        14.14         3.91        16.41 
TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A20F 
       52.41        13.15         0.00        26.24        75.55        79.20 
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        47.41        47.74 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A2A2 TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
       27.16        61.12        30.02        68.65        10.62        32.48 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI 
        0.20        71.31        23.77       209.79        94.19       171.85 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MS TCGA-EE-A2MT 
       63.25        89.26       104.78       145.45       143.93        23.51 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3J4 TCGA-EE-A3J8 TCGA-ER-A195 
       64.04         4.41         6.28       111.85         3.35        34.45 
TCGA-ER-A197 TCGA-ER-A19A TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19H TCGA-ER-A19N 
       10.49         4.54        39.81        11.47       150.12        42.51 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NE TCGA-ER-A2NF 
       49.71        47.18       146.63        73.05        16.87        10.19 
TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A7U8 
       28.67       173.29        68.52        32.05        74.47        26.20 
TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1ZE 
        5.65        10.06       171.78        49.74         8.35        43.92 
TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F9 
       35.28        23.21         3.06        30.90        66.67        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        18.25         1.91 
TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-LH-A9QB 
       53.29        96.92       120.53        34.49        46.92        85.05 
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-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO 
        8.09       185.13        47.54        65.42        12.69        21.90 
TCGA-WE-A8ZT TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-Z2-AA3S 
       10.95         1.94        37.32        24.99        28.21        91.23 

  20P GAIN MUTATED 20P GAIN WILD-TYPE 
              0.76               0.00 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
            346.49             269.03 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
            58.735             42.280 
[1] "0.8 - 346.5 (58.7)" "0.0 - 269.0 (42.3)"
[1] "hr=" "1.3"
D36V2, survival
                    sevent
clus2                  0   1
  20P GAIN MUTATED    64  77
  20P GAIN WILD-TYPE 102 115
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               141                217 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                77                115 
$`20P GAIN MUTATED`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A8GI TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GO 
       27.65        62.07        58.52        94.98       168.26       126.81 
TCGA-FR-A729 TCGA-WE-AAA3 TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q5 
      220.80        21.40        12.99        14.93        16.57       112.57 
TCGA-D3-A1Q9 TCGA-D3-A2JA TCGA-D3-A2JD TCGA-D3-A2JH TCGA-D3-A2JN TCGA-D3-A3C6 
       31.59       115.53        11.87        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-A5GO TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D3-A8GC 
       63.81       135.75       137.92       178.32       125.19        79.59 
TCGA-D3-A8GD TCGA-D3-A8GM TCGA-D3-A8GP TCGA-D9-A1JX TCGA-D9-A3Z3 TCGA-D9-A6E9 
       23.61       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        88.87 
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-A181 TCGA-EE-A20B TCGA-EE-A29A TCGA-EE-A29D TCGA-EE-A29R TCGA-EE-A29T 
       33.73       133.81        63.35        13.97        14.47       369.93 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
      195.02        17.92       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-A2GP 
      173.79       220.24        48.72        75.48       102.12        13.91 
TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MH 
       94.82        21.67       129.27        28.83        19.76        16.96 
TCGA-EE-A2MP TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AE TCGA-EE-A3J3 
      248.65        53.26       124.31       122.73        54.51       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-A199 TCGA-ER-A19B TCGA-ER-A19G TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
        9.17        98.40       302.07         6.44       131.51        61.05 
TCGA-ER-A19P TCGA-ER-A19T TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A3EV TCGA-ER-A42K 
      162.08         8.88        43.82        23.34        46.98        12.95 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A8YD TCGA-FS-A1YX TCGA-FS-A1Z0 
       92.98       174.21        15.72        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        17.46 
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-XV-AB01 TCGA-YD-A9TA 
       49.51        13.25        49.18 

$`20P GAIN WILD-TYPE`
TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A184 TCGA-EE-A29L 
       46.32        13.87        68.25        54.02        68.15         2.60 
TCGA-EE-A2GD TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 TCGA-ER-A198 TCGA-FS-A1ZF 
      340.14       134.40        27.35        31.40        50.76        15.45 
TCGA-FW-A3R5 TCGA-QB-AA9O TCGA-WE-A8K5 TCGA-3N-A9WB TCGA-3N-A9WC TCGA-D3-A1Q3 
       36.95        18.05        61.15        17.03        66.48        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-A2J9 TCGA-D3-A2JB TCGA-D3-A2JC 
       43.43       103.10        65.49        23.77       168.00        86.76 
TCGA-D3-A2JG TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ 
      113.52        12.10       171.58        66.08        59.57       130.72 
TCGA-D3-A3C7 TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MU TCGA-D3-A51E 
       46.98        86.93        24.53         9.34        39.75       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-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       222.51        35.93       135.02        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        43.36        37.35 
TCGA-DA-A95X TCGA-DA-A95Y TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5UN 
       73.94        14.14        13.87        10.36        20.35        58.92 
TCGA-EB-A5VV TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 
        7.04        29.82         8.65        14.70        26.89         4.96 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E 
      151.27        91.56        13.55        85.08        78.97        63.78 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
       72.07        64.64        56.84        18.61        56.42        66.74 
TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A2A0 TCGA-EE-A2A2 TCGA-EE-A2GC TCGA-EE-A2GJ 
       61.28        25.87        46.82        59.64        67.43       107.38 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2MC 
       54.74        79.66        42.77        81.21        44.88        61.51 
TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ 
       47.28       103.27       268.73       103.20       204.66        96.23 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MS 
      180.39       216.66       167.90        47.54        43.23       162.48 
TCGA-EE-A2MT TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH 
       71.21        64.04        28.77        13.81        41.59       138.81 
TCGA-EE-A3J4 TCGA-EE-A3J8 TCGA-EE-A3JE TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A19A 
      127.20        34.32        51.35        35.44        13.94        77.75 
TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19H TCGA-ER-A19N 
       48.89        12.59        13.02        26.37       152.35        44.09 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NE TCGA-ER-A2NF 
       50.89        49.48       148.18       105.07        20.15        28.83 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3PL TCGA-ER-A42L 
       48.99        41.56       247.04        93.01        33.21       149.03 
TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YE TCGA-FS-A1YW 
       27.85        18.77        38.27        34.82       104.42       216.92 
TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1ZB TCGA-FS-A1ZE TCGA-FS-A1ZH TCGA-FS-A1ZP 
      228.59        20.91        48.85        46.45        32.75        74.73 
TCGA-FS-A1ZR TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 
       11.41        53.16        49.48        27.02        77.82        66.67 
TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
       34.03        26.73        54.41        55.59        13.51        19.30 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A266 
        9.90        19.43         2.04       139.89        96.92        10.13 
TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A8LL TCGA-HR-A2OG 
      121.91        39.35        10.42        48.89        21.37         0.23 
TCGA-LH-A9QB TCGA-RP-A690 TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A828 
      368.78         0.20         0.33         0.69       228.16       121.08 
TCGA-W3-AA1O TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1V TCGA-W3-AA1W TCGA-WE-A8K1 
        4.01        69.07       111.09        42.08       219.16        49.05 
TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-AA9Y TCGA-WE-AAA0 
      101.33        58.98        70.52        11.80        12.16        40.41 
TCGA-WE-AAA4 TCGA-YD-A89C TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S 
       24.99         6.90        37.94        14.43        27.58        96.99 
TCGA-Z2-AA3V 
       15.98 

  20P GAIN MUTATED 20P GAIN WILD-TYPE 
              6.44               0.20 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
            369.93             368.78 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
             58.06              49.48 
[1] "6.4 - 369.9 (58.1)" "0.2 - 368.8 (49.5)"
[1] "hr=" "1.1"
D36V3, continuous
                    vv
clus                 I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  20P GAIN MUTATED          8       2      17        9       14        9
  20P GAIN WILD-TYPE        5       5      12        9       14       17
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  20P GAIN MUTATED           5         3         6        17          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         20         35       15
D36V4, multiclass
            clus
vv           20P GAIN MUTATED 20P GAIN WILD-TYPE
  I/II NOS                  8                  5
  STAGE 0                   2                  5
  STAGE I                  17                 12
  STAGE IA                  9                  9
  STAGE IB                 14                 14
  STAGE II                  9                 17
  STAGE IIA                 5                  9
  STAGE IIB                 3                 16
  STAGE IIC                 6                  9
  STAGE III                17                 22
  STAGE IIIA                7                  8
  STAGE IIIB               15                 20
  STAGE IIIC               19                 35
  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      30 35 23 30
  20P GAIN WILD-TYPE    34 38 58 37
D36V5, multiclass
       clus
vv      20P GAIN MUTATED 20P GAIN WILD-TYPE
  T0+T1               30                 34
  T2                  35                 38
  T3                  23                 58
  T4                  30                 37
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  20P GAIN MUTATED    77  28  13  16
  20P GAIN WILD-TYPE 100  37  26  29
D36V6, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  N0               77                100
  N1               28                 37
  N2               13                 26
  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 187  16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED    132    6
  20P GAIN WILD-TYPE  187   16
   clus
vv  20P GAIN MUTATED 20P GAIN WILD-TYPE
  0              132                187
  1                6                 16
[1] 2 2
[1] FALSE
D36V8, binary
                    cls
clus                  0  1
  20P GAIN MUTATED   57 32
  20P GAIN WILD-TYPE 77 58
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     57   32
  20P GAIN WILD-TYPE   77   58
     clus
vv    20P GAIN MUTATED 20P GAIN WILD-TYPE
  NO                57                 77
  YES               32                 58
[1] 2 2
[1] FALSE
D36V9, binary
                    cls
clus                   0   1
  20P GAIN MUTATED    15 132
  20P GAIN WILD-TYPE  32 188
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     15  132
  20P GAIN WILD-TYPE   32  188
     clus
vv    20P GAIN MUTATED 20P GAIN WILD-TYPE
  NO                15                 32
  YES              132                188
[1] 2 2
[1] FALSE
D36V10, continuous
D36V11, binary
                    cls
clus                   0   1
  20P GAIN MUTATED    57  90
  20P GAIN WILD-TYPE  81 139
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     57   90
  20P GAIN WILD-TYPE   81  139
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  FEMALE               57                 81
  MALE                 90                139
[1] 2 2
[1] FALSE
D36V12, binary
                    cls
clus                   0   1
  20P GAIN MUTATED   129  18
  20P GAIN WILD-TYPE 190  29
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED    129   18
  20P GAIN WILD-TYPE  190   29
     clus
vv    20P GAIN MUTATED 20P GAIN WILD-TYPE
  NO               129                190
  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   211
D36V13, multiclass
                           clus
vv                          20P GAIN MUTATED 20P GAIN WILD-TYPE
  ASIAN                                    2                  3
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                  142                211
[1] 3 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   5 211
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      2  141
  20P GAIN WILD-TYPE    5  211
                        clus
vv                       20P GAIN MUTATED 20P GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  5
  NOT HISPANIC OR LATINO              141                211
[1] 2 2
[1] FALSE

Clustering(37) Variable = 20Q GAIN MUTATION ANALYSIS
D37V1, survival
                    sevent
clus2                 0  1
  20Q GAIN MUTATED   64 62
  20Q GAIN WILD-TYPE 64 62
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               126                126 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                62                 62 
$`20Q GAIN MUTATED`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A8GI TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GO 
        9.76        62.07        13.41        31.96       166.75        52.90 
TCGA-FR-A729 TCGA-WE-AAA3 TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q5 
      216.43         7.40        12.99        14.83         8.42       110.93 
TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JP 
       15.75        86.30        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        60.10        64.83       225.11        72.10 
TCGA-DA-A95Z TCGA-EB-A6L9 TCGA-EE-A17Y TCGA-EE-A183 TCGA-EE-A29D TCGA-EE-A29E 
       12.30        18.21        24.89        26.24        12.99         0.26 
TCGA-EE-A29P TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A6 TCGA-EE-A2GB 
       27.16       346.49       185.19       115.43        77.98        26.14 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GU 
       12.95       201.60        18.35        93.63         0.76        81.99 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MG TCGA-EE-A2MP TCGA-EE-A2MS 
      103.13        15.25         5.75        94.19       227.01       143.93 
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-A3J3 TCGA-EE-A3J7 TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A197 
       67.89        45.90       168.85        19.86       135.98        10.49 
TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19G TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19P 
        7.82        53.29       184.60        99.06        59.84       120.76 
TCGA-ER-A19Q TCGA-ER-A19W TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NG TCGA-ER-A3EV 
       49.71       146.63        22.36         4.70        28.67        15.48 
TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1Z0 TCGA-FS-A1Z4 
       32.05         4.50       174.21         4.14       195.98        27.62 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ 
      312.07        32.78         7.82        36.33        78.61       130.95 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A4F8 TCGA-FS-A4FD 
      136.27        35.28         4.47         5.29       173.19        80.68 
TCGA-GF-A4EO TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
       18.25       117.93        96.92        17.06        42.48         7.59 
TCGA-GN-A8LK TCGA-GN-A9SD TCGA-OD-A75X TCGA-QB-A6FS TCGA-W3-A825 TCGA-W3-AA1R 
       43.23        59.41       297.01         7.23         1.97        79.99 
TCGA-W3-AA21 TCGA-WE-A8ZM TCGA-WE-A8ZQ TCGA-WE-A8ZY TCGA-XV-AB01 TCGA-YG-AA3O 
       92.84        65.42        62.89        48.39         6.61        28.21 

$`20Q GAIN WILD-TYPE`
TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A2GD TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 
       38.76        33.24       269.03       134.40        27.35        19.04 
TCGA-FW-A3R5 TCGA-WE-A8K5 TCGA-3N-A9WC TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q6 
       36.95        52.73        60.46        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-A2JB TCGA-D3-A2JG TCGA-D3-A2JO TCGA-D3-A3CC TCGA-D3-A3CF 
       62.86       168.00       107.61        66.08        40.01        24.53 
TCGA-D3-A3MO TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A8GJ 
        9.34       173.85        30.67        11.34        42.05       179.97 
TCGA-D3-A8GK TCGA-D3-A8GR TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A4Z6 TCGA-D9-A6EG 
      120.00        36.53        10.78        15.02        18.44        22.85 
TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I5 TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F8 
      138.67        68.68       110.53        58.85        30.44         8.71 
TCGA-DA-A95W TCGA-DA-A95X TCGA-DA-A95Y TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN 
        0.76        65.03        14.14         3.91        16.41        52.41 
TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29B 
       13.15        20.38         0.00        75.55        79.20        75.22 
TCGA-EE-A29C TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29Q TCGA-EE-A2A2 
       76.14        44.28        47.41        47.74        61.12        30.02 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2MC 
       68.65        10.62        32.48         0.20        71.31        23.77 
TCGA-EE-A2MF TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM 
      209.79       171.85        63.25        89.26       104.78       145.45 
TCGA-EE-A2MT TCGA-EE-A3AF TCGA-EE-A3J4 TCGA-EE-A3J8 TCGA-ER-A195 TCGA-ER-A19A 
       23.51         6.28       111.85         3.35        34.45         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        42.51        47.18        73.05 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A42L TCGA-FR-A7U8 
       16.87        10.19       173.29        68.52        74.47        26.20 
TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1ZE 
        5.65        10.06       171.78        49.74         8.35        43.92 
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-A8ZN 
      120.07        44.05         8.09       185.13        47.54        12.69 
TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-Z2-AA3S 
       21.90        10.95         1.94        37.32        24.99        91.23 

  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
              0.26               0.00 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
            346.49             269.03 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
            58.735             39.910 
[1] "0.3 - 346.5 (58.7)" "0.0 - 269.0 (39.9)"
[1] "hr=" "1.3"
D37V2, survival
                    sevent
clus2                 0  1
  20Q GAIN MUTATED   80 94
  20Q GAIN WILD-TYPE 86 98
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               174                184 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                94                 98 
$`20Q GAIN MUTATED`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A8GI TCGA-EB-A5SH TCGA-EE-A180 TCGA-EE-A184 
       27.65        62.07        58.52        54.02        94.98        68.15 
TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GO TCGA-FR-A729 TCGA-QB-AA9O TCGA-WE-AAA3 
      168.26         2.60       126.81       220.80        18.05        21.40 
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-A2JH TCGA-D3-A2JL TCGA-D3-A2JN 
      115.53        86.76        11.87        42.08       171.58        66.48 
TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3MR TCGA-D3-A3MU 
       59.57        58.06       166.52        60.23       103.59        39.75 
TCGA-D3-A3MV TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A5GO 
       45.30       145.12        32.94        63.81       135.75       137.92 
TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GL TCGA-D3-A8GM 
      178.32       125.19        79.59        23.61        89.13       107.15 
TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D9-A148 TCGA-D9-A1JX TCGA-D9-A3Z3 TCGA-D9-A6E9 
      152.75        29.06       151.53         7.10        22.29         9.90 
TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I2 
       25.18        77.56        76.57        36.03        20.38       176.55 
TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A3F5 TCGA-DA-A95V TCGA-DA-A95Z TCGA-EB-A5UL 
       88.87        65.92       225.96        72.10        13.02        29.29 
TCGA-EB-A6L9 TCGA-EE-A17Y TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A29A TCGA-EE-A29D 
       36.46        27.22        26.89       133.81        63.35        13.97 
TCGA-EE-A29E TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A29X 
       63.78        56.42        14.47       369.93       195.02        17.92 
TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH 
      115.96        39.29        86.14        59.28       173.79       220.24 
TCGA-EE-A2GI TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GU TCGA-EE-A2M5 
       48.72        75.48       102.12        13.91        94.82        21.67 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MP 
      129.27        28.83        19.76       103.20        16.96       248.65 
TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
      162.48        53.26       124.31       122.73        64.04        28.77 
TCGA-EE-A3AE TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3JA 
       54.51        41.59       172.18        36.95        64.08        53.19 
TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19B 
      201.80       134.33       152.81        13.94         9.17        98.40 
TCGA-ER-A19G TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19P TCGA-ER-A19Q 
      302.07         6.44       131.51        61.05       162.08        50.89 
TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NG TCGA-ER-A3EV 
        8.88       148.18        43.82        23.34        48.99        46.98 
TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A8YD 
       33.21        12.95        92.98       174.21        15.72        36.26 
TCGA-FS-A1YX TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZC 
       48.59       202.65        28.08         7.79        27.72       357.37 
TCGA-FS-A1ZD TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZQ 
       53.52         9.70        47.38        23.93       101.26       133.55 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A4F2 TCGA-FS-A4F5 
      148.80        53.16        26.56        27.09        50.14        28.73 
TCGA-FS-A4F8 TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-GF-A4EO TCGA-GF-A6C9 TCGA-GN-A264 
      174.84        80.68        17.46        19.43        15.78       117.93 
TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U9 
       96.92        64.44        62.79        32.48        48.00        22.13 
TCGA-GN-A8LK TCGA-GN-A8LL TCGA-GN-A9SD TCGA-HR-A2OH TCGA-OD-A75X TCGA-QB-A6FS 
       50.10        21.37        59.41        65.88       297.90         7.23 
TCGA-W3-A825 TCGA-W3-AA1R TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K6 TCGA-WE-A8ZM 
       63.02       111.09       105.04        24.03        17.95       101.33 
TCGA-WE-A8ZQ TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-XV-AB01 TCGA-YD-A9TA TCGA-YG-AA3O 
       63.22        35.80        49.51        13.25        49.18        37.94 

$`20Q GAIN WILD-TYPE`
TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EB-A5SG TCGA-EE-A2GD TCGA-EE-A2MR TCGA-EE-A3JD 
       46.32        13.87        68.25       340.14       134.40        27.35 
TCGA-ER-A193 TCGA-ER-A198 TCGA-FS-A1ZF TCGA-FW-A3R5 TCGA-WE-A8K5 TCGA-3N-A9WC 
       31.40        50.76        15.45        36.95        61.15        66.48 
TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA 
       16.67       112.04        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-A2JG TCGA-D3-A2JK TCGA-D3-A2JO TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3CC 
      113.52        12.10        66.08       130.72        46.98        86.93 
TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51N 
       24.53         9.34       174.84        55.73        56.35        22.62 
TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GS TCGA-D3-A8GB TCGA-D3-A8GE TCGA-D3-A8GJ 
       26.89       125.79        18.18        30.84        26.43       241.38 
TCGA-D3-A8GK TCGA-D3-A8GN TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D3-A8GV TCGA-D9-A149 
      170.20       161.00       129.63       117.17       167.70        54.67 
TCGA-D9-A1JW TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A4Z6 TCGA-D9-A6EG TCGA-DA-A1HY 
        3.65        18.12        15.39        18.44        22.95       144.89 
TCGA-DA-A1I1 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A1IB TCGA-DA-A1IC 
      222.51        35.93       135.02        53.92        40.60        68.09 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-DA-A95W TCGA-DA-A95X TCGA-DA-A95Y 
       33.93        10.49        43.36        37.35        73.94        14.14 
TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EE-A17X 
       13.87        10.36        20.35        58.92         7.04        29.82 
TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A20F 
        8.65        33.73        14.70         4.96       151.27        91.56 
TCGA-EE-A20I TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M 
       13.55        85.08        78.97        72.07        64.64        56.84 
TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A2A0 TCGA-EE-A2A2 
       18.61        66.74        61.28        25.87        46.82        59.64 
TCGA-EE-A2GC TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GR TCGA-EE-A2GS 
       67.43       107.38        54.74        79.66        42.77        81.21 
TCGA-EE-A2GT TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MI 
       44.88        61.51        47.28       103.27       268.73       204.66 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MQ 
       96.23       180.39       216.66       167.90        47.54        43.23 
TCGA-EE-A2MT TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J8 TCGA-EE-A3JE 
       71.21        13.81       138.81       127.20        34.32        51.35 
TCGA-ER-A195 TCGA-ER-A19A TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F 
       35.44        77.75        48.89        12.59        13.02        26.37 
TCGA-ER-A19H TCGA-ER-A19N TCGA-ER-A19S TCGA-ER-A1A1 TCGA-ER-A2NE TCGA-ER-A2NF 
      152.35        44.09        49.48       105.07        20.15        28.83 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A42L TCGA-FR-A7U8 TCGA-FR-A7U9 
       41.56       247.04        93.01       149.03        27.85        18.77 
TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z3 
       38.27        34.82       104.42       216.92       228.59        20.91 
TCGA-FS-A1ZB TCGA-FS-A1ZE TCGA-FS-A1ZH TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZW 
       48.85        46.45        32.75        74.73        11.41        49.48 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC 
       27.02        77.82        66.67        34.03        26.73        54.41 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GN-A262 
       55.59        13.51        19.30         9.90         2.04       139.89 
TCGA-GN-A266 TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-HR-A2OG 
       10.13       121.91        39.35        10.42        48.89         0.23 
TCGA-LH-A9QB TCGA-RP-A690 TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A828 
      368.78         0.20         0.33         0.69       228.16       121.08 
TCGA-W3-AA1O TCGA-W3-AA1Q TCGA-W3-AA1V TCGA-W3-AA1W TCGA-WE-A8K1 TCGA-WE-A8ZN 
        4.01        69.07        42.08       219.16        49.05        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 
               2.6                0.2 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
            369.93             368.78 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
             57.24              48.87 
[1] "2.6 - 369.9 (57.2)" "0.2 - 368.8 (48.9)"
[1] "hr=" "1.1"
D37V3, continuous
                    vv
clus                 I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  20Q GAIN MUTATED          9       3      18       10       15       11
  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        16          7
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  20Q GAIN MUTATED           21         24        7
  20Q GAIN WILD-TYPE         14         30       14
D37V4, multiclass
            clus
vv           20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  I/II NOS                  9                  4
  STAGE 0                   3                  4
  STAGE I                  18                 11
  STAGE IA                 10                  8
  STAGE IB                 15                 13
  STAGE II                 11                 15
  STAGE IIA                 5                  9
  STAGE IIB                 3                 16
  STAGE IIC                 8                  7
  STAGE III                23                 16
  STAGE IIIA                8                  7
  STAGE IIIB               21                 14
  STAGE IIIC               24                 30
  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 29 35
  20Q GAIN WILD-TYPE    26 33 52 32
D37V5, multiclass
       clus
vv      20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  T0+T1               38                 26
  T2                  40                 33
  T3                  29                 52
  T4                  35                 32
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  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   160   8
  20Q GAIN WILD-TYPE 159  14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED    160    8
  20Q GAIN WILD-TYPE  159   14
   clus
vv  20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  0              160                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    24 156
  20Q GAIN WILD-TYPE  23 164
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     24  156
  20Q GAIN WILD-TYPE   23  164
     clus
vv    20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  NO                24                 23
  YES              156                164
[1] 2 2
[1] FALSE
D37V10, continuous
D37V11, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED    68 112
  20Q GAIN WILD-TYPE  70 117
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     68  112
  20Q GAIN WILD-TYPE   70  117
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  FEMALE               68                 70
  MALE                112                117
[1] 2 2
[1] FALSE
D37V12, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED   159  21
  20Q GAIN WILD-TYPE 160  26
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED    159   21
  20Q GAIN WILD-TYPE  160   26
     clus
vv    20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  NO               159                160
  YES               21                 26
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  20Q GAIN MUTATED       2                         0   174
  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                                  174                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     3 173
  20Q GAIN WILD-TYPE   4 179
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      3  173
  20Q GAIN WILD-TYPE    4  179
                        clus
vv                       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                  4
  NOT HISPANIC OR LATINO              173                179
[1] 2 2
[1] FALSE

Clustering(38) Variable = 21Q GAIN MUTATION ANALYSIS
D38V1, survival
                    sevent
clus2                  0   1
  21Q GAIN MUTATED    27  21
  21Q GAIN WILD-TYPE 101 103
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                48                204 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                21                103 
$`21Q GAIN MUTATED`
TCGA-D3-A2JF TCGA-D3-A8GI TCGA-EE-A20H TCGA-FR-A729 TCGA-WE-AAA3 TCGA-D3-A1Q3 
       62.07        13.41       166.75       216.43         7.40        15.72 
TCGA-D3-A2J7 TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3MR 
       45.99        43.53        58.06       140.98        40.01        90.21 
TCGA-D3-A5GN TCGA-D3-A5GU TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GM TCGA-D9-A6EC 
       45.70       124.08        78.21        23.61        70.62        69.21 
TCGA-EB-A6L9 TCGA-EE-A29D TCGA-EE-A2A1 TCGA-EE-A2GH TCGA-EE-A2GM TCGA-EE-A2GN 
       18.21        12.99       115.43       201.60        18.35        93.63 
TCGA-EE-A2MP TCGA-EE-A3AA TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-ER-A19B TCGA-ER-A19D 
      227.01       124.31        67.89        45.90        53.29        11.47 
TCGA-ER-A19L TCGA-ER-A19P TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3PL TCGA-FR-A3YN 
       99.06       120.76        10.19        28.67        32.05         4.50 
TCGA-FR-A44A TCGA-FR-A7U8 TCGA-FS-A1Z4 TCGA-FS-A1ZD TCGA-FS-A1ZJ TCGA-FS-A1ZS 
      174.21        26.20        27.62        32.78        36.33       136.27 
TCGA-GF-A4EO TCGA-GN-A8LK TCGA-W3-A825 TCGA-W3-AA1W TCGA-WE-A8ZM TCGA-XV-AB01 
       18.25        43.23         1.97       185.13        65.42         6.61 

$`21Q GAIN WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A2GD TCGA-EE-A2GO 
        9.76        38.76        33.24        31.96       269.03        52.90 
TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 TCGA-FW-A3R5 TCGA-WE-A8K5 TCGA-3N-A9WC 
      134.40        27.35        19.04        36.95        52.73        60.46 
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-A2J8 
      133.25        19.04        76.41        62.60        25.64        62.86 
TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL 
       15.75       168.00        86.30       107.61        36.30       171.58 
TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MU 
       64.83        66.08        59.70        24.53         9.34        23.67 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T 
      173.85        30.67       144.46        31.76        62.70        11.34 
TCGA-D3-A5GL TCGA-D3-A5GR TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GP 
       42.05       177.86       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        68.68       150.61       110.53        60.10 
TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-DA-A95V 
       64.83        58.85        30.44       225.11         8.71        72.10 
TCGA-DA-A95W TCGA-DA-A95X TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5KH 
        0.76        65.03        14.14        12.30         3.91        16.41 
TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
       52.41        13.15        24.89        20.38         0.00        26.24 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G 
       75.55        79.20        75.22        76.14         0.26        44.28 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W 
       47.41        47.74        27.16        61.12       346.49       185.19 
TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GJ TCGA-EE-A2GK 
       30.02        77.98        26.14        12.95        68.65        10.62 
TCGA-EE-A2GL TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 
       32.48         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-A2MS TCGA-EE-A2MT 
       63.25        89.26       104.78       145.45       143.93        23.51 
TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
       53.26       122.73        64.04         4.41        54.51         6.28 
TCGA-EE-A3J4 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 
      111.85         3.35       168.85        19.86       135.98        34.45 
TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19C TCGA-ER-A19G TCGA-ER-A19H 
       10.49         7.82         4.54        39.81       184.60       150.12 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 
       59.84        42.51        49.71        47.18       146.63        73.05 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
       22.36         4.70        16.87       173.29        68.52        15.48 
TCGA-ER-A42L TCGA-FR-A69P TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FS-A1YW TCGA-FS-A1YY 
       74.47         4.14         5.65        10.06       171.78        49.74 
TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1ZC TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZM 
      195.98         8.35       312.07        43.92         7.82        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-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-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-AA1R TCGA-W3-AA1V 
        0.33       174.12       120.07        44.05        79.99         8.09 
TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT 
       92.84        47.54        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        37.32        24.99        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 
            45.945             47.050 
[1] "2.0 - 227.0 (45.9)" "0.0 - 346.5 (47.0)"
[1] "hr=" "1.3"
D38V2, survival
                    sevent
clus2                  0   1
  21Q GAIN MUTATED    32  31
  21Q GAIN WILD-TYPE 134 161
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                63                295 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                31                161 
$`21Q GAIN MUTATED`
TCGA-D3-A2JF TCGA-D3-A8GI TCGA-EE-A184 TCGA-EE-A20H TCGA-EE-A29L TCGA-FR-A729 
       62.07        58.52        68.15       168.26         2.60       220.80 
TCGA-WE-AAA3 TCGA-D3-A1Q3 TCGA-D3-A1Q9 TCGA-D3-A2J7 TCGA-D3-A2JP TCGA-D3-A3C6 
       21.40        16.67        31.59       103.10        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-A8GM TCGA-D9-A6EC TCGA-EB-A6L9 TCGA-EE-A29A 
       79.59        23.61       107.15        77.56        36.46        63.35 
TCGA-EE-A29D TCGA-EE-A29R TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-EE-A2GH 
       13.97        14.47        46.82       115.96        39.29       220.24 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A3AA TCGA-EE-A3J3 
       75.48       102.12       248.65        43.23       124.31       172.18 
TCGA-EE-A3J7 TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19L TCGA-ER-A19P TCGA-ER-A2NF 
       64.08        98.40        12.59       131.51       162.08        28.83 
TCGA-ER-A2NG TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A7U8 
       48.99        33.21        12.95        92.98       174.21        27.85 
TCGA-FS-A1Z4 TCGA-FS-A1ZD TCGA-FS-A1ZJ TCGA-FS-A1ZS TCGA-FS-A4F2 TCGA-FW-A3I3 
       28.08        53.52        47.38       148.80        50.14        17.46 
TCGA-GF-A4EO TCGA-GN-A26D TCGA-GN-A8LK TCGA-W3-A825 TCGA-W3-AA1W TCGA-WE-A8K6 
       19.43        48.00        50.10        63.02       219.16        17.95 
TCGA-WE-A8ZM TCGA-WE-A8ZX TCGA-XV-AB01 
      101.33        35.80        13.25 

$`21Q GAIN WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A180 
       27.65        46.32        13.87        68.25        54.02        94.98 
TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 TCGA-ER-A198 
      340.14       126.81       134.40        27.35        31.40        50.76 
TCGA-FS-A1ZF TCGA-FW-A3R5 TCGA-QB-AA9O TCGA-WE-A8K5 TCGA-3N-A9WB TCGA-3N-A9WC 
       15.45        36.95        18.05        61.15        17.03        66.48 
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-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-A2JC TCGA-D3-A2JD TCGA-D3-A2JG 
       23.77       115.53       168.00        86.76        11.87       113.52 
TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A3BZ 
       42.08        12.10       171.58        66.48        66.08       130.72 
TCGA-D3-A3C7 TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MU TCGA-D3-A51E 
       46.98        60.23        24.53         9.34        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-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-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-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       222.51       176.55        35.93       135.02        88.87 
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-A95X TCGA-DA-A95Y 
      225.96        43.36        72.10        37.35        73.94        14.14 
TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5UL TCGA-EB-A5UN 
       13.02        13.87        10.36        20.35        29.29        58.92 
TCGA-EB-A5VV TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 
        7.04        29.82        27.22         8.65        33.73        14.70 
TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I 
       26.89         4.96       133.81       151.27        91.56        13.55 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M 
       85.08        78.97        63.78        72.07        64.64        56.84 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V 
       18.61        56.42        66.74        61.28       369.93        25.87 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC 
      195.02        17.92        59.64        86.14        59.28        67.43 
TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GP 
      173.79        48.72       107.38        54.74        79.66        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-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB 
      167.90        47.54       162.48        71.21        53.26       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-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JE 
      127.20        36.95        34.32        53.19       201.80        51.35 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A 
      134.33       152.81        35.44        13.94         9.17        77.75 
TCGA-ER-A19C TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J 
       48.89        13.02        26.37       302.07       152.35         6.44 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W 
       61.05        44.09        50.89        49.48         8.88       148.18 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NH TCGA-ER-A3ES 
      105.07        43.82        23.34        20.15        41.56       247.04 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A42L TCGA-FR-A69P TCGA-FR-A7U9 TCGA-FR-A7UA 
       93.01        46.98       149.03        15.72        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-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC 
      202.65        20.91         7.79        27.72        48.85       357.37 
TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP 
       46.45         9.70        32.75        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-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
       26.73        54.41        80.68        55.59        13.51        19.30 
TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        9.90         2.04        15.78       139.89       117.93        96.92 
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-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-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-A828 TCGA-W3-AA1O TCGA-W3-AA1Q TCGA-W3-AA1R 
        0.69       228.16       121.08         4.01        69.07       111.09 
TCGA-W3-AA1V TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8ZN TCGA-WE-A8ZO 
       42.08       105.04        24.03        49.05        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-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 

  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
               2.6                0.2 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
            248.65             369.93 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
             59.57              49.51 
[1] "2.6 - 248.7 (59.6)" "0.2 - 369.9 (49.5)"
[1] "hr=" "1.2"
D38V3, continuous
                    vv
clus                 I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  21Q GAIN MUTATED          4       0       9        2        9        4
  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        37         12
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  21Q GAIN MUTATED            6         13        2
  21Q GAIN WILD-TYPE         29         41       19
D38V4, multiclass
            clus
vv           21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  I/II NOS                  4                  9
  STAGE 0                   0                  7
  STAGE I                   9                 20
  STAGE IA                  2                 16
  STAGE IB                  9                 19
  STAGE II                  4                 22
  STAGE IIA                 3                 11
  STAGE IIB                 1                 18
  STAGE IIC                 5                 10
  STAGE III                 2                 37
  STAGE IIIA                3                 12
  STAGE IIIB                6                 29
  STAGE IIIC               13                 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 15 10
  21Q GAIN WILD-TYPE    53 54 66 57
D38V5, multiclass
       clus
vv      21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  T0+T1               11                 53
  T2                  19                 54
  T3                  15                 66
  T4                  10                 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   9   5  10
  21Q GAIN WILD-TYPE 138  56  34  35
D38V6, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  N0               39                138
  N1                9                 56
  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 258  20
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED     61    2
  21Q GAIN WILD-TYPE  258   20
   clus
vv  21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  0               61                258
  1                2                 20
[1] 2 2
[1] FALSE
D38V8, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED    20  22
  21Q GAIN WILD-TYPE 114  68
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED     20   22
  21Q GAIN WILD-TYPE  114   68
     clus
vv    21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  NO                20                114
  YES               22                 68
[1] 2 2
[1] FALSE
D38V9, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED     8  59
  21Q GAIN WILD-TYPE  39 261
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      8   59
  21Q GAIN WILD-TYPE   39  261
     clus
vv    21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  NO                 8                 39
  YES               59                261
[1] 2 2
[1] FALSE
D38V10, continuous
D38V11, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED    27  40
  21Q GAIN WILD-TYPE 111 189
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED     27   40
  21Q GAIN WILD-TYPE  111  189
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  FEMALE               27                111
  MALE                 40                189
[1] 2 2
[1] FALSE
D38V12, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED    58   9
  21Q GAIN WILD-TYPE 261  38
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED     58    9
  21Q GAIN WILD-TYPE  261   38
     clus
vv    21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  NO                58                261
  YES                9                 38
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  21Q GAIN MUTATED       1                         0    66
  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                                   66                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  65
  21Q GAIN WILD-TYPE   6 287
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      1   65
  21Q GAIN WILD-TYPE    6  287
                        clus
vv                       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO               65                287
[1] 2 2
[1] FALSE

Clustering(39) Variable = 22Q GAIN MUTATION ANALYSIS
D39V1, survival
                    sevent
clus2                 0  1
  22Q GAIN MUTATED   45 45
  22Q GAIN WILD-TYPE 83 79
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                90                162 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                45                 79 
$`22Q GAIN MUTATED`
TCGA-D3-A2JE TCGA-D3-A8GI TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GO 
        9.76        13.41        33.24        31.96       166.75        52.90 
TCGA-EE-A2MR TCGA-EE-A3JD TCGA-FR-A729 TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-3N-A9WD 
      134.40        27.35       216.43        52.73         7.40        12.99 
TCGA-D3-A1Q1 TCGA-D3-A2J7 TCGA-D3-A2JA TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 
        8.42        45.99        15.75        66.08        43.53        58.06 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3MO TCGA-D3-A3MU TCGA-D3-A5GN TCGA-D3-A5GR 
       40.01        59.70         9.34        23.67        45.70       177.86 
TCGA-D3-A8GC TCGA-D3-A8GM TCGA-D9-A3Z1 TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1I1 
       78.21        70.62        15.02        69.21        76.34        68.68 
TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A3F5 TCGA-DA-A95V TCGA-DA-A95Z TCGA-EB-A5KH 
       60.10        64.83       225.11        72.10        12.30        16.41 
TCGA-EB-A6L9 TCGA-EE-A17Y TCGA-EE-A29M TCGA-EE-A29Q TCGA-EE-A29W TCGA-EE-A2GB 
       18.21        24.89        47.74        61.12       185.19        26.14 
TCGA-EE-A2GH TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MJ 
      201.60        18.35        93.63       103.13        15.25        63.25 
TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE 
      143.93        53.26       124.31       122.73         4.41        54.51 
TCGA-EE-A3J7 TCGA-EE-A3JB TCGA-ER-A19C TCGA-ER-A19G TCGA-ER-A19L TCGA-ER-A19M 
       45.90       168.85        39.81       184.60        99.06        59.84 
TCGA-ER-A19W TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ET TCGA-FR-A3YN TCGA-FR-A44A 
      146.63        10.19        28.67        68.52         4.50       174.21 
TCGA-FR-A69P TCGA-FR-A7UA TCGA-FS-A1YY TCGA-FS-A1ZD TCGA-FS-A1ZM TCGA-FS-A1ZQ 
        4.14         5.65        49.74        32.78        78.61       130.95 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A4FD TCGA-FW-A3TU 
      136.27        35.28         4.47        23.21        80.68        55.59 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A8LK 
      117.93        96.92        17.06        42.48         7.59        43.23 
TCGA-QB-A6FS TCGA-W3-AA1R TCGA-WE-A8ZM TCGA-WE-A8ZY TCGA-XV-AB01 TCGA-YG-AA3O 
        7.23        79.99        65.42        48.39         6.61        28.21 

$`22Q GAIN WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EE-A2GD TCGA-ER-A193 TCGA-FW-A3R5 TCGA-3N-A9WC 
       62.07        38.76       269.03        19.04        36.95        60.46 
TCGA-BF-AAP0 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       14.83        15.72        31.89       110.93        49.35       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J8 TCGA-D3-A2JB 
       19.04        76.41        62.60        25.64        62.86       168.00 
TCGA-D3-A2JC TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A3CB 
       86.30       107.61        36.30       171.58        64.83       140.98 
TCGA-D3-A3CF TCGA-D3-A3MR TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K 
       24.53        90.21       173.85        30.67       144.46        31.76 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GU TCGA-D3-A8GD TCGA-D3-A8GJ 
       62.70        11.34        42.05       124.08        23.61       179.97 
TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GP TCGA-D3-A8GR TCGA-D9-A1X3 TCGA-D9-A3Z3 
      120.00        69.53       135.12        36.53        10.78        16.90 
TCGA-D9-A4Z6 TCGA-D9-A6EG TCGA-DA-A1HY TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1IC 
       18.44        22.85       138.67       150.61       110.53        58.85 
TCGA-DA-A3F2 TCGA-DA-A3F8 TCGA-DA-A95W TCGA-DA-A95X TCGA-DA-A95Y TCGA-EB-A44Q 
       30.44         8.71         0.76        65.03        14.14         3.91 
TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20C 
       52.41        13.15        20.38         0.00        26.24        75.55 
TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G 
       79.20        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 
       47.41        27.16       346.49       115.43        30.02        77.98 
TCGA-EE-A2GE TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GP TCGA-EE-A2GR 
       12.95        68.65        10.62        32.48         0.76         0.20 
TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MG 
       71.31        81.99         5.75        23.77       209.79        94.19 
TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MT 
      171.85        89.26       104.78       145.45       227.01        23.51 
TCGA-EE-A3AC TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J8 TCGA-EE-A3JH 
       64.04         6.28        67.89       111.85         3.35        19.86 
TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B 
      135.98        34.45        10.49         7.82         4.54        53.29 
TCGA-ER-A19D TCGA-ER-A19H TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S 
       11.47       150.12        42.51       120.76        49.71        47.18 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A3ES TCGA-ER-A3EV 
       73.05        22.36         4.70        16.87       173.29        15.48 
TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A7U8 TCGA-FR-A8YC TCGA-FS-A1YW TCGA-FS-A1Z0 
       32.05        74.47        26.20        10.06       171.78       195.98 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ 
        8.35        27.62       312.07        43.92         7.82        36.33 
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-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 
       11.54        19.30         9.90        18.25         1.91        53.29 
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-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-A8ZN TCGA-WE-A8ZO 
        8.09       185.13        92.84        47.54        12.69        21.90 
TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-Z2-AA3S 
       62.89        10.95         1.94        37.32        24.99        91.23 

  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
              4.14               0.00 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
            225.11             346.49 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
            51.235             43.215 
[1] "4.1 - 225.1 (51.2)" "0.0 - 346.5 (43.2)"
[1] "hr=" "1"  
D39V2, survival
                    sevent
clus2                  0   1
  22Q GAIN MUTATED    56  66
  22Q GAIN WILD-TYPE 110 126
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
               122                236 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                66                126 
$`22Q GAIN MUTATED`
TCGA-D3-A2JE TCGA-D3-A8GI TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A180 TCGA-EE-A20H 
       27.65        58.52        68.25        54.02        94.98       168.26 
TCGA-EE-A29L TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-FR-A729 TCGA-WE-A8K5 
        2.60       126.81       134.40        27.35       220.80        61.15 
TCGA-WE-AAA3 TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q9 TCGA-D3-A2J7 TCGA-D3-A2JA 
       21.40        12.99        16.57        31.59       103.10       115.53 
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-A8GM TCGA-D3-A8GQ TCGA-D9-A148 TCGA-D9-A3Z1 TCGA-D9-A6E9 TCGA-D9-A6EA 
      107.15        29.06       151.53        15.39         9.90        25.18 
TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I7 
       77.56        76.57        36.03        20.38       222.51        88.87 
TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A3F5 TCGA-DA-A95V TCGA-DA-A95Z 
       53.92        65.92        40.60       225.96        72.10        13.02 
TCGA-EB-A5KH TCGA-EB-A5UL TCGA-EB-A6L9 TCGA-EE-A17Y TCGA-EE-A29M TCGA-EE-A29N 
       20.35        29.29        36.46        27.22        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-A2M6 TCGA-EE-A2M7 
      220.24        48.72        75.48       102.12       129.27        28.83 
TCGA-EE-A2MJ TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB 
       96.23        43.23       162.48        53.26       124.31       122.73 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AG TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3JB 
       28.77        54.51        41.59        36.95        64.08       201.80 
TCGA-ER-A19C TCGA-ER-A19G TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19W TCGA-ER-A2NF 
       48.89       302.07       131.51        61.05       148.18        28.83 
TCGA-ER-A2NG TCGA-ER-A3ET TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A7UA 
       48.99        93.01        92.98       174.21        15.72        38.27 
TCGA-FS-A1YY TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZD TCGA-FS-A1ZH TCGA-FS-A1ZM 
      228.59         7.79        27.72        53.52        32.75       101.26 
TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A4F2 
      133.55       148.80        53.16        26.56        49.48        50.14 
TCGA-FS-A4F5 TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-GN-A264 TCGA-GN-A265 
       28.73        80.68        17.46        55.59       117.93        96.92 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U7 TCGA-GN-A8LK 
       64.44        62.79        32.48        48.00        10.42        50.10 
TCGA-HR-A2OH TCGA-QB-A6FS TCGA-W3-AA1R TCGA-WE-A8ZM TCGA-WE-A8ZY TCGA-XV-AB01 
       65.88         7.23       111.09       101.33        49.51        13.25 
TCGA-YD-A89C TCGA-YG-AA3O 
        6.90        37.94 

$`22Q GAIN WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EE-A184 TCGA-EE-A2GD TCGA-ER-A193 
       62.07        46.32        13.87        68.15       340.14        31.40 
TCGA-ER-A198 TCGA-FS-A1ZF TCGA-FW-A3R5 TCGA-QB-AA9O TCGA-3N-A9WB TCGA-3N-A9WC 
       50.76        15.45        36.95        18.05        17.03        66.48 
TCGA-BF-AAP0 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       14.93        16.67       112.04       112.57        71.80       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-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK 
      168.00        86.76        11.87       113.52        42.08        12.10 
TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CF 
      171.58        66.48       130.72        46.98       166.52        24.53 
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-A5GO TCGA-D3-A5GU 
       22.62        63.81        26.89       125.79       137.92       125.19 
TCGA-D3-A8GB TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL 
       30.84        23.61        26.43       241.38       170.20        89.13 
TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D3-A8GV TCGA-D9-A149 
      161.00       152.75       129.63       117.17       167.70        54.67 
TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A1X3 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6EG 
        3.65         7.10        18.12        22.29        18.44        22.95 
TCGA-DA-A1HY TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1IC TCGA-DA-A3F2 
      144.89       176.55        35.93       135.02        68.09        33.93 
TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-DA-A95W TCGA-DA-A95X TCGA-DA-A95Y TCGA-EB-A44Q 
       10.49        43.36        37.35        73.94        14.14        13.87 
TCGA-EB-A44R TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 
       10.36        58.92         7.04        29.82         8.65        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-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-A2GE 
       46.82       115.96        59.64        86.14        67.43       173.79 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
      107.38        54.74        79.66        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-A2MK 
      103.27       268.73       103.20        16.96       204.66       180.39 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MT TCGA-EE-A3AC 
      216.66       167.90        47.54       248.65        71.21        64.04 
TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J8 TCGA-EE-A3JA 
       13.81       138.81       172.18       127.20        34.32        53.19 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 
       51.35       134.33       152.81        35.44        13.94         9.17 
TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19H 
       77.75        98.40        12.59        13.02        26.37       152.35 
TCGA-ER-A19J TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T 
        6.44        44.09       162.08        50.89        49.48         8.88 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NH TCGA-ER-A3ES 
      105.07        43.82        23.34        20.15        41.56       247.04 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A7U8 TCGA-FR-A7U9 
       46.98        33.21        12.95       149.03        27.85        18.77 
TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1Z0 
       34.82        36.26       104.42       216.92        48.59       202.65 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZE TCGA-FS-A1ZG 
       20.91        28.08        48.85       357.37        46.45         9.70 
TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZY TCGA-FS-A1ZZ 
       47.38        23.93        74.73        11.41        27.09        27.02 
TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC 
       77.82        66.67       174.84        34.03        26.73        54.41 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 
       13.51        19.30         9.90        19.43         2.04        15.78 
TCGA-GN-A262 TCGA-GN-A266 TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-GN-A4U9 
      139.89        10.13       121.91        39.35        48.89        22.13 
TCGA-GN-A8LL TCGA-GN-A9SD TCGA-HR-A2OG TCGA-LH-A9QB TCGA-OD-A75X TCGA-RP-A690 
       21.37        59.41         0.23       368.78       297.90         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-A8JZ TCGA-WE-A8K1 
       69.07        42.08       219.16       105.04        24.03        49.05 
TCGA-WE-A8K6 TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX 
       17.95        58.98        70.52        63.22        11.80        35.80 
TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-YD-A9TA TCGA-YG-AA3P TCGA-Z2-A8RT 
       12.16        40.41        24.99        49.18        14.43        27.58 
TCGA-Z2-AA3S TCGA-Z2-AA3V 
       96.99        15.98 

  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
               2.6                0.2 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
            302.07             369.93 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
             55.05              48.97 
[1] "2.6 - 302.1 (55.0)" "0.2 - 369.9 (49.0)"
[1] "hr=" "1"  
D39V3, continuous
                    vv
clus                 I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  22Q GAIN MUTATED          3       2      10        5        9        7
  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        21          6
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  22Q GAIN MUTATED           13         19        7
  22Q GAIN WILD-TYPE         22         35       14
D39V4, multiclass
            clus
vv           22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  I/II NOS                  3                 10
  STAGE 0                   2                  5
  STAGE I                  10                 19
  STAGE IA                  5                 13
  STAGE IB                  9                 19
  STAGE II                  7                 19
  STAGE IIA                 4                 10
  STAGE IIB                 3                 16
  STAGE IIC                 7                  8
  STAGE III                18                 21
  STAGE IIIA                9                  6
  STAGE IIIB               13                 22
  STAGE IIIC               19                 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 25 20
  22Q GAIN WILD-TYPE    39 43 56 47
D39V5, multiclass
       clus
vv      22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  T0+T1               25                 39
  T2                  30                 43
  T3                  25                 56
  T4                  20                 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  25  18  18
  22Q GAIN WILD-TYPE 126  40  21  27
D39V6, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  N0               51                126
  N1               25                 40
  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 213  14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED    106    8
  22Q GAIN WILD-TYPE  213   14
   clus
vv  22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  0              106                213
  1                8                 14
[1] 2 2
[1] FALSE
D39V8, binary
                    cls
clus                  0  1
  22Q GAIN MUTATED   48 32
  22Q GAIN WILD-TYPE 86 58
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED     48   32
  22Q GAIN WILD-TYPE   86   58
     clus
vv    22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  NO                48                 86
  YES               32                 58
[1] 2 2
[1] FALSE
D39V9, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED    16 110
  22Q GAIN WILD-TYPE  31 210
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED     16  110
  22Q GAIN WILD-TYPE   31  210
     clus
vv    22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  NO                16                 31
  YES              110                210
[1] 2 2
[1] FALSE
D39V10, continuous
D39V11, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED    53  73
  22Q GAIN WILD-TYPE  85 156
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED     53   73
  22Q GAIN WILD-TYPE   85  156
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  FEMALE               53                 85
  MALE                 73                156
[1] 2 2
[1] FALSE
D39V12, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED   109  17
  22Q GAIN WILD-TYPE 210  30
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED    109   17
  22Q GAIN WILD-TYPE  210   30
     clus
vv    22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  NO               109                210
  YES               17                 30
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  22Q GAIN MUTATED       3                         0   121
  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                                  121                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     1 123
  22Q GAIN WILD-TYPE   6 229
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      1  123
  22Q GAIN WILD-TYPE    6  229
                        clus
vv                       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO              123                229
[1] 2 2
[1] FALSE

Clustering(40) Variable = XP GAIN MUTATION ANALYSIS
D40V1, survival
                   sevent
clus2                 0   1
  XP GAIN MUTATED    11  12
  XP GAIN WILD-TYPE 117 112
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               23               229 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               12               112 
$`XP GAIN MUTATED`
TCGA-D3-A2JE TCGA-FR-A729 TCGA-D3-A1Q3 TCGA-D3-A2JA TCGA-D3-A3CE TCGA-D3-A3MU 
        9.76       216.43        15.72        15.75        59.70        23.67 
TCGA-DA-A95V TCGA-DA-A95Z TCGA-EB-A5KH TCGA-EE-A2GN TCGA-EE-A2MU TCGA-EE-A3J7 
       72.10        12.30        16.41        93.63        53.26        45.90 
TCGA-ER-A19M TCGA-ER-A2NC TCGA-FR-A3YN TCGA-FR-A8YC TCGA-FS-A1ZU TCGA-FS-A1ZY 
       59.84        22.36         4.50        10.06         4.47         5.29 
TCGA-FS-A4FD TCGA-GN-A264 TCGA-GN-A265 TCGA-W3-AA1W TCGA-XV-AB01 
       80.68       117.93        96.92       185.13         6.61 

$`XP GAIN WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A8GI TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A20H 
       62.07        38.76        13.41        33.24        31.96       166.75 
TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 TCGA-FW-A3R5 
      269.03        52.90       134.40        27.35        19.04        36.95 
TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 
       52.73         7.40        60.46        12.99        14.83         8.42 
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA 
       31.89       110.93        49.35       133.25        19.04        76.41 
TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JB TCGA-D3-A2JC 
       62.60        25.64        45.99        62.86       168.00        86.30 
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-A3CB TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR 
       58.06       140.98        40.01        24.53         9.34        90.21 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T 
      173.85        30.67       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        68.68       150.61       110.53        60.10 
TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-DA-A95W 
       64.83        58.85        30.44       225.11         8.71         0.76 
TCGA-DA-A95X TCGA-DA-A95Y TCGA-EB-A44Q TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X 
       65.03        14.14         3.91        52.41        18.21        13.15 
TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A20F 
       24.89        20.38         0.00        26.24        75.55        79.20 
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        47.41 
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-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ 
       30.02        77.98        26.14        12.95       201.60        68.65 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
       10.62        32.48        18.35         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-A2MS TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC 
      227.01       143.93        23.51       124.31       122.73        64.04 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J8 
        4.41        54.51         6.28        67.89       111.85         3.35 
TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 
      168.85        19.86       135.98        34.45        10.49         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       184.60       150.12 
TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W 
       99.06        42.51       120.76        49.71        47.18       146.63 
TCGA-ER-A1A1 TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES 
       73.05         4.70        16.87        10.19        28.67       173.29 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A44A TCGA-FR-A69P 
       68.52        15.48        32.05        74.47       174.21         4.14 
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-A1ZG TCGA-FS-A1ZJ 
       27.62       312.07        32.78        43.92         7.82        36.33 
TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A1ZZ 
       78.61       130.95       136.27        35.28        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-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A267 
       19.30         9.90        18.25         1.91        53.29        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-AA21 TCGA-WE-A8K1 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ 
       92.84        47.54        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        37.32        24.99        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 
           216.43            346.49 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
            23.67             47.18 
[1] "4.5 - 216.4 (23.7)" "0.0 - 346.5 (47.2)"
[1] "hr=" "1.3"
D40V2, survival
                   sevent
clus2                 0   1
  XP GAIN MUTATED    15  24
  XP GAIN WILD-TYPE 151 168
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               39               319 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               24               168 
$`XP GAIN MUTATED`
TCGA-D3-A2JE TCGA-EE-A184 TCGA-FR-A729 TCGA-3N-A9WB TCGA-D3-A1Q3 TCGA-D3-A2JA 
       27.65        68.15       220.80        17.03        16.67       115.53 
TCGA-D3-A3CE TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A8GQ TCGA-DA-A3F3 TCGA-DA-A95V 
       60.23        39.75        45.30        29.06        10.49        72.10 
TCGA-DA-A95Z TCGA-EB-A5KH TCGA-EE-A29A TCGA-EE-A29R TCGA-EE-A2GN TCGA-EE-A2MU 
       13.02        20.35        63.35        14.47       102.12        53.26 
TCGA-EE-A3AG TCGA-EE-A3J7 TCGA-ER-A19M TCGA-ER-A2NC TCGA-FR-A3YN TCGA-FR-A8YC 
       41.59        64.08        61.05        43.82        92.98        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-W3-AA1O TCGA-W3-AA1W 
       80.68       117.93        96.92        48.00         4.01       219.16 
TCGA-WE-A8K6 TCGA-XV-AB01 TCGA-YD-A89C 
       17.95        13.25         6.90 

$`XP GAIN WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-D3-A8GI TCGA-EB-A5SG TCGA-EB-A5SH 
       62.07        46.32        13.87        58.52        68.25        54.02 
TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR 
       94.98       168.26         2.60       340.14       126.81       134.40 
TCGA-EE-A3JD TCGA-ER-A193 TCGA-ER-A198 TCGA-FS-A1ZF TCGA-FW-A3R5 TCGA-QB-AA9O 
       27.35        31.40        50.76        15.45        36.95        18.05 
TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 
       61.15        21.40        66.48        12.99        14.93        16.57 
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-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK 
      168.00        86.76        11.87       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-A3CB TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR 
       46.98       166.52        86.93        24.53         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-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-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       222.51       176.55        35.93       135.02        88.87 
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-A95W TCGA-DA-A95X TCGA-DA-A95Y TCGA-EB-A44Q TCGA-EB-A44R 
       43.36        37.35        73.94        14.14        13.87        10.36 
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-A185 TCGA-EE-A20B 
        8.65        33.73        14.70        26.89         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-A29M TCGA-EE-A29N TCGA-EE-A29P 
       63.78        72.07        64.64        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-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
       67.43       173.79       220.24        48.72       107.38        54.74 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT 
       79.66        75.48        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-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-A3AE TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 
       28.77        54.51        13.81       138.81       172.18       127.20 
TCGA-EE-A3J5 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JE TCGA-EE-A3JH 
       36.95        34.32        53.19       201.80        51.35       134.33 
TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B 
      152.81        35.44        13.94         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       302.07       152.35 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S 
        6.44       131.51        44.09       162.08        50.89        49.48 
TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF 
        8.88       148.18       105.07        23.34        20.15        28.83 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL 
       48.99        41.56       247.04        93.01        46.98        33.21 
TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A7U9 
       12.95       149.03       174.21        15.72        27.85        18.77 
TCGA-FR-A7UA TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
       38.27       104.42       216.92        48.59       228.59       202.65 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD 
       20.91        28.08         7.79        48.85       357.37        53.52 
TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ 
       46.45         9.70        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-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
       54.41        17.46        55.59        13.51        19.30         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A266 TCGA-GN-A267 
       19.43         2.04        15.78       139.89        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-A8LK TCGA-GN-A8LL TCGA-GN-A9SD TCGA-HR-A2OG TCGA-HR-A2OH 
       22.13        50.10        21.37        59.41         0.23        65.88 
TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-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-AA1Q TCGA-W3-AA1R TCGA-W3-AA1V 
      228.16        63.02       121.08        69.07       111.09        42.08 
TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO 
      105.04        24.03        49.05       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-AAA4 TCGA-YD-A9TA TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S 
       24.99        49.18        37.94        14.43        27.58        96.99 
TCGA-Z2-AA3V 
       15.98 

  XP GAIN MUTATED XP GAIN WILD-TYPE 
             4.01              0.20 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
           220.80            369.93 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
            41.59             53.92 
[1] "4.0 - 220.8 (41.6)" "0.2 - 369.9 (53.9)"
[1] "hr=" "1.6"
D40V3, continuous
                   vv
clus                I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  XP GAIN MUTATED          1       1       2        3        4        5
  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         4          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         31         51       20
D40V4, multiclass
            clus
vv           XP GAIN MUTATED XP GAIN WILD-TYPE
  I/II NOS                 1                12
  STAGE 0                  1                 6
  STAGE I                  2                27
  STAGE IA                 3                15
  STAGE IB                 4                24
  STAGE II                 5                21
  STAGE IIA                1                13
  STAGE IIB                2                17
  STAGE IIC                5                10
  STAGE III                4                35
  STAGE IIIA               3                12
  STAGE IIIB               4                31
  STAGE IIIC               3                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
  XP GAIN MUTATED       8  9  9  7
  XP GAIN WILD-TYPE    56 64 72 60
D40V5, multiclass
       clus
vv      XP GAIN MUTATED XP GAIN WILD-TYPE
  T0+T1               8                56
  T2                  9                64
  T3                  9                72
  T4                  7                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
  XP GAIN MUTATED    22   6   6   2
  XP GAIN WILD-TYPE 155  59  33  43
D40V6, multiclass
    clus
vv   XP GAIN MUTATED XP GAIN WILD-TYPE
  N0              22               155
  N1               6                59
  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 283  21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED     36    1
  XP GAIN WILD-TYPE  283   21
   clus
vv  XP GAIN MUTATED XP GAIN WILD-TYPE
  0              36               283
  1               1                21
[1] 2 2
[1] FALSE
D40V8, binary
                   cls
clus                  0   1
  XP GAIN MUTATED    13  12
  XP GAIN WILD-TYPE 121  78
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED     13   12
  XP GAIN WILD-TYPE  121   78
     clus
vv    XP GAIN MUTATED XP GAIN WILD-TYPE
  NO               13               121
  YES              12                78
[1] 2 2
[1] FALSE
D40V9, binary
                   cls
clus                  0   1
  XP GAIN MUTATED     6  36
  XP GAIN WILD-TYPE  41 284
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED      6   36
  XP GAIN WILD-TYPE   41  284
     clus
vv    XP GAIN MUTATED XP GAIN WILD-TYPE
  NO                6                41
  YES              36               284
[1] 2 2
[1] FALSE
D40V10, continuous
D40V11, binary
                   cls
clus                  0   1
  XP GAIN MUTATED    14  28
  XP GAIN WILD-TYPE 124 201
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED     14   28
  XP GAIN WILD-TYPE  124  201
        clus
vv       XP GAIN MUTATED XP GAIN WILD-TYPE
  FEMALE              14               124
  MALE                28               201
[1] 2 2
[1] FALSE
D40V12, binary
                   cls
clus                  0   1
  XP GAIN MUTATED    40   2
  XP GAIN WILD-TYPE 279  45
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED     40    2
  XP GAIN WILD-TYPE  279   45
     clus
vv    XP GAIN MUTATED XP GAIN WILD-TYPE
  NO               40               279
  YES               2                45
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  XP GAIN MUTATED       1                         0    41
  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                                  41               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  41
  XP GAIN WILD-TYPE   7 311
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED      0   41
  XP GAIN WILD-TYPE    7  311
                        clus
vv                       XP GAIN MUTATED XP GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 7
  NOT HISPANIC OR LATINO              41               311
[1] 2 2
[1] FALSE

Clustering(41) Variable = XQ GAIN MUTATION ANALYSIS
D41V1, survival
                   sevent
clus2                 0   1
  XQ GAIN MUTATED    11  16
  XQ GAIN WILD-TYPE 117 108
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               27               225 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               16               108 
$`XQ GAIN MUTATED`
TCGA-D3-A2JE TCGA-FR-A729 TCGA-D3-A1Q3 TCGA-D3-A2JA TCGA-D3-A2JG TCGA-D3-A3CE 
        9.76       216.43        15.72        15.75       107.61        59.70 
TCGA-D3-A3MU TCGA-DA-A95V TCGA-DA-A95Z TCGA-EB-A5KH TCGA-EE-A2GN TCGA-EE-A2MU 
       23.67        72.10        12.30        16.41        93.63        53.26 
TCGA-EE-A3J7 TCGA-ER-A19M TCGA-ER-A2NC TCGA-ER-A2ND TCGA-FR-A3YN TCGA-FR-A8YC 
       45.90        59.84        22.36         4.70         4.50        10.06 
TCGA-FS-A1ZG TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A4FD TCGA-FW-A3TV TCGA-GN-A264 
        7.82         4.47         5.29        80.68        11.54       117.93 
TCGA-GN-A268 TCGA-WE-A8ZT TCGA-XV-AB01 
       42.48        10.95         6.61 

$`XQ GAIN WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A8GI TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A20H 
       62.07        38.76        13.41        33.24        31.96       166.75 
TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 TCGA-FW-A3R5 
      269.03        52.90       134.40        27.35        19.04        36.95 
TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 
       52.73         7.40        60.46        12.99        14.83         8.42 
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA 
       31.89       110.93        49.35       133.25        19.04        76.41 
TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JB TCGA-D3-A2JC 
       62.60        25.64        45.99        62.86       168.00        86.30 
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-A3CB TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A51E 
      140.98        40.01        24.53         9.34        90.21       173.85 
TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL 
       30.67       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        68.68       150.61       110.53        60.10        64.83 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-DA-A95W TCGA-DA-A95X 
       58.85        30.44       225.11         8.71         0.76        65.03 
TCGA-DA-A95Y TCGA-EB-A44Q TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y 
       14.14         3.91        52.41        18.21        13.15        24.89 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29B 
       20.38         0.00        26.24        75.55        79.20        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        47.41        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-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK 
       77.98        26.14        12.95       201.60        68.65        10.62 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU 
       32.48        18.35         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-A2MS TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
      143.93        23.51       124.31       122.73        64.04         4.41 
TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J8 TCGA-EE-A3JB 
       54.51         6.28        67.89       111.85         3.35       168.85 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A 
       19.86       135.98        34.45        10.49         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       184.60       150.12        99.06 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 
       42.51       120.76        49.71        47.18       146.63        73.05 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
       16.87        10.19        28.67       173.29        68.52        15.48 
TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A7UA 
       32.05        74.47       174.21         4.14        26.20         5.65 
TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZC 
      171.78        49.74       195.98         8.35        27.62       312.07 
TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS 
       32.78        43.92        36.33        78.61       130.95       136.27 
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-FW-A3TU TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 
       13.28        55.59        19.30         9.90        18.25         1.91 
TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 
       53.29        96.92        17.06         7.59       120.53        34.49 
TCGA-GN-A4U8 TCGA-GN-A8LK TCGA-GN-A9SD TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS 
       46.92        43.23        59.41        85.05       297.01         7.23 
TCGA-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        47.54        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        37.32 
TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-Z2-AA3S 
       24.99        28.21        91.23 

  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
             4.47              0.00 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
           216.43            346.49 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
            16.41             47.74 
[1] "4.5 - 216.4 (16.4)" "0.0 - 346.5 (47.7)"
[1] "hr=" "2"  
D41V2, survival
                   sevent
clus2                 0   1
  XQ GAIN MUTATED    16  27
  XQ GAIN WILD-TYPE 150 165
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               43               315 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               27               165 
$`XQ GAIN MUTATED`
TCGA-D3-A2JE TCGA-EE-A184 TCGA-FR-A729 TCGA-3N-A9WB TCGA-D3-A1Q3 TCGA-D3-A2JA 
       27.65        68.15       220.80        17.03        16.67       115.53 
TCGA-D3-A2JG TCGA-D3-A3CE TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A8GQ TCGA-DA-A3F3 
      113.52        60.23        39.75        45.30        29.06        10.49 
TCGA-DA-A95V TCGA-DA-A95Z TCGA-EB-A5KH TCGA-EE-A29A TCGA-EE-A29R TCGA-EE-A2GN 
       72.10        13.02        20.35        63.35        14.47       102.12 
TCGA-EE-A2MU TCGA-EE-A3AG TCGA-EE-A3J7 TCGA-ER-A19M TCGA-ER-A2NC TCGA-ER-A2ND 
       53.26        41.59        64.08        61.05        43.82        23.34 
TCGA-FR-A3YN TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FS-A1ZG TCGA-FS-A1ZK TCGA-FS-A1ZP 
       92.98        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-XV-AB01 
       62.79        48.00         4.01        17.95        11.80        13.25 
TCGA-YD-A89C 
        6.90 

$`XQ GAIN WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-D3-A8GI TCGA-EB-A5SG TCGA-EB-A5SH 
       62.07        46.32        13.87        58.52        68.25        54.02 
TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR 
       94.98       168.26         2.60       340.14       126.81       134.40 
TCGA-EE-A3JD TCGA-ER-A193 TCGA-ER-A198 TCGA-FS-A1ZF TCGA-FW-A3R5 TCGA-QB-AA9O 
       27.35        31.40        50.76        15.45        36.95        18.05 
TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 
       61.15        21.40        66.48        12.99        14.93        16.57 
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-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL 
      168.00        86.76        11.87        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-A3CB TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A51E 
      166.52        86.93        24.53         9.34       103.59       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-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-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 
      222.51       176.55        35.93       135.02        88.87        53.92 
TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 
       65.92        40.60        68.09        33.93       225.96        43.36 
TCGA-DA-A95W TCGA-DA-A95X TCGA-DA-A95Y TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5UL 
       37.35        73.94        14.14        13.87        10.36        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-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-A29D TCGA-EE-A29E 
       91.56        13.55        85.08        78.97        13.97        63.78 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
       72.07        64.64        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-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-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU 
       75.48        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-A2MS TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
      162.48        71.21       124.31       122.73        64.04        28.77 
TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 
       54.51        13.81       138.81       172.18       127.20        36.95 
TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI 
       34.32        53.19       201.80        51.35       134.33       152.81 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C 
       35.44        13.94         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       302.07       152.35         6.44 
TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T 
      131.51        44.09       162.08        50.89        49.48         8.88 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH 
      148.18       105.07        20.15        28.83        48.99        41.56 
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-A44A TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YE 
      174.21        15.72        27.85        18.77        38.27       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-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS 
       32.75        47.38       101.26       133.55        11.41       148.80 
TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 
       53.16        49.48        27.02        77.82        50.14        66.67 
TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FW-A3I3 
       28.73       174.84        34.03        26.73        54.41        17.46 
TCGA-FW-A3TU TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 
       55.59        19.30         9.90        19.43         2.04       139.89 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 
       96.92        10.13        64.44        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-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-AA1Q 
        0.33         0.69       228.16        63.02       121.08        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-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-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-YD-A9TA TCGA-YG-AA3O TCGA-YG-AA3P 
       12.16        40.41        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 
            36.26             54.41 
[1] "4.0 - 220.8 (36.3)" "0.2 - 369.9 (54.4)"
[1] "hr=" "1.9"
D41V3, continuous
                   vv
clus                I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  XQ GAIN MUTATED          0       1       2        3        4        4
  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         4          4
  XQ GAIN WILD-TYPE        13        16        10        35         11
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  XQ GAIN MUTATED            5          5        2
  XQ GAIN WILD-TYPE         30         49       19
D41V4, multiclass
            clus
vv           XQ GAIN MUTATED XQ GAIN WILD-TYPE
  I/II NOS                 0                13
  STAGE 0                  1                 6
  STAGE I                  2                27
  STAGE IA                 3                15
  STAGE IB                 4                24
  STAGE II                 4                22
  STAGE IIA                1                13
  STAGE IIB                3                16
  STAGE IIC                5                10
  STAGE III                4                35
  STAGE IIIA               4                11
  STAGE IIIB               5                30
  STAGE IIIC               5                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
  XQ GAIN MUTATED      10  9 10  8
  XQ GAIN WILD-TYPE    54 64 71 59
D41V5, multiclass
       clus
vv      XQ GAIN MUTATED XQ GAIN WILD-TYPE
  T0+T1              10                54
  T2                  9                64
  T3                 10                71
  T4                  8                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
  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    38   2
  XQ GAIN WILD-TYPE 281  20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     38    2
  XQ GAIN WILD-TYPE  281   20
   clus
vv  XQ GAIN MUTATED XQ GAIN WILD-TYPE
  0              38               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  38
  XQ GAIN WILD-TYPE  41 282
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      6   38
  XQ GAIN WILD-TYPE   41  282
     clus
vv    XQ GAIN MUTATED XQ GAIN WILD-TYPE
  NO                6                41
  YES              38               282
[1] 2 2
[1] FALSE
D41V10, continuous
D41V11, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED    17  27
  XQ GAIN WILD-TYPE 121 202
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     17   27
  XQ GAIN WILD-TYPE  121  202
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  FEMALE              17               121
  MALE                27               202
[1] 2 2
[1] FALSE
D41V12, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED    42   2
  XQ GAIN WILD-TYPE 277  45
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     42    2
  XQ GAIN WILD-TYPE  277   45
     clus
vv    XQ GAIN MUTATED XQ GAIN WILD-TYPE
  NO               42               277
  YES               2                45
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  XQ GAIN MUTATED       1                         0    43
  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                                  43               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  43
  XQ GAIN WILD-TYPE   7 309
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      0   43
  XQ GAIN WILD-TYPE    7  309
                        clus
vv                       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 7
  NOT HISPANIC OR LATINO              43               309
[1] 2 2
[1] FALSE

Clustering(42) Variable = 1P LOSS MUTATION ANALYSIS
D42V1, survival
                   sevent
clus2                 0   1
  1P LOSS MUTATED    21  16
  1P LOSS WILD-TYPE 107 108
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               37               215 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               16               108 
$`1P LOSS MUTATED`
TCGA-EE-A20H TCGA-EE-A2GO TCGA-ER-A193 TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-D3-A1Q4 
      166.75        52.90        19.04        52.73         7.40        31.89 
TCGA-D3-A2JO TCGA-D3-A3CC TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D9-A1X3 TCGA-D9-A4Z6 
       66.08        40.01        45.70       177.86        10.78        18.44 
TCGA-DA-A1I2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-DA-A95V TCGA-EE-A2GE TCGA-EE-A2GH 
      150.61       225.11         8.71        72.10        12.95       201.60 
TCGA-EE-A2GR TCGA-EE-A2MK TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A3AD TCGA-EE-A3J3 
        0.20        89.26       227.01       143.93         4.41        67.89 
TCGA-ER-A197 TCGA-ER-A19C TCGA-ER-A19L TCGA-ER-A2ND TCGA-ER-A2NG TCGA-ER-A3EV 
       10.49        39.81        99.06         4.70        28.67        15.48 
TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A4F8 TCGA-FW-A3TV TCGA-WE-A8ZM TCGA-WE-A8ZQ 
       35.28        23.21       173.19        11.54        65.42        62.89 
TCGA-WE-AA9Y 
        1.94 

$`1P LOSS WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A8GI TCGA-EB-A5SG TCGA-EE-A180 
        9.76        62.07        38.76        13.41        33.24        31.96 
TCGA-EE-A2GD TCGA-EE-A2MR TCGA-EE-A3JD TCGA-FR-A729 TCGA-FW-A3R5 TCGA-3N-A9WC 
      269.03       134.40        27.35       216.43        36.95        60.46 
TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q5 TCGA-D3-A1Q6 
       12.99        14.83         8.42        15.72       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-A2JG TCGA-D3-A2JH 
       62.86        15.75       168.00        86.30       107.61        36.30 
TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CE 
      171.58        64.83        43.53        58.06       140.98        59.70 
TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F 
       24.53         9.34        90.21        23.67       173.85        30.67 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GU 
      144.46        31.76        62.70        11.34        42.05       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-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA 
       76.34       138.67        68.68       110.53        60.10        64.83 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A95W TCGA-DA-A95X TCGA-DA-A95Y TCGA-DA-A95Z 
       58.85        30.44         0.76        65.03        14.14        12.30 
TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y 
        3.91        16.41        52.41        18.21        13.15        24.89 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29B 
       20.38         0.00        26.24        75.55        79.20        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        47.41        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-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
       77.98        26.14        68.65        10.62        32.48        18.35 
TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 
       93.63         0.76        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-A2MM TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB 
      104.78       145.45        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-A199 TCGA-ER-A19A 
      168.85        19.86       135.98        34.45         7.82         4.54 
TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19M TCGA-ER-A19N 
       53.29        11.47       184.60       150.12        59.84        42.51 
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        73.05        22.36 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3PL TCGA-ER-A42L 
       16.87        10.19       173.29        68.52        32.05        74.47 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FR-A8YC 
        4.50       174.21         4.14        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-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ 
       32.78        43.92         7.82        36.33        78.61       130.95 
TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 
      136.27         4.47         5.29         3.06        30.90        66.67 
TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
       13.28        80.68        55.59        19.30         9.90        18.25 
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-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-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-A8ZY 
       92.84        47.54        12.69        21.90        10.95        48.39 
TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-XV-AB01 TCGA-YG-AA3O TCGA-Z2-AA3S 
       37.32        24.99         6.61        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 
            40.01             47.18 
[1] "0.2 - 227.0 (40.0)" "0.0 - 346.5 (47.2)"
[1] "hr=" "1.2"
D42V2, survival
                   sevent
clus2                 0   1
  1P LOSS MUTATED    28  22
  1P LOSS WILD-TYPE 138 170
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               50               308 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               22               170 
$`1P LOSS MUTATED`
TCGA-EE-A20H TCGA-EE-A2GO TCGA-ER-A193 TCGA-QB-AA9O TCGA-WE-A8K5 TCGA-WE-AAA3 
      168.26       126.81        31.40        18.05        61.15        21.40 
TCGA-D3-A1Q4 TCGA-D3-A1Q9 TCGA-D3-A2JO TCGA-D3-A3CC TCGA-D3-A3MV TCGA-D3-A5GN 
      112.04        31.59        66.08        86.93        45.30       135.75 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D9-A1X3 TCGA-D9-A4Z6 TCGA-DA-A1I2 TCGA-DA-A1I8 
      178.32        18.18        18.12        18.44       176.55        53.92 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-DA-A95V TCGA-EB-A44R TCGA-EE-A29R TCGA-EE-A2GE 
      225.96        43.36        72.10        10.36        14.47       173.79 
TCGA-EE-A2GH TCGA-EE-A2GR TCGA-EE-A2MK TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A3AD 
      220.24        42.77       180.39       248.65       162.48        28.77 
TCGA-EE-A3J3 TCGA-ER-A197 TCGA-ER-A19C TCGA-ER-A19L TCGA-ER-A2ND TCGA-ER-A2NG 
      172.18        13.94        48.89       131.51        23.34        48.99 
TCGA-ER-A2NH TCGA-ER-A3EV TCGA-FR-A7U9 TCGA-FS-A1Z7 TCGA-FS-A1ZT TCGA-FS-A1ZW 
       41.56        46.98        18.77         7.79        53.16        49.48 
TCGA-FS-A4F8 TCGA-FW-A3TV TCGA-GN-A26D TCGA-WE-A8ZM TCGA-WE-A8ZQ TCGA-WE-AA9Y 
      174.84        13.51        48.00       101.33        63.22        12.16 
TCGA-YD-A89C TCGA-YG-AA3P 
        6.90        14.43 

$`1P LOSS WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-D3-A8GI TCGA-EB-A5SG 
       27.65        62.07        46.32        13.87        58.52        68.25 
TCGA-EB-A5SH TCGA-EE-A180 TCGA-EE-A184 TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2MR 
       54.02        94.98        68.15         2.60       340.14       134.40 
TCGA-EE-A3JD TCGA-ER-A198 TCGA-FR-A729 TCGA-FS-A1ZF TCGA-FW-A3R5 TCGA-3N-A9WB 
       27.35        50.76       220.80        15.45        36.95        17.03 
TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q5 
       66.48        12.99        14.93        16.57        16.67       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-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-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       11.87       113.52        42.08        12.10       171.58        66.48 
TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CE 
       59.57       130.72        58.06        46.98       166.52        60.23 
TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F 
       24.53         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-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-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-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 
       54.67         3.65         7.10        15.39        22.29         9.90 
TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY 
       25.18        77.56        22.95        76.57        36.03       144.89 
TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA 
       20.38       222.51        35.93       135.02        88.87        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        37.35        73.94 
TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UL TCGA-EB-A5UN 
       14.14        13.02        13.87        20.35        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-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F 
       14.70        26.89         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-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
       72.07        64.64        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-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-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB 
       47.54        43.23        71.21        53.26       124.31       122.73 
TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J4 
       64.04        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-A3JE 
       36.95        64.08        34.32        53.19       201.80        51.35 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B 
      134.33       152.81        35.44         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       302.07       152.35         6.44 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T 
       61.05        44.09       162.08        50.89        49.48         8.88 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A3ES 
      148.18       105.07        43.82        20.15        28.83       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-A69P TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE 
       15.72        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-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG 
       27.72        48.85       357.37        53.52        46.45         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-A1ZU TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 
       11.41       148.80        26.56        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-A3TU TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
       80.68        17.46        55.59        19.30         9.90        19.43 
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-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 
       64.44        62.79        32.48       121.91        39.35        10.42 
TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A8LL TCGA-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-A8K6 TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-A8ZY 
       17.95        58.98        70.52        11.80        35.80        49.51 
TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-XV-AB01 TCGA-YD-A9TA TCGA-YG-AA3O TCGA-Z2-A8RT 
       40.41        24.99        13.25        49.18        37.94        27.58 
TCGA-Z2-AA3S TCGA-Z2-AA3V 
       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 
            48.94             53.39 
[1] "6.9 - 248.7 (48.9)" "0.2 - 369.9 (53.4)"
[1] "hr=" "1.3"
D42V3, continuous
                   vv
clus                I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  1P LOSS MUTATED          0       0       8        1        1        3
  1P LOSS WILD-TYPE       13       7      21       17       27       23
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  1P LOSS MUTATED           1         2         4         6          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         27         42       19
D42V4, multiclass
            clus
vv           1P LOSS MUTATED 1P LOSS WILD-TYPE
  I/II NOS                 0                13
  STAGE 0                  0                 7
  STAGE I                  8                21
  STAGE IA                 1                17
  STAGE IB                 1                27
  STAGE II                 3                23
  STAGE IIA                1                13
  STAGE IIB                2                17
  STAGE IIC                4                11
  STAGE III                6                33
  STAGE IIIA               0                15
  STAGE IIIB               8                27
  STAGE IIIC              12                42
  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       9 13  9 14
  1P LOSS WILD-TYPE    55 60 72 53
D42V5, multiclass
       clus
vv      1P LOSS MUTATED 1P LOSS WILD-TYPE
  T0+T1               9                55
  T2                 13                60
  T3                  9                72
  T4                 14                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
  1P LOSS MUTATED    20  11   8   8
  1P LOSS WILD-TYPE 157  54  31  37
D42V6, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  N0              20               157
  N1              11                54
  N2               8                31
  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    44   2
  1P LOSS WILD-TYPE 275  20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     44    2
  1P LOSS WILD-TYPE  275   20
   clus
vv  1P LOSS MUTATED 1P LOSS WILD-TYPE
  0              44               275
  1               2                20
[1] 2 2
[1] FALSE
D42V8, binary
                   cls
clus                  0   1
  1P LOSS MUTATED    16  17
  1P LOSS WILD-TYPE 118  73
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     16   17
  1P LOSS WILD-TYPE  118   73
     clus
vv    1P LOSS MUTATED 1P LOSS WILD-TYPE
  NO               16               118
  YES              17                73
[1] 2 2
[1] FALSE
D42V9, binary
                   cls
clus                  0   1
  1P LOSS MUTATED     2  49
  1P LOSS WILD-TYPE  45 271
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      2   49
  1P LOSS WILD-TYPE   45  271
     clus
vv    1P LOSS MUTATED 1P LOSS WILD-TYPE
  NO                2                45
  YES              49               271
[1] 2 2
[1] FALSE
D42V10, continuous
D42V11, binary
                   cls
clus                  0   1
  1P LOSS MUTATED    22  29
  1P LOSS WILD-TYPE 116 200
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     22   29
  1P LOSS WILD-TYPE  116  200
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  FEMALE              22               116
  MALE                29               200
[1] 2 2
[1] FALSE
D42V12, binary
                   cls
clus                  0   1
  1P LOSS MUTATED    46   5
  1P LOSS WILD-TYPE 273  42
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     46    5
  1P LOSS WILD-TYPE  273   42
     clus
vv    1P LOSS MUTATED 1P LOSS WILD-TYPE
  NO               46               273
  YES               5                42
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  1P LOSS MUTATED       1                         0    48
  1P LOSS WILD-TYPE     4                         1   305
D42V13, multiclass
                           clus
vv                          1P LOSS MUTATED 1P LOSS WILD-TYPE
  ASIAN                                   1                 4
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  48               305
[1] 3 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  50
  1P LOSS WILD-TYPE   6 302
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      1   50
  1P LOSS WILD-TYPE    6  302
                        clus
vv                       1P LOSS MUTATED 1P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 6
  NOT HISPANIC OR LATINO              50               302
[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 118 114
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               20               232 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               10               114 
$`1Q LOSS MUTATED`
TCGA-EE-A20H TCGA-ER-A193 TCGA-WE-AAA3 TCGA-D3-A2JO TCGA-D3-A3CC TCGA-D3-A5GR 
      166.75        19.04         7.40        66.08        40.01       177.86 
TCGA-D9-A1X3 TCGA-D9-A4Z6 TCGA-DA-A1I2 TCGA-DA-A3F8 TCGA-DA-A95V TCGA-EE-A2M6 
       10.78        18.44       150.61         8.71        72.10       103.13 
TCGA-EE-A2MP TCGA-EE-A3J3 TCGA-ER-A19C TCGA-ER-A2NG TCGA-ER-A3EV TCGA-FS-A4F8 
      227.01        67.89        39.81        28.67        15.48       173.19 
TCGA-W3-AA1V TCGA-WE-A8ZQ 
        8.09        62.89 

$`1Q LOSS WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A8GI TCGA-EB-A5SG TCGA-EE-A180 
        9.76        62.07        38.76        13.41        33.24        31.96 
TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-FR-A729 TCGA-FW-A3R5 
      269.03        52.90       134.40        27.35       216.43        36.95 
TCGA-WE-A8K5 TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q3 
       52.73        60.46        12.99        14.83         8.42        15.72 
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA 
       31.89       110.93        49.35       133.25        19.04        76.41 
TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JB 
       62.60        25.64        45.99        62.86        15.75       168.00 
TCGA-D3-A2JC TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JP 
       86.30       107.61        36.30       171.58        64.83        43.53 
TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR 
       58.06       140.98        59.70        24.53         9.34        90.21 
TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R 
       23.67       173.85        30.67       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-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-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY 
       15.02        16.90        69.21        22.85        76.34       138.67 
TCGA-DA-A1I1 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 
       68.68       110.53        60.10        64.83        58.85        30.44 
TCGA-DA-A3F5 TCGA-DA-A95W TCGA-DA-A95X TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q 
      225.11         0.76        65.03        14.14        12.30         3.91 
TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A181 
       16.41        52.41        18.21        13.15        24.89        20.38 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29C 
        0.00        26.24        75.55        79.20        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        47.41        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-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
       26.14        12.95       201.60        68.65        10.62        32.48 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU 
       18.35        93.63         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-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MS TCGA-EE-A2MT 
       63.25        89.26       104.78       145.45       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-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH 
        6.28       111.85        45.90         3.35       168.85        19.86 
TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B 
      135.98        34.45        10.49         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       184.60       150.12        99.06        59.84        42.51 
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        73.05        22.36 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3PL 
        4.70        16.87        10.19       173.29        68.52        32.05 
TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A7UA 
       74.47         4.50       174.21         4.14        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-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM 
      312.07        32.78        43.92         7.82        36.33        78.61 
TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY 
      130.95       136.27        35.28         4.47        23.21         5.29 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TU 
        3.06        30.90        66.67        13.28        80.68        55.59 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 
       11.54        19.30         9.90        18.25         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-A8LK TCGA-GN-A9SD TCGA-LH-A9QB TCGA-OD-A75X 
       34.49        46.92        43.23        59.41        85.05       297.01 
TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 
        7.23         0.20         0.33       174.12         1.97       120.07 
TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8ZM 
       44.05        79.99       185.13        92.84        47.54        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        37.32 
TCGA-WE-AAA4 TCGA-XV-AB01 TCGA-YG-AA3O TCGA-Z2-AA3S 
       24.99         6.61        28.21        91.23 

  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
              7.4               0.0 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
           227.01            346.49 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
           51.450            46.455 
[1] "7.4 - 227.0 (51.5)" "0.0 - 346.5 (46.5)"
[1] "hr=" "1.1"
D43V2, survival
                   sevent
clus2                 0   1
  1Q LOSS MUTATED    13  14
  1Q LOSS WILD-TYPE 153 178
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               27               331 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               14               178 
$`1Q LOSS MUTATED`
TCGA-EE-A20H TCGA-ER-A193 TCGA-QB-AA9O TCGA-WE-AAA3 TCGA-D3-A1Q9 TCGA-D3-A2JO 
      168.26        31.40        18.05        21.40        31.59        66.08 
TCGA-D3-A3CC TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D9-A1X3 TCGA-D9-A4Z6 TCGA-DA-A1I2 
       86.93       178.32        18.18        18.12        18.44       176.55 
TCGA-DA-A1I8 TCGA-DA-A3F8 TCGA-DA-A95V TCGA-EE-A29X TCGA-EE-A2M6 TCGA-EE-A2MP 
       53.92        43.36        72.10        17.92       129.27       248.65 
TCGA-EE-A3J3 TCGA-ER-A19C TCGA-ER-A2NG TCGA-ER-A3EV TCGA-FR-A7U9 TCGA-FS-A4F8 
      172.18        48.89        48.99        46.98        18.77       174.84 
TCGA-W3-AA1V TCGA-WE-A8ZQ TCGA-YD-A89C 
       42.08        63.22         6.90 

$`1Q LOSS WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-D3-A8GI TCGA-EB-A5SG 
       27.65        62.07        46.32        13.87        58.52        68.25 
TCGA-EB-A5SH TCGA-EE-A180 TCGA-EE-A184 TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2GO 
       54.02        94.98        68.15         2.60       340.14       126.81 
TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A198 TCGA-FR-A729 TCGA-FS-A1ZF TCGA-FW-A3R5 
      134.40        27.35        50.76       220.80        15.45        36.95 
TCGA-WE-A8K5 TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 
       61.15        17.03        66.48        12.99        14.93        16.57 
TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       16.67       112.04       112.57        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-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH 
      115.53       168.00        86.76        11.87       113.52        42.08 
TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 
       12.10       171.58        66.48        59.57       130.72        58.06 
TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR 
       46.98       166.52        60.23        24.53         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-A5GU TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GE 
      137.92       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-A148 TCGA-D9-A149 
       29.06       129.63       117.17       167.70       151.53        54.67 
TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA 
        3.65         7.10        15.39        22.29         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-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IB 
      222.51        35.93       135.02        88.87        65.92        40.60 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A95W TCGA-DA-A95X 
       68.09        33.93        10.49       225.96        37.35        73.94 
TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5UL 
       14.14        13.02        13.87        10.36        20.35        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-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-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D 
       91.56        13.55        63.35        85.08        78.97        13.97 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P 
       63.78        72.07        64.64        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-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-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
       67.43       173.79       220.24        48.72       107.38        54.74 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
       79.66        75.48       102.12        13.91        42.77        81.21 
TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC 
       44.88        94.82        21.67        28.83        19.76        61.51 
TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
       47.28       103.27       268.73       103.20        16.96       204.66 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MQ 
       96.23       180.39       216.66       167.90        47.54        43.23 
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-A3JE 
       36.95        64.08        34.32        53.19       201.80        51.35 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A 
      134.33       152.81        35.44        13.94         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       302.07       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        44.09       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       105.07        43.82        23.34 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3PL 
       20.15        28.83        41.56       247.04        93.01        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-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-A1ZG TCGA-FS-A1ZH 
       48.85       357.37        53.52        46.45         9.70        32.75 
TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR 
       47.38        23.93       101.26        74.73       133.55        11.41 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ 
      148.80        53.16        26.56        49.48        27.09        27.02 
TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F9 TCGA-FS-A4FB 
       77.82        50.14        66.67        28.73        34.03        26.73 
TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
       54.41        80.68        17.46        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        19.43         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-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-AA1W TCGA-W3-AA21 
      121.08         4.01        69.07       111.09       219.16       105.04 
TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO 
       24.03        49.05        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-AAA4 
       11.80        35.80        49.51        12.16        40.41        24.99 
TCGA-XV-AB01 TCGA-YD-A9TA TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S 
       13.25        49.18        37.94        14.43        27.58        96.99 
TCGA-Z2-AA3V 
       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 
            48.89             53.19 
[1] "6.9 - 248.7 (48.9)" "0.2 - 369.9 (53.2)"
[1] "hr=" "1.1"
D43V3, continuous
                   vv
clus                I/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       25
                   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        36         15
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  1Q LOSS MUTATED            2          6        1
  1Q LOSS WILD-TYPE         33         48       20
D43V4, multiclass
            clus
vv           1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  I/II NOS                 0                13
  STAGE 0                  0                 7
  STAGE I                  5                24
  STAGE IA                 1                17
  STAGE IB                 2                26
  STAGE II                 1                25
  STAGE IIA                1                13
  STAGE IIB                1                18
  STAGE IIC                3                12
  STAGE III                3                36
  STAGE IIIA               0                15
  STAGE IIIB               2                33
  STAGE IIIC               6                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
  1Q LOSS MUTATED       5  6  6  8
  1Q LOSS WILD-TYPE    59 67 75 59
D43V5, multiclass
       clus
vv      1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  T0+T1               5                59
  T2                  6                67
  T3                  6                75
  T4                  8                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
  1Q LOSS MUTATED    13   3   5   4
  1Q LOSS WILD-TYPE 164  62  34  41
D43V6, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  N0              13               164
  N1               3                62
  N2               5                34
  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 295  21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED     24    1
  1Q LOSS WILD-TYPE  295   21
   clus
vv  1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  0              24               295
  1               1                21
[1] 2 2
[1] FALSE
D43V8, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED     9  10
  1Q LOSS WILD-TYPE 125  80
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      9   10
  1Q LOSS WILD-TYPE  125   80
     clus
vv    1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  NO                9               125
  YES              10                80
[1] 2 2
[1] FALSE
D43V9, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED     1  26
  1Q LOSS WILD-TYPE  46 294
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      1   26
  1Q LOSS WILD-TYPE   46  294
     clus
vv    1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  NO                1                46
  YES              26               294
[1] 2 2
[1] FALSE
D43V10, continuous
D43V11, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED    11  16
  1Q LOSS WILD-TYPE 127 213
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED     11   16
  1Q LOSS WILD-TYPE  127  213
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  FEMALE              11               127
  MALE                16               213
[1] 2 2
[1] FALSE
D43V12, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED    25   2
  1Q LOSS WILD-TYPE 294  45
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED     25    2
  1Q LOSS WILD-TYPE  294   45
     clus
vv    1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  NO               25               294
  YES               2                45
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  1Q LOSS MUTATED       0                         0    26
  1Q LOSS WILD-TYPE     5                         1   327
D43V13, multiclass
                           clus
vv                          1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  ASIAN                                   0                 5
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  26               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"
D43V14, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED     0  27
  1Q LOSS WILD-TYPE   7 325
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      0   27
  1Q LOSS WILD-TYPE    7  325
                        clus
vv                       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 7
  NOT HISPANIC OR LATINO              27               325
[1] 2 2
[1] FALSE

Clustering(44) Variable = 2P LOSS MUTATION ANALYSIS
D44V1, survival
                   sevent
clus2                 0   1
  2P LOSS MUTATED    14  19
  2P LOSS WILD-TYPE 114 105
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               33               219 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               19               105 
$`2P LOSS MUTATED`
TCGA-EE-A180 TCGA-D3-A2JC TCGA-D3-A2JG TCGA-D3-A3C6 TCGA-D3-A3CF TCGA-D3-A3MR 
       31.96        86.30       107.61        58.06        24.53        90.21 
TCGA-D3-A3MU TCGA-D3-A51T TCGA-D3-A8GM TCGA-D9-A1X3 TCGA-D9-A3Z3 TCGA-DA-A1I2 
       23.67        11.34        70.62        10.78        16.90       150.61 
TCGA-DA-A95V TCGA-EE-A20F TCGA-EE-A29P TCGA-EE-A2GH TCGA-EE-A2GR TCGA-EE-A2MJ 
       72.10        79.20        27.16       201.60         0.20        63.25 
TCGA-EE-A2MK TCGA-EE-A2MS TCGA-EE-A3AD TCGA-EE-A3J3 TCGA-ER-A19C TCGA-ER-A19P 
       89.26       143.93         4.41        67.89        39.81       120.76 
TCGA-ER-A3PL TCGA-FR-A8YC TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-GN-A264 
       32.05        10.06       171.78        49.74       195.98       117.93 
TCGA-GN-A267 TCGA-W3-AA21 TCGA-WE-AA9Y 
       17.06        92.84         1.94 

$`2P LOSS WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A8GI TCGA-EB-A5SG TCGA-EE-A20H 
        9.76        62.07        38.76        13.41        33.24       166.75 
TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 TCGA-FR-A729 
      269.03        52.90       134.40        27.35        19.04       216.43 
TCGA-FW-A3R5 TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 
       36.95        52.73         7.40        60.46        12.99        14.83 
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
        8.42        15.72        31.89       110.93        49.35       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-A2JA TCGA-D3-A2JB TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
       15.75       168.00        36.30       171.58        64.83        66.08 
TCGA-D3-A2JP TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3MO TCGA-D3-A51E 
       43.53       140.98        40.01        59.70         9.34       173.85 
TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A5GL TCGA-D3-A5GN 
       30.67       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        68.68       110.53        60.10 
TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-DA-A95W 
       64.83        58.85        30.44       225.11         8.71         0.76 
TCGA-DA-A95X TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN 
       65.03        14.14        12.30         3.91        16.41        52.41 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
       18.21        13.15        24.89        20.38         0.00        26.24 
TCGA-EE-A20C TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G 
       75.55        75.22        76.14        12.99         0.26        44.28 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 
       47.41        47.74        61.12       346.49       185.19       115.43 
TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GJ TCGA-EE-A2GK 
       30.02        77.98        26.14        12.95        68.65        10.62 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2GU 
       32.48        18.35        93.63         0.76        71.31        81.99 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MG 
      103.13        15.25         5.75        23.77       209.79        94.19 
TCGA-EE-A2MI TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MT TCGA-EE-A2MU 
      171.85       104.78       145.45       227.01        23.51        53.26 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J4 
      124.31       122.73        64.04        54.51         6.28       111.85 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 
       45.90         3.35       168.85        19.86       135.98        34.45 
TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19G 
       10.49         7.82         4.54        53.29        11.47       184.60 
TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A19S 
      150.12        99.06        59.84        42.51        49.71        47.18 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF 
      146.63        73.05        22.36         4.70        16.87        10.19 
TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A42L TCGA-FR-A3YN 
       28.67       173.29        68.52        15.48        74.47         4.50 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FS-A1Z3 TCGA-FS-A1Z4 
      174.21         4.14        26.20         5.65         8.35        27.62 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM 
      312.07        32.78        43.92         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        18.25         1.91 
TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 
       53.29        96.92        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-AA1V TCGA-W3-AA1W TCGA-WE-A8K1 TCGA-WE-A8ZM TCGA-WE-A8ZN 
       79.99         8.09       185.13        47.54        65.42        12.69 
TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AAA0 TCGA-WE-AAA4 
       21.90        62.89        10.95        48.39        37.32        24.99 
TCGA-XV-AB01 TCGA-YG-AA3O TCGA-Z2-AA3S 
        6.61        28.21        91.23 

  2P LOSS MUTATED 2P LOSS WILD-TYPE 
              0.2               0.0 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
           201.60            346.49 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
            63.25             45.70 
[1] "0.2 - 201.6 (63.2)" "0.0 - 346.5 (45.7)"
[1] "hr=" "1.1"
D44V2, survival
                   sevent
clus2                 0   1
  2P LOSS MUTATED    22  24
  2P LOSS WILD-TYPE 144 168
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               46               312 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               24               168 
$`2P LOSS MUTATED`
TCGA-EE-A180 TCGA-D3-A2JC TCGA-D3-A2JG TCGA-D3-A3C6 TCGA-D3-A3CF TCGA-D3-A3MR 
       94.98        86.76       113.52        58.06        24.53       103.59 
TCGA-D3-A3MU TCGA-D3-A51T TCGA-D3-A5GO TCGA-D3-A8GM TCGA-D3-A8GS TCGA-D9-A149 
       39.75        26.89       137.92       107.15       117.17        54.67 
TCGA-D9-A1X3 TCGA-D9-A3Z3 TCGA-D9-A6EA TCGA-DA-A1I2 TCGA-DA-A95V TCGA-EE-A20B 
       18.12        22.29        25.18       176.55        72.10       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-W3-AA21 TCGA-WE-AA9Y TCGA-YG-AA3P 
       65.88       105.04        12.16        14.43 

$`2P LOSS WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-D3-A8GI TCGA-EB-A5SG 
       27.65        62.07        46.32        13.87        58.52        68.25 
TCGA-EB-A5SH TCGA-EE-A184 TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2GO 
       54.02        68.15       168.26         2.60       340.14       126.81 
TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 TCGA-ER-A198 TCGA-FR-A729 TCGA-FS-A1ZF 
      134.40        27.35        31.40        50.76       220.80        15.45 
TCGA-FW-A3R5 TCGA-QB-AA9O TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-3N-A9WB TCGA-3N-A9WC 
       36.95        18.05        61.15        21.40        17.03        66.48 
TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 
       12.99        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-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-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
       11.87        42.08        12.10       171.58        66.48        66.08 
TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE 
       59.57       130.72        46.98       166.52        86.93        60.23 
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-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-A148 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 
      129.63       167.70       151.53         3.65         7.10        15.39 
TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW 
       18.44         9.90        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       222.51        35.93       135.02        88.87 
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        43.36        37.35        73.94        14.14        13.02 
TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV 
       13.87        10.36        20.35        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-A185 TCGA-EE-A20C TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C 
       26.89         4.96       151.27        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-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-A2GE TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
       59.28       173.79        48.72       107.38        54.74        79.66 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU 
       75.48       102.12        13.91        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-A2ML 
      103.27       268.73       103.20        16.96       204.66       216.66 
TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MT TCGA-EE-A2MU 
      167.90        47.54       248.65        43.23        71.21        53.26 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG 
      124.31       122.73        64.04        54.51        13.81        41.59 
TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB 
      138.81       127.20        36.95        64.08        34.32       201.80 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A 
      134.33       152.81        35.44        13.94         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       302.07       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        44.09        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       105.07        43.82        23.34        20.15 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
       28.83        48.99        41.56       247.04        93.01        46.98 
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-A7U9 TCGA-FR-A7UA TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YX TCGA-FS-A1Z3 
       18.77        38.27        36.26       104.42        48.59        20.91 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD 
       28.08         7.79        27.72        48.85       357.37        53.52 
TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM 
       46.45         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 
       17.46        55.59        13.51        19.30         9.90        19.43 
TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A268 
        2.04        15.78       139.89        96.92        10.13        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-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS 
       50.10        21.37        59.41       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-WE-A8JZ 
        4.01        69.07       111.09        42.08       219.16        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-AAA0 TCGA-WE-AAA4 TCGA-XV-AB01 
       11.80        35.80        49.51        40.41        24.99        13.25 
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 

  2P LOSS MUTATED 2P LOSS WILD-TYPE 
             0.23              0.20 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
           228.59            369.93 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
           66.655            49.480 
[1] "0.2 - 228.6 (66.7)" "0.2 - 369.9 (49.5)"
[1] "hr=" "1.3"
D44V3, continuous
                   vv
clus                I/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       22
                   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        32         12
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  2P LOSS MUTATED            3          4        3
  2P LOSS WILD-TYPE         32         50       18
D44V4, multiclass
            clus
vv           2P LOSS MUTATED 2P LOSS WILD-TYPE
  I/II NOS                 1                12
  STAGE 0                  0                 7
  STAGE I                  5                24
  STAGE IA                 1                17
  STAGE IB                 4                24
  STAGE II                 4                22
  STAGE IIA                1                13
  STAGE IIB                4                15
  STAGE IIC                3                12
  STAGE III                7                32
  STAGE IIIA               3                12
  STAGE IIIB               3                32
  STAGE IIIC               4                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
  2P LOSS MUTATED       7  8 12 15
  2P LOSS WILD-TYPE    57 65 69 52
D44V5, multiclass
       clus
vv      2P LOSS MUTATED 2P LOSS WILD-TYPE
  T0+T1               7                57
  T2                  8                65
  T3                 12                69
  T4                 15                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
  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    40   3
  2P LOSS WILD-TYPE 279  19
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED     40    3
  2P LOSS WILD-TYPE  279   19
   clus
vv  2P LOSS MUTATED 2P LOSS WILD-TYPE
  0              40               279
  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  47
  2P LOSS WILD-TYPE  44 273
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      3   47
  2P LOSS WILD-TYPE   44  273
     clus
vv    2P LOSS MUTATED 2P LOSS WILD-TYPE
  NO                3                44
  YES              47               273
[1] 2 2
[1] FALSE
D44V10, continuous
D44V11, binary
                   cls
clus                  0   1
  2P LOSS MUTATED    21  29
  2P LOSS WILD-TYPE 117 200
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED     21   29
  2P LOSS WILD-TYPE  117  200
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  FEMALE              21               117
  MALE                29               200
[1] 2 2
[1] FALSE
D44V12, binary
                   cls
clus                  0   1
  2P LOSS MUTATED    45   5
  2P LOSS WILD-TYPE 274  42
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED     45    5
  2P LOSS WILD-TYPE  274   42
     clus
vv    2P LOSS MUTATED 2P LOSS WILD-TYPE
  NO               45               274
  YES               5                42
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  2P LOSS MUTATED       0                         0    47
  2P LOSS WILD-TYPE     5                         1   306
D44V13, multiclass
                           clus
vv                          2P LOSS MUTATED 2P LOSS WILD-TYPE
  ASIAN                                   0                 5
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  47               306
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V14, binary
                   cls
clus                  0   1
  2P LOSS MUTATED     2  46
  2P LOSS WILD-TYPE   5 306
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      2   46
  2P LOSS WILD-TYPE    5  306
                        clus
vv                       2P LOSS MUTATED 2P LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                 5
  NOT HISPANIC OR LATINO              46               306
[1] 2 2
[1] FALSE

Clustering(45) Variable = 2Q LOSS MUTATION ANALYSIS
D45V1, survival
                   sevent
clus2                 0   1
  2Q LOSS MUTATED    12  22
  2Q LOSS WILD-TYPE 116 102
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               34               218 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               22               102 
$`2Q LOSS MUTATED`
TCGA-EE-A180 TCGA-D3-A2JG TCGA-D3-A3C6 TCGA-D3-A3CF TCGA-D3-A3MR TCGA-D3-A3MU 
       31.96       107.61        58.06        24.53        90.21        23.67 
TCGA-D3-A51T TCGA-D3-A8GM TCGA-D9-A1X3 TCGA-DA-A95V TCGA-EE-A20C TCGA-EE-A20F 
       11.34        70.62        10.78        72.10        75.55        79.20 
TCGA-EE-A29D TCGA-EE-A29P TCGA-EE-A2GH TCGA-EE-A2GR TCGA-EE-A2MJ TCGA-EE-A2MK 
       12.99        27.16       201.60         0.20        63.25        89.26 
TCGA-EE-A2MS TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-ER-A19C TCGA-ER-A19P TCGA-ER-A2ND 
      143.93         6.28        67.89        39.81       120.76         4.70 
TCGA-ER-A3PL TCGA-FR-A8YC TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1ZQ 
       32.05        10.06       171.78        49.74       195.98       130.95 
TCGA-GN-A267 TCGA-W3-A828 TCGA-W3-AA21 TCGA-WE-AA9Y 
       17.06       120.07        92.84         1.94 

$`2Q LOSS WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A8GI TCGA-EB-A5SG TCGA-EE-A20H 
        9.76        62.07        38.76        13.41        33.24       166.75 
TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 TCGA-FR-A729 
      269.03        52.90       134.40        27.35        19.04       216.43 
TCGA-FW-A3R5 TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 
       36.95        52.73         7.40        60.46        12.99        14.83 
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
        8.42        15.72        31.89       110.93        49.35       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-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN 
       15.75       168.00        86.30        36.30       171.58        64.83 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3MO 
       66.08        43.53       140.98        40.01        59.70         9.34 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A5GL 
      173.85        30.67       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        68.68 
TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 
      150.61       110.53        60.10        64.83        58.85        30.44 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-DA-A95W TCGA-DA-A95X TCGA-DA-A95Y TCGA-DA-A95Z 
      225.11         8.71         0.76        65.03        14.14        12.30 
TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y 
        3.91        16.41        52.41        18.21        13.15        24.89 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E 
       20.38         0.00        26.24        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        47.41        47.74        61.12       346.49       185.19 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GJ 
      115.43        30.02        77.98        26.14        12.95        68.65 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GS 
       10.62        32.48        18.35        93.63         0.76        71.31 
TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MF 
       81.99       103.13        15.25         5.75        23.77       209.79 
TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MT 
       94.19       171.85       104.78       145.45       227.01        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-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI 
      111.85        45.90         3.35       168.85        19.86       135.98 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19D 
       34.45        10.49         7.82         4.54        53.29        11.47 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19Q 
      184.60       150.12        99.06        59.84        42.51        49.71 
TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NF 
       47.18       146.63        73.05        22.36        16.87        10.19 
TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A42L TCGA-FR-A3YN 
       28.67       173.29        68.52        15.48        74.47         4.50 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FS-A1Z3 TCGA-FS-A1Z4 
      174.21         4.14        26.20         5.65         8.35        27.62 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM 
      312.07        32.78        43.92         7.82        36.33        78.61 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ 
      136.27        35.28         4.47        23.21         5.29         3.06 
TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TU 
       30.90        66.67       173.19        13.28        80.68        55.59 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 
       11.54        19.30         9.90        18.25         1.91        53.29 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 
      117.93        96.92        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-AA1Q TCGA-W3-AA1R 
        0.20         0.33       174.12         1.97        44.05        79.99 
TCGA-W3-AA1V TCGA-W3-AA1W TCGA-WE-A8K1 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO 
        8.09       185.13        47.54        65.42        12.69        21.90 
TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-XV-AB01 
       62.89        10.95        48.39        37.32        24.99         6.61 
TCGA-YG-AA3O TCGA-Z2-AA3S 
       28.21        91.23 

  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
              0.2               0.0 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
           201.60            346.49 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
           60.655            45.800 
[1] "0.2 - 201.6 (60.7)" "0.0 - 346.5 (45.8)"
[1] "hr=" "1.4"
D45V2, survival
                   sevent
clus2                 0   1
  2Q LOSS MUTATED    20  27
  2Q LOSS WILD-TYPE 146 165
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               47               311 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               27               165 
$`2Q LOSS MUTATED`
TCGA-EE-A180 TCGA-D3-A2JG TCGA-D3-A3C6 TCGA-D3-A3CF TCGA-D3-A3MR TCGA-D3-A3MU 
       94.98       113.52        58.06        24.53       103.59        39.75 
TCGA-D3-A51T TCGA-D3-A8GM TCGA-D3-A8GS TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1X3 
       26.89       107.15       117.17       151.53        54.67        18.12 
TCGA-D9-A6EA TCGA-DA-A95V TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I 
       25.18        72.10       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-W3-A828 TCGA-W3-AA21 TCGA-WE-AA9Y TCGA-YG-AA3P 
       65.88       121.08       105.04        12.16        14.43 

$`2Q LOSS WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-D3-A8GI TCGA-EB-A5SG 
       27.65        62.07        46.32        13.87        58.52        68.25 
TCGA-EB-A5SH TCGA-EE-A184 TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2GO 
       54.02        68.15       168.26         2.60       340.14       126.81 
TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 TCGA-ER-A198 TCGA-FR-A729 TCGA-FS-A1ZF 
      134.40        27.35        31.40        50.76       220.80        15.45 
TCGA-FW-A3R5 TCGA-QB-AA9O TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-3N-A9WB TCGA-3N-A9WC 
       36.95        18.05        61.15        21.40        17.03        66.48 
TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 
       12.99        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-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-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       86.76        11.87        42.08        12.10       171.58        66.48 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CC 
       66.08        59.57       130.72        46.98       166.52        86.93 
TCGA-D3-A3CE TCGA-D3-A3MO TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
       60.23         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-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-A8GV TCGA-D9-A1JW TCGA-D9-A1JX 
      152.75        29.06       129.63       167.70         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-A1I1 TCGA-DA-A1I2 
       76.57        36.03       144.89        20.38       222.51       176.55 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB 
       35.93       135.02        88.87        53.92        65.92        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        43.36        37.35 
TCGA-DA-A95X TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH 
       73.94        14.14        13.02        13.87        10.36        20.35 
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-A185 TCGA-EE-A29A 
        8.65        33.73        14.70        26.89         4.96        63.35 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M 
       85.08        78.97        63.78        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-A2GB TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
       86.14        59.28       173.79        48.72       107.38        54.74 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2GT 
       79.66        75.48       102.12        13.91        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-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-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
       53.26       124.31       122.73        64.04        28.77        54.51 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 
       41.59       138.81       127.20        36.95        64.08        34.32 
TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 
      201.80       134.33       152.81        35.44        13.94         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       302.07 
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        44.09        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       105.07        43.82        20.15 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
       28.83        48.99        41.56       247.04        93.01        46.98 
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-A7U9 TCGA-FR-A7UA TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YX TCGA-FS-A1Z3 
       18.77        38.27        36.26       104.42        48.59        20.91 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD 
       28.08         7.79        27.72        48.85       357.37        53.52 
TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM 
       46.45         9.70        32.75        47.38        23.93       101.26 
TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW 
       74.73        11.41       148.80        53.16        26.56        49.48 
TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 
       27.09        27.02        77.82        50.14        66.67        28.73 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 
      174.84        34.03        26.73        54.41        80.68        17.46 
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        19.43         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-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-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS 
       50.10        21.37        59.41       368.78       297.90         7.23 
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-WE-A8JZ TCGA-WE-A8K1 
       69.07       111.09        42.08       219.16        24.03        49.05 
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-AAA0 TCGA-WE-AAA4 TCGA-XV-AB01 TCGA-YD-A89C 
       35.80        49.51        40.41        24.99        13.25         6.90 
TCGA-YD-A9TA TCGA-YG-AA3O TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
       49.18        37.94        27.58        96.99        15.98 

  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
             0.23              0.20 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
           228.59            369.93 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
            65.88             49.48 
[1] "0.2 - 228.6 (65.9)" "0.2 - 369.9 (49.5)"
[1] "hr=" "1.1"
D45V3, continuous
                   vv
clus                I/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       22
                   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        35         12
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  2Q LOSS MUTATED            2          7        3
  2Q LOSS WILD-TYPE         33         47       18
D45V4, multiclass
            clus
vv           2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  I/II NOS                 2                11
  STAGE 0                  1                 6
  STAGE I                  5                24
  STAGE IA                 1                17
  STAGE IB                 4                24
  STAGE II                 4                22
  STAGE IIA                1                13
  STAGE IIB                4                15
  STAGE IIC                3                12
  STAGE III                4                35
  STAGE IIIA               3                12
  STAGE IIIB               2                33
  STAGE IIIC               7                47
  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 68 54
D45V5, multiclass
       clus
vv      2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  T0+T1               7                57
  T2                  8                65
  T3                 13                68
  T4                 13                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
  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    41   4
  2Q LOSS WILD-TYPE 278  18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED     41    4
  2Q LOSS WILD-TYPE  278   18
   clus
vv  2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  0              41               278
  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  49
  2Q LOSS WILD-TYPE  45 271
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      2   49
  2Q LOSS WILD-TYPE   45  271
     clus
vv    2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  NO                2                45
  YES              49               271
[1] 2 2
[1] FALSE
D45V10, continuous
D45V11, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED    21  30
  2Q LOSS WILD-TYPE 117 199
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED     21   30
  2Q LOSS WILD-TYPE  117  199
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  FEMALE              21               117
  MALE                30               199
[1] 2 2
[1] FALSE
D45V12, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED    43   8
  2Q LOSS WILD-TYPE 276  39
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED     43    8
  2Q LOSS WILD-TYPE  276   39
     clus
vv    2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  NO               43               276
  YES               8                39
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  2Q LOSS MUTATED       0                         0    48
  2Q LOSS WILD-TYPE     5                         1   305
D45V13, multiclass
                           clus
vv                          2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  ASIAN                                   0                 5
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  48               305
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V14, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED     2  47
  2Q LOSS WILD-TYPE   5 305
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      2   47
  2Q LOSS WILD-TYPE    5  305
                        clus
vv                       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                 5
  NOT HISPANIC OR LATINO              47               305
[1] 2 2
[1] FALSE

Clustering(46) Variable = 3P LOSS MUTATION ANALYSIS
D46V1, survival
                   sevent
clus2                 0   1
  3P LOSS MUTATED    22  25
  3P LOSS WILD-TYPE 106  99
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               47               205 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               25                99 
$`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-A2JN TCGA-D3-A3C6 TCGA-D3-A5GU TCGA-D3-A8GP TCGA-D9-A1X3 TCGA-D9-A4Z6 
       64.83        58.06       124.08       135.12        10.78        18.44 
TCGA-DA-A1HV TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A95Y TCGA-EE-A17Y 
       76.34       150.61       110.53        60.10        14.14        24.89 
TCGA-EE-A20C TCGA-EE-A29G TCGA-EE-A29P TCGA-EE-A2GH TCGA-EE-A2M6 TCGA-EE-A2MF 
       75.55        44.28        27.16       201.60       103.13       209.79 
TCGA-EE-A3AA TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-EE-A3JB TCGA-ER-A195 TCGA-ER-A197 
      124.31        67.89        45.90       168.85        34.45        10.49 
TCGA-ER-A19H TCGA-ER-A19S TCGA-ER-A2ND TCGA-ER-A2NG TCGA-FR-A8YC TCGA-FS-A1ZM 
      150.12        47.18         4.70        28.67        10.06        78.61 
TCGA-FS-A1ZQ TCGA-FS-A4F8 TCGA-FS-A4FD TCGA-FW-A3TU TCGA-GF-A6C8 TCGA-GN-A262 
      130.95       173.19        80.68        55.59         1.91        53.29 
TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 TCGA-WE-AAA4 TCGA-Z2-AA3S 
      117.93        17.06        42.48        24.99        91.23 

$`3P LOSS WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A8GI TCGA-EB-A5SG TCGA-EE-A180 
        9.76        62.07        38.76        13.41        33.24        31.96 
TCGA-EE-A20H TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 
      166.75       269.03        52.90       134.40        27.35        19.04 
TCGA-FR-A729 TCGA-FW-A3R5 TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-3N-A9WC TCGA-3N-A9WD 
      216.43        36.95        52.73         7.40        60.46        12.99 
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q6 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB 
        8.42        15.72        49.35        19.04        76.41        62.60 
TCGA-D3-A2J6 TCGA-D3-A2J8 TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JG TCGA-D3-A2JH 
       25.64        62.86       168.00        86.30       107.61        36.30 
TCGA-D3-A2JL TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE 
      171.58        66.08        43.53       140.98        40.01        59.70 
TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F 
       24.53         9.34        90.21        23.67       173.85        30.67 
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-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6EC TCGA-D9-A6EG 
       70.62        36.53        15.02        16.90        69.21        22.85 
TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 
      138.67        68.68        64.83        58.85        30.44       225.11 
TCGA-DA-A3F8 TCGA-DA-A95V TCGA-DA-A95W TCGA-DA-A95X TCGA-DA-A95Z TCGA-EB-A44Q 
        8.71        72.10         0.76        65.03        12.30         3.91 
TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A182 
       16.41        52.41        18.21        13.15        20.38         0.00 
TCGA-EE-A183 TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
       26.24        79.20        75.22        76.14        12.99         0.26 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 
       47.41        47.74        61.12       346.49       185.19       115.43 
TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GJ TCGA-EE-A2GK 
       30.02        77.98        26.14        12.95        68.65        10.62 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
       32.48        18.35        93.63         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-A2MS 
       63.25        89.26       104.78       145.45       227.01       143.93 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
       23.51        53.26       122.73        64.04         4.41        54.51 
TCGA-EE-A3AF TCGA-EE-A3J4 TCGA-EE-A3J8 TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A199 
        6.28       111.85         3.35        19.86       135.98         7.82 
TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19L 
        4.54        53.29        39.81        11.47       184.60        99.06 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19W TCGA-ER-A1A1 
       59.84        42.51       120.76        49.71       146.63        73.05 
TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
       22.36        16.87        10.19       173.29        68.52        15.48 
TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A7U8 
       32.05        74.47         4.50       174.21         4.14        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-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZS 
      312.07        32.78        43.92         7.82        36.33       136.27 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 
       35.28         4.47        23.21         5.29         3.06        30.90 
TCGA-FS-A4F4 TCGA-FS-A4F9 TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
       66.67        13.28        11.54        19.30         9.90        18.25 
TCGA-GN-A265 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-GN-A8LK 
       96.92         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-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO 
      185.13        92.84        47.54        65.42        12.69        21.90 
TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-XV-AB01 
       62.89        10.95        48.39         1.94        37.32         6.61 
TCGA-YG-AA3O 
       28.21 

  3P LOSS MUTATED 3P LOSS WILD-TYPE 
             1.91              0.00 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
           209.79            346.49 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
            58.06             43.53 
[1] "1.9 - 209.8 (58.1)" "0.0 - 346.5 (43.5)"
[1] "hr=" "1"  
D46V2, survival
                   sevent
clus2                 0   1
  3P LOSS MUTATED    28  30
  3P LOSS WILD-TYPE 138 162
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               58               300 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               30               162 
$`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-A2JN TCGA-D3-A3C6 TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GP TCGA-D9-A1X3 
       66.48        58.06       125.19        30.84       152.75        18.12 
TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I2 
       18.44         9.90        25.18        76.57        36.03       176.55 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A95Y TCGA-EE-A17Y TCGA-EE-A20C TCGA-EE-A29G 
      135.02        88.87        14.14        27.22       151.27        72.07 
TCGA-EE-A29P TCGA-EE-A2GC TCGA-EE-A2GH TCGA-EE-A2M6 TCGA-EE-A2MF TCGA-EE-A3AA 
       56.42        67.43       220.24       129.27       268.73       124.31 
TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-EE-A3JB TCGA-ER-A195 TCGA-ER-A197 
       41.59       172.18        64.08       201.80        35.44        13.94 
TCGA-ER-A19H TCGA-ER-A19S TCGA-ER-A2ND TCGA-ER-A2NG TCGA-FR-A7U9 TCGA-FR-A8YC 
      152.35        49.48        23.34        48.99        18.77        34.82 
TCGA-FS-A1YX TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A4F8 TCGA-FS-A4FD TCGA-FW-A3TU 
       48.59       101.26       133.55       174.84        80.68        55.59 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A4U9 
        2.04       139.89       117.93        64.44        62.79        22.13 
TCGA-WE-A8ZX TCGA-WE-AAA4 TCGA-YG-AA3P TCGA-Z2-AA3S 
       35.80        24.99        14.43        96.99 

$`3P LOSS WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-D3-A8GI TCGA-EB-A5SG 
       27.65        62.07        46.32        13.87        58.52        68.25 
TCGA-EB-A5SH TCGA-EE-A180 TCGA-EE-A184 TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GD 
       54.02        94.98        68.15       168.26         2.60       340.14 
TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 TCGA-ER-A198 TCGA-FR-A729 
      126.81       134.40        27.35        31.40        50.76       220.80 
TCGA-FS-A1ZF TCGA-FW-A3R5 TCGA-QB-AA9O TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-3N-A9WB 
       15.45        36.95        18.05        61.15        21.40        17.03 
TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q6 TCGA-D3-A1Q8 
       66.48        12.99        16.57        16.67        71.80        28.08 
TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J8 TCGA-D3-A2J9 
       31.59        90.90        95.74        43.43        65.49        23.77 
TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK 
      168.00        86.76        11.87       113.52        42.08        12.10 
TCGA-D3-A2JL TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3CB 
      171.58        66.08        59.57       130.72        46.98       166.52 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU 
       86.93        60.23        24.53         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-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-A8GJ 
      178.32        18.18        79.59        23.61        26.43       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-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HY TCGA-DA-A1I0 
       15.39        22.29        77.56        22.95       144.89        20.38 
TCGA-DA-A1I1 TCGA-DA-A1I4 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
      222.51        35.93        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        43.36        72.10        37.35 
TCGA-DA-A95X TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5UL 
       73.94        13.02        13.87        10.36        20.35        29.29 
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-A185 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20I 
       14.70        26.89         4.96       133.81        91.56        13.55 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H 
       63.35        85.08        78.97        13.97        63.78        64.64 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T 
       56.84        18.61        66.74        14.47        61.28       369.93 
TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
       25.87       195.02        17.92        46.82       115.96        59.64 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GJ 
       39.29        86.14        59.28       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-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M7 TCGA-EE-A2M8 
       81.21        44.88        94.82        21.67        28.83        19.76 
TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
       61.51        47.28       103.27       103.20        16.96       204.66 
TCGA-EE-A2MJ TCGA-EE-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-A2MU TCGA-EE-A3AB TCGA-EE-A3AC 
       43.23       162.48        71.21        53.26       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-A3J8 TCGA-EE-A3JA TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A199 
       34.32        53.19        51.35       134.33       152.81         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 
      302.07         6.44       131.51        61.05        44.09       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       105.07        43.82        20.15 
TCGA-ER-A2NF TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL 
       28.83        41.56       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-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-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK 
       53.52        46.45         9.70        32.75        47.38        23.93 
TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW 
       74.73        11.41       148.80        53.16        26.56        49.48 
TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 
       27.09        27.02        77.82        50.14        66.67        28.73 
TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FW-A3I3 TCGA-FW-A3TV TCGA-FW-A5DY 
       34.03        26.73        54.41        17.46        13.51        19.30 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C9 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A26A 
        9.90        19.43        15.78        96.92        10.13        32.48 
TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A8LK 
       48.00       121.91        39.35        10.42        48.89        50.10 
TCGA-GN-A8LL TCGA-GN-A9SD TCGA-HR-A2OG TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X 
       21.37        59.41         0.23        65.88       368.78       297.90 
TCGA-QB-A6FS TCGA-RP-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-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-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 
       70.52        63.22        11.80        49.51        12.16        40.41 
TCGA-XV-AB01 TCGA-YD-A89C TCGA-YD-A9TA TCGA-YG-AA3O TCGA-Z2-A8RT TCGA-Z2-AA3V 
       13.25         6.90        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 
           65.460            49.495 
[1] "2.0 - 268.7 (65.5)" "0.2 - 369.9 (49.5)"
[1] "hr=" "1.2"
D46V3, continuous
                   vv
clus                I/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       26
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  3P LOSS MUTATED           0         5         2         7          4
  3P LOSS WILD-TYPE        14        14        13        32         11
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  3P LOSS MUTATED            7         10        2
  3P LOSS WILD-TYPE         28         44       19
D46V4, multiclass
            clus
vv           3P LOSS MUTATED 3P LOSS WILD-TYPE
  I/II NOS                 2                11
  STAGE 0                  1                 6
  STAGE I                  6                23
  STAGE IA                 1                17
  STAGE IB                 4                24
  STAGE II                 0                26
  STAGE IIA                0                14
  STAGE IIB                5                14
  STAGE IIC                2                13
  STAGE III                7                32
  STAGE IIIA               4                11
  STAGE IIIB               7                28
  STAGE IIIC              10                44
  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 11 11
  3P LOSS WILD-TYPE    51 61 70 56
D46V5, multiclass
       clus
vv      3P LOSS MUTATED 3P LOSS WILD-TYPE
  T0+T1              13                51
  T2                 12                61
  T3                 11                70
  T4                 11                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
  3P LOSS MUTATED    23  13   9   7
  3P LOSS WILD-TYPE 154  52  30  38
D46V6, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  N0              23               154
  N1              13                52
  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    51   2
  3P LOSS WILD-TYPE 268  20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     51    2
  3P LOSS WILD-TYPE  268   20
   clus
vv  3P LOSS MUTATED 3P LOSS WILD-TYPE
  0              51               268
  1               2                20
[1] 2 2
[1] FALSE
D46V8, binary
                   cls
clus                  0   1
  3P LOSS MUTATED    19  15
  3P LOSS WILD-TYPE 115  75
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     19   15
  3P LOSS WILD-TYPE  115   75
     clus
vv    3P LOSS MUTATED 3P LOSS WILD-TYPE
  NO               19               115
  YES              15                75
[1] 2 2
[1] FALSE
D46V9, binary
                   cls
clus                  0   1
  3P LOSS MUTATED     7  53
  3P LOSS WILD-TYPE  40 267
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      7   53
  3P LOSS WILD-TYPE   40  267
     clus
vv    3P LOSS MUTATED 3P LOSS WILD-TYPE
  NO                7                40
  YES              53               267
[1] 2 2
[1] FALSE
D46V10, continuous
D46V11, binary
                   cls
clus                  0   1
  3P LOSS MUTATED    26  34
  3P LOSS WILD-TYPE 112 195
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     26   34
  3P LOSS WILD-TYPE  112  195
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  FEMALE              26               112
  MALE                34               195
[1] 2 2
[1] FALSE
D46V12, binary
                   cls
clus                  0   1
  3P LOSS MUTATED    55   5
  3P LOSS WILD-TYPE 264  42
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     55    5
  3P LOSS WILD-TYPE  264   42
     clus
vv    3P LOSS MUTATED 3P LOSS WILD-TYPE
  NO               55               264
  YES               5                42
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3P LOSS MUTATED       1                         0    58
  3P LOSS WILD-TYPE     4                         1   295
D46V13, multiclass
                           clus
vv                          3P LOSS MUTATED 3P LOSS WILD-TYPE
  ASIAN                                   1                 4
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  58               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"
D46V14, binary
                   cls
clus                  0   1
  3P LOSS MUTATED     1  58
  3P LOSS WILD-TYPE   6 294
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      1   58
  3P LOSS WILD-TYPE    6  294
                        clus
vv                       3P LOSS MUTATED 3P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 6
  NOT HISPANIC OR LATINO              58               294
[1] 2 2
[1] FALSE

Clustering(47) Variable = 3Q LOSS MUTATION ANALYSIS
D47V1, survival
                   sevent
clus2                 0   1
  3Q LOSS MUTATED    17  22
  3Q LOSS WILD-TYPE 111 102
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               39               213 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               22               102 
$`3Q LOSS MUTATED`
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A3C6 TCGA-D3-A5GU TCGA-D3-A8GP 
       31.89       110.93       133.25        58.06       124.08       135.12 
TCGA-D3-A8GR TCGA-D9-A1X3 TCGA-D9-A4Z6 TCGA-DA-A1HV TCGA-DA-A1I2 TCGA-DA-A1I5 
       36.53        10.78        18.44        76.34       150.61       110.53 
TCGA-DA-A1I7 TCGA-DA-A95V TCGA-DA-A95Y TCGA-EE-A17Y TCGA-EE-A20C TCGA-EE-A29G 
       60.10        72.10        14.14        24.89        75.55        44.28 
TCGA-EE-A29H TCGA-EE-A29P TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A3J3 TCGA-EE-A3JI 
       47.41        27.16       201.60        68.65        67.89       135.98 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A19H TCGA-ER-A19S TCGA-FR-A8YC TCGA-FS-A1ZM 
       34.45        10.49       150.12        47.18        10.06        78.61 
TCGA-FS-A4F8 TCGA-FS-A4FD TCGA-FW-A3TU TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A267 
      173.19        80.68        55.59        53.29       117.93        17.06 
TCGA-GN-A268 TCGA-WE-AAA4 TCGA-Z2-AA3S 
       42.48        24.99        91.23 

$`3Q LOSS WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A8GI TCGA-EB-A5SG TCGA-EE-A180 
        9.76        62.07        38.76        13.41        33.24        31.96 
TCGA-EE-A20H TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 
      166.75       269.03        52.90       134.40        27.35        19.04 
TCGA-FR-A729 TCGA-FW-A3R5 TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-3N-A9WC TCGA-3N-A9WD 
      216.43        36.95        52.73         7.40        60.46        12.99 
TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q6 TCGA-D3-A1Q8 TCGA-D3-A1QA 
       14.83         8.42        15.72        49.35        19.04        76.41 
TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JB 
       62.60        25.64        45.99        62.86        15.75       168.00 
TCGA-D3-A2JC TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
       86.30       107.61        36.30       171.58        64.83        66.08 
TCGA-D3-A2JP TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO 
       43.53       140.98        40.01        59.70        24.53         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K 
       90.21        23.67       173.85        30.67       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-D9-A3Z1 
       23.61       179.97       120.00        69.53        70.62        15.02 
TCGA-D9-A3Z3 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1IA 
       16.90        69.21        22.85       138.67        68.68        64.83 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-DA-A95W TCGA-DA-A95X 
       58.85        30.44       225.11         8.71         0.76        65.03 
TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X 
       12.30         3.91        16.41        52.41        18.21        13.15 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29C 
       20.38         0.00        26.24        79.20        75.22        76.14 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29M TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W 
       12.99         0.26        47.74        61.12       346.49       185.19 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GK 
      115.43        30.02        77.98        26.14        12.95        10.62 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
       32.48        18.35        93.63         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-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB 
      227.01       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-ER-A199 TCGA-ER-A19A TCGA-ER-A19B 
        3.35       168.85        19.86         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       184.60        99.06        59.84        42.51 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
      120.76        49.71       146.63        73.05        22.36         4.70 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
       16.87        10.19        28.67       173.29        68.52        15.48 
TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A7U8 
       32.05        74.47         4.50       174.21         4.14        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-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZQ 
      312.07        32.78        43.92         7.82        36.33       130.95 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ 
      136.27        35.28         4.47        23.21         5.29         3.06 
TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F9 TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
       30.90        66.67        13.28        11.54        19.30         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A265 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 
       18.25         1.91        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-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        47.54        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-XV-AB01 TCGA-YG-AA3O 
       37.32         6.61        28.21 

  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
            10.06              0.00 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
           201.60            346.49 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
            60.10             43.53 
[1] "10.1 - 201.6 (60.1)" "0.0 - 346.5 (43.5)" 
[1] "hr=" "1"  
D47V2, survival
                   sevent
clus2                 0   1
  3Q LOSS MUTATED    23  27
  3Q LOSS WILD-TYPE 143 165
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               50               308 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               27               165 
$`3Q LOSS MUTATED`
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A3C6 TCGA-D3-A5GU TCGA-D3-A8GP 
      112.04       112.57       133.25        58.06       125.19       152.75 
TCGA-D3-A8GR TCGA-D9-A1X3 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-DA-A1HV 
      129.63        18.12        18.44         9.90        25.18        76.57 
TCGA-DA-A1HW TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A95V TCGA-DA-A95Y 
       36.03       176.55       135.02        88.87        72.10        14.14 
TCGA-EE-A17Y TCGA-EE-A20C TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29P TCGA-EE-A2GC 
       27.22       151.27        72.07        64.64        56.42        67.43 
TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3JI TCGA-ER-A195 
      220.24       107.38        41.59       172.18       152.81        35.44 
TCGA-ER-A197 TCGA-ER-A19H TCGA-ER-A19S TCGA-FR-A7U9 TCGA-FR-A8YC TCGA-FS-A1YX 
       13.94       152.35        49.48        18.77        34.82        48.59 
TCGA-FS-A1ZM TCGA-FS-A4F8 TCGA-FS-A4FD TCGA-FW-A3TU TCGA-GN-A262 TCGA-GN-A264 
      101.26       174.84        80.68        55.59       139.89       117.93 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A4U9 TCGA-GN-A8LL TCGA-WE-A8ZX TCGA-WE-AAA4 
       64.44        62.79        22.13        21.37        35.80        24.99 
TCGA-YG-AA3P TCGA-Z2-AA3S 
       14.43        96.99 

$`3Q LOSS WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-D3-A8GI TCGA-EB-A5SG 
       27.65        62.07        46.32        13.87        58.52        68.25 
TCGA-EB-A5SH TCGA-EE-A180 TCGA-EE-A184 TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GD 
       54.02        94.98        68.15       168.26         2.60       340.14 
TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 TCGA-ER-A198 TCGA-FR-A729 
      126.81       134.40        27.35        31.40        50.76       220.80 
TCGA-FS-A1ZF TCGA-FW-A3R5 TCGA-QB-AA9O TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-3N-A9WB 
       15.45        36.95        18.05        61.15        21.40        17.03 
TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q6 
       66.48        12.99        14.93        16.57        16.67        71.80 
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-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-A3CB TCGA-D3-A3CC TCGA-D3-A3CE 
       59.57       130.72        46.98       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-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       26.89       125.79       135.75       137.92       178.32        18.18 
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-A8GQ TCGA-D3-A8GS TCGA-D3-A8GV 
       89.13       107.15       161.00        29.06       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-A6EC TCGA-D9-A6EG TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I4 
       77.56        22.95       144.89        20.38       222.51        35.93 
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-A95Z TCGA-EB-A44Q 
      225.96        43.36        37.35        73.94        13.02        13.87 
TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 
       10.36        20.35        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-A185 
       29.82         8.65        33.73        14.70        26.89         4.96 
TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C 
      133.81        91.56        13.55        63.35        85.08        78.97 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29R 
       13.97        63.78        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-A2GB TCGA-EE-A2GE 
      115.96        59.64        39.29        86.14        59.28       173.79 
TCGA-EE-A2GI TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP 
       48.72        54.74        79.66        75.48       102.12        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-A2MS TCGA-EE-A2MT 
      167.90        47.54       248.65        43.23       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-A3AH TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 
       13.81       138.81       127.20        36.95        64.08        34.32 
TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A199 TCGA-ER-A19A 
       53.19       201.80        51.35       134.33         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       302.07 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
        6.44       131.51        61.05        44.09       162.08        50.89 
TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
        8.88       148.18       105.07        43.82        23.34        20.15 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
       28.83        48.99        41.56       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-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-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ 
      357.37        53.52        46.45         9.70        32.75        47.38 
TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT 
       23.93        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-FW-A3I3 
       66.67        28.73        34.03        26.73        54.41        17.46 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 
       13.51        19.30         9.90        19.43         2.04        15.78 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A4U4 
       96.92        10.13        32.48        48.00       121.91        39.35 
TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A8LK TCGA-GN-A9SD TCGA-HR-A2OG TCGA-HR-A2OH 
       10.42        48.89        50.10        59.41         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-A825 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1Q TCGA-W3-AA1R 
      228.16        63.02       121.08         4.01        69.07       111.09 
TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K6 
       42.08       219.16       105.04        24.03        49.05        17.95 
TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZY 
      101.33        58.98        70.52        63.22        11.80        49.51 
TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-XV-AB01 TCGA-YD-A89C TCGA-YD-A9TA TCGA-YG-AA3O 
       12.16        40.41        13.25         6.90        49.18        37.94 
TCGA-Z2-A8RT TCGA-Z2-AA3V 
       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 
           66.035            49.495 
[1] "9.9 - 220.2 (66.0)" "0.2 - 369.9 (49.5)"
[1] "hr=" "1.1"
D47V3, continuous
                   vv
clus                I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  3Q LOSS MUTATED          1       2       4        3        4        0
  3Q LOSS WILD-TYPE       12       5      25       15       24       26
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  3Q LOSS MUTATED           0         4         4         4          3
  3Q LOSS WILD-TYPE        14        15        11        35         12
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  3Q LOSS MUTATED            6          7        1
  3Q LOSS WILD-TYPE         29         47       20
D47V4, multiclass
            clus
vv           3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  I/II NOS                 1                12
  STAGE 0                  2                 5
  STAGE I                  4                25
  STAGE IA                 3                15
  STAGE IB                 4                24
  STAGE II                 0                26
  STAGE IIA                0                14
  STAGE IIB                4                15
  STAGE IIC                4                11
  STAGE III                4                35
  STAGE IIIA               3                12
  STAGE IIIB               6                29
  STAGE IIIC               7                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
  3Q LOSS MUTATED      11 10  6 12
  3Q LOSS WILD-TYPE    53 63 75 55
D47V5, multiclass
       clus
vv      3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  T0+T1              11                53
  T2                 10                63
  T3                  6                75
  T4                 12                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
  3Q LOSS MUTATED    24   8   8   5
  3Q LOSS WILD-TYPE 153  57  31  40
D47V6, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  N0              24               153
  N1               8                57
  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    43   1
  3Q LOSS WILD-TYPE 276  21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED     43    1
  3Q LOSS WILD-TYPE  276   21
   clus
vv  3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  0              43               276
  1               1                21
[1] 2 2
[1] FALSE
D47V8, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED    17  13
  3Q LOSS WILD-TYPE 117  77
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED     17   13
  3Q LOSS WILD-TYPE  117   77
     clus
vv    3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  NO               17               117
  YES              13                77
[1] 2 2
[1] FALSE
D47V9, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED     5  46
  3Q LOSS WILD-TYPE  42 274
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      5   46
  3Q LOSS WILD-TYPE   42  274
     clus
vv    3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  NO                5                42
  YES              46               274
[1] 2 2
[1] FALSE
D47V10, continuous
D47V11, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED    22  29
  3Q LOSS WILD-TYPE 116 200
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED     22   29
  3Q LOSS WILD-TYPE  116  200
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  FEMALE              22               116
  MALE                29               200
[1] 2 2
[1] FALSE
D47V12, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED    46   5
  3Q LOSS WILD-TYPE 273  42
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED     46    5
  3Q LOSS WILD-TYPE  273   42
     clus
vv    3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  NO               46               273
  YES               5                42
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3Q LOSS MUTATED       1                         0    49
  3Q LOSS WILD-TYPE     4                         1   304
D47V13, multiclass
                           clus
vv                          3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  ASIAN                                   1                 4
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  49               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"
D47V14, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED     1  49
  3Q LOSS WILD-TYPE   6 303
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      1   49
  3Q LOSS WILD-TYPE    6  303
                        clus
vv                       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 6
  NOT HISPANIC OR LATINO              49               303
[1] 2 2
[1] FALSE

Clustering(48) Variable = 4P LOSS MUTATION ANALYSIS
D48V1, survival
                   sevent
clus2                 0   1
  4P LOSS MUTATED    25  31
  4P LOSS WILD-TYPE 103  93
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               56               196 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               31                93 
$`4P LOSS MUTATED`
TCGA-D3-A8GI TCGA-EE-A180 TCGA-EE-A2GO TCGA-ER-A193 TCGA-WE-AAA3 TCGA-D3-A1Q1 
       13.41        31.96        52.90        19.04         7.40         8.42 
TCGA-D3-A1Q4 TCGA-D3-A2J6 TCGA-D3-A2JA TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A3CC 
       31.89        25.64        15.75        64.83        66.08        40.01 
TCGA-D3-A3MR TCGA-D3-A51F TCGA-D3-A8GC TCGA-D3-A8GM TCGA-D9-A3Z3 TCGA-D9-A4Z6 
       90.21        30.67        78.21        70.62        16.90        18.44 
TCGA-D9-A6EC TCGA-DA-A3F8 TCGA-DA-A95X TCGA-EB-A5KH TCGA-EE-A17Y TCGA-EE-A20C 
       69.21         8.71        65.03        16.41        24.89        75.55 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29M TCGA-EE-A29T TCGA-EE-A29W 
       75.22        76.14        12.99        47.74       346.49       185.19 
TCGA-EE-A2GH TCGA-EE-A2GM TCGA-EE-A2M6 TCGA-EE-A2MM TCGA-EE-A2MS TCGA-EE-A3J8 
      201.60        18.35       103.13       145.45       143.93         3.35 
TCGA-ER-A197 TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19S TCGA-ER-A2ND TCGA-ER-A2NG 
       10.49        53.29        11.47        47.18         4.70        28.67 
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-YG-AA3O 
        1.94        28.21 

$`4P LOSS WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A20H TCGA-EE-A2GD 
        9.76        62.07        38.76        33.24       166.75       269.03 
TCGA-EE-A2MR TCGA-EE-A3JD TCGA-FR-A729 TCGA-FW-A3R5 TCGA-WE-A8K5 TCGA-3N-A9WC 
      134.40        27.35       216.43        36.95        52.73        60.46 
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-A2JB 
       19.04        76.41        62.60        45.99        62.86       168.00 
TCGA-D3-A2JC TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JP TCGA-D3-A3C6 
       86.30       107.61        36.30       171.58        43.53        58.06 
TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MU TCGA-D3-A51E 
      140.98        59.70        24.53         9.34        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-A5GR TCGA-D3-A5GU TCGA-D3-A8GD TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL 
      177.86       124.08        23.61       179.97       120.00        69.53 
TCGA-D3-A8GP TCGA-D3-A8GR TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A6EG TCGA-DA-A1HV 
      135.12        36.53        10.78        15.02        22.85        76.34 
TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA 
      138.67        68.68       150.61       110.53        60.10        64.83 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A95V TCGA-DA-A95W TCGA-DA-A95Y 
       58.85        30.44       225.11        72.10         0.76        14.14 
TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A181 
       12.30         3.91        52.41        18.21        13.15        20.38 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20F TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H 
        0.00        26.24        79.20         0.26        44.28        47.41 
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-A2GE TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GP 
       12.95        68.65        10.62        32.48        93.63         0.76 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC 
        0.20        71.31        81.99        15.25         5.75        23.77 
TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML 
      209.79        94.19       171.85        63.25        89.26       104.78 
TCGA-EE-A2MP TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC 
      227.01        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-A3JB TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A199 TCGA-ER-A19A 
      168.85        19.86       135.98        34.45         7.82         4.54 
TCGA-ER-A19C TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
       39.81       184.60       150.12        99.06        59.84        42.51 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE 
      120.76        49.71       146.63        73.05        22.36        16.87 
TCGA-ER-A2NF TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A 
       10.19       173.29        68.52        32.05         4.50       174.21 
TCGA-FR-A69P TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z3 
        4.14         5.65        10.06       171.78        49.74         8.35 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM 
      312.07        32.78        43.92         7.82        36.33        78.61 
TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY 
      130.95       136.27        35.28         4.47        23.21         5.29 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TV 
        3.06        30.90        66.67        13.28        80.68        11.54 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
       19.30         9.90        18.25        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-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-A828 TCGA-W3-AA1Q TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 
      174.12       120.07        44.05       185.13        92.84        47.54 
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-AAA0 TCGA-WE-AAA4 TCGA-XV-AB01 TCGA-Z2-AA3S 
       37.32        24.99         6.61        91.23 

  4P LOSS MUTATED 4P LOSS WILD-TYPE 
             1.91              0.00 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
           346.49            312.07 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
           31.925            47.475 
[1] "1.9 - 346.5 (31.9)" "0.0 - 312.1 (47.5)"
[1] "hr=" "1.3"
D48V2, survival
                   sevent
clus2                 0   1
  4P LOSS MUTATED    37  41
  4P LOSS WILD-TYPE 129 151
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               78               280 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               41               151 
$`4P LOSS MUTATED`
TCGA-D3-A8GI TCGA-EE-A180 TCGA-EE-A2GO TCGA-ER-A193 TCGA-WE-AAA3 TCGA-D3-A1Q1 
       58.52        94.98       126.81        31.40        21.40        16.57 
TCGA-D3-A1Q4 TCGA-D3-A2J6 TCGA-D3-A2JA TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A3CC 
      112.04        43.43       115.53        66.48        66.08        86.93 
TCGA-D3-A3MR TCGA-D3-A3MV TCGA-D3-A51F TCGA-D3-A51N TCGA-D3-A8GC TCGA-D3-A8GM 
      103.59        45.30        55.73        22.62        79.59       107.15 
TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6EC TCGA-DA-A1HW 
      151.53        54.67        22.29        18.44        77.56        36.03 
TCGA-DA-A3F8 TCGA-DA-A95X TCGA-EB-A44R TCGA-EB-A5KH TCGA-EE-A17Y TCGA-EE-A20B 
       43.36        73.94        10.36        20.35        27.22       133.81 
TCGA-EE-A20C TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29M TCGA-EE-A29T 
      151.27        85.08        78.97        13.97        56.84       369.93 
TCGA-EE-A29W TCGA-EE-A2A5 TCGA-EE-A2GH TCGA-EE-A2GM TCGA-EE-A2M5 TCGA-EE-A2M6 
      195.02        39.29       220.24        75.48        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-A197 TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19S TCGA-ER-A19T 
       13.94        98.40        12.59        13.02        49.48         8.88 
TCGA-ER-A2ND TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3EV TCGA-ER-A42L TCGA-FR-A7U8 
       23.34        48.99        41.56        46.98       149.03        27.85 
TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1ZA TCGA-FS-A4F8 TCGA-FW-A3TU TCGA-GF-A6C8 
      202.65        28.08        27.72       174.84        55.59         2.04 
TCGA-GF-A6C9 TCGA-GN-A266 TCGA-GN-A4U3 TCGA-W3-A825 TCGA-W3-AA1R TCGA-W3-AA1V 
       15.78        10.13       121.91        63.02       111.09        42.08 
TCGA-WE-A8JZ TCGA-WE-A8ZX TCGA-WE-AA9Y TCGA-YD-A9TA TCGA-YG-AA3O TCGA-Z2-A8RT 
       24.03        35.80        12.16        49.18        37.94        27.58 

$`4P LOSS WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EB-A5SG TCGA-EB-A5SH 
       27.65        62.07        46.32        13.87        68.25        54.02 
TCGA-EE-A184 TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2MR TCGA-EE-A3JD 
       68.15       168.26         2.60       340.14       134.40        27.35 
TCGA-ER-A198 TCGA-FR-A729 TCGA-FS-A1ZF TCGA-FW-A3R5 TCGA-QB-AA9O TCGA-WE-A8K5 
       50.76       220.80        15.45        36.95        18.05        61.15 
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-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-A3CB TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO 
       58.06        46.98       166.52        60.23        24.53         9.34 
TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R 
       39.75       174.84        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-A8GD TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GK 
      125.19        30.84        23.61        26.43       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-A1JW TCGA-D9-A1JX TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A6E9 
      167.70         3.65         7.10        18.12        15.39         9.90 
TCGA-D9-A6EA TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 
       25.18        22.95        76.57       144.89        20.38       222.51 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA 
      176.55        35.93       135.02        88.87        53.92        65.92 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A95V 
       40.60        68.09        33.93        10.49       225.96        72.10 
TCGA-DA-A95W TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5UL TCGA-EB-A5UN 
       37.35        14.14        13.02        13.87        29.29        58.92 
TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 
        7.04        36.46        29.82         8.65        33.73        14.70 
TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29E 
       26.89         4.96        91.56        13.55        63.35        63.78 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
       72.07        64.64        18.61        56.42        66.74        14.47 
TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
       61.28        25.87        17.92        46.82       115.96        59.64 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GJ 
       86.14        59.28        67.43       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-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-A2MK TCGA-EE-A2ML TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MT TCGA-EE-A2MU 
      180.39       216.66        47.54       248.65        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-A3JA 
      138.81       172.18       127.20        36.95        64.08        53.19 
TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A199 TCGA-ER-A19A 
      201.80       134.33       152.81        35.44         9.17        77.75 
TCGA-ER-A19C TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L 
       48.89        26.37       302.07       152.35         6.44       131.51 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19W TCGA-ER-A1A1 
       61.05        44.09       162.08        50.89       148.18       105.07 
TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3PL 
       43.82        20.15        28.83       247.04        93.01        33.21 
TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A7U9 TCGA-FR-A7UA 
       12.95        92.98       174.21        15.72        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-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP 
        9.70        32.75        47.38        23.93       101.26        74.73 
TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW 
      133.55        11.41       148.80        53.16        26.56        49.48 
TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 
       27.09        27.02        77.82        50.14        66.67        28.73 
TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TV 
       34.03        26.73        54.41        80.68        17.46        13.51 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
       19.30         9.90        19.43       139.89       117.93        96.92 
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-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-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-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO 
      105.04        49.05        17.95       101.33        58.98        70.52 
TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-XV-AB01 
       63.22        11.80        49.51        40.41        24.99        13.25 
TCGA-YD-A89C TCGA-YG-AA3P TCGA-Z2-AA3S TCGA-Z2-AA3V 
        6.90        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 
           49.085            53.390 
[1] "2.0 - 369.9 (49.1)" "0.2 - 368.8 (53.4)"
[1] "hr=" "1"  
D48V3, continuous
                   vv
clus                I/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       19
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  4P LOSS MUTATED           0         6         2         7          4
  4P LOSS WILD-TYPE        14        13        13        32         11
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  4P LOSS MUTATED           12         13        3
  4P LOSS WILD-TYPE         23         41       18
D48V4, multiclass
            clus
vv           4P LOSS MUTATED 4P LOSS WILD-TYPE
  I/II NOS                 1                12
  STAGE 0                  2                 5
  STAGE I                  6                23
  STAGE IA                 2                16
  STAGE IB                 6                22
  STAGE II                 7                19
  STAGE IIA                0                14
  STAGE IIB                6                13
  STAGE IIC                2                13
  STAGE III                7                32
  STAGE IIIA               4                11
  STAGE IIIB              12                23
  STAGE IIIC              13                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
  4P LOSS MUTATED      13 15 23 11
  4P LOSS WILD-TYPE    51 58 58 56
D48V5, multiclass
       clus
vv      4P LOSS MUTATED 4P LOSS WILD-TYPE
  T0+T1              13                51
  T2                 15                58
  T3                 23                58
  T4                 11                56
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  4P LOSS MUTATED    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 249  18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     70    4
  4P LOSS WILD-TYPE  249   18
   clus
vv  4P LOSS MUTATED 4P LOSS WILD-TYPE
  0              70               249
  1               4                18
[1] 2 2
[1] FALSE
D48V8, binary
                   cls
clus                  0   1
  4P LOSS MUTATED    32  19
  4P LOSS WILD-TYPE 102  71
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     32   19
  4P LOSS WILD-TYPE  102   71
     clus
vv    4P LOSS MUTATED 4P LOSS WILD-TYPE
  NO               32               102
  YES              19                71
[1] 2 2
[1] FALSE
D48V9, binary
                   cls
clus                  0   1
  4P LOSS MUTATED    10  70
  4P LOSS WILD-TYPE  37 250
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     10   70
  4P LOSS WILD-TYPE   37  250
     clus
vv    4P LOSS MUTATED 4P LOSS WILD-TYPE
  NO               10                37
  YES              70               250
[1] 2 2
[1] FALSE
D48V10, continuous
D48V11, binary
                   cls
clus                  0   1
  4P LOSS MUTATED    31  49
  4P LOSS WILD-TYPE 107 180
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     31   49
  4P LOSS WILD-TYPE  107  180
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  FEMALE              31               107
  MALE                49               180
[1] 2 2
[1] FALSE
D48V12, binary
                   cls
clus                  0   1
  4P LOSS MUTATED    70  10
  4P LOSS WILD-TYPE 249  37
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     70   10
  4P LOSS WILD-TYPE  249   37
     clus
vv    4P LOSS MUTATED 4P LOSS WILD-TYPE
  NO               70               249
  YES              10                37
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  4P LOSS MUTATED       3                         0    75
  4P LOSS WILD-TYPE     2                         1   278
D48V13, multiclass
                           clus
vv                          4P LOSS MUTATED 4P LOSS WILD-TYPE
  ASIAN                                   3                 2
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  75               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"
D48V14, binary
                   cls
clus                  0   1
  4P LOSS MUTATED     1  77
  4P LOSS WILD-TYPE   6 275
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      1   77
  4P LOSS WILD-TYPE    6  275
                        clus
vv                       4P LOSS MUTATED 4P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 6
  NOT HISPANIC OR LATINO              77               275
[1] 2 2
[1] FALSE

Clustering(49) Variable = 4Q LOSS MUTATION ANALYSIS
D49V1, survival
                   sevent
clus2                 0   1
  4Q LOSS MUTATED    25  31
  4Q LOSS WILD-TYPE 103  93
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               56               196 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               31                93 
$`4Q LOSS MUTATED`
TCGA-D3-A8GI TCGA-EE-A180 TCGA-EE-A2GO TCGA-ER-A193 TCGA-WE-AAA3 TCGA-D3-A1Q1 
       13.41        31.96        52.90        19.04         7.40         8.42 
TCGA-D3-A1Q4 TCGA-D3-A1Q8 TCGA-D3-A2JA TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A3CC 
       31.89        19.04        15.75        64.83        66.08        40.01 
TCGA-D3-A3MR TCGA-D3-A51F TCGA-D3-A8GC TCGA-D3-A8GM TCGA-D9-A3Z3 TCGA-D9-A4Z6 
       90.21        30.67        78.21        70.62        16.90        18.44 
TCGA-DA-A3F8 TCGA-DA-A95V TCGA-DA-A95X TCGA-EB-A5KH TCGA-EE-A17Y TCGA-EE-A181 
        8.71        72.10        65.03        16.41        24.89        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-A2M6 TCGA-EE-A2MM TCGA-EE-A2MS TCGA-EE-A3J8 TCGA-ER-A197 
       18.35       103.13       145.45       143.93         3.35        10.49 
TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19S TCGA-ER-A2ND TCGA-ER-A2NG TCGA-ER-A3EV 
       53.29        11.47        47.18         4.70        28.67        15.48 
TCGA-ER-A42L TCGA-FR-A7U8 TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A4F8 TCGA-FW-A3TU 
       74.47        26.20       195.98        27.62       173.19        55.59 
TCGA-GF-A6C8 TCGA-GN-A4U3 TCGA-GN-A8LK TCGA-W3-A825 TCGA-W3-AA1R TCGA-W3-AA1V 
        1.91       120.53        43.23         1.97        79.99         8.09 
TCGA-WE-AA9Y TCGA-YG-AA3O 
        1.94        28.21 

$`4Q LOSS WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A20H TCGA-EE-A2GD 
        9.76        62.07        38.76        33.24       166.75       269.03 
TCGA-EE-A2MR TCGA-EE-A3JD TCGA-FR-A729 TCGA-FW-A3R5 TCGA-WE-A8K5 TCGA-3N-A9WC 
      134.40        27.35       216.43        36.95        52.73        60.46 
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-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-A2JH TCGA-D3-A2JL TCGA-D3-A2JP TCGA-D3-A3C6 
       86.30       107.61        36.30       171.58        43.53        58.06 
TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MU TCGA-D3-A51E 
      140.98        59.70        24.53         9.34        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-A5GR TCGA-D3-A5GU TCGA-D3-A8GD TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL 
      177.86       124.08        23.61       179.97       120.00        69.53 
TCGA-D3-A8GP TCGA-D3-A8GR TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A6EC TCGA-D9-A6EG 
      135.12        36.53        10.78        15.02        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        68.68       150.61       110.53        60.10 
TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A95W TCGA-DA-A95Y 
       64.83        58.85        30.44       225.11         0.76        14.14 
TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A182 
       12.30         3.91        52.41        18.21        13.15         0.00 
TCGA-EE-A183 TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G 
       26.24        79.20        75.22        12.99         0.26        44.28 
TCGA-EE-A29H TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 
       47.41        27.16        61.12       115.43        30.02        77.98 
TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN 
       26.14        12.95        68.65        10.62        32.48        93.63 
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-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB 
      104.78       227.01        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-A3JB TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A199 
       45.90       168.85        19.86       135.98        34.45         7.82 
TCGA-ER-A19A TCGA-ER-A19C TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M 
        4.54        39.81       184.60       150.12        99.06        59.84 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
       42.51       120.76        49.71       146.63        73.05        22.36 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3PL TCGA-FR-A3YN 
       16.87        10.19       173.29        68.52        32.05         4.50 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FS-A1YW TCGA-FS-A1YY 
      174.21         4.14         5.65        10.06       171.78        49.74 
TCGA-FS-A1Z3 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ 
        8.35       312.07        32.78        43.92         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-A4F9 TCGA-FS-A4FD 
        5.29         3.06        30.90        66.67        13.28        80.68 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GN-A262 TCGA-GN-A264 
       11.54        19.30         9.90        18.25        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-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-A828 TCGA-W3-AA1Q TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 
      174.12       120.07        44.05       185.13        92.84        47.54 
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-AAA0 TCGA-WE-AAA4 TCGA-XV-AB01 TCGA-Z2-AA3S 
       37.32        24.99         6.61        91.23 

  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
             1.91              0.00 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
           346.49            312.07 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
           31.925            47.965 
[1] "1.9 - 346.5 (31.9)" "0.0 - 312.1 (48.0)"
[1] "hr=" "1.3"
D49V2, survival
                   sevent
clus2                 0   1
  4Q LOSS MUTATED    41  43
  4Q LOSS WILD-TYPE 125 149
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               84               274 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               43               149 
$`4Q LOSS MUTATED`
TCGA-D3-A8GI TCGA-EE-A180 TCGA-EE-A2GO TCGA-ER-A193 TCGA-QB-AA9O TCGA-WE-AAA3 
       58.52        94.98       126.81        31.40        18.05        21.40 
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-A8GM TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A3Z3 TCGA-D9-A4Z6 
       79.59       107.15       151.53        54.67        22.29        18.44 
TCGA-D9-A6E9 TCGA-DA-A1HW TCGA-DA-A3F8 TCGA-DA-A95V TCGA-DA-A95X TCGA-EB-A44R 
        9.90        36.03        43.36        72.10        73.94        10.36 
TCGA-EB-A5KH TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A29C 
       20.35        27.22        33.73       133.81       151.27        78.97 
TCGA-EE-A29M TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A5 TCGA-EE-A2GH TCGA-EE-A2GI 
       56.84       369.93       195.02        39.29       220.24        48.72 
TCGA-EE-A2GM TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2MM TCGA-EE-A2MQ TCGA-EE-A2MS 
       75.48        21.67       129.27       167.90        43.23       162.48 
TCGA-EE-A3AG TCGA-EE-A3J8 TCGA-EE-A3JE TCGA-ER-A197 TCGA-ER-A19B TCGA-ER-A19D 
       41.59        34.32        51.35        13.94        98.40        12.59 
TCGA-ER-A19E TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A2ND TCGA-ER-A2NG TCGA-ER-A2NH 
       13.02        49.48         8.88        23.34        48.99        41.56 
TCGA-ER-A3EV TCGA-ER-A42L TCGA-FR-A7U8 TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1ZA 
       46.98       149.03        27.85       202.65        28.08        27.72 
TCGA-FS-A4F8 TCGA-FW-A3TU TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A266 TCGA-GN-A4U3 
      174.84        55.59         2.04        15.78        10.13       121.91 
TCGA-GN-A8LK TCGA-HR-A2OH TCGA-W3-A825 TCGA-W3-AA1R TCGA-W3-AA1V TCGA-WE-A8JZ 
       50.10        65.88        63.02       111.09        42.08        24.03 
TCGA-WE-A8K6 TCGA-WE-A8ZX TCGA-WE-AA9Y TCGA-YD-A9TA TCGA-YG-AA3O TCGA-Z2-A8RT 
       17.95        35.80        12.16        49.18        37.94        27.58 

$`4Q LOSS WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EB-A5SG TCGA-EB-A5SH 
       27.65        62.07        46.32        13.87        68.25        54.02 
TCGA-EE-A184 TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2MR TCGA-EE-A3JD 
       68.15       168.26         2.60       340.14       134.40        27.35 
TCGA-ER-A198 TCGA-FR-A729 TCGA-FS-A1ZF TCGA-FW-A3R5 TCGA-WE-A8K5 TCGA-3N-A9WB 
       50.76       220.80        15.45        36.95        61.15        17.03 
TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q3 TCGA-D3-A1Q5 TCGA-D3-A1Q6 
       66.48        12.99        14.93        16.67       112.57        71.80 
TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
      133.25        31.59        90.90        95.74        43.43       103.10 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG 
       65.49        23.77       168.00        86.76        11.87       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-A3CB TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MU TCGA-D3-A51E 
      166.52        60.23        24.53         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-A6EC TCGA-D9-A6EG 
        7.10        18.12        15.39        25.18        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       222.51       176.55        35.93 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
      135.02        88.87        53.92        65.92        40.60        68.09 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A95W TCGA-DA-A95Y TCGA-DA-A95Z 
       33.93        10.49       225.96        37.35        14.14        13.02 
TCGA-EB-A44Q TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X 
       13.87        29.29        58.92         7.04        36.46        29.82 
TCGA-EE-A17Z TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20F TCGA-EE-A20I 
        8.65        14.70        26.89         4.96        91.56        13.55 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H 
       63.35        85.08        13.97        63.78        72.07        64.64 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V 
       18.61        56.42        66.74        14.47        61.28        25.87 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB 
       17.92        46.82       115.96        59.64        86.14        59.28 
TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN 
       67.43       173.79       107.38        54.74        79.66       102.12 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M7 
       13.91        42.77        81.21        44.88        94.82        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-A2MN 
       16.96       204.66        96.23       180.39       216.66        47.54 
TCGA-EE-A2MP TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC 
      248.65        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-A3JH TCGA-EE-A3JI 
       36.95        64.08        53.19       201.80       134.33       152.81 
TCGA-ER-A195 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19C TCGA-ER-A19F TCGA-ER-A19G 
       35.44         9.17        77.75        48.89        26.37       302.07 
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        44.09       162.08 
TCGA-ER-A19Q TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NF 
       50.89       148.18       105.07        43.82        20.15        28.83 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A 
      247.04        93.01        33.21        12.95        92.98       174.21 
TCGA-FR-A69P TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE 
       15.72        18.77        38.27        34.82        36.26       104.42 
TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1Z7 TCGA-FS-A1ZB 
      216.92        48.59       228.59        20.91         7.79        48.85 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ 
      357.37        53.52        46.45         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-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
       80.68        17.46        13.51        19.30         9.90        19.43 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
      139.89       117.93        96.92        64.44        62.79        32.48 
TCGA-GN-A26D TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LL 
       48.00        39.35        10.42        48.89        22.13        21.37 
TCGA-GN-A9SD TCGA-HR-A2OG TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 
       59.41         0.23       368.78       297.90         7.23         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-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO 
      219.16       105.04        49.05       101.33        58.98        70.52 
TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-XV-AB01 
       63.22        11.80        49.51        40.41        24.99        13.25 
TCGA-YD-A89C TCGA-YG-AA3P TCGA-Z2-AA3S TCGA-Z2-AA3V 
        6.90        14.43        96.99        15.98 

  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
             2.04              0.20 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
           369.93            368.78 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
           47.850            54.215 
[1] "2.0 - 369.9 (47.8)" "0.2 - 368.8 (54.2)"
[1] "hr=" "1.1"
D49V3, continuous
                   vv
clus                I/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       18
                   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        31         11
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  4Q LOSS MUTATED           14         13        4
  4Q LOSS WILD-TYPE         21         41       17
D49V4, multiclass
            clus
vv           4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  I/II NOS                 0                13
  STAGE 0                  2                 5
  STAGE I                  6                23
  STAGE IA                 3                15
  STAGE IB                 7                21
  STAGE II                 8                18
  STAGE IIA                0                14
  STAGE IIB                4                15
  STAGE IIC                3                12
  STAGE III                8                31
  STAGE IIIA               4                11
  STAGE IIIB              14                21
  STAGE IIIC              13                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
  4Q LOSS MUTATED      17 14 22 12
  4Q LOSS WILD-TYPE    47 59 59 55
D49V5, multiclass
       clus
vv      4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  T0+T1              17                47
  T2                 14                59
  T3                 22                59
  T4                 12                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
  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 247  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     72    5
  4Q LOSS WILD-TYPE  247   17
   clus
vv  4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  0              72               247
  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  34 248
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     13   72
  4Q LOSS WILD-TYPE   34  248
     clus
vv    4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  NO               13                34
  YES              72               248
[1] 2 2
[1] FALSE
D49V10, continuous
D49V11, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED    35  50
  4Q LOSS WILD-TYPE 103 179
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     35   50
  4Q LOSS WILD-TYPE  103  179
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  FEMALE              35               103
  MALE                50               179
[1] 2 2
[1] FALSE
D49V12, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED    73  12
  4Q LOSS WILD-TYPE 246  35
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     73   12
  4Q LOSS WILD-TYPE  246   35
     clus
vv    4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  NO               73               246
  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   274
D49V13, multiclass
                           clus
vv                          4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  ASIAN                                   3                 2
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  79               274
[1] 3 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   6 271
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      1   81
  4Q LOSS WILD-TYPE    6  271
                        clus
vv                       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 6
  NOT HISPANIC OR LATINO              81               271
[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 104  93
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               55               197 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               31                93 
$`5P LOSS MUTATED`
TCGA-EE-A2GD TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A2JB TCGA-D3-A2JG TCGA-D3-A2JL 
      269.03        12.99         8.42       168.00       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        24.53        10.78        18.44        76.34 
TCGA-DA-A3F5 TCGA-DA-A95Y TCGA-EB-A5KH TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A29C 
      225.11        14.14        16.41        13.15        24.89        76.14 
TCGA-EE-A29E TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A2A2 TCGA-EE-A2GB TCGA-EE-A2GE 
        0.26        47.74        27.16        30.02        26.14        12.95 
TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GR TCGA-EE-A2MM TCGA-EE-A2MU TCGA-EE-A3AB 
      201.60        68.65         0.20       145.45        53.26       122.73 
TCGA-EE-A3AD TCGA-EE-A3J7 TCGA-EE-A3JB TCGA-ER-A199 TCGA-ER-A2NE TCGA-ER-A2NG 
        4.41        45.90       168.85         7.82        16.87        28.67 
TCGA-FR-A69P TCGA-FS-A1ZD TCGA-FS-A1ZG TCGA-FS-A1ZM TCGA-FS-A1ZT TCGA-FS-A1ZW 
        4.14        32.78         7.82        78.61        35.28        23.21 
TCGA-FS-A1ZY TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A267 
        5.29        66.67       173.19         1.91        53.29        17.06 
TCGA-GN-A268 TCGA-GN-A4U3 TCGA-GN-A8LK TCGA-OD-A75X TCGA-W3-AA1R TCGA-WE-A8ZY 
       42.48       120.53        43.23       297.01        79.99        48.39 
TCGA-WE-AAA4 
       24.99 

$`5P LOSS WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A8GI TCGA-EB-A5SG TCGA-EE-A180 
        9.76        62.07        38.76        13.41        33.24        31.96 
TCGA-EE-A20H TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 TCGA-FR-A729 
      166.75        52.90       134.40        27.35        19.04       216.43 
TCGA-FW-A3R5 TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-3N-A9WC TCGA-BF-AAP0 TCGA-D3-A1Q3 
       36.95        52.73         7.40        60.46        14.83        15.72 
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA 
       31.89       110.93        49.35       133.25        19.04        76.41 
TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JC 
       62.60        25.64        45.99        62.86        15.75        86.30 
TCGA-D3-A2JH TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CE 
       36.30        64.83        43.53        58.06       140.98        59.70 
TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51J 
        9.34        90.21        23.67       173.85        30.67       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-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6EC 
       70.62       135.12        36.53        15.02        16.90        69.21 
TCGA-D9-A6EG TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 
       22.85       138.67        68.68       150.61       110.53        60.10 
TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F8 TCGA-DA-A95V TCGA-DA-A95W 
       64.83        58.85        30.44         8.71        72.10         0.76 
TCGA-DA-A95X TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A181 
       65.03        12.30         3.91        52.41        18.21        20.38 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29D 
        0.00        26.24        75.55        79.20        75.22        12.99 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 
       44.28        47.41        61.12       346.49       185.19       115.43 
TCGA-EE-A2A6 TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP 
       77.98        10.62        32.48        18.35        93.63         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-A2MS TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AE 
      227.01       143.93        23.51       124.31        64.04        54.51 
TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J8 TCGA-EE-A3JH TCGA-EE-A3JI 
        6.28        67.89       111.85         3.35        19.86       135.98 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D 
       34.45        10.49         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 
      184.60       150.12        99.06        59.84        42.51       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        73.05        22.36         4.70 
TCGA-ER-A2NF TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42L 
       10.19       173.29        68.52        15.48        32.05        74.47 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FS-A1YW 
        4.50       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-A1ZE 
       49.74       195.98         8.35        27.62       312.07        43.92 
TCGA-FS-A1ZJ TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZZ TCGA-FS-A4F0 
       36.33       130.95       136.27         4.47         3.06        30.90 
TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
       13.28        80.68        55.59        11.54        19.30         9.90 
TCGA-GF-A4EO TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A26A TCGA-GN-A4U4 TCGA-GN-A4U8 
       18.25       117.93        96.92         7.59        34.49        46.92 
TCGA-GN-A9SD TCGA-LH-A9QB TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 TCGA-W3-A824 
       59.41        85.05         7.23         0.20         0.33       174.12 
TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1Q TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 
        1.97       120.07        44.05         8.09       185.13        92.84 
TCGA-WE-A8K1 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT 
       47.54        65.42        12.69        21.90        62.89        10.95 
TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-XV-AB01 TCGA-YG-AA3O TCGA-Z2-AA3S 
        1.94        37.32         6.61        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 
            35.28             49.35 
[1] "0.2 - 297.0 (35.3)" "0.0 - 346.5 (49.4)"
[1] "hr=" "1.2"
D50V2, survival
                   sevent
clus2                 0   1
  5P LOSS MUTATED    33  43
  5P LOSS WILD-TYPE 133 149
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               76               282 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               43               149 
$`5P LOSS MUTATED`
TCGA-EE-A184 TCGA-EE-A2GD TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A2JB TCGA-D3-A2JD 
       68.15       340.14        12.99        16.57       168.00        11.87 
TCGA-D3-A2JG TCGA-D3-A2JL TCGA-D3-A2JO TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3MV 
      113.52       171.58        66.08        86.93        24.53        45.30 
TCGA-D3-A5GO TCGA-D3-A8GB TCGA-D3-A8GN TCGA-D9-A1X3 TCGA-D9-A4Z6 TCGA-DA-A1HV 
      137.92        30.84       161.00        18.12        18.44        76.57 
TCGA-DA-A1HW TCGA-DA-A3F5 TCGA-DA-A95Y TCGA-EB-A5KH TCGA-EB-A5UL TCGA-EE-A17X 
       36.03       225.96        14.14        20.35        29.29        29.82 
TCGA-EE-A17Y TCGA-EE-A185 TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29M TCGA-EE-A29P 
       27.22         4.96        78.97        63.78        56.84        56.42 
TCGA-EE-A2A2 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       59.64        59.28       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-A3AB 
       42.77        44.88       167.90        43.23        53.26       122.73 
TCGA-EE-A3AD TCGA-EE-A3AH TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3JB TCGA-ER-A199 
       28.77       138.81        36.95        64.08       201.80         9.17 
TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A2NH TCGA-FR-A69P TCGA-FS-A1ZD TCGA-FS-A1ZG 
       20.15        48.99        41.56        15.72        53.52         9.70 
TCGA-FS-A1ZM TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F2 TCGA-FS-A4F4 
      101.26        53.16        49.48        27.09        50.14        66.67 
TCGA-FS-A4F8 TCGA-FS-A4FB TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A266 TCGA-GN-A267 
      174.84        26.73         2.04       139.89        10.13        64.44 
TCGA-GN-A268 TCGA-GN-A4U3 TCGA-GN-A8LK TCGA-HR-A2OG TCGA-HR-A2OH TCGA-OD-A75X 
       62.79       121.91        50.10         0.23        65.88       297.90 
TCGA-W3-AA1R TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AAA4 
      111.09        35.80        49.51        24.99 

$`5P LOSS WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-D3-A8GI TCGA-EB-A5SG 
       27.65        62.07        46.32        13.87        58.52        68.25 
TCGA-EB-A5SH TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GO TCGA-EE-A2MR 
       54.02        94.98       168.26         2.60       126.81       134.40 
TCGA-EE-A3JD TCGA-ER-A193 TCGA-ER-A198 TCGA-FR-A729 TCGA-FS-A1ZF TCGA-FW-A3R5 
       27.35        31.40        50.76       220.80        15.45        36.95 
TCGA-QB-AA9O TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-3N-A9WB TCGA-3N-A9WC TCGA-BF-AAP0 
       18.05        61.15        21.40        17.03        66.48        14.93 
TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       16.67       112.04       112.57        71.80       133.25        28.08 
TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 
       31.59        90.90        95.74        43.43       103.10        65.49 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JN 
       23.77       115.53        86.76        42.08        12.10        66.48 
TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CE 
       59.57       130.72        58.06        46.98       166.52        60.23 
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-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-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-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-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA 
        3.65         7.10        15.39        22.29         9.90        25.18 
TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 
       77.56        22.95       144.89        20.38       222.51       176.55 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB 
       35.93       135.02        88.87        53.92        65.92        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        43.36        72.10        37.35 
TCGA-DA-A95X TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5UN TCGA-EB-A5VV 
       73.94        13.02        13.87        10.36        58.92         7.04 
TCGA-EB-A6L9 TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20B 
       36.46         8.65        33.73        14.70        26.89       133.81 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29D 
      151.27        91.56        13.55        63.35        85.08        13.97 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
       72.07        64.64        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-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GC TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
       39.29        86.14        67.43        54.74        79.66        75.48 
TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 
      102.12        13.91        81.21        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-A2MN TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AC 
       47.54       248.65       162.48        71.21       124.31        64.04 
TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J8 
       54.51        13.81        41.59       172.18       127.20        34.32 
TCGA-EE-A3JA TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 
       53.19        51.35       134.33       152.81        35.44        13.94 
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 
      302.07       152.35         6.44       131.51        61.05        44.09 
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       105.07 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NF TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
       43.82        23.34        28.83       247.04        93.01        46.98 
TCGA-ER-A3PL TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A7U8 
       33.21        12.95       149.03        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-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-A1ZH TCGA-FS-A1ZJ 
       27.72        48.85       357.37        46.45        32.75        47.38 
TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZU 
       23.93        74.73       133.55        11.41       148.80        26.56 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F5 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FS-A4FD 
       27.02        77.82        28.73        34.03        54.41        80.68 
TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
       17.46        55.59        13.51        19.30         9.90        19.43 
TCGA-GF-A6C9 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U4 
       15.78       117.93        96.92        32.48        48.00        39.35 
TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LL TCGA-GN-A9SD TCGA-LH-A9QB 
       10.42        48.89        22.13        21.37        59.41       368.78 
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-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO 
       24.03        49.05        17.95       101.33        58.98        70.52 
TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-XV-AB01 TCGA-YD-A89C 
       63.22        11.80        12.16        40.41        13.25         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 

  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             52.27 
[1] "0.2 - 340.1 (51.6)" "0.2 - 369.9 (52.3)"
[1] "hr=" "1.1"
D50V3, continuous
                   vv
clus                I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  5P LOSS MUTATED          3       3       6        4        4        5
  5P LOSS WILD-TYPE       10       4      23       14       24       21
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  5P LOSS MUTATED           3         4         4        10          4
  5P LOSS WILD-TYPE        11        15        11        29         11
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  5P LOSS MUTATED           10         13        0
  5P LOSS WILD-TYPE         25         41       21
D50V4, multiclass
            clus
vv           5P LOSS MUTATED 5P LOSS WILD-TYPE
  I/II NOS                 3                10
  STAGE 0                  3                 4
  STAGE I                  6                23
  STAGE IA                 4                14
  STAGE IB                 4                24
  STAGE II                 5                21
  STAGE IIA                3                11
  STAGE IIB                4                15
  STAGE IIC                4                11
  STAGE III               10                29
  STAGE IIIA               4                11
  STAGE IIIB              10                25
  STAGE IIIC              13                41
  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      13 16 18 17
  5P LOSS WILD-TYPE    51 57 63 50
D50V5, multiclass
       clus
vv      5P LOSS MUTATED 5P LOSS WILD-TYPE
  T0+T1              13                51
  T2                 16                57
  T3                 18                63
  T4                 17                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
  5P LOSS MUTATED    33  21   8   9
  5P LOSS WILD-TYPE 144  44  31  36
D50V6, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  N0              33               144
  N1              21                44
  N2               8                31
  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 247  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED     72    0
  5P LOSS WILD-TYPE  247   22
   clus
vv  5P LOSS MUTATED 5P LOSS WILD-TYPE
  0              72               247
  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     7  72
  5P LOSS WILD-TYPE  40 248
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      7   72
  5P LOSS WILD-TYPE   40  248
     clus
vv    5P LOSS MUTATED 5P LOSS WILD-TYPE
  NO                7                40
  YES              72               248
[1] 2 2
[1] FALSE
D50V10, continuous
D50V11, binary
                   cls
clus                  0   1
  5P LOSS MUTATED    32  47
  5P LOSS WILD-TYPE 106 182
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED     32   47
  5P LOSS WILD-TYPE  106  182
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  FEMALE              32               106
  MALE                47               182
[1] 2 2
[1] FALSE
D50V12, binary
                   cls
clus                  0   1
  5P LOSS MUTATED    68  11
  5P LOSS WILD-TYPE 251  36
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED     68   11
  5P LOSS WILD-TYPE  251   36
     clus
vv    5P LOSS MUTATED 5P LOSS WILD-TYPE
  NO               68               251
  YES              11                36
[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   279
D50V13, multiclass
                           clus
vv                          5P LOSS MUTATED 5P LOSS WILD-TYPE
  ASIAN                                   2                 3
  BLACK OR AFRICAN AMERICAN               1                 0
  WHITE                                  74               279
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V14, binary
                   cls
clus                  0   1
  5P LOSS MUTATED     0  74
  5P LOSS WILD-TYPE   7 278
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      0   74
  5P LOSS WILD-TYPE    7  278
                        clus
vv                       5P LOSS MUTATED 5P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 7
  NOT HISPANIC OR LATINO              74               278
[1] 2 2
[1] FALSE

Clustering(51) Variable = 5Q LOSS MUTATION ANALYSIS
D51V1, survival
                   sevent
clus2                0  1
  5Q LOSS MUTATED   32 38
  5Q LOSS WILD-TYPE 96 86
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               70               182 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               38                86 
$`5Q LOSS MUTATED`
TCGA-D3-A8GI TCGA-EE-A20H TCGA-EE-A2GD TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q8 
       13.41       166.75       269.03        12.99        14.83        19.04 
TCGA-D3-A2JB TCGA-D3-A2JG TCGA-D3-A2JL TCGA-D3-A2JO TCGA-D3-A3C6 TCGA-D3-A3CC 
      168.00       107.61       171.58        66.08        58.06        40.01 
TCGA-D3-A3CF TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A4Z6 
       24.53        42.05        45.70        10.78        15.02        18.44 
TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A3F5 TCGA-DA-A95Y 
       69.21        76.34       110.53        60.10       225.11        14.14 
TCGA-EB-A5KH TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29M 
       16.41        13.15        24.89        76.14         0.26        47.74 
TCGA-EE-A29P TCGA-EE-A2A2 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ 
       27.16        30.02        26.14        12.95       201.60        68.65 
TCGA-EE-A2GM TCGA-EE-A2GR TCGA-EE-A2M6 TCGA-EE-A2MJ TCGA-EE-A2MM TCGA-EE-A3AB 
       18.35         0.20       103.13        63.25       145.45       122.73 
TCGA-EE-A3AD TCGA-EE-A3J7 TCGA-EE-A3JB TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A2NE 
        4.41        45.90       168.85         7.82        53.29        16.87 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1ZG TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZT 
      174.21         4.14         7.82        78.61       130.95        35.28 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-GF-A6C8 TCGA-GN-A262 
       23.21         5.29        66.67       173.19         1.91        53.29 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A4U3 TCGA-GN-A8LK TCGA-OD-A75X TCGA-W3-A825 
       17.06        42.48       120.53        43.23       297.01         1.97 
TCGA-W3-AA1R TCGA-W3-AA1V TCGA-WE-A8ZY TCGA-WE-AAA4 
       79.99         8.09        48.39        24.99 

$`5Q LOSS WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A2GO 
        9.76        62.07        38.76        33.24        31.96        52.90 
TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 TCGA-FR-A729 TCGA-FW-A3R5 TCGA-WE-A8K5 
      134.40        27.35        19.04       216.43        36.95        52.73 
TCGA-WE-AAA3 TCGA-3N-A9WC TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 
        7.40        60.46         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-A2J7 
       49.35       133.25        76.41        62.60        25.64        45.99 
TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JH TCGA-D3-A2JN TCGA-D3-A2JP 
       62.86        15.75        86.30        36.30        64.83        43.53 
TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E 
      140.98        59.70         9.34        90.21        23.67       173.85 
TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GR 
       30.67       144.46        31.76        62.70        11.34       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-A3Z3 TCGA-D9-A6EG TCGA-DA-A1HY 
       70.62       135.12        36.53        16.90        22.85       138.67 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F8 
       68.68       150.61        64.83        58.85        30.44         8.71 
TCGA-DA-A95V TCGA-DA-A95W TCGA-DA-A95X TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5UN 
       72.10         0.76        65.03        12.30         3.91        52.41 
TCGA-EB-A6L9 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A20F 
       18.21        20.38         0.00        26.24        75.55        79.20 
TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29Q TCGA-EE-A29T 
       75.22        12.99        44.28        47.41        61.12       346.49 
TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A6 TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN 
      185.19       115.43        77.98        10.62        32.48        93.63 
TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC 
        0.76        71.31        81.99        15.25         5.75        23.77 
TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MP 
      209.79        94.19       171.85        89.26       104.78       227.01 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AE 
      143.93        23.51        53.26       124.31        64.04        54.51 
TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J8 TCGA-EE-A3JH TCGA-EE-A3JI 
        6.28        67.89       111.85         3.35        19.86       135.98 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A19A TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19G 
       34.45        10.49         4.54        39.81        11.47       184.60 
TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
      150.12        99.06        59.84        42.51       120.76        49.71 
TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NF 
       47.18       146.63        73.05        22.36         4.70        10.19 
TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42L 
       28.67       173.29        68.52        15.48        32.05        74.47 
TCGA-FR-A3YN TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FS-A1YW TCGA-FS-A1YY 
        4.50        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        43.92 
TCGA-FS-A1ZJ TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F9 
       36.33       136.27         4.47         3.06        30.90        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        18.25 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A26A TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-GN-A9SD 
      117.93        96.92         7.59        34.49        46.92        59.41 
TCGA-LH-A9QB TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A828 
       85.05         7.23         0.20         0.33       174.12       120.07 
TCGA-W3-AA1Q TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8ZM TCGA-WE-A8ZN 
       44.05       185.13        92.84        47.54        65.42        12.69 
TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-XV-AB01 
       21.90        62.89        10.95         1.94        37.32         6.61 
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 
           42.855            47.475 
[1] "0.2 - 297.0 (42.9)" "0.0 - 346.5 (47.5)"
[1] "hr=" "1.2"
D51V2, survival
                   sevent
clus2                 0   1
  5Q LOSS MUTATED    40  53
  5Q LOSS WILD-TYPE 126 139
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               93               265 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               53               139 
$`5Q LOSS MUTATED`
TCGA-D3-A8GI TCGA-EE-A20H TCGA-EE-A2GD TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q8 
       58.52       168.26       340.14        12.99        14.93        28.08 
TCGA-D3-A2JB TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JO 
      168.00        11.87       113.52        12.10       171.58        66.08 
TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3MV TCGA-D3-A5GL TCGA-D3-A5GN 
       58.06        86.93        24.53        45.30       125.79       135.75 
TCGA-D3-A5GO TCGA-D9-A1JX TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A4Z6 TCGA-D9-A6EC 
      137.92         7.10        18.12        15.39        18.44        77.56 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A3F5 
       76.57        36.03        20.38       135.02        88.87       225.96 
TCGA-DA-A95Y TCGA-EB-A5KH TCGA-EB-A5UL TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A185 
       14.14        20.35        29.29        29.82        27.22         4.96 
TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29V TCGA-EE-A2A2 
       78.97        63.78        56.84        56.42        25.87        59.64 
TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GM 
       59.28       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        41.56       174.21        15.72 
TCGA-FS-A1ZB TCGA-FS-A1ZG TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZT TCGA-FS-A1ZW 
       48.85         9.70       101.26       133.55        53.16        49.48 
TCGA-FS-A1ZY TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4FB TCGA-GF-A6C8 
       27.09        50.14        66.67       174.84        26.73         2.04 
TCGA-GN-A262 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A4U3 TCGA-GN-A8LK 
      139.89        10.13        64.44        62.79       121.91        50.10 
TCGA-HR-A2OG TCGA-HR-A2OH TCGA-OD-A75X TCGA-W3-A825 TCGA-W3-AA1R TCGA-W3-AA1V 
        0.23        65.88       297.90        63.02       111.09        42.08 
TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AAA4 
       35.80        49.51        24.99 

$`5Q LOSS WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EB-A5SG TCGA-EB-A5SH 
       27.65        62.07        46.32        13.87        68.25        54.02 
TCGA-EE-A180 TCGA-EE-A184 TCGA-EE-A29L TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD 
       94.98        68.15         2.60       126.81       134.40        27.35 
TCGA-ER-A193 TCGA-ER-A198 TCGA-FR-A729 TCGA-FS-A1ZF TCGA-FW-A3R5 TCGA-QB-AA9O 
       31.40        50.76       220.80        15.45        36.95        18.05 
TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-3N-A9WB TCGA-3N-A9WC TCGA-D3-A1Q1 TCGA-D3-A1Q3 
       61.15        21.40        17.03        66.48        16.57        16.67 
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A1QA 
      112.04       112.57        71.80       133.25        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-A2JC TCGA-D3-A2JH TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C7 
       86.76        42.08        66.48        59.57       130.72        46.98 
TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E 
      166.52        60.23         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-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GC 
       26.89       178.32        18.18       125.19        30.84        79.59 
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-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-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA 
      151.53        54.67         3.65        22.29         9.90        25.18 
TCGA-D9-A6EG TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I8 
       22.95       144.89       222.51       176.55        35.93        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        43.36 
TCGA-DA-A95V TCGA-DA-A95W TCGA-DA-A95X TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A44R 
       72.10        37.35        73.94        13.02        13.87        10.36 
TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 
       58.92         7.04        36.46         8.65        33.73        14.70 
TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29A 
       26.89       133.81       151.27        91.56        13.55        63.35 
TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29N TCGA-EE-A29Q 
       85.08        13.97        72.07        64.64        18.61        66.74 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 
       14.47        61.28       369.93       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-A2GN TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M7 
      102.12        13.91        81.21        94.82        21.67        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-A2MK TCGA-EE-A2ML TCGA-EE-A2MN TCGA-EE-A2MP 
       16.96       204.66       180.39       216.66        47.54       248.65 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AE 
      162.48        71.21        53.26       124.31        64.04        54.51 
TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J8 TCGA-EE-A3JA 
       13.81        41.59       172.18       127.20        34.32        53.19 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A19A 
       51.35       134.33       152.81        35.44        13.94        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       302.07       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        44.09       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       105.07        43.82        23.34 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL 
       28.83        48.99       247.04        93.01        46.98        33.21 
TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA 
       12.95       149.03        92.98        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-A1ZC 
      202.65        20.91        28.08         7.79        27.72       357.37 
TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZP 
       53.52        46.45        32.75        47.38        23.93        74.73 
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-A3TU TCGA-FW-A3TV 
       34.03        54.41        80.68        17.46        55.59        13.51 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C9 TCGA-GN-A264 TCGA-GN-A265 
       19.30         9.90        19.43        15.78       117.93        96.92 
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-A8LL TCGA-GN-A9SD TCGA-LH-A9QB TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 
       21.37        59.41       368.78         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-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-AA9Y TCGA-WE-AAA0 TCGA-XV-AB01 
       70.52        63.22        11.80        12.16        40.41        13.25 
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 

  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 
            56.84             50.76 
[1] "0.2 - 340.1 (56.8)" "0.2 - 369.9 (50.8)"
[1] "hr=" "1"  
D51V3, continuous
                   vv
clus                I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  5Q LOSS MUTATED          4       3       9        4        5        9
  5Q LOSS WILD-TYPE        9       4      20       14       23       17
                   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        28         10
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  5Q LOSS MUTATED           10         14        4
  5Q LOSS WILD-TYPE         25         40       17
D51V4, multiclass
            clus
vv           5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  I/II NOS                 4                 9
  STAGE 0                  3                 4
  STAGE I                  9                20
  STAGE IA                 4                14
  STAGE IB                 5                23
  STAGE II                 9                17
  STAGE IIA                2                12
  STAGE IIB                4                15
  STAGE IIC                5                10
  STAGE III               11                28
  STAGE IIIA               5                10
  STAGE IIIB              10                25
  STAGE IIIC              14                40
  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 18 22 22
  5Q LOSS WILD-TYPE    47 55 59 45
D51V5, multiclass
       clus
vv      5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  T0+T1              17                47
  T2                 18                55
  T3                 22                59
  T4                 22                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
  5Q LOSS MUTATED    45  22  10  10
  5Q LOSS WILD-TYPE 132  43  29  35
D51V6, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  N0              45               132
  N1              22                43
  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    86   4
  5Q LOSS WILD-TYPE 233  18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     86    4
  5Q LOSS WILD-TYPE  233   18
   clus
vv  5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  0              86               233
  1               4                18
[1] 2 2
[1] FALSE
D51V8, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED    32  26
  5Q LOSS WILD-TYPE 102  64
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     32   26
  5Q LOSS WILD-TYPE  102   64
     clus
vv    5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  NO               32               102
  YES              26                64
[1] 2 2
[1] FALSE
D51V9, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED     8  89
  5Q LOSS WILD-TYPE  39 231
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      8   89
  5Q LOSS WILD-TYPE   39  231
     clus
vv    5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  NO                8                39
  YES              89               231
[1] 2 2
[1] FALSE
D51V10, continuous
D51V11, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED    37  60
  5Q LOSS WILD-TYPE 101 169
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     37   60
  5Q LOSS WILD-TYPE  101  169
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  FEMALE              37               101
  MALE                60               169
[1] 2 2
[1] FALSE
D51V12, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED    80  17
  5Q LOSS WILD-TYPE 239  30
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     80   17
  5Q LOSS WILD-TYPE  239   30
     clus
vv    5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  NO               80               239
  YES              17                30
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  5Q LOSS MUTATED       2                         1    92
  5Q LOSS WILD-TYPE     3                         0   261
D51V13, multiclass
                           clus
vv                          5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  ASIAN                                   2                 3
  BLACK OR AFRICAN AMERICAN               1                 0
  WHITE                                  92               261
[1] 3 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  92
  5Q LOSS WILD-TYPE   7 260
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      0   92
  5Q LOSS WILD-TYPE    7  260
                        clus
vv                       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 7
  NOT HISPANIC OR LATINO              92               260
[1] 2 2
[1] FALSE

Clustering(52) Variable = 6P LOSS MUTATION ANALYSIS
D52V1, survival
                   sevent
clus2                 0   1
  6P LOSS MUTATED    22  27
  6P LOSS WILD-TYPE 106  97
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               49               203 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               27                97 
$`6P LOSS MUTATED`
TCGA-D3-A8GI TCGA-EE-A180 TCGA-D3-A1Q4 TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2JC 
       13.41        31.96        31.89        25.64        45.99        86.30 
TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A5GR TCGA-D3-A8GC TCGA-D3-A8GD 
       36.30       171.58        64.83       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        68.68        58.85 
TCGA-DA-A3F5 TCGA-EB-A44Q TCGA-EE-A17Y TCGA-EE-A183 TCGA-EE-A29D TCGA-EE-A29G 
      225.11         3.91        24.89        26.24        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-A2MT TCGA-EE-A3J4 TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A2NE 
       23.77        23.51       111.85        53.29        11.47        16.87 
TCGA-ER-A42L TCGA-FR-A69P TCGA-FR-A8YC TCGA-FS-A1ZC TCGA-FS-A1ZG TCGA-FS-A1ZM 
       74.47         4.14        10.06       312.07         7.82        78.61 
TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FW-A3TU TCGA-GN-A267 TCGA-GN-A4U4 
      130.95       136.27        35.28        55.59        17.06        34.49 
TCGA-QB-A6FS 
        7.23 

$`6P LOSS WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A20H TCGA-EE-A2GD 
        9.76        62.07        38.76        33.24       166.75       269.03 
TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 TCGA-FR-A729 TCGA-FW-A3R5 
       52.90       134.40        27.35        19.04       216.43        36.95 
TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 
       52.73         7.40        60.46        12.99        14.83         8.42 
TCGA-D3-A1Q3 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA 
       15.72       110.93        49.35       133.25        19.04        76.41 
TCGA-D3-A1QB TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JG TCGA-D3-A2JO 
       62.60        62.86        15.75       168.00       107.61        66.08 
TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF 
       43.53        58.06       140.98        40.01        59.70        24.53 
TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51J 
        9.34        90.21        23.67       173.85        30.67       144.46 
TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GU 
       31.76        62.70        11.34        42.05        45.70       124.08 
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-DA-A1HV TCGA-DA-A1I2 TCGA-DA-A1I5 
       15.02        16.90        18.44        76.34       150.61       110.53 
TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A3F2 TCGA-DA-A3F8 TCGA-DA-A95V TCGA-DA-A95W 
       60.10        64.83        30.44         8.71        72.10         0.76 
TCGA-DA-A95X TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A6L9 
       65.03        14.14        12.30        16.41        52.41        18.21 
TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29B 
       13.15        20.38         0.00        75.55        79.20        75.22 
TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29T 
       76.14         0.26        47.41        47.74        27.16       346.49 
TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ 
       30.02        77.98        26.14        12.95       201.60        68.65 
TCGA-EE-A2GK TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
       10.62        18.35        93.63         0.76         0.20        71.31 
TCGA-EE-A2GU TCGA-EE-A2M8 TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ 
       81.99         5.75       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-A2MU 
       89.26       104.78       145.45       227.01       143.93        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-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI 
       67.89        45.90         3.35       168.85        19.86       135.98 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19C TCGA-ER-A19G 
       34.45        10.49         7.82         4.54        39.81       184.60 
TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
      150.12        99.06        59.84        42.51       120.76        49.71 
TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NF 
       47.18       146.63        73.05        22.36         4.70        10.19 
TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN 
       28.67       173.29        68.52        15.48        32.05         4.50 
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-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZJ TCGA-FS-A1ZU 
        8.35        27.62        32.78        43.92        36.33         4.47 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 
       23.21         5.29         3.06        30.90        66.67       173.19 
TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
       13.28        80.68        11.54        19.30         9.90        18.25 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A268 TCGA-GN-A26A 
        1.91        53.29       117.93        96.92        42.48         7.59 
TCGA-GN-A4U3 TCGA-GN-A4U8 TCGA-GN-A8LK TCGA-GN-A9SD TCGA-LH-A9QB TCGA-OD-A75X 
      120.53        46.92        43.23        59.41        85.05       297.01 
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        47.54        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-XV-AB01 TCGA-YG-AA3O TCGA-Z2-AA3S 
       37.32        24.99         6.61        28.21        91.23 

  6P LOSS MUTATED 6P LOSS WILD-TYPE 
             3.91              0.00 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
           312.07            346.49 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
            44.28             47.18 
[1] "3.9 - 312.1 (44.3)" "0.0 - 346.5 (47.2)"
[1] "hr=" "1.1"
D52V2, survival
                   sevent
clus2                 0   1
  6P LOSS MUTATED    28  40
  6P LOSS WILD-TYPE 138 152
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               68               290 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               40               152 
$`6P LOSS MUTATED`
TCGA-D3-A3ML TCGA-D3-A8GI TCGA-EE-A180 TCGA-D3-A1Q4 TCGA-D3-A1Q9 TCGA-D3-A2J6 
       13.87        58.52        94.98       112.04        31.59        43.43 
TCGA-D3-A2J7 TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN 
      103.10        86.76        11.87        42.08       171.58        66.48 
TCGA-D3-A3MV TCGA-D3-A51N TCGA-D3-A5GR TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GM 
       45.30        22.62       178.32        79.59        23.61       107.15 
TCGA-D3-A8GN TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HY TCGA-DA-A1I1 
      161.00        25.18        77.56        22.95       144.89       222.51 
TCGA-DA-A1I4 TCGA-DA-A1I8 TCGA-DA-A1IC TCGA-DA-A3F5 TCGA-EB-A44Q TCGA-EE-A17Y 
       35.93        53.92        68.09       225.96        13.87        27.22 
TCGA-EE-A183 TCGA-EE-A29A TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29Q TCGA-EE-A29W 
       26.89        63.35        13.97        72.07        66.74       195.02 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2GL TCGA-EE-A2M5 TCGA-EE-A2M6 
       17.92        46.82       115.96        79.66        21.67       129.27 
TCGA-EE-A2M7 TCGA-EE-A2MC TCGA-EE-A2MT TCGA-EE-A3J4 TCGA-ER-A19B TCGA-ER-A19D 
       28.83        61.51        71.21       127.20        98.40        12.59 
TCGA-ER-A19T TCGA-ER-A2NE TCGA-ER-A42L TCGA-FR-A69P TCGA-FR-A8YC TCGA-FS-A1YX 
        8.88        20.15       149.03        15.72        34.82        48.59 
TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZG TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZR 
       48.85       357.37         9.70       101.26       133.55        11.41 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FW-A3TU TCGA-GN-A267 TCGA-GN-A4U4 TCGA-HR-A2OG 
      148.80        53.16        55.59        64.44        39.35         0.23 
TCGA-QB-A6FS TCGA-YG-AA3P 
        7.23        14.43 

$`6P LOSS WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A184 
       27.65        62.07        46.32        68.25        54.02        68.15 
TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD 
      168.26         2.60       340.14       126.81       134.40        27.35 
TCGA-ER-A193 TCGA-ER-A198 TCGA-FR-A729 TCGA-FS-A1ZF TCGA-FW-A3R5 TCGA-QB-AA9O 
       31.40        50.76       220.80        15.45        36.95        18.05 
TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 
       61.15        21.40        17.03        66.48        12.99        14.93 
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       16.57        16.67       112.57        71.80       133.25        28.08 
TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB 
       90.90        95.74        65.49        23.77       115.53       168.00 
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-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO 
       46.98       166.52        86.93        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-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-A5GS TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GK 
       18.18       125.19        30.84        26.43       241.38       170.20 
TCGA-D3-A8GL TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D3-A8GV 
       89.13       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-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I0 
       22.29        18.44         9.90        76.57        36.03        20.38 
TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A3F2 
      176.55       135.02        88.87        65.92        40.60        33.93 
TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-DA-A95V TCGA-DA-A95W TCGA-DA-A95X TCGA-DA-A95Y 
       10.49        43.36        72.10        37.35        73.94        14.14 
TCGA-DA-A95Z TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV 
       13.02        10.36        20.35        29.29        58.92         7.04 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A185 
       36.46        29.82         8.65        33.73        14.70         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-A29H TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29R 
       63.78        64.64        56.84        18.61        56.42        14.47 
TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
       61.28       369.93        25.87        59.64        39.29        86.14 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       59.28        67.43       173.79       220.24        48.72       107.38 
TCGA-EE-A2GK TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
       54.74        75.48       102.12        13.91        42.77        81.21 
TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M8 TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF 
       44.88        94.82        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-A2MS TCGA-EE-A2MU 
      167.90        47.54       248.65        43.23       162.48        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-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 
       41.59       138.81       172.18        36.95        64.08        34.32 
TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 
       53.19       201.80        51.35       134.33       152.81        35.44 
TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19C TCGA-ER-A19E TCGA-ER-A19F 
       13.94         9.17        77.75        48.89        13.02        26.37 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
      302.07       152.35         6.44       131.51        61.05        44.09 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
      162.08        50.89        49.48       148.18       105.07        43.82 
TCGA-ER-A2ND TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET 
       23.34        28.83        48.99        41.56       247.04        93.01 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A7U8 
       46.98        33.21        12.95        92.98       174.21        27.85 
TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YY 
       18.77        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-A1ZD 
      202.65        20.91        28.08         7.79        27.72        53.52 
TCGA-FS-A1ZE TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZU 
       46.45        32.75        47.38        23.93        74.73        26.56 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 
       49.48        27.09        27.02        77.82        50.14        66.67 
TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD 
       28.73       174.84        34.03        26.73        54.41        80.68 
TCGA-FW-A3I3 TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 
       17.46        13.51        19.30         9.90        19.43         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-A26A TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A4U9 
       32.48        48.00       121.91        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-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-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO 
       24.03        49.05        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-AAA4 TCGA-XV-AB01 TCGA-YD-A89C TCGA-YD-A9TA TCGA-YG-AA3O TCGA-Z2-A8RT 
       24.99        13.25         6.90        49.18        37.94        27.58 
TCGA-Z2-AA3S TCGA-Z2-AA3V 
       96.99        15.98 

  6P LOSS MUTATED 6P LOSS WILD-TYPE 
             0.23              0.20 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
           357.37            369.93 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
           54.755            50.825 
[1] "0.2 - 357.4 (54.8)" "0.2 - 369.9 (50.8)"
[1] "hr=" "1.1"
D52V3, continuous
                   vv
clus                I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  6P LOSS MUTATED          6       3       6        1        5        5
  6P LOSS WILD-TYPE        7       4      23       17       23       21
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  6P LOSS MUTATED           3         5         1         8          6
  6P LOSS WILD-TYPE        11        14        14        31          9
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  6P LOSS MUTATED            4         12        2
  6P LOSS WILD-TYPE         31         42       19
D52V4, multiclass
            clus
vv           6P LOSS MUTATED 6P LOSS WILD-TYPE
  I/II NOS                 6                 7
  STAGE 0                  3                 4
  STAGE I                  6                23
  STAGE IA                 1                17
  STAGE IB                 5                23
  STAGE II                 5                21
  STAGE IIA                3                11
  STAGE IIB                5                14
  STAGE IIC                1                14
  STAGE III                8                31
  STAGE IIIA               6                 9
  STAGE IIIB               4                31
  STAGE IIIC              12                42
  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
  6P LOSS MUTATED      10 15 18 12
  6P LOSS WILD-TYPE    54 58 63 55
D52V5, multiclass
       clus
vv      6P LOSS MUTATED 6P LOSS WILD-TYPE
  T0+T1              10                54
  T2                 15                58
  T3                 18                63
  T4                 12                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
  6P LOSS MUTATED    36  13  10   8
  6P LOSS WILD-TYPE 141  52  29  37
D52V6, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  N0              36               141
  N1              13                52
  N2              10                29
  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    65   2
  6P LOSS WILD-TYPE 254  20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     65    2
  6P LOSS WILD-TYPE  254   20
   clus
vv  6P LOSS MUTATED 6P LOSS WILD-TYPE
  0              65               254
  1               2                20
[1] 2 2
[1] FALSE
D52V8, binary
                   cls
clus                  0   1
  6P LOSS MUTATED    24  20
  6P LOSS WILD-TYPE 110  70
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     24   20
  6P LOSS WILD-TYPE  110   70
     clus
vv    6P LOSS MUTATED 6P LOSS WILD-TYPE
  NO               24               110
  YES              20                70
[1] 2 2
[1] FALSE
D52V9, binary
                   cls
clus                  0   1
  6P LOSS MUTATED     8  62
  6P LOSS WILD-TYPE  39 258
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      8   62
  6P LOSS WILD-TYPE   39  258
     clus
vv    6P LOSS MUTATED 6P LOSS WILD-TYPE
  NO                8                39
  YES              62               258
[1] 2 2
[1] FALSE
D52V10, continuous
D52V11, binary
                   cls
clus                  0   1
  6P LOSS MUTATED    23  47
  6P LOSS WILD-TYPE 115 182
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     23   47
  6P LOSS WILD-TYPE  115  182
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  FEMALE              23               115
  MALE                47               182
[1] 2 2
[1] FALSE
D52V12, binary
                   cls
clus                  0   1
  6P LOSS MUTATED    60  10
  6P LOSS WILD-TYPE 259  37
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     60   10
  6P LOSS WILD-TYPE  259   37
     clus
vv    6P LOSS MUTATED 6P LOSS WILD-TYPE
  NO               60               259
  YES              10                37
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  6P LOSS MUTATED       2                         0    66
  6P LOSS WILD-TYPE     3                         1   287
D52V13, multiclass
                           clus
vv                          6P LOSS MUTATED 6P LOSS WILD-TYPE
  ASIAN                                   2                 3
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  66               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"
D52V14, binary
                   cls
clus                  0   1
  6P LOSS MUTATED     1  66
  6P LOSS WILD-TYPE   6 286
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      1   66
  6P LOSS WILD-TYPE    6  286
                        clus
vv                       6P LOSS MUTATED 6P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 6
  NOT HISPANIC OR LATINO              66               286
[1] 2 2
[1] FALSE

Clustering(53) Variable = 6Q LOSS MUTATION ANALYSIS
D53V1, survival
                   sevent
clus2                0  1
  6Q LOSS MUTATED   66 57
  6Q LOSS WILD-TYPE 62 67
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
              123               129 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               57                67 
$`6Q LOSS MUTATED`
TCGA-D3-A2JF TCGA-D3-A8GI TCGA-EE-A180 TCGA-EE-A2GD TCGA-EE-A2GO TCGA-FW-A3R5 
       62.07        13.41        31.96       269.03        52.90        36.95 
TCGA-WE-AAA3 TCGA-3N-A9WC TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A2J6 
        7.40        60.46         8.42        31.89       110.93        25.64 
TCGA-D3-A2J7 TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN 
       45.99       168.00        86.30        36.30       171.58        64.83 
TCGA-D3-A2JO TCGA-D3-A3C6 TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51J TCGA-D3-A51T 
       66.08        58.06        90.21        23.67       144.46        11.34 
TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GL 
       42.05        45.70       177.86        78.21        23.61        69.53 
TCGA-D3-A8GM TCGA-D3-A8GP TCGA-D9-A3Z3 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV 
       70.62       135.12        16.90        69.21        22.85        76.34 
TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F5 
      138.67        68.68        60.10        64.83        58.85       225.11 
TCGA-DA-A95V TCGA-DA-A95W TCGA-DA-A95Y TCGA-EB-A44Q TCGA-EB-A5UN TCGA-EE-A17Y 
       72.10         0.76        14.14         3.91        52.41        24.89 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29G 
       20.38         0.00        26.24        76.14        12.99        44.28 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 
       47.41        47.74        61.12       346.49       185.19       115.43 
TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GL TCGA-EE-A2GN 
       30.02        77.98        26.14        12.95        32.48        93.63 
TCGA-EE-A2GP TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MC TCGA-EE-A2MF 
        0.76        81.99       103.13        15.25        23.77       209.79 
TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AC TCGA-EE-A3AD 
      227.01       143.93        23.51        53.26        64.04         4.41 
TCGA-EE-A3AF TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3JB TCGA-EE-A3JH TCGA-ER-A195 
        6.28       111.85        45.90       168.85        19.86        34.45 
TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A2NE 
        7.82        53.29        11.47        42.51       120.76        16.87 
TCGA-ER-A2NF TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A8YC 
       10.19        32.05        74.47         4.14        26.20        10.06 
TCGA-FS-A1Z0 TCGA-FS-A1ZC TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ 
      195.98       312.07         7.82        36.33        78.61       130.95 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZZ TCGA-FW-A3TU TCGA-GF-A4EO TCGA-GN-A264 
      136.27        35.28         3.06        55.59        18.25       117.93 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 
       17.06        42.48         7.59       120.53        34.49        46.92 
TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A693 TCGA-W3-AA1R TCGA-WE-A8ZM 
       85.05       297.01         7.23         0.33        79.99        65.42 
TCGA-WE-A8ZQ TCGA-WE-AAA4 TCGA-YG-AA3O 
       62.89        24.99        28.21 

$`6Q LOSS WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A20H TCGA-EE-A2MR TCGA-EE-A3JD 
        9.76        38.76        33.24       166.75       134.40        27.35 
TCGA-ER-A193 TCGA-FR-A729 TCGA-WE-A8K5 TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q3 
       19.04       216.43        52.73        12.99        14.83        15.72 
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-A2JG TCGA-D3-A2JP TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE 
       15.75       107.61        43.53       140.98        40.01        59.70 
TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51K TCGA-D3-A51R 
       24.53         9.34       173.85        30.67        31.76        62.70 
TCGA-D3-A5GU TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GR TCGA-D9-A1X3 TCGA-D9-A3Z1 
      124.08       179.97       120.00        36.53        10.78        15.02 
TCGA-D9-A4Z6 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A3F2 TCGA-DA-A3F8 TCGA-DA-A95X 
       18.44       150.61       110.53        30.44         8.71        65.03 
TCGA-DA-A95Z TCGA-EB-A5KH TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A20C TCGA-EE-A20F 
       12.30        16.41        18.21        13.15        75.55        79.20 
TCGA-EE-A29B TCGA-EE-A29E TCGA-EE-A29P TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK 
       75.22         0.26        27.16       201.60        68.65        10.62 
TCGA-EE-A2GM TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2M8 TCGA-EE-A2MG TCGA-EE-A2MI 
       18.35         0.20        71.31         5.75        94.19       171.85 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A3AA TCGA-EE-A3AB 
       63.25        89.26       104.78       145.45       124.31       122.73 
TCGA-EE-A3AE TCGA-EE-A3J3 TCGA-EE-A3J8 TCGA-EE-A3JI TCGA-ER-A197 TCGA-ER-A19A 
       54.51        67.89         3.35       135.98        10.49         4.54 
TCGA-ER-A19C TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19Q 
       39.81       184.60       150.12        99.06        59.84        49.71 
TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NG 
       47.18       146.63        73.05        22.36         4.70        28.67 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A7UA 
      173.29        68.52        15.48         4.50       174.21         5.65 
TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZD TCGA-FS-A1ZE 
      171.78        49.74         8.35        27.62        32.78        43.92 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 
        4.47        23.21         5.29        30.90        66.67       173.19 
TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 
       13.28        80.68        11.54        19.30         9.90         1.91 
TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A8LK TCGA-GN-A9SD TCGA-RP-A690 TCGA-W3-A824 
       53.29        96.92        43.23        59.41         0.20       174.12 
TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1Q TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 
        1.97       120.07        44.05         8.09       185.13        92.84 
TCGA-WE-A8K1 TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AA9Y 
       47.54        12.69        21.90        10.95        48.39         1.94 
TCGA-WE-AAA0 TCGA-XV-AB01 TCGA-Z2-AA3S 
       37.32         6.61        91.23 

  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
              0.0               0.2 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
           346.49            216.43 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
            47.41             43.92 
[1] "0.0 - 346.5 (47.4)" "0.2 - 216.4 (43.9)"
[1] "hr=" "1.3"
D53V2, survival
                   sevent
clus2                 0   1
  6Q LOSS MUTATED    77  90
  6Q LOSS WILD-TYPE  89 102
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
              167               191 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               90               102 
$`6Q LOSS MUTATED`
TCGA-D3-A2JF TCGA-D3-A3ML TCGA-D3-A8GI TCGA-EE-A180 TCGA-EE-A184 TCGA-EE-A2GD 
       62.07        13.87        58.52        94.98        68.15       340.14 
TCGA-EE-A2GO TCGA-FS-A1ZF TCGA-FW-A3R5 TCGA-WE-AAA3 TCGA-3N-A9WB TCGA-3N-A9WC 
      126.81        15.45        36.95        21.40        17.03        66.48 
TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q9 TCGA-D3-A2J6 TCGA-D3-A2J7 
       16.57       112.04       112.57        31.59        43.43       103.10 
TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN 
      168.00        86.76        11.87        42.08       171.58        66.48 
TCGA-D3-A2JO TCGA-D3-A3C6 TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51J 
       66.08        58.06       103.59        39.75        45.30       145.12 
TCGA-D3-A51N TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A8GC 
       22.62        26.89       125.79       135.75       178.32        79.59 
TCGA-D3-A8GD TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D9-A148 
       23.61        89.13       107.15       161.00       152.75       151.53 
TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z3 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG 
        3.65         7.10        22.29        25.18        77.56        22.95 
TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I4 TCGA-DA-A1I7 TCGA-DA-A1I8 
       76.57       144.89       222.51        35.93        88.87        53.92 
TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F5 TCGA-DA-A95V TCGA-DA-A95W TCGA-DA-A95Y 
       65.92        68.09       225.96        72.10        37.35        14.14 
TCGA-EB-A44Q TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A182 
       13.87        29.29        58.92        27.22        33.73        14.70 
TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29D 
       26.89         4.96        13.55        63.35        78.97        13.97 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29T 
       72.07        64.64        56.84        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-A2GE TCGA-EE-A2GL TCGA-EE-A2GN 
       39.29        86.14        59.28       173.79        79.66       102.12 
TCGA-EE-A2GP TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MC 
       13.91        94.82        21.67       129.27        28.83        61.51 
TCGA-EE-A2MF TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AC 
      268.73       248.65       162.48        71.21        53.26        64.04 
TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3JB 
       28.77        13.81        41.59       127.20        64.08       201.80 
TCGA-EE-A3JH TCGA-ER-A195 TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19F 
      134.33        35.44         9.17        98.40        12.59        26.37 
TCGA-ER-A19J TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19T TCGA-ER-A2NE TCGA-ER-A2NF 
        6.44        44.09       162.08         8.88        20.15        28.83 
TCGA-ER-A3PL TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A8YC 
       33.21        12.95       149.03        15.72        27.85        34.82 
TCGA-FR-A8YD TCGA-FS-A1YX TCGA-FS-A1Z0 TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZG 
       36.26        48.59       202.65        48.85       357.37         9.70 
TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS 
       32.75        47.38       101.26       133.55        11.41       148.80 
TCGA-FS-A1ZT TCGA-FS-A1ZZ TCGA-FS-A4F5 TCGA-FS-A4FB TCGA-FW-A3I3 TCGA-FW-A3TU 
       53.16        27.02        28.73        26.73        17.46        55.59 
TCGA-GF-A4EO TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 
       19.43       117.93        64.44        62.79        32.48       121.91 
TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LL TCGA-HR-A2OG 
       39.35        10.42        48.89        22.13        21.37         0.23 
TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A693 TCGA-W3-AA1R TCGA-WE-A8JZ 
      368.78       297.90         7.23         0.33       111.09        24.03 
TCGA-WE-A8ZM TCGA-WE-A8ZQ TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-YG-AA3P 
      101.33        63.22        24.99        37.94        14.43 

$`6Q LOSS WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A20H TCGA-EE-A29L 
       27.65        46.32        68.25        54.02       168.26         2.60 
TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 TCGA-ER-A198 TCGA-FR-A729 TCGA-QB-AA9O 
      134.40        27.35        31.40        50.76       220.80        18.05 
TCGA-WE-A8K5 TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q3 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       61.15        12.99        14.93        16.67        71.80       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA 
       28.08        90.90        95.74        65.49        23.77       115.53 
TCGA-D3-A2JG TCGA-D3-A2JK TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3CB 
      113.52        12.10        59.57       130.72        46.98       166.52 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A51E TCGA-D3-A51F 
       86.93        60.23        24.53         9.34       174.84        55.73 
TCGA-D3-A51H TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A5GO TCGA-D3-A5GS TCGA-D3-A5GU 
       56.35        32.94        63.81       137.92        18.18       125.19 
TCGA-D3-A8GB TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GQ TCGA-D3-A8GR 
       30.84        26.43       241.38       170.20        29.06       129.63 
TCGA-D3-A8GS TCGA-D3-A8GV TCGA-D9-A149 TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A4Z6 
      117.17       167.70        54.67        18.12        15.39        18.44 
TCGA-D9-A6E9 TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1IB 
        9.90        36.03        20.38       176.55       135.02        40.60 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-DA-A95X TCGA-DA-A95Z TCGA-EB-A44R 
       33.93        10.49        43.36        73.94        13.02        10.36 
TCGA-EB-A5KH TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A20B 
       20.35         7.04        36.46        29.82         8.65       133.81 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29E TCGA-EE-A29N TCGA-EE-A29P 
      151.27        91.56        85.08        63.78        18.61        56.42 
TCGA-EE-A29R TCGA-EE-A2GC TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
       14.47        67.43       220.24        48.72       107.38        54.74 
TCGA-EE-A2GM TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2M8 TCGA-EE-A2MD 
       75.48        42.77        81.21        44.88        19.76        47.28 
TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK 
      103.27       103.20        16.96       204.66        96.23       180.39 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A3AA TCGA-EE-A3AB 
      216.66       167.90        47.54        43.23       124.31       122.73 
TCGA-EE-A3AE TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J5 TCGA-EE-A3J8 TCGA-EE-A3JA 
       54.51       138.81       172.18        36.95        34.32        53.19 
TCGA-EE-A3JE TCGA-EE-A3JI TCGA-ER-A197 TCGA-ER-A19A TCGA-ER-A19C TCGA-ER-A19E 
       51.35       152.81        13.94        77.75        48.89        13.02 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19Q TCGA-ER-A19S 
      302.07       152.35       131.51        61.05        50.89        49.48 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NG TCGA-ER-A2NH 
      148.18       105.07        43.82        23.34        48.99        41.56 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A7U9 
      247.04        93.01        46.98        92.98       174.21        18.77 
TCGA-FR-A7UA TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1Z4 
       38.27       104.42       216.92       228.59        20.91        28.08 
TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZK TCGA-FS-A1ZP 
        7.79        27.72        53.52        46.45        23.93        74.73 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 
       26.56        49.48        27.09        77.82        50.14        66.67 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3TV TCGA-FW-A5DY 
      174.84        34.03        54.41        80.68        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-A26D TCGA-GN-A8LK TCGA-GN-A9SD TCGA-HR-A2OH TCGA-RP-A690 TCGA-RP-A694 
       48.00        50.10        59.41        65.88         0.20         0.69 
TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1Q TCGA-W3-AA1V 
      228.16        63.02       121.08         4.01        69.07        42.08 
TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8K6 TCGA-WE-A8ZN TCGA-WE-A8ZO 
      219.16       105.04        49.05        17.95        58.98        70.52 
TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-XV-AB01 
       11.80        35.80        49.51        12.16        40.41        13.25 
TCGA-YD-A89C TCGA-YD-A9TA TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
        6.90        49.18        27.58        96.99        15.98 

  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
             0.23              0.20 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
           369.93            302.07 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
            53.92             50.76 
[1] "0.2 - 369.9 (53.9)" "0.2 - 302.1 (50.8)"
[1] "hr=" "1"  
D53V3, continuous
                   vv
clus                I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  6Q LOSS MUTATED          7       4      12        8       13        9
  6Q LOSS WILD-TYPE        6       3      17       10       15       17
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  6Q LOSS MUTATED           7         8         7        19          8
  6Q LOSS WILD-TYPE         7        11         8        20          7
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  6Q LOSS MUTATED           16         28        8
  6Q LOSS WILD-TYPE         19         26       13
D53V4, multiclass
            clus
vv           6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  I/II NOS                 7                 6
  STAGE 0                  4                 3
  STAGE I                 12                17
  STAGE IA                 8                10
  STAGE IB                13                15
  STAGE II                 9                17
  STAGE IIA                7                 7
  STAGE IIB                8                11
  STAGE IIC                7                 8
  STAGE III               19                20
  STAGE IIIA               8                 7
  STAGE IIIB              16                19
  STAGE IIIC              28                26
  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
  6Q LOSS MUTATED      29 37 35 29
  6Q LOSS WILD-TYPE    35 36 46 38
D53V5, multiclass
       clus
vv      6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  T0+T1              29                35
  T2                 37                36
  T3                 35                46
  T4                 29                38
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  6Q LOSS MUTATED   78 34 20 22
  6Q LOSS WILD-TYPE 99 31 19 23
D53V6, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  N0              78                99
  N1              34                31
  N2              20                19
  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"
D53V7, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED   152   9
  6Q LOSS WILD-TYPE 167  13
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED    152    9
  6Q LOSS WILD-TYPE  167   13
   clus
vv  6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  0             152               167
  1               9                13
[1] 2 2
[1] FALSE
D53V8, binary
                   cls
clus                 0  1
  6Q LOSS MUTATED   58 48
  6Q LOSS WILD-TYPE 76 42
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     58   48
  6Q LOSS WILD-TYPE   76   42
     clus
vv    6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  NO               58                76
  YES              48                42
[1] 2 2
[1] FALSE
D53V9, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED    23 149
  6Q LOSS WILD-TYPE  24 171
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     23  149
  6Q LOSS WILD-TYPE   24  171
     clus
vv    6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  NO               23                24
  YES             149               171
[1] 2 2
[1] FALSE
D53V10, continuous
D53V11, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED    69 103
  6Q LOSS WILD-TYPE  69 126
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     69  103
  6Q LOSS WILD-TYPE   69  126
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  FEMALE              69                69
  MALE               103               126
[1] 2 2
[1] FALSE
D53V12, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED   148  24
  6Q LOSS WILD-TYPE 171  23
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED    148   24
  6Q LOSS WILD-TYPE  171   23
     clus
vv    6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  NO              148               171
  YES              24                23
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  6Q LOSS MUTATED       2                         1   164
  6Q LOSS WILD-TYPE     3                         0   189
D53V13, multiclass
                           clus
vv                          6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  ASIAN                                   2                 3
  BLACK OR AFRICAN AMERICAN               1                 0
  WHITE                                 164               189
[1] 3 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   4 188
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      3  164
  6Q LOSS WILD-TYPE    4  188
                        clus
vv                       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   3                 4
  NOT HISPANIC OR LATINO             164               188
[1] 2 2
[1] FALSE

Clustering(54) Variable = 7P LOSS MUTATION ANALYSIS
D54V1, survival
                   sevent
clus2                 0   1
  7P LOSS MUTATED     6   6
  7P LOSS WILD-TYPE 122 118
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               12               240 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                6               118 
$`7P LOSS MUTATED`
TCGA-D3-A8GI TCGA-D3-A1QA TCGA-D3-A3CE TCGA-DA-A3F8 TCGA-EE-A20C TCGA-EE-A29M 
       13.41        76.41        59.70         8.71        75.55        47.74 
TCGA-EE-A3JI TCGA-FR-A7U8 TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-W3-A828 
      135.98        26.20       136.27        35.28         4.47       120.07 

$`7P LOSS WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A20H 
        9.76        62.07        38.76        33.24        31.96       166.75 
TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 TCGA-FR-A729 
      269.03        52.90       134.40        27.35        19.04       216.43 
TCGA-FW-A3R5 TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 
       36.95        52.73         7.40        60.46        12.99        14.83 
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
        8.42        15.72        31.89       110.93        49.35       133.25 
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-A2JB TCGA-D3-A2JC TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN 
      168.00        86.30       107.61        36.30       171.58        64.83 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CF 
       66.08        43.53        58.06       140.98        40.01        24.53 
TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51J 
        9.34        90.21        23.67       173.85        30.67       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        68.68 
TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 
      150.61       110.53        60.10        64.83        58.85        30.44 
TCGA-DA-A3F5 TCGA-DA-A95V TCGA-DA-A95W TCGA-DA-A95X TCGA-DA-A95Y TCGA-DA-A95Z 
      225.11        72.10         0.76        65.03        14.14        12.30 
TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y 
        3.91        16.41        52.41        18.21        13.15        24.89 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29C 
       20.38         0.00        26.24        79.20        75.22        76.14 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29P TCGA-EE-A29Q 
       12.99         0.26        44.28        47.41        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-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-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 
       93.63         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-A2MS 
       63.25        89.26       104.78       145.45       227.01       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-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A 
      168.85        19.86        34.45        10.49         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       184.60       150.12        99.06 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W 
       59.84        42.51       120.76        49.71        47.18       146.63 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
       73.05        22.36         4.70        16.87        10.19        28.67 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A3YN 
      173.29        68.52        15.48        32.05        74.47         4.50 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FS-A1YW TCGA-FS-A1YY 
      174.21         4.14         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        43.92 
TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZW TCGA-FS-A1ZY 
        7.82        36.33        78.61       130.95        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        18.25         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-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        47.54 
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-XV-AB01 TCGA-YG-AA3O TCGA-Z2-AA3S 
        1.94        37.32        24.99         6.61        28.21        91.23 

  7P LOSS MUTATED 7P LOSS WILD-TYPE 
             4.47              0.00 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
           136.27            346.49 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
           53.720            45.945 
[1] "4.5 - 136.3 (53.7)" "0.0 - 346.5 (45.9)"
[1] "hr=" "1.1"
D54V2, survival
                   sevent
clus2                 0   1
  7P LOSS MUTATED     7  11
  7P LOSS WILD-TYPE 159 181
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               18               340 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               11               181 
$`7P LOSS MUTATED`
TCGA-D3-A8GI TCGA-ER-A198 TCGA-D3-A1QA TCGA-D3-A3CE TCGA-D3-A3MV TCGA-DA-A3F8 
       58.52        50.76        90.90        60.23        45.30        43.36 
TCGA-EB-A44R TCGA-EE-A20C TCGA-EE-A29M TCGA-EE-A2A5 TCGA-EE-A3JA TCGA-EE-A3JI 
       10.36       151.27        56.84        39.29        53.19       152.81 
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-D3-A2JE TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EB-A5SG TCGA-EB-A5SH 
       27.65        62.07        46.32        13.87        68.25        54.02 
TCGA-EE-A180 TCGA-EE-A184 TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2GO 
       94.98        68.15       168.26         2.60       340.14       126.81 
TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 TCGA-FR-A729 TCGA-FS-A1ZF TCGA-FW-A3R5 
      134.40        27.35        31.40       220.80        15.45        36.95 
TCGA-QB-AA9O TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD 
       18.05        61.15        21.40        17.03        66.48        12.99 
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-A2J6 TCGA-D3-A2J7 
      133.25        28.08        31.59        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-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-A3CB TCGA-D3-A3CC 
       59.57       130.72        58.06        46.98       166.52        86.93 
TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F 
       24.53         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-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-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-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-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 
      222.51       176.55        35.93       135.02        88.87        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-A95V TCGA-DA-A95W TCGA-DA-A95X TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q 
       72.10        37.35        73.94        14.14        13.02        13.87 
TCGA-EB-A5KH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X 
       20.35        29.29        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-A185 
       27.22         8.65        33.73        14.70        26.89         4.96 
TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C 
      133.81        91.56        13.55        63.35        85.08        78.97 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29N TCGA-EE-A29P 
       13.97        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-A2A6 TCGA-EE-A2GB 
       17.92        46.82       115.96        59.64        86.14        59.28 
TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
       67.43       173.79       220.24        48.72       107.38        54.74 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
       79.66        75.48       102.12        13.91        42.77        81.21 
TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 
       44.88        94.82        21.67       129.27        28.83        19.76 
TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-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-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA 
      248.65        43.23       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-A3JE TCGA-EE-A3JH TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 
      201.80        51.35       134.33        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 
      302.07       152.35         6.44       131.51        61.05        44.09 
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       105.07 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH 
       43.82        23.34        20.15        28.83        48.99        41.56 
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-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC 
       92.98       174.21        15.72        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-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-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZW TCGA-FS-A1ZY 
      101.26        74.73       133.55        11.41        49.48        27.09 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 
       27.02        77.82        50.14        66.67        28.73       174.84 
TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU 
       34.03        26.73        54.41        80.68        17.46        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        19.43         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-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-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-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-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-AAA4 TCGA-XV-AB01 TCGA-YD-A89C TCGA-YD-A9TA TCGA-YG-AA3O 
       40.41        24.99        13.25         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 

  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            51.120 
[1] "10.4 - 152.8 (53.2)" "0.2 - 369.9 (51.1)" 
[1] "hr=" "1.2"
D54V3, continuous
                   vv
clus                I/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       25
                   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        37         15
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  7P LOSS MUTATED            3          1        0
  7P LOSS WILD-TYPE         32         53       21
D54V4, multiclass
            clus
vv           7P LOSS MUTATED 7P LOSS WILD-TYPE
  I/II NOS                 0                13
  STAGE 0                  1                 6
  STAGE I                  2                27
  STAGE IA                 1                17
  STAGE IB                 4                24
  STAGE II                 1                25
  STAGE IIA                0                14
  STAGE IIB                0                19
  STAGE IIC                2                13
  STAGE III                2                37
  STAGE IIIA               0                15
  STAGE IIIB               3                32
  STAGE IIIC               1                53
  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 80 65
D54V5, multiclass
       clus
vv      7P LOSS MUTATED 7P LOSS WILD-TYPE
  T0+T1               2                62
  T2                  9                64
  T3                  1                80
  T4                  2                65
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  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 301  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED     18    0
  7P LOSS WILD-TYPE  301   22
   clus
vv  7P LOSS MUTATED 7P LOSS WILD-TYPE
  0              18               301
  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  45 304
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      2   16
  7P LOSS WILD-TYPE   45  304
     clus
vv    7P LOSS MUTATED 7P LOSS WILD-TYPE
  NO                2                45
  YES              16               304
[1] 2 2
[1] FALSE
D54V10, continuous
D54V11, binary
                   cls
clus                  0   1
  7P LOSS MUTATED     5  13
  7P LOSS WILD-TYPE 133 216
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      5   13
  7P LOSS WILD-TYPE  133  216
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  FEMALE               5               133
  MALE                13               216
[1] 2 2
[1] FALSE
D54V12, binary
                   cls
clus                  0   1
  7P LOSS MUTATED    16   2
  7P LOSS WILD-TYPE 303  45
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED     16    2
  7P LOSS WILD-TYPE  303   45
     clus
vv    7P LOSS MUTATED 7P LOSS WILD-TYPE
  NO               16               303
  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   336
D54V13, multiclass
                           clus
vv                          7P LOSS MUTATED 7P LOSS WILD-TYPE
  ASIAN                                   1                 4
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  17               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"
D54V14, binary
                   cls
clus                  0   1
  7P LOSS MUTATED     0  18
  7P LOSS WILD-TYPE   7 334
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      0   18
  7P LOSS WILD-TYPE    7  334
                        clus
vv                       7P LOSS MUTATED 7P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 7
  NOT HISPANIC OR LATINO              18               334
[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 123 116
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               13               239 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                8               116 
$`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        93.63       135.98 
TCGA-ER-A19W TCGA-FS-A1ZE TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A4F0 TCGA-W3-A828 
      146.63        43.92        35.28         4.47        30.90       120.07 
TCGA-WE-A8ZM 
       65.42 

$`7Q LOSS WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A8GI TCGA-EB-A5SG TCGA-EE-A180 
        9.76        62.07        38.76        13.41        33.24        31.96 
TCGA-EE-A20H TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 
      166.75       269.03        52.90       134.40        27.35        19.04 
TCGA-FR-A729 TCGA-FW-A3R5 TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-3N-A9WC TCGA-3N-A9WD 
      216.43        36.95        52.73         7.40        60.46        12.99 
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-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 
      133.25        19.04        62.60        25.64        45.99        62.86 
TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL 
       15.75       168.00        86.30       107.61        36.30       171.58 
TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CC 
       64.83        66.08        43.53        58.06       140.98        40.01 
TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F 
       24.53         9.34        90.21        23.67       173.85        30.67 
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-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-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-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 
       68.68       150.61       110.53        60.10        64.83        58.85 
TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-DA-A95V TCGA-DA-A95W TCGA-DA-A95X 
       30.44       225.11         8.71        72.10         0.76        65.03 
TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A6L9 
       14.14        12.30         3.91        16.41        52.41        18.21 
TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20C 
       13.15        24.89        20.38         0.00        26.24        75.55 
TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H 
       79.20        75.22        76.14         0.26        44.28        47.41 
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-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK 
       77.98        26.14        12.95       201.60        68.65        10.62 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU 
       32.48        18.35         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-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-ER-A195 TCGA-ER-A197 TCGA-ER-A199 
        3.35       168.85        19.86        34.45        10.49         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       184.60       150.12 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S 
       99.06        59.84        42.51       120.76        49.71        47.18 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
       73.05        22.36         4.70        16.87        10.19        28.67 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A3YN 
      173.29        68.52        15.48        32.05        74.47         4.50 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FS-A1YW 
      174.21         4.14        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-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZW 
        7.82        36.33        78.61       130.95       136.27        23.21 
TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FD 
        5.29         3.06        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        18.25         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-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        47.54 
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-XV-AB01 TCGA-YG-AA3O TCGA-Z2-AA3S 
       37.32        24.99         6.61        28.21        91.23 

  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
             4.47              0.00 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
           146.63            346.49 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
             59.7              45.9 
[1] "4.5 - 146.6 (59.7)" "0.0 - 346.5 (45.9)"
[1] "hr=" "1.3"
D55V2, survival
                   sevent
clus2                 0   1
  7Q LOSS MUTATED     5  12
  7Q LOSS WILD-TYPE 161 180
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               17               341 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               12               180 
$`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-D3-A2JE TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-D3-A8GI TCGA-EB-A5SG 
       27.65        62.07        46.32        13.87        58.52        68.25 
TCGA-EB-A5SH TCGA-EE-A180 TCGA-EE-A184 TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GD 
       54.02        94.98        68.15       168.26         2.60       340.14 
TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 TCGA-ER-A198 TCGA-FR-A729 
      126.81       134.40        27.35        31.40        50.76       220.80 
TCGA-FS-A1ZF TCGA-FW-A3R5 TCGA-QB-AA9O TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-3N-A9WB 
       15.45        36.95        18.05        61.15        21.40        17.03 
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-A1QB 
      112.57        71.80       133.25        28.08        31.59        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-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-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-A3CB TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU 
      166.52        86.93        24.53         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-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-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-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       222.51       176.55        35.93 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
      135.02        88.87        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        43.36        72.10        37.35 
TCGA-DA-A95X TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UL 
       73.94        14.14        13.02        13.87        20.35        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-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-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-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
       72.07        64.64        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-A2GE 
      115.96        59.64        86.14        59.28        67.43       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-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-A2MS 
      216.66       167.90        47.54       248.65        43.23       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-A3JB TCGA-EE-A3JE TCGA-EE-A3JH 
       36.95        64.08        34.32       201.80        51.35       134.33 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C 
       35.44        13.94         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       302.07       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        44.09       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       105.07        43.82        23.34        20.15        28.83 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL 
       48.99        41.56       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-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW 
       18.77        38.27        34.82        36.26       104.42       216.92 
TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 
       48.59       228.59       202.65        20.91        28.08         7.79 
TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZG TCGA-FS-A1ZH 
       27.72        48.85       357.37        53.52         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-A4F2 TCGA-FS-A4F4 
      148.80        49.48        27.09        27.02        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 
       17.46        55.59        13.51        19.30         9.90        19.43 
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-A9SD TCGA-HR-A2OG 
       10.42        48.89        22.13        50.10        59.41         0.23 
TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-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-AA1O TCGA-W3-AA1Q TCGA-W3-AA1R 
        0.69       228.16        63.02         4.01        69.07       111.09 
TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K6 
       42.08       219.16       105.04        24.03        49.05        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-AAA4 TCGA-XV-AB01 TCGA-YD-A89C TCGA-YD-A9TA 
       12.16        40.41        24.99        13.25         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 

  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
            10.36              0.20 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
           152.81            369.93 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
            56.84             50.76 
[1] "10.4 - 152.8 (56.8)" "0.2 - 369.9 (50.8)" 
[1] "hr=" "1.4"
D55V3, continuous
                   vv
clus                I/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       25
                   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        37         15
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  7Q LOSS MUTATED            2          1        0
  7Q LOSS WILD-TYPE         33         53       21
D55V4, multiclass
            clus
vv           7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  I/II NOS                 0                13
  STAGE 0                  0                 7
  STAGE I                  1                28
  STAGE IA                 0                18
  STAGE IB                 4                24
  STAGE II                 1                25
  STAGE IIA                1                13
  STAGE IIB                1                18
  STAGE IIC                3                12
  STAGE III                2                37
  STAGE IIIA               0                15
  STAGE IIIB               2                33
  STAGE IIIC               1                53
  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 79 63
D55V5, multiclass
       clus
vv      7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  T0+T1               1                63
  T2                  7                66
  T3                  2                79
  T4                  4                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
  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 303  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED     16    0
  7Q LOSS WILD-TYPE  303   22
   clus
vv  7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  0              16               303
  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  46 304
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      1   16
  7Q LOSS WILD-TYPE   46  304
     clus
vv    7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  NO                1                46
  YES              16               304
[1] 2 2
[1] FALSE
D55V10, continuous
D55V11, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED     6  11
  7Q LOSS WILD-TYPE 132 218
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      6   11
  7Q LOSS WILD-TYPE  132  218
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  FEMALE               6               132
  MALE                11               218
[1] 2 2
[1] FALSE
D55V12, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED    14   3
  7Q LOSS WILD-TYPE 305  44
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED     14    3
  7Q LOSS WILD-TYPE  305   44
     clus
vv    7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  NO               14               305
  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   337
D55V13, multiclass
                           clus
vv                          7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  ASIAN                                   1                 4
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  16               337
[1] 3 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   7 335
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      0   17
  7Q LOSS WILD-TYPE    7  335
                        clus
vv                       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 7
  NOT HISPANIC OR LATINO              17               335
[1] 2 2
[1] FALSE

Clustering(56) Variable = 8P LOSS MUTATION ANALYSIS
D56V1, survival
                   sevent
clus2                 0   1
  8P LOSS MUTATED    20  31
  8P LOSS WILD-TYPE 108  93
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               51               201 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               31                93 
$`8P LOSS MUTATED`
TCGA-EE-A180 TCGA-FW-A3R5 TCGA-WE-AAA3 TCGA-D3-A1Q1 TCGA-D3-A2J6 TCGA-D3-A2JA 
       31.96        36.95         7.40         8.42        25.64        15.75 
TCGA-D3-A2JG TCGA-D3-A2JL TCGA-D3-A3C6 TCGA-D3-A3MO TCGA-D3-A5GN TCGA-D3-A8GC 
      107.61       171.58        58.06         9.34        45.70        78.21 
TCGA-D3-A8GM TCGA-DA-A1IA TCGA-EB-A6L9 TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A29C 
       70.62        64.83        18.21        26.24        75.55        76.14 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A2GS TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI 
       47.41        47.74        71.31       209.79        94.19       171.85 
TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AC 
      145.45       227.01       143.93        53.26       124.31        64.04 
TCGA-EE-A3J3 TCGA-EE-A3JI TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19S TCGA-ER-A2ND 
       67.89       135.98        10.49         7.82        47.18         4.70 
TCGA-ER-A2NE TCGA-ER-A3PL TCGA-FR-A8YC TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1ZC 
       16.87        32.05        10.06        49.74       195.98       312.07 
TCGA-FS-A1ZT TCGA-GN-A264 TCGA-GN-A265 TCGA-OD-A75X TCGA-QB-A6FS TCGA-W3-AA1R 
       35.28       117.93        96.92       297.01         7.23        79.99 
TCGA-WE-A8ZY TCGA-WE-AAA0 TCGA-Z2-AA3S 
       48.39        37.32        91.23 

$`8P LOSS WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A8GI TCGA-EB-A5SG TCGA-EE-A20H 
        9.76        62.07        38.76        13.41        33.24       166.75 
TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 TCGA-FR-A729 
      269.03        52.90       134.40        27.35        19.04       216.43 
TCGA-WE-A8K5 TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
       52.73        60.46        12.99        14.83        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-A2JB TCGA-D3-A2JC TCGA-D3-A2JH TCGA-D3-A2JN 
       45.99        62.86       168.00        86.30        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        24.53 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K 
       90.21        23.67       173.85        30.67       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        68.68       150.61       110.53        60.10        58.85 
TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-DA-A95V TCGA-DA-A95W TCGA-DA-A95X 
       30.44       225.11         8.71        72.10         0.76        65.03 
TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EE-A17X 
       14.14        12.30         3.91        16.41        52.41        13.15 
TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29D 
       24.89        20.38         0.00        79.20        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-A2GE TCGA-EE-A2GH 
      115.43        30.02        77.98        26.14        12.95       201.60 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP 
       68.65        10.62        32.48        18.35        93.63         0.76 
TCGA-EE-A2GR TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC 
        0.20        81.99       103.13        15.25         5.75        23.77 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MT TCGA-EE-A3AB TCGA-EE-A3AD 
       63.25        89.26       104.78        23.51       122.73         4.41 
TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB 
       54.51         6.28       111.85        45.90         3.35       168.85 
TCGA-EE-A3JH TCGA-ER-A195 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D 
       19.86        34.45         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 
      184.60       150.12        99.06        59.84        42.51       120.76 
TCGA-ER-A19Q TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NF TCGA-ER-A2NG 
       49.71       146.63        73.05        22.36        10.19        28.67 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A 
      173.29        68.52        15.48        74.47         4.50       174.21 
TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FS-A1YW TCGA-FS-A1Z3 TCGA-FS-A1Z4 
        4.14        26.20         5.65       171.78         8.35        27.62 
TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ 
       32.78        43.92         7.82        36.33        78.61       130.95 
TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 
      136.27         4.47        23.21         5.29         3.06        30.90 
TCGA-FS-A4F4 TCGA-FS-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-A267 
       19.30         9.90        18.25         1.91        53.29        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-RP-A690 TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A825 
       59.41        85.05         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        47.54 
TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-AA9Y 
       65.42        12.69        21.90        62.89        10.95         1.94 
TCGA-WE-AAA4 TCGA-XV-AB01 TCGA-YG-AA3O 
       24.99         6.61        28.21 

  8P LOSS MUTATED 8P LOSS WILD-TYPE 
              4.7               0.0 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
           312.07            346.49 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
            58.06             43.23 
[1] "4.7 - 312.1 (58.1)" "0.0 - 346.5 (43.2)"
[1] "hr=" "1"  
D56V2, survival
                   sevent
clus2                 0   1
  8P LOSS MUTATED    28  38
  8P LOSS WILD-TYPE 138 154
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               66               292 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               38               154 
$`8P LOSS MUTATED`
TCGA-EE-A180 TCGA-FW-A3R5 TCGA-QB-AA9O TCGA-WE-AAA3 TCGA-D3-A1Q1 TCGA-D3-A2J6 
       94.98        36.95        18.05        21.40        16.57        43.43 
TCGA-D3-A2JA TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JL TCGA-D3-A3C6 TCGA-D3-A3MO 
      115.53        11.87       113.52       171.58        58.06         9.34 
TCGA-D3-A51N TCGA-D3-A5GN TCGA-D3-A8GC TCGA-D3-A8GM TCGA-D9-A148 TCGA-D9-A1JW 
       22.62       135.75        79.59       107.15       151.53         3.65 
TCGA-D9-A6EA TCGA-DA-A1IA TCGA-EB-A6L9 TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A29C 
       25.18        65.92        36.46        26.89       151.27        78.97 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29V TCGA-EE-A2A5 TCGA-EE-A2GI TCGA-EE-A2GS 
       64.64        56.84        25.87        39.29        48.72        81.21 
TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP 
      268.73       103.20       204.66       167.90        47.54       248.65 
TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3J3 TCGA-EE-A3JI 
      162.48        53.26       124.31        64.04       172.18       152.81 
TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A2ND TCGA-ER-A2NE 
       13.94         9.17        49.48         8.88        23.34        20.15 
TCGA-ER-A3PL TCGA-FR-A8YC TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1ZA TCGA-FS-A1ZC 
       33.21        34.82       228.59       202.65        27.72       357.37 
TCGA-FS-A1ZT TCGA-GN-A264 TCGA-GN-A265 TCGA-OD-A75X TCGA-QB-A6FS TCGA-W3-AA1R 
       53.16       117.93        96.92       297.90         7.23       111.09 
TCGA-WE-A8JZ TCGA-WE-A8ZY TCGA-WE-AAA0 TCGA-YD-A9TA TCGA-YG-AA3P TCGA-Z2-AA3S 
       24.03        49.51        40.41        49.18        14.43        96.99 

$`8P LOSS WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-D3-A8GI TCGA-EB-A5SG 
       27.65        62.07        46.32        13.87        58.52        68.25 
TCGA-EB-A5SH TCGA-EE-A184 TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2GO 
       54.02        68.15       168.26         2.60       340.14       126.81 
TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 TCGA-ER-A198 TCGA-FR-A729 TCGA-FS-A1ZF 
      134.40        27.35        31.40        50.76       220.80        15.45 
TCGA-WE-A8K5 TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q3 
       61.15        17.03        66.48        12.99        14.93        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-A2JB 
       90.90        95.74       103.10        65.49        23.77       168.00 
TCGA-D3-A2JC TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP 
       86.76        42.08        12.10        66.48        66.08        59.57 
TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF 
      130.72        46.98       166.52        86.93        60.23        24.53 
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-A5GO 
      145.12        32.94        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-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-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-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 
       76.57        36.03       144.89        20.38       222.51       176.55 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IB TCGA-DA-A1IC 
       35.93       135.02        88.87        53.92        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        43.36        72.10        37.35 
TCGA-DA-A95X TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH 
       73.94        14.14        13.02        13.87        10.36        20.35 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
       29.29        58.92         7.04        29.82        27.22         8.65 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20I 
       33.73        14.70         4.96       133.81        91.56        13.55 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29N 
       63.35        85.08        13.97        63.78        72.07        18.61 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29W 
       56.42        66.74        14.47        61.28       369.93       195.02 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB 
       17.92        46.82       115.96        59.64        86.14        59.28 
TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
       67.43       173.79       220.24       107.38        54.74        79.66 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GT TCGA-EE-A2GU 
       75.48       102.12        13.91        42.77        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-A2MH TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MQ 
      103.27        16.96        96.23       180.39       216.66        43.23 
TCGA-EE-A2MT TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG 
       71.21       122.73        28.77        54.51        13.81        41.59 
TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA 
      138.81       127.20        36.95        64.08        34.32        53.19 
TCGA-EE-A3JB TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A195 TCGA-ER-A19A TCGA-ER-A19B 
      201.80        51.35       134.33        35.44        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       302.07       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        44.09       162.08        50.89 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH 
      148.18       105.07        43.82        28.83        48.99        41.56 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A3YN 
      247.04        93.01        46.98        12.95       149.03        92.98 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YD 
      174.21        15.72        27.85        18.77        38.27        36.26 
TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 
      104.42       216.92        48.59        20.91        28.08         7.79 
TCGA-FS-A1ZB TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ 
       48.85        53.52        46.45         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-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-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
       80.68        17.46        55.59        13.51        19.30         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A266 TCGA-GN-A267 
       19.43         2.04        15.78       139.89        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-GN-A9SD TCGA-HR-A2OG 
       48.89        22.13        50.10        21.37        59.41         0.23 
TCGA-HR-A2OH TCGA-LH-A9QB TCGA-RP-A690 TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 
       65.88       368.78         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-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-AA9Y TCGA-WE-AAA4 TCGA-XV-AB01 
       63.22        11.80        35.80        12.16        24.99        13.25 
TCGA-YD-A89C TCGA-YG-AA3O TCGA-Z2-A8RT TCGA-Z2-AA3V 
        6.90        37.94        27.58        15.98 

  8P LOSS MUTATED 8P LOSS WILD-TYPE 
             3.65              0.20 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
           357.37            369.93 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
           55.050            50.825 
[1] "3.6 - 357.4 (55.0)" "0.2 - 369.9 (50.8)"
[1] "hr=" "1.1"
D56V3, continuous
                   vv
clus                I/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       24
                   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        33         13
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  8P LOSS MUTATED            4         11        3
  8P LOSS WILD-TYPE         31         43       18
D56V4, multiclass
            clus
vv           8P LOSS MUTATED 8P LOSS WILD-TYPE
  I/II NOS                 2                11
  STAGE 0                  3                 4
  STAGE I                  7                22
  STAGE IA                 6                12
  STAGE IB                 6                22
  STAGE II                 2                24
  STAGE IIA                2                12
  STAGE IIB                5                14
  STAGE IIC                0                15
  STAGE III                6                33
  STAGE IIIA               2                13
  STAGE IIIB               4                31
  STAGE IIIC              11                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 71 56
D56V5, multiclass
       clus
vv      8P LOSS MUTATED 8P LOSS WILD-TYPE
  T0+T1              14                50
  T2                 15                58
  T3                 10                71
  T4                 11                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
  8P LOSS MUTATED    34   8   7  11
  8P LOSS WILD-TYPE 143  57  32  34
D56V6, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  N0              34               143
  N1               8                57
  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"
D56V7, binary
                   cls
clus                  0   1
  8P LOSS MUTATED    58   4
  8P LOSS WILD-TYPE 261  18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     58    4
  8P LOSS WILD-TYPE  261   18
   clus
vv  8P LOSS MUTATED 8P LOSS WILD-TYPE
  0              58               261
  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  58
  8P LOSS WILD-TYPE  39 262
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      8   58
  8P LOSS WILD-TYPE   39  262
     clus
vv    8P LOSS MUTATED 8P LOSS WILD-TYPE
  NO                8                39
  YES              58               262
[1] 2 2
[1] FALSE
D56V10, continuous
D56V11, binary
                   cls
clus                  0   1
  8P LOSS MUTATED    22  44
  8P LOSS WILD-TYPE 116 185
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     22   44
  8P LOSS WILD-TYPE  116  185
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  FEMALE              22               116
  MALE                44               185
[1] 2 2
[1] FALSE
D56V12, binary
                   cls
clus                  0   1
  8P LOSS MUTATED    57   9
  8P LOSS WILD-TYPE 262  38
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     57    9
  8P LOSS WILD-TYPE  262   38
     clus
vv    8P LOSS MUTATED 8P LOSS WILD-TYPE
  NO               57               262
  YES               9                38
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  8P LOSS MUTATED       1                         0    63
  8P LOSS WILD-TYPE     4                         1   290
D56V13, multiclass
                           clus
vv                          8P LOSS MUTATED 8P LOSS WILD-TYPE
  ASIAN                                   1                 4
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  63               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"
D56V14, binary
                   cls
clus                  0   1
  8P LOSS MUTATED     1  64
  8P LOSS WILD-TYPE   6 288
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      1   64
  8P LOSS WILD-TYPE    6  288
                        clus
vv                       8P LOSS MUTATED 8P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 6
  NOT HISPANIC OR LATINO              64               288
[1] 2 2
[1] FALSE

Clustering(57) Variable = 8Q LOSS MUTATION ANALYSIS
D57V1, survival
                   sevent
clus2                 0   1
  8Q LOSS MUTATED     7  12
  8Q LOSS WILD-TYPE 121 112
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               19               233 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               12               112 
$`8Q LOSS MUTATED`
TCGA-EE-A180 TCGA-FW-A3R5 TCGA-D3-A2JL TCGA-D3-A8GC TCGA-D3-A8GM TCGA-DA-A1IA 
       31.96        36.95       171.58        78.21        70.62        64.83 
TCGA-EE-A20C TCGA-EE-A29M TCGA-EE-A2MI TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MS 
       75.55        47.74       171.85       145.45       227.01       143.93 
TCGA-EE-A2MU TCGA-EE-A3JI TCGA-ER-A199 TCGA-ER-A2NE TCGA-ER-A3PL TCGA-W3-AA1R 
       53.26       135.98         7.82        16.87        32.05        79.99 
TCGA-WE-A8ZY 
       48.39 

$`8Q LOSS WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A8GI TCGA-EB-A5SG TCGA-EE-A20H 
        9.76        62.07        38.76        13.41        33.24       166.75 
TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 TCGA-FR-A729 
      269.03        52.90       134.40        27.35        19.04       216.43 
TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 
       52.73         7.40        60.46        12.99        14.83         8.42 
TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       15.72        31.89       110.93        49.35       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-A2JG TCGA-D3-A2JH TCGA-D3-A2JN TCGA-D3-A2JO 
      168.00        86.30       107.61        36.30        64.83        66.08 
TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF 
       43.53        58.06       140.98        40.01        59.70        24.53 
TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51J 
        9.34        90.21        23.67       173.85        30.67       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        68.68       150.61       110.53 
TCGA-DA-A1I7 TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-DA-A95V 
       60.10        58.85        30.44       225.11         8.71        72.10 
TCGA-DA-A95W TCGA-DA-A95X TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5KH 
        0.76        65.03        14.14        12.30         3.91        16.41 
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-A183 TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
       26.24        79.20        75.22        76.14        12.99         0.26 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W 
       44.28        47.41        27.16        61.12       346.49       185.19 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH 
      115.43        30.02        77.98        26.14        12.95       201.60 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP 
       68.65        10.62        32.48        18.35        93.63         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-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML 
       23.77       209.79        94.19        63.25        89.26       104.78 
TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
       23.51       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-A3JB 
        6.28        67.89       111.85        45.90         3.35       168.85 
TCGA-EE-A3JH TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C 
       19.86        34.45        10.49         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       184.60       150.12        99.06        59.84        42.51 
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        73.05        22.36 
TCGA-ER-A2ND TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
        4.70        10.19        28.67       173.29        68.52        15.48 
TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A7UA 
       74.47         4.50       174.21         4.14        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-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM 
      312.07        32.78        43.92         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        18.25         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-AA1V TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 
      120.07        44.05         8.09       185.13        92.84        47.54 
TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-AA9Y 
       65.42        12.69        21.90        62.89        10.95         1.94 
TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-XV-AB01 TCGA-YG-AA3O TCGA-Z2-AA3S 
       37.32        24.99         6.61        28.21        91.23 

  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
             7.82              0.00 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
           227.01            346.49 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
            70.62             44.05 
[1] "7.8 - 227.0 (70.6)" "0.0 - 346.5 (44.0)"
[1] "hr=" "1"  
D57V2, survival
                   sevent
clus2                 0   1
  8Q LOSS MUTATED    10  15
  8Q LOSS WILD-TYPE 156 177
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               25               333 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               15               177 
$`8Q LOSS MUTATED`
TCGA-EE-A180 TCGA-FW-A3R5 TCGA-D3-A2JD TCGA-D3-A2JL TCGA-D3-A8GC TCGA-D3-A8GM 
       94.98        36.95        11.87       171.58        79.59       107.15 
TCGA-D9-A6EA TCGA-DA-A1IA TCGA-EE-A20C TCGA-EE-A29M TCGA-EE-A2MI TCGA-EE-A2MM 
       25.18        65.92       151.27        56.84       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-W3-AA1R TCGA-WE-A8JZ TCGA-WE-A8ZY 
       20.15        33.21        27.72       111.09        24.03        49.51 
TCGA-YG-AA3P 
       14.43 

$`8Q LOSS WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-D3-A8GI TCGA-EB-A5SG 
       27.65        62.07        46.32        13.87        58.52        68.25 
TCGA-EB-A5SH TCGA-EE-A184 TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2GO 
       54.02        68.15       168.26         2.60       340.14       126.81 
TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 TCGA-ER-A198 TCGA-FR-A729 TCGA-FS-A1ZF 
      134.40        27.35        31.40        50.76       220.80        15.45 
TCGA-QB-AA9O TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD 
       18.05        61.15        21.40        17.03        66.48        12.99 
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-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-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP 
      113.52        42.08        12.10        66.48        66.08        59.57 
TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE 
      130.72        58.06        46.98       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-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-A8GD TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GK 
      125.19        30.84        23.61        26.43       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-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-A1I1 TCGA-DA-A1I2 
       76.57        36.03       144.89        20.38       222.51       176.55 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IB TCGA-DA-A1IC 
       35.93       135.02        88.87        53.92        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        43.36        72.10        37.35 
TCGA-DA-A95X TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH 
       73.94        14.14        13.02        13.87        10.36        20.35 
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-A185 TCGA-EE-A20B 
        8.65        33.73        14.70        26.89         4.96       133.81 
TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D 
       91.56        13.55        63.35        85.08        78.97        13.97 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
       63.78        72.07        64.64        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-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
       67.43       173.79       220.24        48.72       107.38        54.74 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
       79.66        75.48       102.12        13.91        42.77        81.21 
TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 
       44.88        94.82        21.67       129.27        28.83        19.76 
TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH 
       61.51        47.28       103.27       268.73       103.20        16.96 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MT 
       96.23       180.39       216.66        47.54        43.23        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-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-A3JB TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A195 
       34.32        53.19       201.80        51.35       134.33        35.44 
TCGA-ER-A197 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19F 
       13.94        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 
      302.07       152.35         6.44       131.51        61.05        44.09 
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       105.07 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES 
       43.82        23.34        28.83        48.99        41.56       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-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-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-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP 
        9.70        32.75        47.38        23.93       101.26        74.73 
TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW 
      133.55        11.41       148.80        53.16        26.56        49.48 
TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 
       27.09        27.02        77.82        50.14        66.67        28.73 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 
      174.84        34.03        26.73        54.41        80.68        17.46 
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        19.43         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-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-AA1V TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8K6 TCGA-WE-A8ZM 
       42.08       219.16       105.04        49.05        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-AAA0 TCGA-WE-AAA4 TCGA-XV-AB01 TCGA-YD-A89C TCGA-YD-A9TA TCGA-YG-AA3O 
       40.41        24.99        13.25         6.90        49.18        37.94 
TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
       27.58        96.99        15.98 

  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
             9.17              0.20 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
           248.65            369.93 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
            56.84             50.89 
[1] "9.2 - 248.7 (56.8)" "0.2 - 369.9 (50.9)"
[1] "hr=" "1"  
D57V3, continuous
                   vv
clus                I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  8Q LOSS MUTATED          1       2       3        1        2        2
  8Q LOSS WILD-TYPE       12       5      26       17       26       24
                   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        37         15
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  8Q LOSS MUTATED            3          4        1
  8Q LOSS WILD-TYPE         32         50       20
D57V4, multiclass
            clus
vv           8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  I/II NOS                 1                12
  STAGE 0                  2                 5
  STAGE I                  3                26
  STAGE IA                 1                17
  STAGE IB                 2                26
  STAGE II                 2                24
  STAGE IIA                1                13
  STAGE IIB                3                16
  STAGE IIC                0                15
  STAGE III                2                37
  STAGE IIIA               0                15
  STAGE IIIB               3                32
  STAGE IIIC               4                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
  8Q LOSS MUTATED       1  6  5  8
  8Q LOSS WILD-TYPE    63 67 76 59
D57V5, multiclass
       clus
vv      8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  T0+T1               1                63
  T2                  6                67
  T3                  5                76
  T4                  8                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
  8Q LOSS MUTATED    16   3   2   3
  8Q LOSS WILD-TYPE 161  62  37  42
D57V6, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  N0              16               161
  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    24   1
  8Q LOSS WILD-TYPE 295  21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED     24    1
  8Q LOSS WILD-TYPE  295   21
   clus
vv  8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  0              24               295
  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  24
  8Q LOSS WILD-TYPE  46 296
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      1   24
  8Q LOSS WILD-TYPE   46  296
     clus
vv    8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  NO                1                46
  YES              24               296
[1] 2 2
[1] FALSE
D57V10, continuous
D57V11, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED     9  16
  8Q LOSS WILD-TYPE 129 213
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      9   16
  8Q LOSS WILD-TYPE  129  213
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  FEMALE               9               129
  MALE                16               213
[1] 2 2
[1] FALSE
D57V12, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED    21   4
  8Q LOSS WILD-TYPE 298  43
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED     21    4
  8Q LOSS WILD-TYPE  298   43
     clus
vv    8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  NO               21               298
  YES               4                43
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  8Q LOSS MUTATED       0                         0    23
  8Q LOSS WILD-TYPE     5                         1   330
D57V13, multiclass
                           clus
vv                          8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  ASIAN                                   0                 5
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  23               330
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V14, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED     1  23
  8Q LOSS WILD-TYPE   6 329
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      1   23
  8Q LOSS WILD-TYPE    6  329
                        clus
vv                       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 6
  NOT HISPANIC OR LATINO              23               329
[1] 2 2
[1] FALSE

Clustering(58) Variable = 9P LOSS MUTATION ANALYSIS
D58V1, survival
                   sevent
clus2                0  1
  9P LOSS MUTATED   75 87
  9P LOSS WILD-TYPE 53 37
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              162                90 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               87                37 
$`9P LOSS MUTATED`
TCGA-D3-A2JF TCGA-D3-A8GI TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GD 
       62.07        13.41        33.24        31.96       166.75       269.03 
TCGA-EE-A2GO TCGA-EE-A2MR TCGA-ER-A193 TCGA-FR-A729 TCGA-FW-A3R5 TCGA-WE-A8K5 
       52.90       134.40        19.04       216.43        36.95        52.73 
TCGA-WE-AAA3 TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 
        7.40        14.83         8.42        31.89       110.93        49.35 
TCGA-D3-A1Q8 TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JL 
       19.04        25.64        45.99       168.00        86.30       171.58 
TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3MO 
       64.83        43.53        58.06        40.01        24.53         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51J TCGA-D3-A51T TCGA-D3-A5GL 
       90.21        23.67       173.85       144.46        11.34        42.05 
TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D3-A8GL TCGA-D3-A8GP TCGA-D3-A8GR TCGA-D9-A1X3 
      177.86       124.08        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-A1IA TCGA-DA-A1IC TCGA-DA-A3F5 
       68.68       150.61       110.53        64.83        58.85       225.11 
TCGA-DA-A95X TCGA-DA-A95Y TCGA-EB-A44Q TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y 
       65.03        14.14         3.91        52.41        13.15        24.89 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29D 
       20.38         0.00        75.55        79.20        76.14        12.99 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29W TCGA-EE-A2GB 
        0.26        44.28        27.16        61.12       185.19        26.14 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP 
       12.95       201.60        32.48        18.35        93.63         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-A2MS TCGA-EE-A3AA 
       89.26       104.78       145.45       227.01       143.93       124.31 
TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J7 
      122.73         4.41        54.51         6.28        67.89        45.90 
TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 
        3.35       168.85        19.86       135.98        34.45        10.49 
TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19H TCGA-ER-A19L 
        7.82        53.29        39.81        11.47       150.12        99.06 
TCGA-ER-A19M TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A2ND 
       59.84       120.76        49.71        47.18       146.63         4.70 
TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A3YN 
       28.67       173.29        15.48        32.05        74.47         4.50 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A8YC TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z3 
      174.21         4.14        10.06       171.78        49.74         8.35 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZW 
      312.07        32.78        78.61       130.95       136.27        23.21 
TCGA-FS-A1ZY TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F9 TCGA-FW-A3TU TCGA-GF-A4EO 
        5.29        30.90        66.67        13.28        55.59        18.25 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 
        1.91        53.29        96.92        42.48         7.59       120.53 
TCGA-GN-A8LK TCGA-GN-A9SD TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A693 TCGA-W3-A825 
       43.23        59.41       297.01         7.23         0.33         1.97 
TCGA-W3-A828 TCGA-W3-AA1R TCGA-W3-AA1V TCGA-W3-AA21 TCGA-WE-A8ZM TCGA-WE-A8ZN 
      120.07        79.99         8.09        92.84        65.42        12.69 
TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZY TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-Z2-AA3S 
       21.90        62.89        48.39        24.99        28.21        91.23 

$`9P LOSS WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A3C8 TCGA-EE-A3JD TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q3 
        9.76        38.76        27.35        60.46        12.99        15.72 
TCGA-D3-A1Q7 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JG 
      133.25        76.41        62.60        62.86        15.75       107.61 
TCGA-D3-A2JH TCGA-D3-A2JO TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A51F TCGA-D3-A51K 
       36.30        66.08       140.98        59.70        30.67        31.76 
TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GJ TCGA-D3-A8GK 
       62.70        45.70        78.21        23.61       179.97       120.00 
TCGA-D3-A8GM TCGA-D9-A6EC TCGA-DA-A1I7 TCGA-DA-A3F2 TCGA-DA-A3F8 TCGA-DA-A95V 
       70.62        69.21        60.10        30.44         8.71        72.10 
TCGA-DA-A95W TCGA-DA-A95Z TCGA-EB-A5KH TCGA-EB-A6L9 TCGA-EE-A183 TCGA-EE-A29B 
        0.76        12.30        16.41        18.21        26.24        75.22 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29T TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 
       47.41        47.74       346.49       115.43        30.02        77.98 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2M7 TCGA-EE-A2MC TCGA-EE-A2MG TCGA-EE-A2MI 
       68.65        10.62        15.25        23.77        94.19       171.85 
TCGA-EE-A2MJ TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AC TCGA-EE-A3J4 TCGA-ER-A19A 
       63.25        23.51        53.26        64.04       111.85         4.54 
TCGA-ER-A19G TCGA-ER-A19N TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NF 
      184.60        42.51        73.05        22.36        16.87        10.19 
TCGA-ER-A3ET TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1ZE 
       68.52        26.20         5.65       195.98        27.62        43.92 
TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZZ TCGA-FS-A4F8 
        7.82        36.33        35.28         4.47         3.06       173.19 
TCGA-FS-A4FD TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GN-A264 TCGA-GN-A267 
       80.68        11.54        19.30         9.90       117.93        17.06 
TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-LH-A9QB TCGA-RP-A690 TCGA-W3-A824 TCGA-W3-AA1Q 
       34.49        46.92        85.05         0.20       174.12        44.05 
TCGA-W3-AA1W TCGA-WE-A8K1 TCGA-WE-A8ZT TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-XV-AB01 
      185.13        47.54        10.95         1.94        37.32         6.61 

  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 
           49.530            43.215 
[1] "0.0 - 312.1 (49.5)" "0.2 - 346.5 (43.2)"
[1] "hr=" "1.1"
D58V2, survival
                   sevent
clus2                 0   1
  9P LOSS MUTATED    96 131
  9P LOSS WILD-TYPE  70  61
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              227               131 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              131                61 
$`9P LOSS MUTATED`
TCGA-D3-A2JF TCGA-D3-A3ML TCGA-D3-A8GI TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A20H 
       62.07        13.87        58.52        68.25        94.98       168.26 
TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR TCGA-ER-A193 TCGA-FR-A729 
        2.60       340.14       126.81       134.40        31.40       220.80 
TCGA-FS-A1ZF TCGA-FW-A3R5 TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-BF-AAP0 TCGA-D3-A1Q1 
       15.45        36.95        61.15        21.40        14.93        16.57 
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q8 TCGA-D3-A2J6 TCGA-D3-A2J7 
      112.04       112.57        71.80        28.08        43.43       103.10 
TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JP 
      168.00        86.76        12.10       171.58        66.48        59.57 
TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR 
       58.06        46.98        86.93        24.53         9.34       103.59 
TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51J TCGA-D3-A51N TCGA-D3-A51T 
       39.75        45.30       174.84       145.12        22.62        26.89 
TCGA-D3-A5GL TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GL 
      125.79       137.92       178.32       125.19        30.84        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       222.51       176.55        35.93 
TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F5 TCGA-DA-A95X 
      135.02        53.92        65.92        68.09       225.96        73.94 
TCGA-DA-A95Y TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X 
       14.14        13.87        10.36        29.29        58.92        29.82 
TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C 
       27.22        33.73        14.70         4.96       133.81       151.27 
TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G 
       91.56        13.55        78.97        13.97        63.78        72.07 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W 
       18.61        56.42        66.74        61.28        25.87       195.02 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A5 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GE 
       17.92        46.82        39.29        59.28        67.43       173.79 
TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP 
      220.24        48.72        79.66        75.48       102.12        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-A2MS TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE 
      248.65       162.48       124.31       122.73        28.77        54.51 
TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-EE-A3J8 
       13.81        41.59       138.81       172.18        64.08        34.32 
TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 
       53.19       201.80       134.33       152.81        35.44        13.94 
TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F 
        9.17        98.40        48.89        12.59        13.02        26.37 
TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S 
      152.35       131.51        61.05       162.08        50.89        49.48 
TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A2ND TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES 
        8.88       148.18        23.34        48.99        41.56       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-A8YC TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z3 
       15.72        34.82       216.92        48.59       228.59        20.91 
TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZH 
        7.79        27.72        48.85       357.37        53.52        32.75 
TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZW TCGA-FS-A1ZY 
      101.26       133.55        11.41       148.80        49.48        27.09 
TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F9 TCGA-FS-A4FB 
       77.82        50.14        66.67        28.73        34.03        26.73 
TCGA-FS-A4FC TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 
       54.41        17.46        55.59        19.43         2.04        15.78 
TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U3 
      139.89        96.92        62.79        32.48        48.00       121.91 
TCGA-GN-A4U7 TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A8LL TCGA-GN-A9SD TCGA-HR-A2OG 
       10.42        22.13        50.10        21.37        59.41         0.23 
TCGA-HR-A2OH TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A825 
       65.88       297.90         7.23         0.33         0.69        63.02 
TCGA-W3-A828 TCGA-W3-AA1R TCGA-W3-AA1V TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K6 
      121.08       111.09        42.08       105.04        24.03        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-AAA4 TCGA-YG-AA3O TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
       24.99        37.94        27.58        96.99        15.98 

$`9P LOSS WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A3C8 TCGA-EB-A5SH TCGA-EE-A184 TCGA-EE-A3JD TCGA-ER-A198 
       27.65        46.32        54.02        68.15        27.35        50.76 
TCGA-QB-AA9O TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q3 TCGA-D3-A1Q7 
       18.05        17.03        66.48        12.99        16.67       133.25 
TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA 
       31.59        90.90        95.74        65.49        23.77       115.53 
TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JO TCGA-D3-A3BZ TCGA-D3-A3CB 
       11.87       113.52        42.08        66.08       130.72       166.52 
TCGA-D3-A3CE TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A5GN 
       60.23        55.73        56.35        32.94        63.81       135.75 
TCGA-D3-A5GS TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GK 
       18.18        79.59        23.61        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        88.87        40.60        33.93        10.49 
TCGA-DA-A3F8 TCGA-DA-A95V TCGA-DA-A95W TCGA-DA-A95Z TCGA-EB-A5KH TCGA-EB-A5VV 
       43.36        72.10        37.35        13.02        20.35         7.04 
TCGA-EB-A6L9 TCGA-EE-A17Z TCGA-EE-A183 TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29H 
       36.46         8.65        26.89        63.35        85.08        64.64 
TCGA-EE-A29M TCGA-EE-A29R TCGA-EE-A29T TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 
       56.84        14.47       369.93       115.96        59.64        86.14 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2M7 TCGA-EE-A2MC 
      107.38        54.74        44.88        21.67        28.83        61.51 
TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MQ TCGA-EE-A2MT 
      103.27       103.20       204.66        96.23        43.23        71.21 
TCGA-EE-A2MU TCGA-EE-A3AC TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3JE TCGA-ER-A19A 
       53.26        64.04       127.20        36.95        51.35        77.75 
TCGA-ER-A19G TCGA-ER-A19J TCGA-ER-A19N TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE 
      302.07         6.44        44.09       105.07        43.82        20.15 
TCGA-ER-A2NF TCGA-ER-A3ET TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YD 
       28.83        93.01        27.85        18.77        38.27        36.26 
TCGA-FR-A8YE TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ 
      104.42       202.65        28.08        46.45         9.70        47.38 
TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZZ TCGA-FS-A4F8 
       23.93        74.73        53.16        26.56        27.02       174.84 
TCGA-FS-A4FD TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GN-A264 TCGA-GN-A266 
       80.68        13.51        19.30         9.90       117.93        10.13 
TCGA-GN-A267 TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-LH-A9QB TCGA-RP-A690 TCGA-W3-A824 
       64.44        39.35        48.89       368.78         0.20       228.16 
TCGA-W3-AA1O TCGA-W3-AA1Q TCGA-W3-AA1W TCGA-WE-A8K1 TCGA-WE-A8ZT TCGA-WE-AA9Y 
        4.01        69.07       219.16        49.05        11.80        12.16 
TCGA-WE-AAA0 TCGA-XV-AB01 TCGA-YD-A89C TCGA-YD-A9TA TCGA-YG-AA3P 
       40.41        13.25         6.90        49.18        14.43 

  9P LOSS MUTATED 9P LOSS WILD-TYPE 
             0.23              0.20 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
           357.37            369.93 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
            54.67             47.38 
[1] "0.2 - 357.4 (54.7)" "0.2 - 369.9 (47.4)"
[1] "hr=" "1.1"
D58V3, continuous
                   vv
clus                I/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        8
                   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        12          8
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  9P LOSS MUTATED           24         31       14
  9P LOSS WILD-TYPE         11         23        7
D58V4, multiclass
            clus
vv           9P LOSS MUTATED 9P LOSS WILD-TYPE
  I/II NOS                11                 2
  STAGE 0                  4                 3
  STAGE I                 19                10
  STAGE IA                 9                 9
  STAGE IB                18                10
  STAGE II                18                 8
  STAGE IIA                9                 5
  STAGE IIB               12                 7
  STAGE IIC               10                 5
  STAGE III               27                12
  STAGE IIIA               7                 8
  STAGE IIIB              24                11
  STAGE IIIC              31                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 54 43
  9P LOSS WILD-TYPE    25 24 27 24
D58V5, multiclass
       clus
vv      9P LOSS MUTATED 9P LOSS WILD-TYPE
  T0+T1              39                25
  T2                 49                24
  T3                 54                27
  T4                 43                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  25
  9P LOSS WILD-TYPE  60  22  15  20
D58V6, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  N0             117                60
  N1              43                22
  N2              24                15
  N3              25                20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V7, binary
                   cls
clus                  0   1
  9P LOSS MUTATED   203  15
  9P LOSS WILD-TYPE 116   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED    203   15
  9P LOSS WILD-TYPE  116    7
   clus
vv  9P LOSS MUTATED 9P LOSS WILD-TYPE
  0             203               116
  1              15                 7
[1] 2 2
[1] FALSE
D58V8, binary
                   cls
clus                 0  1
  9P LOSS MUTATED   85 58
  9P LOSS WILD-TYPE 49 32
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     85   58
  9P LOSS WILD-TYPE   49   32
     clus
vv    9P LOSS MUTATED 9P LOSS WILD-TYPE
  NO               85                49
  YES              58                32
[1] 2 2
[1] FALSE
D58V9, binary
                   cls
clus                  0   1
  9P LOSS MUTATED    26 209
  9P LOSS WILD-TYPE  21 111
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     26  209
  9P LOSS WILD-TYPE   21  111
     clus
vv    9P LOSS MUTATED 9P LOSS WILD-TYPE
  NO               26                21
  YES             209               111
[1] 2 2
[1] FALSE
D58V10, continuous
D58V11, binary
                   cls
clus                  0   1
  9P LOSS MUTATED    98 137
  9P LOSS WILD-TYPE  40  92
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     98  137
  9P LOSS WILD-TYPE   40   92
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  FEMALE              98                40
  MALE               137                92
[1] 2 2
[1] FALSE
D58V12, binary
                   cls
clus                  0   1
  9P LOSS MUTATED   209  26
  9P LOSS WILD-TYPE 110  21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED    209   26
  9P LOSS WILD-TYPE  110   21
     clus
vv    9P LOSS MUTATED 9P LOSS WILD-TYPE
  NO              209               110
  YES              26                21
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  9P LOSS MUTATED       3                         1   224
  9P LOSS WILD-TYPE     2                         0   129
D58V13, multiclass
                           clus
vv                          9P LOSS MUTATED 9P LOSS WILD-TYPE
  ASIAN                                   3                 2
  BLACK OR AFRICAN AMERICAN               1                 0
  WHITE                                 224               129
[1] 3 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     2 227
  9P LOSS WILD-TYPE   5 125
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      2  227
  9P LOSS WILD-TYPE    5  125
                        clus
vv                       9P LOSS MUTATED 9P LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                 5
  NOT HISPANIC OR LATINO             227               125
[1] 2 2
[1] FALSE

Clustering(59) Variable = 9Q LOSS MUTATION ANALYSIS
D59V1, survival
                   sevent
clus2                0  1
  9Q LOSS MUTATED   60 69
  9Q LOSS WILD-TYPE 68 55
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
              129               123 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               69                55 
$`9Q LOSS MUTATED`
TCGA-D3-A8GI TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GD TCGA-EE-A2MR 
       13.41        33.24        31.96       166.75       269.03       134.40 
TCGA-ER-A193 TCGA-FR-A729 TCGA-FW-A3R5 TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q5 
       19.04       216.43        36.95        14.83         8.42       110.93 
TCGA-D3-A1Q6 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A2J7 TCGA-D3-A2JL TCGA-D3-A2JP 
       49.35        19.04        76.41        45.99       171.58        43.53 
TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51J TCGA-D3-A51T 
       58.06        40.01        90.21        23.67       144.46        11.34 
TCGA-D3-A5GL TCGA-D3-A5GU TCGA-D3-A8GD TCGA-D3-A8GL TCGA-D3-A8GP TCGA-D3-A8GR 
       42.05       124.08        23.61        69.53       135.12        36.53 
TCGA-D9-A1X3 TCGA-DA-A1HV TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1IA 
       10.78        76.34        68.68       150.61       110.53        64.83 
TCGA-DA-A1IC TCGA-DA-A3F5 TCGA-DA-A95X TCGA-EB-A5UN TCGA-EE-A17Y TCGA-EE-A181 
       58.85       225.11        65.03        52.41        24.89        20.38 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29P TCGA-EE-A29Q 
       75.55        79.20        12.99        44.28        27.16        61.12 
TCGA-EE-A29W TCGA-EE-A2A2 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ 
      185.19        30.02        26.14        12.95       201.60        68.65 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2M6 
       32.48        18.35        93.63         0.76        71.31       103.13 
TCGA-EE-A2M8 TCGA-EE-A2MF TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP 
        5.75       209.79        89.26       104.78       145.45       227.01 
TCGA-EE-A2MS TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
      143.93       124.31       122.73         4.41        54.51         6.28 
TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 
        3.35       168.85        19.86       135.98        34.45        10.49 
TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19H TCGA-ER-A19M 
        7.82        53.29        39.81        11.47       150.12        59.84 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19W TCGA-ER-A2ND TCGA-ER-A3EV TCGA-ER-A3PL 
      120.76        49.71       146.63         4.70        15.48        32.05 
TCGA-ER-A42L TCGA-FR-A69P TCGA-FR-A8YC TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z3 
       74.47         4.14        10.06       171.78        49.74         8.35 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZW 
      312.07        32.78        78.61       130.95       136.27        23.21 
TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FW-A3TV TCGA-GF-A4EO TCGA-GF-A6C8 
        5.29         3.06        30.90        11.54        18.25         1.91 
TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A8LK 
       53.29        96.92        42.48         7.59       120.53        43.23 
TCGA-GN-A9SD TCGA-OD-A75X TCGA-RP-A693 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1R 
       59.41       297.01         0.33         1.97       120.07        79.99 
TCGA-W3-AA1V TCGA-W3-AA21 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZY 
        8.09        92.84        65.42        12.69        21.90        48.39 
TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-Z2-AA3S 
       24.99        28.21        91.23 

$`9Q LOSS WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EE-A2GO TCGA-EE-A3JD TCGA-WE-A8K5 
        9.76        62.07        38.76        52.90        27.35        52.73 
TCGA-WE-AAA3 TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q7 
        7.40        60.46        12.99        15.72        31.89       133.25 
TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC 
       62.60        25.64        62.86        15.75       168.00        86.30 
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-A3MO TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51K TCGA-D3-A51R 
       24.53         9.34       173.85        30.67        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-A3F8 TCGA-DA-A95V TCGA-DA-A95W TCGA-DA-A95Y 
       60.10        30.44         8.71        72.10         0.76        14.14 
TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A182 
       12.30         3.91        16.41        18.21        13.15         0.00 
TCGA-EE-A183 TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29M 
       26.24        75.22        76.14         0.26        47.41        47.74 
TCGA-EE-A29T TCGA-EE-A2A1 TCGA-EE-A2A6 TCGA-EE-A2GK TCGA-EE-A2GR TCGA-EE-A2GU 
      346.49       115.43        77.98        10.62         0.20        81.99 
TCGA-EE-A2M7 TCGA-EE-A2MC TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MT 
       15.25        23.77        94.19       171.85        63.25        23.51 
TCGA-EE-A2MU TCGA-EE-A3AC TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-ER-A19A 
       53.26        64.04        67.89       111.85        45.90         4.54 
TCGA-ER-A19G TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A19S TCGA-ER-A1A1 TCGA-ER-A2NC 
      184.60        99.06        42.51        47.18        73.05        22.36 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-FR-A3YN 
       16.87        10.19        28.67       173.29        68.52         4.50 
TCGA-FR-A44A TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1ZE 
      174.21        26.20         5.65       195.98        27.62        43.92 
TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A4F4 TCGA-FS-A4F8 
        7.82        36.33        35.28         4.47        66.67       173.19 
TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GN-A264 
       13.28        80.68        55.59        19.30         9.90       117.93 
TCGA-GN-A267 TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-LH-A9QB TCGA-QB-A6FS TCGA-RP-A690 
       17.06        34.49        46.92        85.05         7.23         0.20 
TCGA-W3-A824 TCGA-W3-AA1Q TCGA-W3-AA1W TCGA-WE-A8K1 TCGA-WE-A8ZQ TCGA-WE-A8ZT 
      174.12        44.05       185.13        47.54        62.89        10.95 
TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-XV-AB01 
        1.94        37.32         6.61 

  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 
            49.71             44.05 
[1] "0.3 - 312.1 (49.7)" "0.0 - 346.5 (44.0)"
[1] "hr=" "1"  
D59V2, survival
                   sevent
clus2                 0   1
  9Q LOSS MUTATED    77 102
  9Q LOSS WILD-TYPE  89  90
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
              179               179 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
              102                90 
$`9Q LOSS MUTATED`
TCGA-D3-A8GI TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GD 
       58.52        68.25        94.98       168.26         2.60       340.14 
TCGA-EE-A2MR TCGA-ER-A193 TCGA-FR-A729 TCGA-FS-A1ZF TCGA-FW-A3R5 TCGA-BF-AAP0 
      134.40        31.40       220.80        15.45        36.95        14.93 
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A2J7 
       16.57       112.57        71.80        28.08        90.90       103.10 
TCGA-D3-A2JL TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CC TCGA-D3-A3MR 
      171.58        59.57        58.06        46.98        86.93       103.59 
TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51J TCGA-D3-A51N TCGA-D3-A51T TCGA-D3-A5GL 
       39.75        45.30       145.12        22.62        26.89       125.79 
TCGA-D3-A5GO TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GD TCGA-D3-A8GL TCGA-D3-A8GP 
      137.92       125.19        30.84        23.61        89.13       152.75 
TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1X3 TCGA-D9-A6E9 
      129.63       117.17       151.53        54.67        18.12         9.90 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
       76.57        36.03       222.51       176.55        35.93       135.02 
TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F5 TCGA-DA-A95X TCGA-EB-A44R 
       53.92        65.92        68.09       225.96        73.94        10.36 
TCGA-EB-A5UN TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F 
       58.92        27.22        33.73       133.81       151.27        91.56 
TCGA-EE-A20I TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
       13.55        13.97        72.07        18.61        56.42        66.74 
TCGA-EE-A29S TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A2 TCGA-EE-A2GB 
       61.28       195.02        17.92        46.82        59.64        59.28 
TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GL 
       67.43       173.79       220.24        48.72       107.38        79.66 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2M6 TCGA-EE-A2M8 
       75.48       102.12        13.91        81.21       129.27        19.76 
TCGA-EE-A2MF TCGA-EE-A2MH TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP 
      268.73        16.96       180.39       216.66       167.90       248.65 
TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE 
       43.23       162.48       124.31       122.73        28.77        54.51 
TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3J5 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB 
       13.81        41.59        36.95        34.32        53.19       201.80 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 
       51.35       134.33       152.81        35.44        13.94         9.17 
TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19H TCGA-ER-A19M 
       98.40        48.89        12.59        26.37       152.35        61.05 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A2ND TCGA-ER-A2NH 
      162.08        50.89         8.88       148.18        23.34        41.56 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A69P TCGA-FR-A8YC TCGA-FS-A1YW 
       46.98        33.21       149.03        15.72        34.82       216.92 
TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD 
      228.59        20.91        27.72        48.85       357.37        53.52 
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-A3TV TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 
       54.41        17.46        13.51        19.43         2.04        15.78 
TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U3 
      139.89        96.92        62.79        32.48        48.00       121.91 
TCGA-GN-A4U7 TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A8LL TCGA-GN-A9SD TCGA-HR-A2OG 
       10.42        22.13        50.10        21.37        59.41         0.23 
TCGA-HR-A2OH TCGA-OD-A75X TCGA-RP-A693 TCGA-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-D3-A2JE TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EB-A5SH TCGA-EE-A184 
       27.65        62.07        46.32        13.87        54.02        68.15 
TCGA-EE-A2GO TCGA-EE-A3JD TCGA-ER-A198 TCGA-QB-AA9O TCGA-WE-A8K5 TCGA-WE-AAA3 
      126.81        27.35        50.76        18.05        61.15        21.40 
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-A2JC TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK 
      168.00        86.76        11.87       113.52        42.08        12.10 
TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A3BZ TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3CF 
       66.48        66.08       130.72       166.52        60.23        24.53 
TCGA-D3-A3MO TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51K TCGA-D3-A51R 
        9.34       174.84        55.73        56.35        32.94        63.81 
TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A8GC TCGA-D3-A8GE TCGA-D3-A8GJ 
      135.75       178.32        18.18        79.59        26.43       241.38 
TCGA-D3-A8GK TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GQ TCGA-D3-A8GV TCGA-D9-A1JW 
      170.20       107.15       161.00        29.06       167.70         3.65 
TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6EA TCGA-D9-A6EC 
        7.10        15.39        22.29        18.44        25.18        77.56 
TCGA-D9-A6EG TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I7 TCGA-DA-A1IB TCGA-DA-A3F2 
       22.95       144.89        20.38        88.87        40.60        33.93 
TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-DA-A95V TCGA-DA-A95W TCGA-DA-A95Y TCGA-DA-A95Z 
       10.49        43.36        72.10        37.35        14.14        13.02 
TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UL TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X 
       13.87        20.35        29.29         7.04        36.46        29.82 
TCGA-EE-A17Z TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A29A TCGA-EE-A29B 
        8.65        14.70        26.89         4.96        63.35        85.08 
TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29R TCGA-EE-A29T 
       78.97        63.78        64.64        56.84        14.47       369.93 
TCGA-EE-A29V TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GK TCGA-EE-A2GR 
       25.87       115.96        39.29        86.14        54.74        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-ER-A19A TCGA-ER-A19E TCGA-ER-A19G TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19N 
       77.75        13.02       302.07         6.44       131.51        44.09 
TCGA-ER-A19S TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
       49.48       105.07        43.82        20.15        28.83        48.99 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A7U8 
      247.04        93.01        12.95        92.98       174.21        27.85 
TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YX TCGA-FS-A1Z0 
       18.77        38.27        36.26       104.42        48.59       202.65 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZK 
       28.08         7.79        46.45         9.70        47.38        23.93 
TCGA-FS-A1ZP TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 
       74.73        53.16        26.56        66.67       174.84        34.03 
TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GN-A264 TCGA-GN-A266 
       80.68        55.59        19.30         9.90       117.93        10.13 
TCGA-GN-A267 TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-LH-A9QB TCGA-QB-A6FS TCGA-RP-A690 
       64.44        39.35        48.89       368.78         7.23         0.20 
TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-AA1O TCGA-W3-AA1Q TCGA-W3-AA1W TCGA-WE-A8K1 
        0.69       228.16         4.01        69.07       219.16        49.05 
TCGA-WE-A8K6 TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-XV-AB01 
       17.95        63.22        11.80        12.16        40.41        13.25 
TCGA-YD-A89C TCGA-YD-A9TA TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3V 
        6.90        49.18        14.43        27.58        15.98 

  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
             0.23              0.20 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
           357.37            369.93 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
            58.52             47.38 
[1] "0.2 - 357.4 (58.5)" "0.2 - 369.9 (47.4)"
[1] "hr=" "1.1"
D59V3, continuous
                   vv
clus                I/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       14
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  9Q LOSS MUTATED           8        11         9        22          6
  9Q LOSS WILD-TYPE         6         8         6        17          9
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  9Q LOSS MUTATED           22         18       12
  9Q LOSS WILD-TYPE         13         36        9
D59V4, multiclass
            clus
vv           9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  I/II NOS                 8                 5
  STAGE 0                  3                 4
  STAGE I                 16                13
  STAGE IA                 6                12
  STAGE IB                14                14
  STAGE II                12                14
  STAGE IIA                8                 6
  STAGE IIB               11                 8
  STAGE IIC                9                 6
  STAGE III               22                17
  STAGE IIIA               6                 9
  STAGE IIIB              22                13
  STAGE IIIC              18                36
  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 35
  9Q LOSS WILD-TYPE    31 36 39 32
D59V5, multiclass
       clus
vv      9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  T0+T1              33                31
  T2                 37                36
  T3                 42                39
  T4                 35                32
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  9Q LOSS MUTATED   94 32 21 17
  9Q LOSS WILD-TYPE 83 33 18 28
D59V6, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  N0              94                83
  N1              32                33
  N2              21                18
  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 160   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED    159   13
  9Q LOSS WILD-TYPE  160    9
   clus
vv  9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  0             159               160
  1              13                 9
[1] 2 2
[1] FALSE
D59V8, binary
                   cls
clus                 0  1
  9Q LOSS MUTATED   71 42
  9Q LOSS WILD-TYPE 63 48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     71   42
  9Q LOSS WILD-TYPE   63   48
     clus
vv    9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  NO               71                63
  YES              42                48
[1] 2 2
[1] FALSE
D59V9, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED    21 164
  9Q LOSS WILD-TYPE  26 156
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     21  164
  9Q LOSS WILD-TYPE   26  156
     clus
vv    9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  NO               21                26
  YES             164               156
[1] 2 2
[1] FALSE
D59V10, continuous
D59V11, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED    79 106
  9Q LOSS WILD-TYPE  59 123
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     79  106
  9Q LOSS WILD-TYPE   59  123
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  FEMALE              79                59
  MALE               106               123
[1] 2 2
[1] FALSE
D59V12, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED   160  25
  9Q LOSS WILD-TYPE 159  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED    160   25
  9Q LOSS WILD-TYPE  159   22
     clus
vv    9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  NO              160               159
  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   176
D59V13, multiclass
                           clus
vv                          9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  ASIAN                                   2                 3
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                 177               176
[1] 3 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   4 174
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      3  178
  9Q LOSS WILD-TYPE    4  174
                        clus
vv                       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   3                 4
  NOT HISPANIC OR LATINO             178               174
[1] 2 2
[1] FALSE

Clustering(60) Variable = 10P LOSS MUTATION ANALYSIS
D60V1, survival
                    sevent
clus2                 0  1
  10P LOSS MUTATED   71 72
  10P LOSS WILD-TYPE 57 52
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
               143                109 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                72                 52 
$`10P LOSS MUTATED`
TCGA-D3-A8GI TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GO TCGA-FR-A729 TCGA-WE-AAA3 
       13.41        31.96       166.75        52.90       216.43         7.40 
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-A2JG 
       49.35       133.25        19.04        15.75        86.30       107.61 
TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO 
       64.83        66.08        43.53        59.70        24.53         9.34 
TCGA-D3-A3MU TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51T TCGA-D3-A5GN 
       23.67        30.67       144.46        31.76        11.34        45.70 
TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GJ TCGA-D3-A8GP 
      177.86       124.08        78.21        23.61       179.97       135.12 
TCGA-D3-A8GR TCGA-D9-A1X3 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6EG TCGA-DA-A1I1 
       36.53        10.78        16.90        18.44        22.85        68.68 
TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A3F5 TCGA-DA-A95V 
      150.61       110.53        60.10        64.83       225.11        72.10 
TCGA-DA-A95W TCGA-DA-A95Y TCGA-EB-A5UN TCGA-EE-A181 TCGA-EE-A20F TCGA-EE-A29G 
        0.76        14.14        52.41        20.38        79.20        44.28 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W 
       47.41        47.74        27.16        61.12       346.49       185.19 
TCGA-EE-A2A2 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GM 
       30.02        26.14        12.95       201.60        68.65        18.35 
TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 
       93.63         0.76         0.20        71.31        81.99       103.13 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MG TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MP 
       15.25         5.75        94.19        89.26       145.45       227.01 
TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE 
      143.93        53.26       124.31       122.73         4.41        54.51 
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       168.85        19.86 
TCGA-EE-A3JI TCGA-ER-A199 TCGA-ER-A19D TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19P 
      135.98         7.82        11.47       150.12        99.06       120.76 
TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NG 
       47.18       146.63        22.36         4.70        16.87        28.67 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A 
       68.52        15.48        32.05        74.47         4.50       174.21 
TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1ZC TCGA-FS-A1ZD 
        4.14        26.20       195.98         8.35       312.07        32.78 
TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZU TCGA-FS-A1ZW 
        7.82        36.33        78.61       130.95         4.47        23.21 
TCGA-FS-A1ZY TCGA-FS-A4F4 TCGA-FS-A4FD TCGA-FW-A3TV TCGA-GF-A4EO TCGA-GN-A264 
        5.29        66.67        80.68        11.54        18.25       117.93 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A8LK TCGA-GN-A9SD 
       17.06        42.48         7.59       120.53        43.23        59.41 
TCGA-OD-A75X TCGA-RP-A693 TCGA-W3-A825 TCGA-W3-AA21 TCGA-WE-A8ZM TCGA-WE-A8ZQ 
      297.01         0.33         1.97        92.84        65.42        62.89 
TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-Z2-AA3S 
       48.39         1.94        24.99        28.21        91.23 

$`10P LOSS WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A2GD TCGA-EE-A2MR 
        9.76        62.07        38.76        33.24       269.03       134.40 
TCGA-EE-A3JD TCGA-ER-A193 TCGA-FW-A3R5 TCGA-WE-A8K5 TCGA-D3-A1Q3 TCGA-D3-A1QA 
       27.35        19.04        36.95        52.73        15.72        76.41 
TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JB TCGA-D3-A2JH 
       62.60        25.64        45.99        62.86       168.00        36.30 
TCGA-D3-A2JL TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3MR TCGA-D3-A51E 
      171.58        58.06       140.98        40.01        90.21       173.85 
TCGA-D3-A51R TCGA-D3-A5GL TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D9-A3Z1 
       62.70        42.05       120.00        69.53        70.62        15.02 
TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F8 
       69.21        76.34       138.67        58.85        30.44         8.71 
TCGA-DA-A95X TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A6L9 TCGA-EE-A17X 
       65.03        12.30         3.91        16.41        18.21        13.15 
TCGA-EE-A17Y TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A29B TCGA-EE-A29C 
       24.89         0.00        26.24        75.55        75.22        76.14 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A2A1 TCGA-EE-A2A6 TCGA-EE-A2GK TCGA-EE-A2GL 
       12.99         0.26       115.43        77.98        10.62        32.48 
TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MT 
       23.77       209.79       171.85        63.25       104.78        23.51 
TCGA-EE-A3AC TCGA-EE-A3AF TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A19A TCGA-ER-A19B 
       64.04         6.28        34.45        10.49         4.54        53.29 
TCGA-ER-A19C TCGA-ER-A19G TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A1A1 
       39.81       184.60        59.84        42.51        49.71        73.05 
TCGA-ER-A2NF TCGA-ER-A3ES TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FS-A1YW TCGA-FS-A1YY 
       10.19       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        43.92       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-RP-A690 TCGA-W3-A824 TCGA-W3-A828 TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1V 
        0.20       174.12       120.07        44.05        79.99         8.09 
TCGA-W3-AA1W TCGA-WE-A8K1 TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-AAA0 
      185.13        47.54        12.69        21.90        10.95        37.32 
TCGA-XV-AB01 
        6.61 

  10P LOSS MUTATED 10P LOSS WILD-TYPE 
               0.2                0.0 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
            346.49             269.03 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
             47.74              43.92 
[1] "0.2 - 346.5 (47.7)" "0.0 - 269.0 (43.9)"
[1] "hr=" "1.1"
D60V2, survival
                    sevent
clus2                  0   1
  10P LOSS MUTATED    92 106
  10P LOSS WILD-TYPE  74  86
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
               198                160 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
               106                 86 
$`10P LOSS MUTATED`
TCGA-D3-A8GI TCGA-EB-A5SH TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GO 
       58.52        54.02        94.98       168.26         2.60       126.81 
TCGA-FR-A729 TCGA-FS-A1ZF TCGA-WE-AAA3 TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 
      220.80        15.45        21.40        66.48        12.99        14.93 
TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       16.57       112.04       112.57        71.80       133.25        28.08 
TCGA-D3-A1Q9 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JK 
       31.59       115.53        86.76        11.87       113.52        12.10 
TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C7 TCGA-D3-A3CE TCGA-D3-A3CF 
       66.48        66.08        59.57        46.98        60.23        24.53 
TCGA-D3-A3MO TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K 
        9.34        39.75        45.30        55.73       145.12        32.94 
TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D3-A8GC 
       26.89       135.75       137.92       178.32       125.19        79.59 
TCGA-D3-A8GD TCGA-D3-A8GJ TCGA-D3-A8GP TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D3-A8GV 
       23.61       241.38       152.75       129.63       117.17       167.70 
TCGA-D9-A149 TCGA-D9-A1X3 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EA 
       54.67        18.12        22.29        18.44         9.90        25.18 
TCGA-D9-A6EG TCGA-DA-A1HW TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
       22.95        36.03       222.51       176.55        35.93       135.02 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A3F5 TCGA-DA-A95V TCGA-DA-A95W 
       88.87        53.92        65.92       225.96        72.10        37.35 
TCGA-DA-A95Y TCGA-EB-A44R TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17Z TCGA-EE-A181 
       14.14        10.36        29.29        58.92         8.65        33.73 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29G TCGA-EE-A29H 
        4.96       133.81        91.56        13.55        72.07        64.64 
TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A29X 
       56.84        56.42        66.74       369.93       195.02        17.92 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GH 
       59.64        39.29        59.28        67.43       173.79       220.24 
TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR 
       48.72       107.38        75.48       102.12        13.91        42.77 
TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MG 
       81.21        94.82       129.27        28.83        19.76       103.20 
TCGA-EE-A2MH TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MU 
       16.96       180.39       167.90       248.65       162.48        53.26 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AH TCGA-EE-A3J3 
      124.31       122.73        28.77        54.51       138.81       172.18 
TCGA-EE-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-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A199 TCGA-ER-A19D TCGA-ER-A19E 
       51.35       134.33       152.81         9.17        12.59        13.02 
TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19P TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W 
      152.35       131.51       162.08        49.48         8.88       148.18 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ET 
       43.82        23.34        20.15        48.99        41.56        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-A69P TCGA-FR-A7U8 TCGA-FR-A8YE TCGA-FS-A1YX TCGA-FS-A1Z0 TCGA-FS-A1Z3 
       15.72        27.85       104.42        48.59       202.65        20.91 
TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZG TCGA-FS-A1ZH 
        7.79        27.72       357.37        53.52         9.70        32.75 
TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZU TCGA-FS-A1ZW 
       47.38       101.26       133.55        11.41        26.56        49.48 
TCGA-FS-A1ZY TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4FD TCGA-FW-A3TV TCGA-GF-A4EO 
       27.09        66.67        28.73        80.68        13.51        19.43 
TCGA-GN-A264 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 
      117.93        10.13        64.44        62.79        32.48       121.91 
TCGA-GN-A4U7 TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A8LL TCGA-GN-A9SD TCGA-HR-A2OG 
       10.42        22.13        50.10        21.37        59.41         0.23 
TCGA-HR-A2OH TCGA-OD-A75X TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A825 TCGA-W3-AA21 
       65.88       297.90         0.33         0.69        63.02       105.04 
TCGA-WE-A8JZ TCGA-WE-A8ZM TCGA-WE-A8ZQ TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AA9Y 
       24.03       101.33        63.22        35.80        49.51        12.16 
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-D3-A2JE TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EB-A5SG TCGA-EE-A184 
       27.65        62.07        46.32        13.87        68.25        68.15 
TCGA-EE-A2GD TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 TCGA-ER-A198 TCGA-FW-A3R5 
      340.14       134.40        27.35        31.40        50.76        36.95 
TCGA-QB-AA9O TCGA-WE-A8K5 TCGA-3N-A9WB TCGA-D3-A1Q3 TCGA-D3-A1QA TCGA-D3-A1QB 
       18.05        61.15        17.03        16.67        90.90        95.74 
TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JH 
       43.43       103.10        65.49        23.77       168.00        42.08 
TCGA-D3-A2JL TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3MR 
      171.58       130.72        58.06       166.52        86.93       103.59 
TCGA-D3-A51E TCGA-D3-A51H TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A5GL TCGA-D3-A5GS 
      174.84        56.35        22.62        63.81       125.79        18.18 
TCGA-D3-A8GB TCGA-D3-A8GE TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GN 
       30.84        26.43       170.20        89.13       107.15       161.00 
TCGA-D3-A8GQ TCGA-D9-A148 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A6EC 
       29.06       151.53         3.65         7.10        15.39        77.56 
TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
       76.57       144.89        20.38        40.60        68.09        33.93 
TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-DA-A95X TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5KH 
       10.49        43.36        73.94        13.02        13.87        20.35 
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-A20C TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
      151.27        63.35        85.08        78.97        13.97        63.78 
TCGA-EE-A29N TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A2A0 TCGA-EE-A2A1 
       18.61        14.47        61.28        25.87        46.82       115.96 
TCGA-EE-A2A6 TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2MC 
       86.14        54.74        79.66        44.88        21.67        61.51 
TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2ML 
       47.28       103.27       268.73       204.66        96.23       216.66 
TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MT TCGA-EE-A3AC TCGA-EE-A3AF TCGA-EE-A3AG 
       47.54        43.23        71.21        64.04        13.81        41.59 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19F 
       35.44        13.94        77.75        98.40        48.89        26.37 
TCGA-ER-A19G TCGA-ER-A19J TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A1A1 
      302.07         6.44        61.05        44.09        50.89       105.07 
TCGA-ER-A2NF TCGA-ER-A3ES TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD 
       28.83       247.04        18.77        38.27        34.82        36.26 
TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z4 TCGA-FS-A1ZB TCGA-FS-A1ZE TCGA-FS-A1ZK 
      216.92       228.59        28.08        48.85        46.45        23.93 
TCGA-FS-A1ZP TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 
       74.73       148.80        53.16        27.02        77.82        50.14 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FW-A3I3 TCGA-FW-A3TU 
      174.84        34.03        26.73        54.41        17.46        55.59 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A265 
       19.30         9.90         2.04        15.78       139.89        96.92 
TCGA-GN-A26D TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-LH-A9QB TCGA-QB-A6FS TCGA-RP-A690 
       48.00        39.35        48.89       368.78         7.23         0.20 
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-AA1W TCGA-WE-A8K1 TCGA-WE-A8K6 TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT 
      219.16        49.05        17.95        58.98        70.52        11.80 
TCGA-WE-AAA0 TCGA-XV-AB01 TCGA-YD-A89C TCGA-Z2-A8RT 
       40.41        13.25         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              48.87 
[1] "0.2 - 369.9 (54.6)" "0.2 - 368.8 (48.9)"
[1] "hr=" "1.1"
D60V3, continuous
                    vv
clus                 I/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       11
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  10P LOSS MUTATED           5         6         9        25         11
  10P LOSS WILD-TYPE         9        13         6        14          4
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  10P LOSS MUTATED           19         33       10
  10P LOSS WILD-TYPE         16         21       11
D60V4, multiclass
            clus
vv           10P LOSS MUTATED 10P LOSS WILD-TYPE
  I/II NOS                  8                  5
  STAGE 0                   4                  3
  STAGE I                  17                 12
  STAGE IA                 12                  6
  STAGE IB                 15                 13
  STAGE II                 15                 11
  STAGE IIA                 5                  9
  STAGE IIB                 6                 13
  STAGE IIC                 9                  6
  STAGE III                25                 14
  STAGE IIIA               11                  4
  STAGE IIIB               19                 16
  STAGE IIIC               33                 21
  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 34 48
  10P LOSS WILD-TYPE    24 31 47 19
D60V5, multiclass
       clus
vv      10P LOSS MUTATED 10P LOSS WILD-TYPE
  T0+T1               40                 24
  T2                  42                 31
  T3                  34                 47
  T4                  48                 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"
                    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 138  12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED    181   10
  10P LOSS WILD-TYPE  138   12
   clus
vv  10P LOSS MUTATED 10P LOSS WILD-TYPE
  0              181                138
  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  24 139
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     23  181
  10P LOSS WILD-TYPE   24  139
     clus
vv    10P LOSS MUTATED 10P LOSS WILD-TYPE
  NO                23                 24
  YES              181                139
[1] 2 2
[1] FALSE
D60V10, continuous
D60V11, binary
                    cls
clus                   0   1
  10P LOSS MUTATED    86 118
  10P LOSS WILD-TYPE  52 111
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     86  118
  10P LOSS WILD-TYPE   52  111
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  FEMALE               86                 52
  MALE                118                111
[1] 2 2
[1] FALSE
D60V12, binary
                    cls
clus                   0   1
  10P LOSS MUTATED   176  28
  10P LOSS WILD-TYPE 143  19
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED    176   28
  10P LOSS WILD-TYPE  143   19
     clus
vv    10P LOSS MUTATED 10P LOSS WILD-TYPE
  NO               176                143
  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   156
D60V13, multiclass
                           clus
vv                          10P LOSS MUTATED 10P LOSS WILD-TYPE
  ASIAN                                    1                  4
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                  197                156
[1] 3 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   3 157
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      4  195
  10P LOSS WILD-TYPE    3  157
                        clus
vv                       10P LOSS MUTATED 10P LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                  3
  NOT HISPANIC OR LATINO              195                157
[1] 2 2
[1] FALSE

Clustering(61) Variable = 10Q LOSS MUTATION ANALYSIS
D61V1, survival
                    sevent
clus2                 0  1
  10Q LOSS MUTATED   77 77
  10Q LOSS WILD-TYPE 51 47
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
               154                 98 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                77                 47 
$`10Q LOSS MUTATED`
TCGA-D3-A8GI TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GD TCGA-EE-A2GO TCGA-ER-A193 
       13.41        31.96       166.75       269.03        52.90        19.04 
TCGA-FR-A729 TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 
      216.43        52.73         7.40        12.99        14.83         8.42 
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A2JA 
       31.89       110.93        49.35       133.25        19.04        15.75 
TCGA-D3-A2JC TCGA-D3-A2JG TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP 
       86.30       107.61       171.58        64.83        66.08        43.53 
TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51F 
       58.06        59.70         9.34        90.21        23.67        30.67 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GU 
      144.46        31.76        11.34        45.70       177.86       124.08 
TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GM TCGA-D3-A8GP TCGA-D9-A1X3 TCGA-D9-A3Z3 
       78.21        23.61        70.62       135.12        10.78        16.90 
TCGA-D9-A4Z6 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 
       18.44        69.21        22.85        68.68       150.61       110.53 
TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-DA-A95V TCGA-DA-A95W 
       60.10        64.83       225.11         8.71        72.10         0.76 
TCGA-DA-A95Y TCGA-EB-A5UN TCGA-EE-A181 TCGA-EE-A20F TCGA-EE-A29D TCGA-EE-A29G 
       14.14        52.41        20.38        79.20        12.99        44.28 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W 
       47.41        47.74        27.16        61.12       346.49       185.19 
TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ 
       30.02        77.98        26.14        12.95       201.60        68.65 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU 
       18.35        93.63         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-A199 TCGA-ER-A19C 
        3.35       168.85        19.86       135.98         7.82        39.81 
TCGA-ER-A19D TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19P TCGA-ER-A19S TCGA-ER-A19W 
       11.47       150.12        99.06       120.76        47.18       146.63 
TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42L 
       22.36        16.87        28.67        15.48        32.05        74.47 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FS-A1YY TCGA-FS-A1Z0 
        4.50       174.21         4.14        26.20        49.74       195.98 
TCGA-FS-A1Z3 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ 
        8.35       312.07        32.78        36.33        78.61       130.95 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F4 TCGA-FS-A4FD TCGA-FW-A3TV 
        4.47        23.21         5.29        66.67        80.68        11.54 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A26A 
       18.25         1.91        53.29       117.93        17.06         7.59 
TCGA-GN-A4U3 TCGA-GN-A4U8 TCGA-GN-A8LK TCGA-GN-A9SD TCGA-OD-A75X TCGA-RP-A693 
      120.53        46.92        43.23        59.41       297.01         0.33 
TCGA-W3-A825 TCGA-W3-AA21 TCGA-WE-A8ZM TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZY 
        1.97        92.84        65.42        62.89        10.95        48.39 
TCGA-WE-AA9Y TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-Z2-AA3S 
        1.94        24.99        28.21        91.23 

$`10Q LOSS WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A2MR TCGA-EE-A3JD 
        9.76        62.07        38.76        33.24       134.40        27.35 
TCGA-FW-A3R5 TCGA-3N-A9WC TCGA-D3-A1Q3 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 
       36.95        60.46        15.72        76.41        62.60        25.64 
TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JB TCGA-D3-A2JH TCGA-D3-A3CB TCGA-D3-A3CC 
       45.99        62.86       168.00        36.30       140.98        40.01 
TCGA-D3-A3CF TCGA-D3-A51E TCGA-D3-A51R TCGA-D3-A5GL TCGA-D3-A8GJ TCGA-D3-A8GK 
       24.53       173.85        62.70        42.05       179.97       120.00 
TCGA-D3-A8GL TCGA-D3-A8GR TCGA-D9-A3Z1 TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1IC 
       69.53        36.53        15.02        76.34       138.67        58.85 
TCGA-DA-A3F2 TCGA-DA-A95X TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A6L9 
       30.44        65.03        12.30         3.91        16.41        18.21 
TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A29B 
       13.15        24.89         0.00        26.24        75.55        75.22 
TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A2A1 TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2MC 
       76.14         0.26       115.43        10.62        32.48        23.77 
TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AC TCGA-ER-A195 
       63.25       104.78       143.93        23.51        64.04        34.45 
TCGA-ER-A197 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19G TCGA-ER-A19M TCGA-ER-A19N 
       10.49         4.54        53.29       184.60        59.84        42.51 
TCGA-ER-A19Q TCGA-ER-A1A1 TCGA-ER-A2ND TCGA-ER-A2NF TCGA-ER-A3ES TCGA-ER-A3ET 
       49.71        73.05         4.70        10.19       173.29        68.52 
TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FS-A1YW TCGA-FS-A1Z4 TCGA-FS-A1ZE TCGA-FS-A1ZG 
        5.65        10.06       171.78        27.62        43.92         7.82 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F8 TCGA-FS-A4F9 
      136.27        35.28         3.06        30.90       173.19        13.28 
TCGA-FW-A3TU TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GN-A265 TCGA-GN-A268 TCGA-GN-A4U4 
       55.59        19.30         9.90        96.92        42.48        34.49 
TCGA-LH-A9QB TCGA-QB-A6FS TCGA-RP-A690 TCGA-W3-A824 TCGA-W3-A828 TCGA-W3-AA1Q 
       85.05         7.23         0.20       174.12       120.07        44.05 
TCGA-W3-AA1R TCGA-W3-AA1V TCGA-W3-AA1W TCGA-WE-A8K1 TCGA-WE-A8ZN TCGA-WE-A8ZO 
       79.99         8.09       185.13        47.54        12.69        21.90 
TCGA-WE-AAA0 TCGA-XV-AB01 
       37.32         6.61 

  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 
            49.545             41.030 
[1] "0.2 - 346.5 (49.5)" "0.0 - 185.1 (41.0)"
[1] "hr=" "1.2"
D61V2, survival
                    sevent
clus2                  0   1
  10Q LOSS MUTATED   103 114
  10Q LOSS WILD-TYPE  63  78
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
               217                141 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
               114                 78 
$`10Q LOSS MUTATED`
TCGA-D3-A8GI TCGA-EB-A5SH TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GD 
       58.52        54.02        94.98       168.26         2.60       340.14 
TCGA-EE-A2GO TCGA-ER-A193 TCGA-FR-A729 TCGA-FS-A1ZF TCGA-WE-A8K5 TCGA-WE-AAA3 
      126.81        31.40       220.80        15.45        61.15        21.40 
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-A8GM TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GS 
       79.59        23.61       107.15       161.00       152.75       117.17 
TCGA-D3-A8GV TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1X3 TCGA-D9-A3Z3 TCGA-D9-A4Z6 
      167.70       151.53        54.67        18.12        22.29        18.44 
TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HW TCGA-DA-A1I1 
        9.90        25.18        77.56        22.95        36.03       222.51 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA 
      176.55        35.93       135.02        88.87        53.92        65.92 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-DA-A95V TCGA-DA-A95W TCGA-DA-A95Y TCGA-EB-A44R 
      225.96        43.36        72.10        37.35        14.14        10.36 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A185 TCGA-EE-A20B 
       29.29        58.92         8.65        33.73         4.96       133.81 
TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M 
       91.56        13.55        13.97        72.07        64.64        56.84 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A2 
       56.42        66.74       369.93       195.02        17.92        59.64 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GH 
       39.29        86.14        59.28        67.43       173.79       220.24 
TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR 
       48.72       107.38        75.48       102.12        13.91        42.77 
TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MD 
       81.21        94.82       129.27        28.83        19.76        47.28 
TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2MM 
      268.73       103.20        16.96       204.66       180.39       167.90 
TCGA-EE-A2MP TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE 
      248.65        53.26       124.31       122.73        28.77        54.51 
TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 
       13.81        41.59       138.81       172.18       127.20        36.95 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JE TCGA-EE-A3JH 
       64.08        34.32        53.19       201.80        51.35       134.33 
TCGA-EE-A3JI TCGA-ER-A199 TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19H 
      152.81         9.17        48.89        12.59        13.02       152.35 
TCGA-ER-A19L TCGA-ER-A19P TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A2NC 
      131.51       162.08        49.48         8.88       148.18        43.82 
TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K 
       20.15        48.99        41.56        46.98        33.21        12.95 
TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A8YE 
      149.03        92.98       174.21        15.72        27.85       104.42 
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-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ 
      357.37        53.52        32.75        47.38       101.26       133.55 
TCGA-FS-A1ZR TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F4 TCGA-FS-A4F5 
       11.41        26.56        49.48        27.09        66.67        28.73 
TCGA-FS-A4FB TCGA-FS-A4FD TCGA-FW-A3TV TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 
       26.73        80.68        13.51        19.43         2.04       139.89 
TCGA-GN-A264 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U7 
      117.93        10.13        64.44        32.48       121.91        10.42 
TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A9SD TCGA-HR-A2OG TCGA-HR-A2OH 
       48.89        22.13        50.10        59.41         0.23        65.88 
TCGA-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-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-A8ZY 
       17.95       101.33        63.22        11.80        35.80        49.51 
TCGA-WE-AA9Y TCGA-WE-AAA4 TCGA-YD-A9TA TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-AA3S 
       12.16        24.99        49.18        37.94        14.43        96.99 
TCGA-Z2-AA3V 
       15.98 

$`10Q LOSS WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EB-A5SG TCGA-EE-A184 
       27.65        62.07        46.32        13.87        68.25        68.15 
TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A198 TCGA-FW-A3R5 TCGA-QB-AA9O TCGA-3N-A9WB 
      134.40        27.35        50.76        36.95        18.05        17.03 
TCGA-3N-A9WC TCGA-D3-A1Q3 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       66.48        16.67        90.90        95.74        43.43       103.10 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JH TCGA-D3-A3BZ TCGA-D3-A3CB 
       65.49        23.77       168.00        42.08       130.72       166.52 
TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A51E TCGA-D3-A51H TCGA-D3-A51R TCGA-D3-A5GL 
       86.93        24.53       174.84        56.35        63.81       125.79 
TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GQ TCGA-D3-A8GR 
       26.43       241.38       170.20        89.13        29.06       129.63 
TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I0 
        3.65         7.10        15.39        76.57       144.89        20.38 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A95X TCGA-DA-A95Z 
       40.60        68.09        33.93        10.49        73.94        13.02 
TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y 
       13.87        20.35         7.04        36.46        29.82        27.22 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C 
       14.70        26.89       151.27        63.35        85.08        78.97 
TCGA-EE-A29E TCGA-EE-A29N TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A2A0 
       63.78        18.61        14.47        61.28        25.87        46.82 
TCGA-EE-A2A1 TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2MC 
      115.96        54.74        79.66        44.88        21.67        61.51 
TCGA-EE-A2ME TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MS 
      103.27        96.23       216.66        47.54        43.23       162.48 
TCGA-EE-A2MT TCGA-EE-A3AC TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A19A TCGA-ER-A19B 
       71.21        64.04        35.44        13.94        77.75        98.40 
TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19J TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19Q 
       26.37       302.07         6.44        61.05        44.09        50.89 
TCGA-ER-A1A1 TCGA-ER-A2ND TCGA-ER-A2NF TCGA-ER-A3ES TCGA-ER-A3ET TCGA-FR-A7U9 
      105.07        23.34        28.83       247.04        93.01        18.77 
TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FS-A1YW TCGA-FS-A1Z4 TCGA-FS-A1ZB 
       38.27        34.82        36.26       216.92        28.08        48.85 
TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZS TCGA-FS-A1ZT 
       46.45         9.70        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-A4FC 
       27.02        77.82        50.14       174.84        34.03        54.41 
TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C9 TCGA-GN-A265 
       17.46        55.59        19.30         9.90        15.78        96.92 
TCGA-GN-A268 TCGA-GN-A26D TCGA-GN-A4U4 TCGA-GN-A8LL TCGA-LH-A9QB TCGA-QB-A6FS 
       62.79        48.00        39.35        21.37       368.78         7.23 
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-XV-AB01 TCGA-YD-A89C TCGA-Z2-A8RT 
       13.25         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              48.85 
[1] "0.2 - 369.9 (54.0)" "0.2 - 368.8 (48.9)"
[1] "hr=" "1.2"
D61V3, continuous
                    vv
clus                 I/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       12
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  10Q LOSS MUTATED           5        10         8        28         11
  10Q LOSS WILD-TYPE         9         9         7        11          4
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  10Q LOSS MUTATED           22         32       14
  10Q LOSS WILD-TYPE         13         22        7
D61V4, multiclass
            clus
vv           10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  I/II NOS                 10                  3
  STAGE 0                   3                  4
  STAGE I                  19                 10
  STAGE IA                 13                  5
  STAGE IB                 16                 12
  STAGE II                 14                 12
  STAGE IIA                 5                  9
  STAGE IIB                10                  9
  STAGE IIC                 8                  7
  STAGE III                28                 11
  STAGE IIIA               11                  4
  STAGE IIIB               22                 13
  STAGE IIIC               32                 22
  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 40 46
  10Q LOSS WILD-TYPE    19 26 41 21
D61V5, multiclass
       clus
vv      10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  T0+T1               45                 19
  T2                  47                 26
  T3                  40                 41
  T4                  46                 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
  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 126   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED    193   15
  10Q LOSS WILD-TYPE  126    7
   clus
vv  10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  0              193                126
  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  19 124
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     28  196
  10Q LOSS WILD-TYPE   19  124
     clus
vv    10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  NO                28                 19
  YES              196                124
[1] 2 2
[1] FALSE
D61V10, continuous
D61V11, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED    92 132
  10Q LOSS WILD-TYPE  46  97
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     92  132
  10Q LOSS WILD-TYPE   46   97
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  FEMALE               92                 46
  MALE                132                 97
[1] 2 2
[1] FALSE
D61V12, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED   193  31
  10Q LOSS WILD-TYPE 126  16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED    193   31
  10Q LOSS WILD-TYPE  126   16
     clus
vv    10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  NO               193                126
  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   136
D61V13, multiclass
                           clus
vv                          10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  ASIAN                                    1                  4
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                  217                136
[1] 3 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   3 137
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      4  215
  10Q LOSS WILD-TYPE    3  137
                        clus
vv                       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                  3
  NOT HISPANIC OR LATINO              215                137
[1] 2 2
[1] FALSE

Clustering(62) Variable = 11P LOSS MUTATION ANALYSIS
D62V1, survival
                    sevent
clus2                 0  1
  11P LOSS MUTATED   42 41
  11P LOSS WILD-TYPE 86 83
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                83                169 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                41                 83 
$`11P LOSS MUTATED`
TCGA-D3-A8GI TCGA-EB-A5SG TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-D3-A1Q1 TCGA-D3-A1Q5 
       13.41        33.24        52.73         7.40         8.42       110.93 
TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2JB TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A3C6 
       25.64        45.99       168.00       171.58        64.83        58.06 
TCGA-D3-A3CC TCGA-D3-A3MO TCGA-D3-A51E TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GU 
       40.01         9.34       173.85        45.70       177.86       124.08 
TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GM TCGA-D3-A8GP TCGA-D9-A3Z3 TCGA-D9-A4Z6 
       78.21        23.61        70.62       135.12        16.90        18.44 
TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1I1 TCGA-DA-A1I5 TCGA-DA-A3F5 TCGA-DA-A95V 
       22.85        76.34        68.68       110.53       225.11        72.10 
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        10.49         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-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A7UA 
       15.48        74.47         4.50       174.21         4.14         5.65 
TCGA-FS-A1Z3 TCGA-FS-A1ZM TCGA-FS-A1ZW TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 
        8.35        78.61        23.21        66.67       173.19        13.28 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A9SD TCGA-W3-AA1R 
       53.29       117.93        17.06         7.59        59.41        79.99 
TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-AAA4 TCGA-YG-AA3O 
       65.42        12.69        21.90        24.99        28.21 

$`11P LOSS WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GD 
        9.76        62.07        38.76        31.96       166.75       269.03 
TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 TCGA-FR-A729 TCGA-FW-A3R5 
       52.90       134.40        27.35        19.04       216.43        36.95 
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-A2JG TCGA-D3-A2JH TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3CB 
       86.30       107.61        36.30        66.08        43.53       140.98 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51F TCGA-D3-A51J 
       59.70        24.53        90.21        23.67        30.67       144.46 
TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A8GJ TCGA-D3-A8GK 
       31.76        62.70        11.34        42.05       179.97       120.00 
TCGA-D3-A8GL TCGA-D3-A8GR TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A6EC TCGA-DA-A1HY 
       69.53        36.53        10.78        15.02        69.21       138.67 
TCGA-DA-A1I2 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F8 
      150.61        60.10        64.83        58.85        30.44         8.71 
TCGA-DA-A95W TCGA-DA-A95X TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5KH 
        0.76        65.03        14.14        12.30         3.91        16.41 
TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A183 
       52.41        18.21        13.15        24.89        20.38        26.24 
TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29T 
       79.20        75.22         0.26        44.28        47.41       346.49 
TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GH TCGA-EE-A2GJ 
      185.19       115.43        77.98        26.14       201.60        68.65 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
       10.62        32.48        93.63         0.76         0.20        71.31 
TCGA-EE-A2GU TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MG 
       81.99        15.25         5.75        23.77       209.79        94.19 
TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MT TCGA-EE-A3AA 
      171.85        89.26       104.78       145.45        23.51       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       168.85       135.98 
TCGA-ER-A195 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19M 
       34.45         4.54        53.29       184.60       150.12        59.84 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
       42.51       120.76        49.71       146.63        73.05        22.36 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3PL TCGA-FR-A7U8 TCGA-FR-A8YC 
       10.19        28.67       173.29        32.05        26.20        10.06 
TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD 
      171.78        49.74       195.98        27.62       312.07        32.78 
TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT 
       43.92         7.82        36.33       130.95       136.27        35.28 
TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4FD TCGA-FW-A3TU 
        4.47         5.29         3.06        30.90        80.68        55.59 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A265 
       11.54        19.30         9.90        18.25         1.91        96.92 
TCGA-GN-A268 TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-GN-A8LK TCGA-LH-A9QB 
       42.48       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-AA1V TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 
      120.07        44.05         8.09       185.13        92.84        47.54 
TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-XV-AB01 
       62.89        10.95        48.39         1.94        37.32         6.61 
TCGA-Z2-AA3S 
       91.23 

  11P LOSS MUTATED 11P LOSS WILD-TYPE 
               0.0                0.2 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
            227.01             346.49 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
             45.99              46.92 
[1] "0.0 - 227.0 (46.0)" "0.2 - 346.5 (46.9)"
[1] "hr=" "1.1"
D62V2, survival
                    sevent
clus2                  0   1
  11P LOSS MUTATED    58  66
  11P LOSS WILD-TYPE 108 126
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
               124                234 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                66                126 
$`11P LOSS MUTATED`
TCGA-D3-A8GI TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A29L TCGA-FS-A1ZF TCGA-QB-AA9O 
       58.52        68.25        54.02         2.60        15.45        18.05 
TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q9 TCGA-D3-A2J6 
       61.15        21.40        16.57       112.57        31.59        43.43 
TCGA-D3-A2J7 TCGA-D3-A2JB TCGA-D3-A2JD TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A3C6 
      103.10       168.00        11.87       171.58        66.48        58.06 
TCGA-D3-A3C7 TCGA-D3-A3CC TCGA-D3-A3MO TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A5GN 
       46.98        86.93         9.34        45.30       174.84       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-A8GM TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D9-A149 TCGA-D9-A1JX TCGA-D9-A3Z3 
      107.15       161.00       152.75        54.67         7.10        22.29 
TCGA-D9-A4Z6 TCGA-D9-A6EA TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I1 
       18.44        25.18        22.95        76.57        36.03       222.51 
TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A3F5 TCGA-DA-A95V TCGA-EB-A44R TCGA-EB-A5UL 
      135.02        53.92       225.96        72.10        10.36        29.29 
TCGA-EE-A182 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20I TCGA-EE-A29C TCGA-EE-A29D 
       14.70       133.81       151.27        13.55        78.97        13.97 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29V 
       56.84        18.61        56.42        66.74        14.47        25.87 
TCGA-EE-A29X TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GM 
       17.92        59.64        39.29        67.43       173.79        75.48 
TCGA-EE-A2M6 TCGA-EE-A2MJ TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MU 
      129.27        96.23        47.54       248.65       162.48        53.26 
TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 
      122.73        28.77        54.51        36.95        64.08        34.32 
TCGA-EE-A3JA TCGA-EE-A3JH TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19C TCGA-ER-A19D 
       53.19       134.33        13.94         9.17        48.89        12.59 
TCGA-ER-A19L TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A3ET 
      131.51        49.48         8.88        23.34        20.15        93.01 
TCGA-ER-A3EV TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A7UA 
       46.98       149.03        92.98       174.21        15.72        38.27 
TCGA-FS-A1Z3 TCGA-FS-A1ZA TCGA-FS-A1ZH TCGA-FS-A1ZM TCGA-FS-A1ZW TCGA-FS-A4F4 
       20.91        27.72        32.75       101.26        49.48        66.67 
TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FW-A3I3 TCGA-GN-A262 TCGA-GN-A264 
       28.73       174.84        34.03        17.46       139.89       117.93 
TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A4U7 TCGA-GN-A4U9 TCGA-GN-A9SD TCGA-HR-A2OH 
       64.44        32.48        10.42        22.13        59.41        65.88 
TCGA-W3-AA1R TCGA-WE-A8JZ TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-AAA4 
      111.09        24.03       101.33        58.98        70.52        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-D3-A2JE TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EE-A180 TCGA-EE-A184 
       27.65        62.07        46.32        13.87        94.98        68.15 
TCGA-EE-A20H TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 
      168.26       340.14       126.81       134.40        27.35        31.40 
TCGA-ER-A198 TCGA-FR-A729 TCGA-FW-A3R5 TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD 
       50.76       220.80        36.95        17.03        66.48        12.99 
TCGA-BF-AAP0 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       14.93        16.67       112.04        71.80       133.25        28.08 
TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JC 
       90.90        95.74        65.49        23.77       115.53        86.76 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ 
      113.52        42.08        12.10        66.08        59.57       130.72 
TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51F 
      166.52        60.23        24.53       103.59        39.75        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-A8GE TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL 
      125.79       137.92        26.43       241.38       170.20        89.13 
TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D3-A8GV TCGA-D9-A148 TCGA-D9-A1JW 
       29.06       129.63       117.17       167.70       151.53         3.65 
TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-DA-A1HY TCGA-DA-A1I0 
       18.12        15.39         9.90        77.56       144.89        20.38 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
      176.55        35.93        88.87        65.92        40.60        68.09 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-DA-A95W TCGA-DA-A95X TCGA-DA-A95Y 
       33.93        10.49        43.36        37.35        73.94        14.14 
TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 
       13.02        13.87        20.35        58.92         7.04        36.46 
TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A185 
       29.82        27.22         8.65        33.73        26.89         4.96 
TCGA-EE-A20F TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H 
       91.56        63.35        85.08        63.78        72.07        64.64 
TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A6 
       61.28       369.93       195.02        46.82       115.96        86.14 
TCGA-EE-A2GB TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
       59.28       220.24        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-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-A2MT TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AF 
      167.90        43.23        71.21       124.31        64.04        13.81 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3JB TCGA-EE-A3JE 
       41.59       138.81       172.18       127.20       201.80        51.35 
TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19E TCGA-ER-A19F 
      152.81        35.44        77.75        98.40        13.02        26.37 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P 
      302.07       152.35         6.44        61.05        44.09       162.08 
TCGA-ER-A19Q TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NF TCGA-ER-A2NG 
       50.89       148.18       105.07        43.82        28.83        48.99 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A7U8 TCGA-FR-A7U9 
       41.56       247.04        33.21        12.95        27.85        18.77 
TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY 
       34.82        36.26       104.42       216.92        48.59       228.59 
TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD 
      202.65        28.08         7.79        48.85       357.37        53.52 
TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZQ 
       46.45         9.70        47.38        23.93        74.73       133.55 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A1ZZ 
       11.41       148.80        53.16        26.56        27.09        27.02 
TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3TU 
       77.82        50.14        26.73        54.41        80.68        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        19.43         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-XV-AB01 TCGA-YD-A89C TCGA-Z2-AA3S TCGA-Z2-AA3V 
       12.16        40.41        13.25         6.90        96.99        15.98 

  11P LOSS MUTATED 11P LOSS WILD-TYPE 
               2.6                0.2 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
            248.65             369.93 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
            53.225             51.120 
[1] "2.6 - 248.7 (53.2)" "0.2 - 369.9 (51.1)"
[1] "hr=" "1.1"
D62V3, continuous
                    vv
clus                 I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  11P LOSS MUTATED          6       3       9        4       12        6
  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        25         10
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  11P LOSS MUTATED           14         22        9
  11P LOSS WILD-TYPE         21         32       12
D62V4, multiclass
            clus
vv           11P LOSS MUTATED 11P LOSS WILD-TYPE
  I/II NOS                  6                  7
  STAGE 0                   3                  4
  STAGE I                   9                 20
  STAGE IA                  4                 14
  STAGE IB                 12                 16
  STAGE II                  6                 20
  STAGE IIA                 0                 14
  STAGE IIB                 7                 12
  STAGE IIC                 6                  9
  STAGE III                14                 25
  STAGE IIIA                5                 10
  STAGE IIIB               14                 21
  STAGE IIIC               22                 32
  STAGE IV                  9                 12
[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 29
  11P LOSS WILD-TYPE    43 48 58 38
D62V5, multiclass
       clus
vv      11P LOSS MUTATED 11P LOSS WILD-TYPE
  T0+T1               21                 43
  T2                  25                 48
  T3                  23                 58
  T4                  29                 38
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  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   108   9
  11P LOSS WILD-TYPE 211  13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED    108    9
  11P LOSS WILD-TYPE  211   13
   clus
vv  11P LOSS MUTATED 11P LOSS WILD-TYPE
  0              108                211
  1                9                 13
[1] 2 2
[1] FALSE
D62V8, binary
                    cls
clus                  0  1
  11P LOSS MUTATED   45 37
  11P LOSS WILD-TYPE 89 53
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     45   37
  11P LOSS WILD-TYPE   89   53
     clus
vv    11P LOSS MUTATED 11P LOSS WILD-TYPE
  NO                45                 89
  YES               37                 53
[1] 2 2
[1] FALSE
D62V9, binary
                    cls
clus                   0   1
  11P LOSS MUTATED    13 113
  11P LOSS WILD-TYPE  34 207
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     13  113
  11P LOSS WILD-TYPE   34  207
     clus
vv    11P LOSS MUTATED 11P LOSS WILD-TYPE
  NO                13                 34
  YES              113                207
[1] 2 2
[1] FALSE
D62V10, continuous
D62V11, binary
                    cls
clus                   0   1
  11P LOSS MUTATED    59  67
  11P LOSS WILD-TYPE  79 162
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     59   67
  11P LOSS WILD-TYPE   79  162
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  FEMALE               59                 79
  MALE                 67                162
[1] 2 2
[1] FALSE
D62V12, binary
                    cls
clus                   0   1
  11P LOSS MUTATED   112  14
  11P LOSS WILD-TYPE 207  33
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED    112   14
  11P LOSS WILD-TYPE  207   33
     clus
vv    11P LOSS MUTATED 11P LOSS WILD-TYPE
  NO               112                207
  YES               14                 33
[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   235
D62V13, multiclass
                           clus
vv                          11P LOSS MUTATED 11P LOSS WILD-TYPE
  ASIAN                                    1                  4
  BLACK OR AFRICAN AMERICAN                1                  0
  WHITE                                  118                235
[1] 3 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   5 231
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      2  121
  11P LOSS WILD-TYPE    5  231
                        clus
vv                       11P LOSS MUTATED 11P LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  5
  NOT HISPANIC OR LATINO              121                231
[1] 2 2
[1] FALSE

Clustering(63) Variable = 11Q LOSS MUTATION ANALYSIS
D63V1, survival
                    sevent
clus2                 0  1
  11Q LOSS MUTATED   55 49
  11Q LOSS WILD-TYPE 73 75
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
               104                148 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                49                 75 
$`11Q LOSS MUTATED`
TCGA-D3-A8GI TCGA-EB-A5SG TCGA-EE-A180 TCGA-ER-A193 TCGA-WE-A8K5 TCGA-WE-AAA3 
       13.41        33.24        31.96        19.04        52.73         7.40 
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-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A3C6 
       45.99       168.00       171.58        64.83        66.08        58.06 
TCGA-D3-A3CC TCGA-D3-A3MO TCGA-D3-A51E TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GU 
       40.01         9.34       173.85        45.70       177.86       124.08 
TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GJ TCGA-D3-A8GM TCGA-D3-A8GP TCGA-D3-A8GR 
       78.21        23.61       179.97        70.62       135.12        36.53 
TCGA-D9-A3Z3 TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1I1 TCGA-DA-A1I5 TCGA-DA-A3F5 
       16.90        22.85        76.34        68.68       110.53       225.11 
TCGA-DA-A95V TCGA-EB-A44Q TCGA-EE-A182 TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29M 
       72.10         3.91         0.00        76.14        12.99        47.74 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A2A2 TCGA-EE-A2GB TCGA-EE-A2GE 
       27.16        61.12       346.49        30.02        26.14        12.95 
TCGA-EE-A2GM TCGA-EE-A2M6 TCGA-EE-A2MJ TCGA-EE-A2MP TCGA-EE-A2MT TCGA-EE-A2MU 
       18.35       103.13        63.25       227.01        23.51        53.26 
TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JH 
      122.73         4.41        54.51        45.90         3.35        19.86 
TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19L TCGA-ER-A19S 
       10.49         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        28.67        68.52        15.48 
TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A7UA 
       32.05        74.47         4.50       174.21         4.14         5.65 
TCGA-FS-A1Z3 TCGA-FS-A1ZE TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZW TCGA-FS-A1ZZ 
        8.35        43.92        36.33        78.61        23.21         3.06 
TCGA-FS-A4F4 TCGA-FS-A4FD TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A4U3 
       66.67        80.68       117.93        17.06         7.59       120.53 
TCGA-GN-A9SD TCGA-LH-A9QB TCGA-QB-A6FS TCGA-W3-AA1R TCGA-W3-AA1V TCGA-WE-A8K1 
       59.41        85.05         7.23        79.99         8.09        47.54 
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        37.32 
TCGA-WE-AAA4 TCGA-YG-AA3O 
       24.99        28.21 

$`11Q LOSS WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EE-A20H TCGA-EE-A2GD TCGA-EE-A2GO 
        9.76        62.07        38.76       166.75       269.03        52.90 
TCGA-EE-A2MR TCGA-EE-A3JD TCGA-FR-A729 TCGA-FW-A3R5 TCGA-3N-A9WC TCGA-3N-A9WD 
      134.40        27.35       216.43        36.95        60.46        12.99 
TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q6 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A2J8 
       15.72        31.89        49.35        19.04        76.41        62.86 
TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JP TCGA-D3-A3CB 
       15.75        86.30       107.61        36.30        43.53       140.98 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51F TCGA-D3-A51J 
       59.70        24.53        90.21        23.67        30.67       144.46 
TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A8GK TCGA-D3-A8GL 
       31.76        62.70        11.34        42.05       120.00        69.53 
TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A4Z6 TCGA-D9-A6EC TCGA-DA-A1HY TCGA-DA-A1I2 
       10.78        15.02        18.44        69.21       138.67       150.61 
TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F8 TCGA-DA-A95W 
       60.10        64.83        58.85        30.44         8.71         0.76 
TCGA-DA-A95X TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A6L9 
       65.03        14.14        12.30        16.41        52.41        18.21 
TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A20F 
       13.15        24.89        20.38        26.24        75.55        79.20 
TCGA-EE-A29B TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29W TCGA-EE-A2A1 
       75.22         0.26        44.28        47.41       185.19       115.43 
TCGA-EE-A2A6 TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN 
       77.98       201.60        68.65        10.62        32.48        93.63 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M7 TCGA-EE-A2M8 
        0.76         0.20        71.31        81.99        15.25         5.75 
TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML 
       23.77       209.79        94.19       171.85        89.26       104.78 
TCGA-EE-A2MM TCGA-EE-A2MS TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AF TCGA-EE-A3J3 
      145.45       143.93       124.31        64.04         6.28        67.89 
TCGA-EE-A3J4 TCGA-EE-A3JB TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A19A TCGA-ER-A19B 
      111.85       168.85       135.98        34.45         4.54        53.29 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
      184.60       150.12        59.84        42.51       120.76        49.71 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NF TCGA-ER-A3ES TCGA-FR-A7U8 TCGA-FR-A8YC 
       73.05        22.36        10.19       173.29        26.20        10.06 
TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD 
      171.78        49.74       195.98        27.62       312.07        32.78 
TCGA-FS-A1ZG TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZY 
        7.82       130.95       136.27        35.28         4.47         5.29 
TCGA-FS-A4F0 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
       30.90       173.19        13.28        55.59        11.54        19.30 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A268 
        9.90        18.25         1.91        53.29        96.92        42.48 
TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-GN-A8LK TCGA-OD-A75X TCGA-RP-A690 TCGA-RP-A693 
       34.49        46.92        43.23       297.01         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-A8ZQ TCGA-WE-A8ZT TCGA-XV-AB01 TCGA-Z2-AA3S 
       62.89        10.95         6.61        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 
            41.965             49.725 
[1] "0.0 - 346.5 (42.0)" "0.2 - 312.1 (49.7)"
[1] "hr=" "1.1"
D63V2, survival
                    sevent
clus2                  0   1
  11Q LOSS MUTATED    70  76
  11Q LOSS WILD-TYPE  96 116
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
               146                212 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                76                116 
$`11Q LOSS MUTATED`
TCGA-D3-A8GI TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A180 TCGA-EE-A29L TCGA-ER-A193 
       58.52        68.25        54.02        94.98         2.60        31.40 
TCGA-FS-A1ZF TCGA-QB-AA9O TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-BF-AAP0 TCGA-D3-A1Q1 
       15.45        18.05        61.15        21.40        14.93        16.57 
TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
      112.57       133.25        31.59        95.74        43.43       103.10 
TCGA-D3-A2JB TCGA-D3-A2JD TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A3C6 
      168.00        11.87       171.58        66.48        66.08        58.06 
TCGA-D3-A3C7 TCGA-D3-A3CC TCGA-D3-A3MO TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A5GN 
       46.98        86.93         9.34        45.30       174.84       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-A8GJ TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GR TCGA-D9-A149 
      241.38       107.15       161.00       152.75       129.63        54.67 
TCGA-D9-A1JX TCGA-D9-A3Z3 TCGA-D9-A6EA TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW 
        7.10        22.29        25.18        22.95        76.57        36.03 
TCGA-DA-A1I1 TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A3F5 TCGA-DA-A95V TCGA-EB-A44Q 
      222.51       135.02        53.92       225.96        72.10        13.87 
TCGA-EB-A44R TCGA-EB-A5UL TCGA-EE-A182 TCGA-EE-A20B TCGA-EE-A29C TCGA-EE-A29D 
       10.36        29.29        14.70       133.81        78.97        13.97 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29T 
       56.84        18.61        56.42        66.74        14.47       369.93 
TCGA-EE-A29V TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GE 
       25.87        59.64        39.29        59.28        67.43       173.79 
TCGA-EE-A2GM TCGA-EE-A2M6 TCGA-EE-A2MD TCGA-EE-A2MJ TCGA-EE-A2MN TCGA-EE-A2MP 
       75.48       129.27        47.28        96.23        47.54       248.65 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3J5 
       71.21        53.26       122.73        28.77        54.51        36.95 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JH TCGA-ER-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-A19W 
       48.89        12.59       131.51        49.48         8.88       148.18 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL 
       23.34        20.15        48.99        93.01        46.98        33.21 
TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A7UA TCGA-FS-A1Z3 
      149.03        92.98       174.21        15.72        38.27        20.91 
TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZE TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZM 
        7.79        27.72        46.45        32.75        47.38       101.26 
TCGA-FS-A1ZW TCGA-FS-A1ZZ TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4FD TCGA-FW-A3I3 
       49.48        27.02        66.67        28.73        80.68        17.46 
TCGA-GN-A264 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U3 
      117.93        10.13        64.44        32.48        48.00       121.91 
TCGA-GN-A4U7 TCGA-GN-A4U9 TCGA-GN-A9SD TCGA-HR-A2OH TCGA-LH-A9QB TCGA-QB-A6FS 
       10.42        22.13        59.41        65.88       368.78         7.23 
TCGA-W3-AA1R TCGA-W3-AA1V TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8ZM TCGA-WE-A8ZN 
      111.09        42.08        24.03        49.05       101.33        58.98 
TCGA-WE-A8ZO TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-YG-AA3O 
       70.52        49.51        12.16        40.41        24.99        37.94 
TCGA-YG-AA3P TCGA-Z2-A8RT 
       14.43        27.58 

$`11Q LOSS WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EE-A184 TCGA-EE-A20H 
       27.65        62.07        46.32        13.87        68.15       168.26 
TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A198 TCGA-FR-A729 
      340.14       126.81       134.40        27.35        50.76       220.80 
TCGA-FW-A3R5 TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q3 TCGA-D3-A1Q4 
       36.95        17.03        66.48        12.99        16.67       112.04 
TCGA-D3-A1Q6 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA 
       71.80        28.08        90.90        65.49        23.77       115.53 
TCGA-D3-A2JC TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JP TCGA-D3-A3BZ 
       86.76       113.52        42.08        12.10        59.57       130.72 
TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51F 
      166.52        60.23        24.53       103.59        39.75        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-A8GE TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GQ 
      125.79       137.92        26.43       170.20        89.13        29.06 
TCGA-D3-A8GS TCGA-D3-A8GV TCGA-D9-A148 TCGA-D9-A1JW TCGA-D9-A1X3 TCGA-D9-A3Z1 
      117.17       167.70       151.53         3.65        18.12        15.39 
TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 
       18.44         9.90        77.56       144.89        20.38       176.55 
TCGA-DA-A1I4 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
       35.93        88.87        65.92        40.60        68.09        33.93 
TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-DA-A95W TCGA-DA-A95X TCGA-DA-A95Y TCGA-DA-A95Z 
       10.49        43.36        37.35        73.94        14.14        13.02 
TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y 
       20.35        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-A20F 
        8.65        33.73        26.89         4.96       151.27        91.56 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H 
       13.55        63.35        85.08        63.78        72.07        64.64 
TCGA-EE-A29S TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A6 
       61.28       195.02        17.92        46.82       115.96        86.14 
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-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 
       13.91        42.77        81.21        44.88        94.82        21.67 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG 
       28.83        19.76        61.51       103.27       268.73       103.20 
TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MQ 
       16.96       204.66       180.39       216.66       167.90        43.23 
TCGA-EE-A2MS TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH 
      162.48       124.31        64.04        13.81        41.59       138.81 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3JB TCGA-EE-A3JE TCGA-EE-A3JI TCGA-ER-A195 
      172.18       127.20       201.80        51.35       152.81        35.44 
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       302.07       152.35 
TCGA-ER-A19J TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A1A1 
        6.44        61.05        44.09       162.08        50.89       105.07 
TCGA-ER-A2NC TCGA-ER-A2NF TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A42K TCGA-FR-A7U8 
       43.82        28.83        41.56       247.04        12.95        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-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
       34.03        26.73        54.41        55.59        13.51        19.30 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A265 
        9.90        19.43         2.04        15.78       139.89        96.92 
TCGA-GN-A268 TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-GN-A8LK TCGA-GN-A8LL TCGA-HR-A2OG 
       62.79        39.35        48.89        50.10        21.37         0.23 
TCGA-OD-A75X TCGA-RP-A690 TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 
      297.90         0.20         0.33         0.69       228.16        63.02 
TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1Q TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K6 
      121.08         4.01        69.07       219.16       105.04        17.95 
TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-XV-AB01 TCGA-YD-A89C TCGA-YD-A9TA 
       63.22        11.80        35.80        13.25         6.90        49.18 
TCGA-Z2-AA3S TCGA-Z2-AA3V 
       96.99        15.98 

  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
               2.6                0.2 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
            369.93             357.37 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
            49.495             53.340 
[1] "2.6 - 369.9 (49.5)" "0.2 - 357.4 (53.3)"
[1] "hr=" "1"  
D63V3, continuous
                    vv
clus                 I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  11Q LOSS MUTATED          6       3       9        5       13        8
  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        22         10
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  11Q LOSS MUTATED           15         28       10
  11Q LOSS WILD-TYPE         20         26       11
D63V4, multiclass
            clus
vv           11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  I/II NOS                  6                  7
  STAGE 0                   3                  4
  STAGE I                   9                 20
  STAGE IA                  5                 13
  STAGE IB                 13                 15
  STAGE II                  8                 18
  STAGE IIA                 1                 13
  STAGE IIB                 9                 10
  STAGE IIC                 8                  7
  STAGE III                17                 22
  STAGE IIIA                5                 10
  STAGE IIIB               15                 20
  STAGE IIIC               28                 26
  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 31 33
  11Q LOSS WILD-TYPE    40 44 50 34
D63V5, multiclass
       clus
vv      11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  T0+T1               24                 40
  T2                  29                 44
  T3                  31                 50
  T4                  33                 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
  11Q LOSS MUTATED    66  31  14  21
  11Q LOSS WILD-TYPE 111  34  25  24
D63V6, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  N0               66                111
  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   127  10
  11Q LOSS WILD-TYPE 192  12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED    127   10
  11Q LOSS WILD-TYPE  192   12
   clus
vv  11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  0              127                192
  1               10                 12
[1] 2 2
[1] FALSE
D63V8, binary
                    cls
clus                  0  1
  11Q LOSS MUTATED   55 46
  11Q LOSS WILD-TYPE 79 44
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     55   46
  11Q LOSS WILD-TYPE   79   44
     clus
vv    11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  NO                55                 79
  YES               46                 44
[1] 2 2
[1] FALSE
D63V9, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED    16 133
  11Q LOSS WILD-TYPE  31 187
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     16  133
  11Q LOSS WILD-TYPE   31  187
     clus
vv    11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  NO                16                 31
  YES              133                187
[1] 2 2
[1] FALSE
D63V10, continuous
D63V11, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED    71  78
  11Q LOSS WILD-TYPE  67 151
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     71   78
  11Q LOSS WILD-TYPE   67  151
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  FEMALE               71                 67
  MALE                 78                151
[1] 2 2
[1] FALSE
D63V12, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED   127  22
  11Q LOSS WILD-TYPE 192  25
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED    127   22
  11Q LOSS WILD-TYPE  192   25
     clus
vv    11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  NO               127                192
  YES               22                 25
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  11Q LOSS MUTATED       2                         1   140
  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                                  140                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     3 143
  11Q LOSS WILD-TYPE   4 209
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      3  143
  11Q LOSS WILD-TYPE    4  209
                        clus
vv                       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  4
  NOT HISPANIC OR LATINO              143                209
[1] 2 2
[1] FALSE

Clustering(64) Variable = 12P LOSS MUTATION ANALYSIS
D64V1, survival
                    sevent
clus2                  0   1
  12P LOSS MUTATED    20  15
  12P LOSS WILD-TYPE 108 109
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                35                217 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                15                109 
$`12P LOSS MUTATED`
TCGA-D3-A8GI TCGA-FW-A3R5 TCGA-D3-A2J6 TCGA-D3-A2JL TCGA-D3-A2JO TCGA-D3-A5GR 
       13.41        36.95        25.64       171.58        66.08       177.86 
TCGA-D3-A8GD TCGA-D9-A1X3 TCGA-DA-A1I1 TCGA-DA-A95X TCGA-EE-A20C TCGA-EE-A29G 
       23.61        10.78        68.68        65.03        75.55        44.28 
TCGA-EE-A29Q TCGA-EE-A2A2 TCGA-EE-A2GP TCGA-EE-A2MG TCGA-EE-A2MK TCGA-EE-A2MP 
       61.12        30.02         0.76        94.19        89.26       227.01 
TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AE TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-ER-A197 
      143.93        53.26        54.51        67.89        45.90        10.49 
TCGA-ER-A19S TCGA-ER-A2NG TCGA-FS-A1Z4 TCGA-FS-A1ZQ TCGA-FS-A1ZT TCGA-GN-A4U3 
       47.18        28.67        27.62       130.95        35.28       120.53 
TCGA-LH-A9QB TCGA-OD-A75X TCGA-RP-A693 TCGA-W3-AA1V TCGA-WE-A8ZY 
       85.05       297.01         0.33         8.09        48.39 

$`12P LOSS WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A20H 
        9.76        62.07        38.76        33.24        31.96       166.75 
TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 TCGA-FR-A729 
      269.03        52.90       134.40        27.35        19.04       216.43 
TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 
       52.73         7.40        60.46        12.99        14.83         8.42 
TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       15.72        31.89       110.93        49.35       133.25        19.04 
TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JB 
       76.41        62.60        45.99        62.86        15.75       168.00 
TCGA-D3-A2JC TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3C6 
       86.30       107.61        36.30        64.83        43.53        58.06 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR 
      140.98        40.01        59.70        24.53         9.34        90.21 
TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R 
       23.67       173.85        30.67       144.46        31.76        62.70 
TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GU TCGA-D3-A8GC TCGA-D3-A8GJ 
       11.34        42.05        45.70       124.08        78.21       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-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-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 
      150.61       110.53        60.10        64.83        58.85        30.44 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-DA-A95V TCGA-DA-A95W TCGA-DA-A95Y TCGA-DA-A95Z 
      225.11         8.71        72.10         0.76        14.14        12.30 
TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y 
        3.91        16.41        52.41        18.21        13.15        24.89 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29C 
       20.38         0.00        26.24        79.20        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        47.41        47.74        27.16       346.49 
TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH 
      185.19       115.43        77.98        26.14        12.95       201.60 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GR 
       68.65        10.62        32.48        18.35        93.63         0.20 
TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC 
       71.31        81.99       103.13        15.25         5.75        23.77 
TCGA-EE-A2MF TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MT 
      209.79       171.85        63.25       104.78       145.45        23.51 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3J4 
      124.31       122.73        64.04         4.41         6.28       111.85 
TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A199 
        3.35       168.85        19.86       135.98        34.45         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       184.60       150.12 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19W 
       99.06        59.84        42.51       120.76        49.71       146.63 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A3ES 
       73.05        22.36         4.70        16.87        10.19       173.29 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A 
       68.52        15.48        32.05        74.47         4.50       174.21 
TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FS-A1YW TCGA-FS-A1YY 
        4.14        26.20         5.65        10.06       171.78        49.74 
TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG 
      195.98         8.35       312.07        32.78        43.92         7.82 
TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY 
       36.33        78.61       136.27         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        18.25         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-A4U4 TCGA-GN-A4U8 TCGA-GN-A8LK TCGA-GN-A9SD TCGA-QB-A6FS TCGA-RP-A690 
       34.49        46.92        43.23        59.41         7.23         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-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ 
       92.84        47.54        65.42        12.69        21.90        62.89 
TCGA-WE-A8ZT TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-XV-AB01 TCGA-YG-AA3O 
       10.95         1.94        37.32        24.99         6.61        28.21 
TCGA-Z2-AA3S 
       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 
             53.26              44.05 
[1] "0.3 - 297.0 (53.3)" "0.0 - 346.5 (44.0)"
[1] "hr=" "1.3"
D64V2, survival
                    sevent
clus2                  0   1
  12P LOSS MUTATED    29  28
  12P LOSS WILD-TYPE 137 164
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                57                301 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                28                164 
$`12P LOSS MUTATED`
TCGA-D3-A8GI TCGA-EB-A5SH TCGA-FW-A3R5 TCGA-D3-A2J6 TCGA-D3-A2JL TCGA-D3-A2JO 
       58.52        54.02        36.95        43.43       171.58        66.08 
TCGA-D3-A51N TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A8GB TCGA-D3-A8GD 
       22.62       137.92       178.32        18.18        30.84        23.61 
TCGA-D3-A8GN TCGA-D9-A1X3 TCGA-D9-A6EA TCGA-DA-A1I1 TCGA-DA-A95X TCGA-EE-A20B 
      161.00        18.12        25.18       222.51        73.94       133.81 
TCGA-EE-A20C TCGA-EE-A29G TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A2A2 TCGA-EE-A2GP 
      151.27        72.07        66.74        61.28        59.64        13.91 
TCGA-EE-A2MG TCGA-EE-A2MK TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AE 
      103.20       180.39       248.65       162.48        53.26        54.51 
TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-ER-A197 TCGA-ER-A19E TCGA-ER-A19S 
      172.18        64.08        53.19        13.94        13.02        49.48 
TCGA-ER-A19T TCGA-ER-A2NG TCGA-ER-A42K TCGA-FS-A1YX TCGA-FS-A1Z4 TCGA-FS-A1ZA 
        8.88        48.99        12.95        48.59        28.08        27.72 
TCGA-FS-A1ZH TCGA-FS-A1ZQ TCGA-FS-A1ZT TCGA-FS-A4F2 TCGA-FS-A4F5 TCGA-GN-A4U3 
       32.75       133.55        53.16        50.14        28.73       121.91 
TCGA-GN-A8LL TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X TCGA-RP-A693 TCGA-W3-AA1V 
       21.37        65.88       368.78       297.90         0.33        42.08 
TCGA-WE-A8JZ TCGA-WE-A8ZY TCGA-YD-A9TA 
       24.03        49.51        49.18 

$`12P LOSS WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EB-A5SG TCGA-EE-A180 
       27.65        62.07        46.32        13.87        68.25        94.98 
TCGA-EE-A184 TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR 
       68.15       168.26         2.60       340.14       126.81       134.40 
TCGA-EE-A3JD TCGA-ER-A193 TCGA-ER-A198 TCGA-FR-A729 TCGA-FS-A1ZF TCGA-QB-AA9O 
       27.35        31.40        50.76       220.80        15.45        18.05 
TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 
       61.15        21.40        17.03        66.48        12.99        14.93 
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.57        16.67       112.04       112.57        71.80       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J7 TCGA-D3-A2J8 
       28.08        31.59        90.90        95.74       103.10        65.49 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG 
       23.77       115.53       168.00        86.76        11.87       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-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO 
       46.98       166.52        86.93        60.23        24.53         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-A5GU TCGA-D3-A8GC TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL 
      125.19        79.59        26.43       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-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW 
       18.44         9.90        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       135.02        88.87 
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        43.36        72.10        37.35        14.14        13.02 
TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV 
       13.87        10.36        20.35        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-A185 TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
       26.89         4.96        91.56        13.55        63.35        85.08 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N 
       78.97        13.97        63.78        64.64        56.84        18.61 
TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X 
       56.42        14.47       369.93        25.87       195.02        17.92 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC 
       46.82       115.96        39.29        86.14        59.28        67.43 
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-A2GN TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU 
       75.48       102.12        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-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2ML 
      103.27       268.73        16.96       204.66        96.23       216.66 
TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AB 
      167.90        47.54        43.23        71.21       124.31       122.73 
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-A3J8 TCGA-EE-A3JB TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI 
       36.95        34.32       201.80        51.35       134.33       152.81 
TCGA-ER-A195 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D 
       35.44         9.17        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       302.07       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 
       44.09       162.08        50.89       148.18       105.07        43.82 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET 
       23.34        20.15        28.83        41.56       247.04        93.01 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       46.98        33.21       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-A1Z3 TCGA-FS-A1Z7 TCGA-FS-A1ZB 
      216.92       228.59       202.65        20.91         7.79        48.85 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZK 
      357.37        53.52        46.45         9.70        47.38        23.93 
TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZW 
      101.26        74.73        11.41       148.80        26.56        49.48 
TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 
       27.09        27.02        77.82        66.67       174.84        34.03 
TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV 
       26.73        54.41        80.68        17.46        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        19.43         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-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK 
       48.00        39.35        10.42        48.89        22.13        50.10 
TCGA-GN-A9SD TCGA-HR-A2OG TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A694 TCGA-W3-A824 
       59.41         0.23         7.23         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-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO 
      105.04        49.05        17.95       101.33        58.98        70.52 
TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 
       63.22        11.80        35.80        12.16        40.41        24.99 
TCGA-XV-AB01 TCGA-YD-A89C TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S 
       13.25         6.90        37.94        14.43        27.58        96.99 
TCGA-Z2-AA3V 
       15.98 

  12P LOSS MUTATED 12P LOSS WILD-TYPE 
              0.33               0.20 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
            368.78             369.93 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
             53.19              50.89 
[1] "0.3 - 368.8 (53.2)" "0.2 - 369.9 (50.9)"
[1] "hr=" "1.3"
D64V3, continuous
                    vv
clus                 I/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       22
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  12P LOSS MUTATED           2         2         2         7          1
  12P LOSS WILD-TYPE        12        17        13        32         14
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  12P LOSS MUTATED            6          6        6
  12P LOSS WILD-TYPE         29         48       15
D64V4, multiclass
            clus
vv           12P LOSS MUTATED 12P LOSS WILD-TYPE
  I/II NOS                  4                  9
  STAGE 0                   1                  6
  STAGE I                   5                 24
  STAGE IA                  3                 15
  STAGE IB                  5                 23
  STAGE II                  4                 22
  STAGE IIA                 2                 12
  STAGE IIB                 2                 17
  STAGE IIC                 2                 13
  STAGE III                 7                 32
  STAGE IIIA                1                 14
  STAGE IIIB                6                 29
  STAGE IIIC                6                 48
  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 16
  12P LOSS WILD-TYPE    56 63 69 51
D64V5, multiclass
       clus
vv      12P LOSS MUTATED 12P LOSS WILD-TYPE
  T0+T1                8                 56
  T2                  10                 63
  T3                  12                 69
  T4                  16                 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
  12P LOSS MUTATED    28   9   7   7
  12P LOSS WILD-TYPE 149  56  32  38
D64V6, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  N0               28                149
  N1                9                 56
  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    49   6
  12P LOSS WILD-TYPE 270  16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     49    6
  12P LOSS WILD-TYPE  270   16
   clus
vv  12P LOSS MUTATED 12P LOSS WILD-TYPE
  0               49                270
  1                6                 16
[1] 2 2
[1] FALSE
D64V8, binary
                    cls
clus                   0   1
  12P LOSS MUTATED    21  18
  12P LOSS WILD-TYPE 113  72
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     21   18
  12P LOSS WILD-TYPE  113   72
     clus
vv    12P LOSS MUTATED 12P LOSS WILD-TYPE
  NO                21                113
  YES               18                 72
[1] 2 2
[1] FALSE
D64V9, binary
                    cls
clus                   0   1
  12P LOSS MUTATED     5  56
  12P LOSS WILD-TYPE  42 264
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      5   56
  12P LOSS WILD-TYPE   42  264
     clus
vv    12P LOSS MUTATED 12P LOSS WILD-TYPE
  NO                 5                 42
  YES               56                264
[1] 2 2
[1] FALSE
D64V10, continuous
D64V11, binary
                    cls
clus                   0   1
  12P LOSS MUTATED    27  34
  12P LOSS WILD-TYPE 111 195
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     27   34
  12P LOSS WILD-TYPE  111  195
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  FEMALE               27                111
  MALE                 34                195
[1] 2 2
[1] FALSE
D64V12, binary
                    cls
clus                   0   1
  12P LOSS MUTATED    54   7
  12P LOSS WILD-TYPE 265  40
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     54    7
  12P LOSS WILD-TYPE  265   40
     clus
vv    12P LOSS MUTATED 12P LOSS WILD-TYPE
  NO                54                265
  YES                7                 40
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  12P LOSS MUTATED       0                         0    59
  12P LOSS WILD-TYPE     5                         1   294
D64V13, multiclass
                           clus
vv                          12P LOSS MUTATED 12P LOSS WILD-TYPE
  ASIAN                                    0                  5
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   59                294
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V14, binary
                    cls
clus                   0   1
  12P LOSS MUTATED     0  59
  12P LOSS WILD-TYPE   7 293
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      0   59
  12P LOSS WILD-TYPE    7  293
                        clus
vv                       12P LOSS MUTATED 12P LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  7
  NOT HISPANIC OR LATINO               59                293
[1] 2 2
[1] FALSE

Clustering(65) Variable = 12Q LOSS MUTATION ANALYSIS
D65V1, survival
                    sevent
clus2                  0   1
  12Q LOSS MUTATED    24  20
  12Q LOSS WILD-TYPE 104 104
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                44                208 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                20                104 
$`12Q LOSS MUTATED`
TCGA-D3-A8GI TCGA-FW-A3R5 TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A2J6 TCGA-D3-A2JL 
       13.41        36.95        12.99         8.42        25.64       171.58 
TCGA-D3-A3CC TCGA-D3-A5GR TCGA-D3-A8GC TCGA-D9-A1X3 TCGA-D9-A6EC TCGA-DA-A1I1 
       40.01       177.86        78.21        10.78        69.21        68.68 
TCGA-DA-A95X TCGA-EE-A20C TCGA-EE-A29G TCGA-EE-A29Q TCGA-EE-A2A2 TCGA-EE-A2GP 
       65.03        75.55        44.28        61.12        30.02         0.76 
TCGA-EE-A2GR TCGA-EE-A2GU TCGA-EE-A2MG TCGA-EE-A2MK TCGA-EE-A2MP TCGA-EE-A2MS 
        0.20        81.99        94.19        89.26       227.01       143.93 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3J3 TCGA-EE-A3J7 
       53.26       124.31         4.41        54.51        67.89        45.90 
TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19S TCGA-ER-A3PL TCGA-FS-A1Z4 TCGA-FS-A1ZQ 
       10.49         7.82        47.18        32.05        27.62       130.95 
TCGA-FS-A1ZT TCGA-GN-A4U3 TCGA-LH-A9QB TCGA-OD-A75X TCGA-RP-A693 TCGA-W3-AA1R 
       35.28       120.53        85.05       297.01         0.33        79.99 
TCGA-WE-A8ZM TCGA-WE-A8ZY 
       65.42        48.39 

$`12Q LOSS WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A20H 
        9.76        62.07        38.76        33.24        31.96       166.75 
TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 TCGA-FR-A729 
      269.03        52.90       134.40        27.35        19.04       216.43 
TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-3N-A9WC TCGA-BF-AAP0 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
       52.73         7.40        60.46        14.83        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-A2JG 
       45.99        62.86        15.75       168.00        86.30       107.61 
TCGA-D3-A2JH TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CB 
       36.30        64.83        66.08        43.53        58.06       140.98 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E 
       59.70        24.53         9.34        90.21        23.67       173.85 
TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL 
       30.67       144.46        31.76        62.70        11.34        42.05 
TCGA-D3-A5GN TCGA-D3-A5GU TCGA-D3-A8GD TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL 
       45.70       124.08        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-A4Z6 
       70.62       135.12        36.53        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       110.53        60.10 
TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-DA-A95V 
       64.83        58.85        30.44       225.11         8.71        72.10 
TCGA-DA-A95W TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN 
        0.76        14.14        12.30         3.91        16.41        52.41 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
       18.21        13.15        24.89        20.38         0.00        26.24 
TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H 
       79.20        75.22        76.14        12.99         0.26        47.41 
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-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
       26.14        12.95       201.60        68.65        10.62        32.48 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GS TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 
       18.35        93.63        71.31       103.13        15.25         5.75 
TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MM 
       23.77       209.79       171.85        63.25       104.78       145.45 
TCGA-EE-A2MT TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AF TCGA-EE-A3J4 TCGA-EE-A3J8 
       23.51       122.73        64.04         6.28       111.85         3.35 
TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A19A TCGA-ER-A19B 
      168.85        19.86       135.98        34.45         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       184.60       150.12        99.06        59.84 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
       42.51       120.76        49.71       146.63        73.05        22.36 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET 
        4.70        16.87        10.19        28.67       173.29        68.52 
TCGA-ER-A3EV TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A7U8 
       15.48        74.47         4.50       174.21         4.14        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-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM 
      312.07        32.78        43.92         7.82        36.33        78.61 
TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 
      136.27         4.47        23.21         5.29         3.06        30.90 
TCGA-FS-A4F4 TCGA-FS-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        18.25         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-QB-A6FS TCGA-RP-A690 TCGA-W3-A824 TCGA-W3-A825 
       43.23        59.41         7.23         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        47.54 
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        37.32 
TCGA-WE-AAA4 TCGA-XV-AB01 TCGA-YG-AA3O TCGA-Z2-AA3S 
       24.99         6.61        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 
            53.885             43.985 
[1] "0.2 - 297.0 (53.9)" "0.0 - 346.5 (44.0)"
[1] "hr=" "1.2"
D65V2, survival
                    sevent
clus2                  0   1
  12Q LOSS MUTATED    32  33
  12Q LOSS WILD-TYPE 134 159
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                65                293 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                33                159 
$`12Q LOSS MUTATED`
TCGA-D3-A8GI TCGA-EB-A5SH TCGA-FW-A3R5 TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A2J6 
       58.52        54.02        36.95        12.99        16.57        43.43 
TCGA-D3-A2JL TCGA-D3-A3CC TCGA-D3-A51N TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A8GC 
      171.58        86.93        22.62       137.92       178.32        79.59 
TCGA-D3-A8GN TCGA-D9-A1X3 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1I1 TCGA-DA-A95X 
      161.00        18.12        25.18        77.56       222.51        73.94 
TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A29G TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29X 
      133.81       151.27        72.07        66.74        61.28        17.92 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GU TCGA-EE-A2MG 
       59.64        39.29        13.91        42.77        94.82       103.20 
TCGA-EE-A2MK TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AD 
      180.39       248.65       162.48        53.26       124.31        28.77 
TCGA-EE-A3AE TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-ER-A197 TCGA-ER-A199 
       54.51       172.18        64.08        53.19        13.94         9.17 
TCGA-ER-A19E TCGA-ER-A19S TCGA-ER-A3PL TCGA-ER-A42K TCGA-FS-A1YX TCGA-FS-A1Z4 
       13.02        49.48        33.21        12.95        48.59        28.08 
TCGA-FS-A1ZA TCGA-FS-A1ZH TCGA-FS-A1ZQ TCGA-FS-A1ZT TCGA-FS-A4F2 TCGA-FS-A4F5 
       27.72        32.75       133.55        53.16        50.14        28.73 
TCGA-GN-A4U3 TCGA-GN-A8LL TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X TCGA-RP-A693 
      121.91        21.37        65.88       368.78       297.90         0.33 
TCGA-W3-AA1R TCGA-WE-A8JZ TCGA-WE-A8ZM TCGA-WE-A8ZY TCGA-YD-A9TA 
      111.09        24.03       101.33        49.51        49.18 

$`12Q LOSS WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EB-A5SG TCGA-EE-A180 
       27.65        62.07        46.32        13.87        68.25        94.98 
TCGA-EE-A184 TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR 
       68.15       168.26         2.60       340.14       126.81       134.40 
TCGA-EE-A3JD TCGA-ER-A193 TCGA-ER-A198 TCGA-FR-A729 TCGA-FS-A1ZF TCGA-QB-AA9O 
       27.35        31.40        50.76       220.80        15.45        18.05 
TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-3N-A9WB TCGA-3N-A9WC TCGA-BF-AAP0 TCGA-D3-A1Q3 
       61.15        21.40        17.03        66.48        14.93        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-A2JG TCGA-D3-A2JH TCGA-D3-A2JK 
      168.00        86.76        11.87       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-A3CB TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU 
      166.52        60.23        24.53         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-A5GS TCGA-D3-A5GU 
       63.81        26.89       125.79       135.75        18.18       125.19 
TCGA-D3-A8GB TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL 
       30.84        23.61        26.43       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-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY 
       18.44         9.90        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       135.02        88.87        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 
       43.36        72.10        37.35        14.14        13.02        13.87 
TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 
       10.36        20.35        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-A185 TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C 
        4.96        91.56        13.55        63.35        85.08        78.97 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P 
       13.97        63.78        64.64        56.84        18.61        56.42 
TCGA-EE-A29R TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A2A0 TCGA-EE-A2A1 
       14.47       369.93        25.87       195.02        46.82       115.96 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
       86.14        59.28        67.43       173.79       220.24        48.72 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GS 
      107.38        54.74        79.66        75.48       102.12        81.21 
TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC 
       44.88        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-A2MM TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MT TCGA-EE-A3AB 
      216.66       167.90        47.54        43.23        71.21       122.73 
TCGA-EE-A3AC TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J5 
       64.04        13.81        41.59       138.81       127.20        36.95 
TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 
       34.32       201.80        51.35       134.33       152.81        35.44 
TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19G 
       77.75        98.40        48.89        12.59        26.37       302.07 
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        44.09       162.08 
TCGA-ER-A19Q TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
       50.89         8.88       148.18       105.07        43.82        23.34 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET 
       20.15        28.83        48.99        41.56       247.04        93.01 
TCGA-ER-A3EV TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A7U8 
       46.98       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-A1Z7 TCGA-FS-A1ZB TCGA-FS-A1ZC 
      228.59       202.65        20.91         7.79        48.85       357.37 
TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM 
       53.52        46.45         9.70        47.38        23.93       101.26 
TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY 
       74.73        11.41       148.80        26.56        49.48        27.09 
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-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
       54.41        80.68        17.46        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        19.43         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-RP-A690 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 
        0.23         7.23         0.20         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-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT 
       49.05        17.95        58.98        70.52        63.22        11.80 
TCGA-WE-A8ZX TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-XV-AB01 TCGA-YD-A89C 
       35.80        12.16        40.41        24.99        13.25         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 
             54.02              50.10 
[1] "0.3 - 368.8 (54.0)" "0.2 - 369.9 (50.1)"
[1] "hr=" "1.2"
D65V3, continuous
                    vv
clus                 I/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       21
                    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        30         12
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  12Q LOSS MUTATED            6          6        4
  12Q LOSS WILD-TYPE         29         48       17
D65V4, multiclass
            clus
vv           12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  I/II NOS                  4                  9
  STAGE 0                   1                  6
  STAGE I                   5                 24
  STAGE IA                  4                 14
  STAGE IB                  7                 21
  STAGE II                  5                 21
  STAGE IIA                 2                 12
  STAGE IIB                 2                 17
  STAGE IIC                 3                 12
  STAGE III                 9                 30
  STAGE IIIA                3                 12
  STAGE IIIB                6                 29
  STAGE IIIC                6                 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
  12Q LOSS MUTATED      11 13 12 17
  12Q LOSS WILD-TYPE    53 60 69 50
D65V5, multiclass
       clus
vv      12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  T0+T1               11                 53
  T2                  13                 60
  T3                  12                 69
  T4                  17                 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
  12Q LOSS MUTATED    34  11   8   6
  12Q LOSS WILD-TYPE 143  54  31  39
D65V6, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  N0               34                143
  N1               11                 54
  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    58   4
  12Q LOSS WILD-TYPE 261  18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED     58    4
  12Q LOSS WILD-TYPE  261   18
   clus
vv  12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  0               58                261
  1                4                 18
[1] 2 2
[1] FALSE
D65V8, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED    23  18
  12Q LOSS WILD-TYPE 111  72
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED     23   18
  12Q LOSS WILD-TYPE  111   72
     clus
vv    12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  NO                23                111
  YES               18                 72
[1] 2 2
[1] FALSE
D65V9, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED     8  60
  12Q LOSS WILD-TYPE  39 260
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      8   60
  12Q LOSS WILD-TYPE   39  260
     clus
vv    12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  NO                 8                 39
  YES               60                260
[1] 2 2
[1] FALSE
D65V10, continuous
D65V11, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED    29  39
  12Q LOSS WILD-TYPE 109 190
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED     29   39
  12Q LOSS WILD-TYPE  109  190
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  FEMALE               29                109
  MALE                 39                190
[1] 2 2
[1] FALSE
D65V12, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED    61   7
  12Q LOSS WILD-TYPE 258  40
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED     61    7
  12Q LOSS WILD-TYPE  258   40
     clus
vv    12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  NO                61                258
  YES                7                 40
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  12Q LOSS MUTATED       0                         0    66
  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                                   66                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  66
  12Q LOSS WILD-TYPE   7 286
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      0   66
  12Q LOSS WILD-TYPE    7  286
                        clus
vv                       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  7
  NOT HISPANIC OR LATINO               66                286
[1] 2 2
[1] FALSE

Clustering(66) Variable = 13Q LOSS MUTATION ANALYSIS
D66V1, survival
                    sevent
clus2                  0   1
  13Q LOSS MUTATED    34  23
  13Q LOSS WILD-TYPE  94 101
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                57                195 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                23                101 
$`13Q LOSS MUTATED`
TCGA-EE-A2MR TCGA-ER-A193 TCGA-BF-AAP0 TCGA-D3-A1Q8 TCGA-D3-A2J7 TCGA-D3-A2JA 
      134.40        19.04        14.83        19.04        45.99        15.75 
TCGA-D3-A2JC TCGA-D3-A2JL TCGA-D3-A2JP TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A5GL 
       86.30       171.58        43.53        90.21        23.67        42.05 
TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A8GD TCGA-D3-A8GK TCGA-D3-A8GR TCGA-D9-A3Z3 
       45.70       177.86        23.61       120.00        36.53        16.90 
TCGA-DA-A1HV TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1IC TCGA-DA-A95V TCGA-DA-A95X 
       76.34       150.61       110.53        58.85        72.10        65.03 
TCGA-EB-A5UN TCGA-EE-A181 TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29M TCGA-EE-A29Q 
       52.41        20.38        76.14        12.99        47.74        61.12 
TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A6 TCGA-EE-A2GE TCGA-EE-A2GJ TCGA-EE-A2MG 
      346.49       185.19        77.98        12.95        68.65        94.19 
TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3JB 
      143.93        53.26       122.73         4.41        54.51       168.85 
TCGA-EE-A3JH TCGA-ER-A19B TCGA-ER-A19H TCGA-ER-A2NG TCGA-FR-A3YN TCGA-FS-A1ZJ 
       19.86        53.29       150.12        28.67         4.50        36.33 
TCGA-FS-A4F4 TCGA-GN-A8LK TCGA-GN-A9SD TCGA-RP-A693 TCGA-W3-AA1V TCGA-WE-A8ZM 
       66.67        43.23        59.41         0.33         8.09        65.42 
TCGA-WE-A8ZQ TCGA-WE-A8ZY TCGA-YG-AA3O 
       62.89        48.39        28.21 

$`13Q LOSS WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A8GI TCGA-EB-A5SG TCGA-EE-A180 
        9.76        62.07        38.76        13.41        33.24        31.96 
TCGA-EE-A20H TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A3JD TCGA-FR-A729 TCGA-FW-A3R5 
      166.75       269.03        52.90        27.35       216.43        36.95 
TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q3 
       52.73         7.40        60.46        12.99         8.42        15.72 
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1QA TCGA-D3-A1QB 
       31.89       110.93        49.35       133.25        76.41        62.60 
TCGA-D3-A2J6 TCGA-D3-A2J8 TCGA-D3-A2JB TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JN 
       25.64        62.86       168.00       107.61        36.30        64.83 
TCGA-D3-A2JO TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF 
       66.08        58.06       140.98        40.01        59.70        24.53 
TCGA-D3-A3MO TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R 
        9.34       173.85        30.67       144.46        31.76        62.70 
TCGA-D3-A51T TCGA-D3-A5GU TCGA-D3-A8GC TCGA-D3-A8GJ TCGA-D3-A8GL TCGA-D3-A8GM 
       11.34       124.08        78.21       179.97        69.53        70.62 
TCGA-D3-A8GP TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A4Z6 TCGA-D9-A6EC TCGA-D9-A6EG 
      135.12        10.78        15.02        18.44        69.21        22.85 
TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A3F2 TCGA-DA-A3F5 
      138.67        68.68        60.10        64.83        30.44       225.11 
TCGA-DA-A3F8 TCGA-DA-A95W TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5KH 
        8.71         0.76        14.14        12.30         3.91        16.41 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20C 
       18.21        13.15        24.89         0.00        26.24        75.55 
TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29P 
       79.20        75.22         0.26        44.28        47.41        27.16 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2GB TCGA-EE-A2GH TCGA-EE-A2GK TCGA-EE-A2GL 
      115.43        30.02        26.14       201.60        10.62        32.48 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU 
       18.35        93.63         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-A2MI 
      103.13        15.25         5.75        23.77       209.79       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-A3AA TCGA-EE-A3AC TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 
      124.31        64.04         6.28        67.89       111.85        45.90 
TCGA-EE-A3J8 TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A 
        3.35       135.98        34.45        10.49         7.82         4.54 
TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
       39.81        11.47       184.60        99.06        59.84        42.51 
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        73.05        22.36 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
        4.70        16.87        10.19       173.29        68.52        15.48 
TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A7UA 
       32.05        74.47       174.21         4.14        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-A1ZG TCGA-FS-A1ZM TCGA-FS-A1ZQ 
      312.07        32.78        43.92         7.82        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-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV 
       30.90       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        18.25         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-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 TCGA-W3-A824 
       46.92        85.05       297.01         7.23         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-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-AA9Y TCGA-WE-AAA0 
       47.54        12.69        21.90        10.95         1.94        37.32 
TCGA-WE-AAA4 TCGA-XV-AB01 TCGA-Z2-AA3S 
       24.99         6.61        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 
             53.29              42.51 
[1] "0.3 - 346.5 (53.3)" "0.0 - 312.1 (42.5)"
[1] "hr=" "1.4"
D66V2, survival
                    sevent
clus2                  0   1
  13Q LOSS MUTATED    40  42
  13Q LOSS WILD-TYPE 126 150
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                82                276 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                42                150 
$`13Q LOSS MUTATED`
TCGA-EE-A184 TCGA-EE-A2MR TCGA-ER-A193 TCGA-BF-AAP0 TCGA-D3-A1Q8 TCGA-D3-A2J7 
       68.15       134.40        31.40        14.93        28.08       103.10 
TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JL TCGA-D3-A2JP TCGA-D3-A3MR TCGA-D3-A3MU 
      115.53        86.76       171.58        59.57       103.59        39.75 
TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A8GB TCGA-D3-A8GD TCGA-D3-A8GK 
      125.79       135.75       178.32        30.84        23.61       170.20 
TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D3-A8GV TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A3Z3 
      129.63       117.17       167.70       151.53        54.67        22.29 
TCGA-D9-A6EA TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
       25.18        76.57        36.03       176.55        35.93       135.02 
TCGA-DA-A1I8 TCGA-DA-A1IC TCGA-DA-A95V TCGA-DA-A95X TCGA-EB-A5UN TCGA-EE-A181 
       53.92        68.09        72.10        73.94        58.92        33.73 
TCGA-EE-A20I TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29Q 
       13.55        78.97        13.97        56.84        18.61        66.74 
TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A6 TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GJ 
      369.93       195.02        86.14       173.79        48.72       107.38 
TCGA-EE-A2M5 TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AB 
       21.67       103.20        16.96       162.48        53.26       122.73 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AH TCGA-EE-A3J5 TCGA-EE-A3JB TCGA-EE-A3JH 
       28.77        54.51       138.81        36.95       201.80       134.33 
TCGA-ER-A19B TCGA-ER-A19H TCGA-ER-A19T TCGA-ER-A2NG TCGA-FR-A3YN TCGA-FR-A7U9 
       98.40       152.35         8.88        48.99        92.98        18.77 
TCGA-FS-A1ZA TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A4F4 TCGA-GN-A266 TCGA-GN-A26D 
       27.72        32.75        47.38        66.67        10.13        48.00 
TCGA-GN-A4U7 TCGA-GN-A8LK TCGA-GN-A9SD TCGA-RP-A693 TCGA-W3-AA1V TCGA-WE-A8ZM 
       10.42        50.10        59.41         0.33        42.08       101.33 
TCGA-WE-A8ZQ TCGA-WE-A8ZY TCGA-YG-AA3O TCGA-YG-AA3P 
       63.22        49.51        37.94        14.43 

$`13Q LOSS WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-D3-A8GI TCGA-EB-A5SG 
       27.65        62.07        46.32        13.87        58.52        68.25 
TCGA-EB-A5SH TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2GO 
       54.02        94.98       168.26         2.60       340.14       126.81 
TCGA-EE-A3JD TCGA-ER-A198 TCGA-FR-A729 TCGA-FS-A1ZF TCGA-FW-A3R5 TCGA-QB-AA9O 
       27.35        50.76       220.80        15.45        36.95        18.05 
TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 
       61.15        21.40        17.03        66.48        12.99        16.57 
TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q9 
       16.67       112.04       112.57        71.80       133.25        31.59 
TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JB 
       90.90        95.74        43.43        65.49        23.77       168.00 
TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JN TCGA-D3-A2JO 
       11.87       113.52        42.08        12.10        66.48        66.08 
TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE 
      130.72        58.06        46.98       166.52        86.93        60.23 
TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
       24.53         9.34        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-A5GO 
      145.12        32.94        22.62        63.81        26.89       137.92 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GC TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GL 
       18.18       125.19        79.59        26.43       241.38        89.13 
TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D9-A1JW TCGA-D9-A1JX 
      107.15       161.00       152.75        29.06         3.65         7.10 
TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-D9-A6EG 
       18.12        15.39        18.44         9.90        77.56        22.95 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IB 
      144.89        20.38       222.51        88.87        65.92        40.60 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-DA-A95W TCGA-DA-A95Y 
       33.93        10.49       225.96        43.36        37.35        14.14 
TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5UL TCGA-EB-A5VV 
       13.02        13.87        10.36        20.35        29.29         7.04 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A182 TCGA-EE-A183 
       36.46        29.82        27.22         8.65        14.70        26.89 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29A TCGA-EE-A29B 
        4.96       133.81       151.27        91.56        63.35        85.08 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A29S 
       63.78        72.07        64.64        56.42        14.47        61.28 
TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 
       25.87        17.92        46.82       115.96        59.64        39.29 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GH TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
       59.28        67.43       220.24        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-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM 
      268.73       204.66        96.23       180.39       216.66       167.90 
TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AC 
       47.54       248.65        43.23        71.21       124.31        64.04 
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-A3JA TCGA-EE-A3JE TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 
       53.19        51.35       152.81        35.44        13.94         9.17 
TCGA-ER-A19A TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G 
       77.75        48.89        12.59        13.02        26.37       302.07 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
        6.44       131.51        61.05        44.09       162.08        50.89 
TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
       49.48       148.18       105.07        43.82        23.34        20.15 
TCGA-ER-A2NF TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL 
       28.83        41.56       247.04        93.01        46.98        33.21 
TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A7UA 
       12.95       149.03       174.21        15.72        27.85        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-A1ZB TCGA-FS-A1ZC 
      202.65        20.91        28.08         7.79        48.85       357.37 
TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP 
       53.52        46.45         9.70        23.93       101.26        74.73 
TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW 
      133.55        11.41       148.80        53.16        26.56        49.48 
TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F5 TCGA-FS-A4F8 
       27.09        27.02        77.82        50.14        28.73       174.84 
TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU 
       34.03        26.73        54.41        80.68        17.46        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        19.43         2.04        15.78 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
      139.89       117.93        96.92        64.44        62.79        32.48 
TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LL TCGA-HR-A2OG 
      121.91        39.35        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-A694 
       65.88       368.78       297.90         7.23         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-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-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 
       70.52        11.80        35.80        12.16        40.41        24.99 
TCGA-XV-AB01 TCGA-YD-A89C TCGA-YD-A9TA TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
       13.25         6.90        49.18        27.58        96.99        15.98 

  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
              0.33               0.20 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
            369.93             368.78 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
            59.490             49.115 
[1] "0.3 - 369.9 (59.5)" "0.2 - 368.8 (49.1)"
[1] "hr=" "1.2"
D66V3, continuous
                    vv
clus                 I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  13Q LOSS MUTATED          3       2       7        6        8        5
  13Q LOSS WILD-TYPE       10       5      22       12       20       21
                    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        30         13
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  13Q LOSS MUTATED            7          9        7
  13Q LOSS WILD-TYPE         28         45       14
D66V4, multiclass
            clus
vv           13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  I/II NOS                  3                 10
  STAGE 0                   2                  5
  STAGE I                   7                 22
  STAGE IA                  6                 12
  STAGE IB                  8                 20
  STAGE II                  5                 21
  STAGE IIA                 3                 11
  STAGE IIB                 3                 16
  STAGE IIC                 4                 11
  STAGE III                 9                 30
  STAGE IIIA                2                 13
  STAGE IIIB                7                 28
  STAGE IIIC                9                 45
  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      19 14 21 13
  13Q LOSS WILD-TYPE    45 59 60 54
D66V5, multiclass
       clus
vv      13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  T0+T1               19                 45
  T2                  14                 59
  T3                  21                 60
  T4                  13                 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
  13Q LOSS MUTATED    42  13   9   9
  13Q LOSS WILD-TYPE 135  52  30  36
D66V6, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  N0               42                135
  N1               13                 52
  N2                9                 30
  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"
D66V7, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED    69   8
  13Q LOSS WILD-TYPE 250  14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     69    8
  13Q LOSS WILD-TYPE  250   14
   clus
vv  13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  0               69                250
  1                8                 14
[1] 2 2
[1] FALSE
D66V8, binary
                    cls
clus                  0  1
  13Q LOSS MUTATED   39 16
  13Q LOSS WILD-TYPE 95 74
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     39   16
  13Q LOSS WILD-TYPE   95   74
     clus
vv    13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  NO                39                 95
  YES               16                 74
[1] 2 2
[1] FALSE
D66V9, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED     9  73
  13Q LOSS WILD-TYPE  38 247
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      9   73
  13Q LOSS WILD-TYPE   38  247
     clus
vv    13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  NO                 9                 38
  YES               73                247
[1] 2 2
[1] FALSE
D66V10, continuous
D66V11, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED    29  53
  13Q LOSS WILD-TYPE 109 176
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     29   53
  13Q LOSS WILD-TYPE  109  176
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  FEMALE               29                109
  MALE                 53                176
[1] 2 2
[1] FALSE
D66V12, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED    70  12
  13Q LOSS WILD-TYPE 249  35
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     70   12
  13Q LOSS WILD-TYPE  249   35
     clus
vv    13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  NO                70                249
  YES               12                 35
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  13Q LOSS MUTATED       0                         0    79
  13Q LOSS WILD-TYPE     5                         1   274
D66V13, multiclass
                           clus
vv                          13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  ASIAN                                    0                  5
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   79                274
[1] 3 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  79
  13Q LOSS WILD-TYPE   5 273
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      2   79
  13Q LOSS WILD-TYPE    5  273
                        clus
vv                       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  5
  NOT HISPANIC OR LATINO               79                273
[1] 2 2
[1] FALSE

Clustering(67) Variable = 14Q LOSS MUTATION ANALYSIS
D67V1, survival
                    sevent
clus2                 0  1
  14Q LOSS MUTATED   36 38
  14Q LOSS WILD-TYPE 92 86
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                74                178 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                38                 86 
$`14Q LOSS MUTATED`
TCGA-D3-A2JF TCGA-D3-A8GI TCGA-3N-A9WC TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A2J6 
       62.07        13.41        60.46         8.42        31.89        25.64 
TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3MR 
       64.83        66.08        43.53        40.01        59.70        90.21 
TCGA-D3-A51J TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A8GC TCGA-D9-A4Z6 TCGA-DA-A1HV 
      144.46        45.70       177.86        78.21        18.44        76.34 
TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I5 TCGA-DA-A3F5 TCGA-DA-A95V TCGA-EE-A181 
      138.67        68.68       110.53       225.11        72.10        20.38 
TCGA-EE-A29C TCGA-EE-A29G TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GE TCGA-EE-A2GP 
       76.14        44.28        30.02        77.98        12.95         0.76 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MG TCGA-EE-A2MK TCGA-EE-A2MS 
      103.13        15.25         5.75        94.19        89.26       143.93 
TCGA-EE-A3AA TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-EE-A3JB TCGA-EE-A3JI TCGA-ER-A197 
      124.31        67.89        45.90       168.85       135.98        10.49 
TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19S TCGA-ER-A2ND 
        7.82        53.29       184.60       150.12        47.18         4.70 
TCGA-ER-A3PL TCGA-FR-A44A TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZE TCGA-FS-A1ZM 
       32.05       174.21        27.62       312.07        43.92        78.61 
TCGA-FS-A1ZQ TCGA-FS-A1ZT TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FW-A3TU TCGA-GF-A4EO 
      130.95        35.28       173.19        13.28        55.59        18.25 
TCGA-GF-A6C8 TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 
        1.91       117.93        17.06        42.48         7.59       120.53 
TCGA-GN-A8LK TCGA-LH-A9QB TCGA-OD-A75X TCGA-W3-A825 TCGA-W3-AA1V TCGA-WE-A8ZM 
       43.23        85.05       297.01         1.97         8.09        65.42 
TCGA-WE-A8ZY TCGA-YG-AA3O 
       48.39        28.21 

$`14Q LOSS WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GD 
        9.76        38.76        33.24        31.96       166.75       269.03 
TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 TCGA-FR-A729 TCGA-FW-A3R5 
       52.90       134.40        27.35        19.04       216.43        36.95 
TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q3 TCGA-D3-A1Q5 
       52.73         7.40        12.99        14.83        15.72       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-A2JG TCGA-D3-A2JH 
       62.86        15.75       168.00        86.30       107.61        36.30 
TCGA-D3-A2JL TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MU 
      171.58        58.06       140.98        24.53         9.34        23.67 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL 
      173.85        30.67        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-A8GM 
      124.08        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-A6EC 
      135.12        36.53        10.78        15.02        16.90        69.21 
TCGA-D9-A6EG TCGA-DA-A1I2 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 
       22.85       150.61        60.10        64.83        58.85        30.44 
TCGA-DA-A3F8 TCGA-DA-A95W TCGA-DA-A95X TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q 
        8.71         0.76        65.03        14.14        12.30         3.91 
TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A182 
       16.41        52.41        18.21        13.15        24.89         0.00 
TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29E 
       26.24        75.55        79.20        75.22        12.99         0.26 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W 
       47.41        47.74        27.16        61.12       346.49       185.19 
TCGA-EE-A2A1 TCGA-EE-A2GB TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
      115.43        26.14       201.60        68.65        10.62        32.48 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2MC 
       18.35        93.63         0.20        71.31        81.99        23.77 
TCGA-EE-A2MF TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP 
      209.79       171.85        63.25       104.78       145.45       227.01 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
       23.51        53.26       122.73        64.04         4.41        54.51 
TCGA-EE-A3AF TCGA-EE-A3J4 TCGA-EE-A3J8 TCGA-EE-A3JH TCGA-ER-A195 TCGA-ER-A19A 
        6.28       111.85         3.35        19.86        34.45         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        42.51       120.76 
TCGA-ER-A19Q TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NF 
       49.71       146.63        73.05        22.36        16.87        10.19 
TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A42L TCGA-FR-A3YN 
       28.67       173.29        68.52        15.48        74.47         4.50 
TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FS-A1YW TCGA-FS-A1YY 
        4.14        26.20         5.65        10.06       171.78        49.74 
TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1ZD TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZS 
      195.98         8.35        32.78         7.82        36.33       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-A4FD TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GN-A262 TCGA-GN-A265 
       80.68        11.54        19.30         9.90        53.29        96.92 
TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-GN-A9SD TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 
       34.49        46.92        59.41         7.23         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-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-AA9Y 
       47.54        12.69        21.90        62.89        10.95         1.94 
TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-XV-AB01 TCGA-Z2-AA3S 
       37.32        24.99         6.61        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 
            57.645             40.930 
[1] "0.8 - 312.1 (57.6)" "0.0 - 346.5 (40.9)"
[1] "hr=" "1.1"
D67V2, survival
                    sevent
clus2                  0   1
  14Q LOSS MUTATED    50  60
  14Q LOSS WILD-TYPE 116 132
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               110                248 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                60                132 
$`14Q LOSS MUTATED`
TCGA-D3-A2JF TCGA-D3-A8GI TCGA-3N-A9WC TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A2J6 
       62.07        58.52        66.48        16.57       112.04        43.43 
TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3MR 
       66.48        66.08        59.57        86.93        60.23       103.59 
TCGA-D3-A3MV TCGA-D3-A51J TCGA-D3-A51N TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR 
       45.30       145.12        22.62       135.75       137.92       178.32 
TCGA-D3-A8GC TCGA-D3-A8GN TCGA-D3-A8GS TCGA-D9-A149 TCGA-D9-A4Z6 TCGA-D9-A6EA 
       79.59       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       222.51       135.02        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       302.07 
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        19.43         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-D3-A2JE TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A180 
       27.65        46.32        13.87        68.25        54.02        94.98 
TCGA-EE-A184 TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR 
       68.15       168.26         2.60       340.14       126.81       134.40 
TCGA-EE-A3JD TCGA-ER-A193 TCGA-ER-A198 TCGA-FR-A729 TCGA-FS-A1ZF TCGA-FW-A3R5 
       27.35        31.40        50.76       220.80        15.45        36.95 
TCGA-QB-AA9O TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-3N-A9WB TCGA-3N-A9WD TCGA-BF-AAP0 
       18.05        61.15        21.40        17.03        12.99        14.93 
TCGA-D3-A1Q3 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 
       16.67       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-A2JG TCGA-D3-A2JH TCGA-D3-A2JK 
      168.00        86.76        11.87       113.52        42.08        12.10 
TCGA-D3-A2JL TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CF 
      171.58       130.72        58.06        46.98       166.52        24.53 
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        88.87 
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        43.36 
TCGA-DA-A95W TCGA-DA-A95X TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5KH 
       37.35        73.94        14.14        13.02        13.87        20.35 
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-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-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H 
       13.55        63.35        85.08        13.97        63.78        64.64 
TCGA-EE-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-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-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 
      102.12        42.77        81.21        44.88        94.82        21.67 
TCGA-EE-A2MC TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2ML 
       61.51       103.27       268.73       204.66        96.23       216.66 
TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB 
      167.90       248.65        43.23        71.21        53.26       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3J4 
       64.04        28.77        54.51        13.81        41.59       127.20 
TCGA-EE-A3J8 TCGA-EE-A3JH TCGA-ER-A195 TCGA-ER-A19A TCGA-ER-A19C TCGA-ER-A19D 
       34.32       134.33        35.44        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        44.09       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       105.07        43.82        20.15 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
       28.83        48.99        41.56       247.04        93.01        46.98 
TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA 
      149.03        92.98        15.72        27.85        18.77        38.27 
TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 
       34.82        36.26       104.42       216.92       228.59       202.65 
TCGA-FS-A1Z3 TCGA-FS-A1ZB TCGA-FS-A1ZD TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZK 
       20.91        48.85        53.52         9.70        47.38        23.93 
TCGA-FS-A1ZP TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ 
       74.73       148.80        26.56        49.48        27.09        27.02 
TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 
       77.82        66.67        26.73        54.41        80.68        17.46 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A266 
       13.51        19.30         9.90       139.89        96.92        10.13 
TCGA-GN-A26D TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A8LL TCGA-GN-A9SD 
       48.00        39.35        10.42        48.89        21.37        59.41 
TCGA-HR-A2OH TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 
       65.88         7.23         0.20         0.33         0.69       228.16 
TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1W TCGA-W3-AA21 
      121.08         4.01        69.07       111.09       219.16       105.04 
TCGA-WE-A8K1 TCGA-WE-A8K6 TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT 
       49.05        17.95        58.98        70.52        63.22        11.80 
TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-XV-AB01 TCGA-YD-A89C TCGA-YD-A9TA 
       12.16        40.41        24.99        13.25         6.90        49.18 
TCGA-Z2-AA3S TCGA-Z2-AA3V 
       96.99        15.98 

  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
              0.23               0.20 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
            368.78             369.93 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
            55.130             49.115 
[1] "0.2 - 368.8 (55.1)" "0.2 - 369.9 (49.1)"
[1] "hr=" "1.1"
D67V3, continuous
                    vv
clus                 I/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       16
                    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        22         12
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  14Q LOSS MUTATED           11         16        4
  14Q LOSS WILD-TYPE         24         38       17
D67V4, multiclass
            clus
vv           14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  I/II NOS                  5                  8
  STAGE 0                   0                  7
  STAGE I                  12                 17
  STAGE IA                  3                 15
  STAGE IB                  8                 20
  STAGE II                 10                 16
  STAGE IIA                 2                 12
  STAGE IIB                 5                 14
  STAGE IIC                 5                 10
  STAGE III                17                 22
  STAGE IIIA                3                 12
  STAGE IIIB               11                 24
  STAGE IIIC               16                 38
  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 60 44
D67V5, multiclass
       clus
vv      14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  T0+T1               24                 40
  T2                  23                 50
  T3                  21                 60
  T4                  23                 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"
                    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 220  18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     99    4
  14Q LOSS WILD-TYPE  220   18
   clus
vv  14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  0               99                220
  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  32 223
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     15   97
  14Q LOSS WILD-TYPE   32  223
     clus
vv    14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  NO                15                 32
  YES               97                223
[1] 2 2
[1] FALSE
D67V10, continuous
D67V11, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED    46  66
  14Q LOSS WILD-TYPE  92 163
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     46   66
  14Q LOSS WILD-TYPE   92  163
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  FEMALE               46                 92
  MALE                 66                163
[1] 2 2
[1] FALSE
D67V12, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED    99  13
  14Q LOSS WILD-TYPE 220  34
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     99   13
  14Q LOSS WILD-TYPE  220   34
     clus
vv    14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  NO                99                220
  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   246
D67V13, multiclass
                           clus
vv                          14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  ASIAN                                    1                  4
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                  107                246
[1] 3 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   4 245
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      3  107
  14Q LOSS WILD-TYPE    4  245
                        clus
vv                       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  4
  NOT HISPANIC OR LATINO              107                245
[1] 2 2
[1] FALSE

Clustering(68) Variable = 15Q LOSS MUTATION ANALYSIS
D68V1, survival
                    sevent
clus2                  0   1
  15Q LOSS MUTATED    15  19
  15Q LOSS WILD-TYPE 113 105
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                34                218 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                19                105 
$`15Q LOSS MUTATED`
TCGA-EE-A180 TCGA-3N-A9WD TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3MU TCGA-D3-A5GN 
       31.96        12.99        58.06        40.01        23.67        45.70 
TCGA-D3-A8GC TCGA-D9-A6EC TCGA-DA-A1I1 TCGA-DA-A1IA TCGA-DA-A95V TCGA-DA-A95Z 
       78.21        69.21        68.68        64.83        72.10        12.30 
TCGA-EB-A5KH TCGA-EE-A183 TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A2GH TCGA-EE-A2MC 
       16.41        26.24        27.16        61.12       201.60        23.77 
TCGA-EE-A2MF TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3J7 
      209.79        89.26       145.45        53.26       122.73        45.90 
TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A3EV TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1ZM 
       10.49         7.82        15.48       195.98        27.62        78.61 
TCGA-FS-A1ZT TCGA-GN-A8LK TCGA-W3-AA1R TCGA-W3-AA1V 
       35.28        43.23        79.99         8.09 

$`15Q LOSS WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A8GI TCGA-EB-A5SG TCGA-EE-A20H 
        9.76        62.07        38.76        13.41        33.24       166.75 
TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 TCGA-FR-A729 
      269.03        52.90       134.40        27.35        19.04       216.43 
TCGA-FW-A3R5 TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-3N-A9WC TCGA-BF-AAP0 TCGA-D3-A1Q1 
       36.95        52.73         7.40        60.46        14.83         8.42 
TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       15.72        31.89       110.93        49.35       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-A2JG TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN 
      168.00        86.30       107.61        36.30       171.58        64.83 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO 
       66.08        43.53       140.98        59.70        24.53         9.34 
TCGA-D3-A3MR TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R 
       90.21       173.85        30.67       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       110.53        60.10        58.85        30.44       225.11 
TCGA-DA-A3F8 TCGA-DA-A95W TCGA-DA-A95X TCGA-DA-A95Y TCGA-EB-A44Q TCGA-EB-A5UN 
        8.71         0.76        65.03        14.14         3.91        52.41 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A20C 
       18.21        13.15        24.89        20.38         0.00        75.55 
TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G 
       79.20        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 
       47.41        47.74       346.49       185.19       115.43        30.02 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
       77.98        26.14        12.95        68.65        10.62        32.48 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU 
       18.35        93.63         0.76         0.20        71.31        81.99 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ 
      103.13        15.25         5.75        94.19       171.85        63.25 
TCGA-EE-A2ML TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AC 
      104.78       227.01       143.93        23.51       124.31        64.04 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J8 
        4.41        54.51         6.28        67.89       111.85         3.35 
TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A19A TCGA-ER-A19B 
      168.85        19.86       135.98        34.45         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       184.60       150.12        99.06        59.84 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 
       42.51       120.76        49.71        47.18       146.63        73.05 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES 
       22.36         4.70        16.87        10.19        28.67       173.29 
TCGA-ER-A3ET TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       68.52        32.05        74.47         4.50       174.21         4.14 
TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z3 
       26.20         5.65        10.06       171.78        49.74         8.35 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZQ 
      312.07        32.78        43.92         7.82        36.33       130.95 
TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 
      136.27         4.47        23.21         5.29         3.06        30.90 
TCGA-FS-A4F4 TCGA-FS-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        18.25         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-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-A825 TCGA-W3-A828 TCGA-W3-AA1Q TCGA-W3-AA1W 
        0.33       174.12         1.97       120.07        44.05       185.13 
TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ 
       92.84        47.54        65.42        12.69        21.90        62.89 
TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-XV-AB01 
       10.95        48.39         1.94        37.32        24.99         6.61 
TCGA-YG-AA3O TCGA-Z2-AA3S 
       28.21        91.23 

  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
              7.82               0.00 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
            209.79             346.49 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
             45.80              47.05 
[1] "7.8 - 209.8 (45.8)" "0.0 - 346.5 (47.0)"
[1] "hr=" "1.2"
D68V2, survival
                    sevent
clus2                  0   1
  15Q LOSS MUTATED    21  31
  15Q LOSS WILD-TYPE 145 161
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                52                306 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                31                161 
$`15Q LOSS MUTATED`
TCGA-EB-A5SH TCGA-EE-A180 TCGA-EE-A29L TCGA-3N-A9WD TCGA-D3-A3C6 TCGA-D3-A3CC 
       54.02        94.98         2.60        12.99        58.06        86.93 
TCGA-D3-A3MU TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A8GC TCGA-D3-A8GN TCGA-D9-A148 
       39.75       135.75       137.92        79.59       161.00       151.53 
TCGA-D9-A6EC TCGA-DA-A1I1 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A95V TCGA-DA-A95Z 
       77.56       222.51        53.92        65.92        72.10        13.02 
TCGA-EB-A44R TCGA-EB-A5KH TCGA-EE-A183 TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A2A5 
       10.36        20.35        26.89        56.42        66.74        39.29 
TCGA-EE-A2GH TCGA-EE-A2M5 TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MH TCGA-EE-A2MK 
      220.24        21.67        61.51       268.73        16.96       180.39 
TCGA-EE-A2MM TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-EE-A3JE 
      167.90        53.26       122.73        64.08        53.19        51.35 
TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19E TCGA-ER-A3EV TCGA-FS-A1YX TCGA-FS-A1Z0 
       13.94         9.17        13.02        46.98        48.59       202.65 
TCGA-FS-A1Z4 TCGA-FS-A1ZM TCGA-FS-A1ZT TCGA-GN-A266 TCGA-GN-A4U9 TCGA-GN-A8LK 
       28.08       101.26        53.16        10.13        22.13        50.10 
TCGA-GN-A8LL TCGA-W3-AA1R TCGA-W3-AA1V TCGA-WE-A8JZ 
       21.37       111.09        42.08        24.03 

$`15Q LOSS WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-D3-A8GI TCGA-EB-A5SG 
       27.65        62.07        46.32        13.87        58.52        68.25 
TCGA-EE-A184 TCGA-EE-A20H TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD 
       68.15       168.26       340.14       126.81       134.40        27.35 
TCGA-ER-A193 TCGA-ER-A198 TCGA-FR-A729 TCGA-FS-A1ZF TCGA-FW-A3R5 TCGA-QB-AA9O 
       31.40        50.76       220.80        15.45        36.95        18.05 
TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-3N-A9WB TCGA-3N-A9WC TCGA-BF-AAP0 TCGA-D3-A1Q1 
       61.15        21.40        17.03        66.48        14.93        16.57 
TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       16.67       112.04       112.57        71.80       133.25        28.08 
TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 
       31.59        90.90        95.74        43.43       103.10        65.49 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG 
       23.77       115.53       168.00        86.76        11.87       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-A3CB TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO 
      130.72        46.98       166.52        60.23        24.53         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-A51T TCGA-D3-A5GL TCGA-D3-A5GR 
       32.94        22.62        63.81        26.89       125.79       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-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-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A1X3 
      117.17       167.70        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-A1I2 TCGA-DA-A1I4 
       76.57        36.03       144.89        20.38       176.55        35.93 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
      135.02        88.87        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        43.36        37.35        73.94        14.14        13.87 
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-A185 TCGA-EE-A20B TCGA-EE-A20C 
        8.65        33.73        14.70         4.96       133.81       151.27 
TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D 
       91.56        13.55        63.35        85.08        78.97        13.97 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29R 
       63.78        72.07        64.64        56.84        18.61        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-A2GE 
      115.96        59.64        86.14        59.28        67.43       173.79 
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-A2M6 
       13.91        42.77        81.21        44.88        94.82       129.27 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MI 
       28.83        19.76        47.28       103.27       103.20       204.66 
TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MS 
       96.23       216.66        47.54       248.65        43.23       162.48 
TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
       71.21       124.31        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-A3J8 
       41.59       138.81       172.18       127.20        36.95        34.32 
TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A19A TCGA-ER-A19B 
      201.80       134.33       152.81        35.44        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       302.07       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        44.09       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       105.07        43.82        23.34        20.15 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3PL 
       28.83        48.99        41.56       247.04        93.01        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-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW 
       18.77        38.27        34.82        36.26       104.42       216.92 
TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC 
      228.59        20.91         7.79        27.72        48.85       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-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        17.46 
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        19.43         2.04 
TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 
       15.78       139.89       117.93        96.92        64.44        62.79 
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-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-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8K6 
        4.01        69.07       219.16       105.04        49.05        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-XV-AB01 TCGA-YD-A89C 
       49.51        12.16        40.41        24.99        13.25         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 
            53.590             49.825 
[1] "2.6 - 268.7 (53.6)" "0.2 - 369.9 (49.8)"
[1] "hr=" "1.1"
D68V3, continuous
                    vv
clus                 I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  15Q LOSS MUTATED          1       2       9        2        5        3
  15Q LOSS WILD-TYPE       12       5      20       16       23       23
                    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        29         12
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  15Q LOSS MUTATED            5          4        2
  15Q LOSS WILD-TYPE         30         50       19
D68V4, multiclass
            clus
vv           15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  I/II NOS                  1                 12
  STAGE 0                   2                  5
  STAGE I                   9                 20
  STAGE IA                  2                 16
  STAGE IB                  5                 23
  STAGE II                  3                 23
  STAGE IIA                 0                 14
  STAGE IIB                 1                 18
  STAGE IIC                 5                 10
  STAGE III                10                 29
  STAGE IIIA                3                 12
  STAGE IIIB                5                 30
  STAGE IIIC                4                 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
  15Q LOSS MUTATED       8 16  6 15
  15Q LOSS WILD-TYPE    56 57 75 52
D68V5, multiclass
       clus
vv      15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  T0+T1                8                 56
  T2                  16                 57
  T3                   6                 75
  T4                  15                 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
  15Q LOSS MUTATED    32   8   5   5
  15Q LOSS WILD-TYPE 145  57  34  40
D68V6, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  N0               32                145
  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    48   3
  15Q LOSS WILD-TYPE 271  19
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED     48    3
  15Q LOSS WILD-TYPE  271   19
   clus
vv  15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  0               48                271
  1                3                 19
[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  48
  15Q LOSS WILD-TYPE  41 272
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      6   48
  15Q LOSS WILD-TYPE   41  272
     clus
vv    15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  NO                 6                 41
  YES               48                272
[1] 2 2
[1] FALSE
D68V10, continuous
D68V11, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED    19  35
  15Q LOSS WILD-TYPE 119 194
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED     19   35
  15Q LOSS WILD-TYPE  119  194
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  FEMALE               19                119
  MALE                 35                194
[1] 2 2
[1] FALSE
D68V12, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED    49   5
  15Q LOSS WILD-TYPE 270  42
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED     49    5
  15Q LOSS WILD-TYPE  270   42
     clus
vv    15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  NO                49                270
  YES                5                 42
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  15Q LOSS MUTATED       2                         0    51
  15Q LOSS WILD-TYPE     3                         1   302
D68V13, multiclass
                           clus
vv                          15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  ASIAN                                    2                  3
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   51                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"
D68V14, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED     0  53
  15Q LOSS WILD-TYPE   7 299
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      0   53
  15Q LOSS WILD-TYPE    7  299
                        clus
vv                       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  7
  NOT HISPANIC OR LATINO               53                299
[1] 2 2
[1] FALSE

Clustering(69) Variable = 16P LOSS MUTATION ANALYSIS
D69V1, survival
                    sevent
clus2                  0   1
  16P LOSS MUTATED    23  22
  16P LOSS WILD-TYPE 105 102
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                45                207 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                22                102 
$`16P LOSS MUTATED`
TCGA-EE-A180 TCGA-EE-A2GO TCGA-ER-A193 TCGA-FW-A3R5 TCGA-WE-A8K5 TCGA-D3-A1Q4 
       31.96        52.90        19.04        36.95        52.73        31.89 
TCGA-D3-A1Q5 TCGA-D3-A1QA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JL TCGA-D3-A2JN 
      110.93        76.41       168.00        86.30       171.58        64.83 
TCGA-D3-A2JO TCGA-D3-A3CC TCGA-D3-A8GD TCGA-D3-A8GM TCGA-D9-A6EC TCGA-DA-A1I2 
       66.08        40.01        23.61        70.62        69.21       150.61 
TCGA-DA-A95X TCGA-EE-A181 TCGA-EE-A29D TCGA-EE-A29M TCGA-EE-A29W TCGA-EE-A2GH 
       65.03        20.38        12.99        47.74       185.19       201.60 
TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3JI TCGA-ER-A197 
       89.26       145.45        53.26       122.73       135.98        10.49 
TCGA-ER-A2ND TCGA-FR-A8YC TCGA-FS-A1Z0 TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW 
        4.70        10.06       195.98        35.28         4.47        23.21 
TCGA-FW-A3TU TCGA-GN-A262 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A4U3 TCGA-OD-A75X 
       55.59        53.29        17.06        42.48       120.53       297.01 
TCGA-WE-A8ZQ TCGA-YG-AA3O TCGA-Z2-AA3S 
       62.89        28.21        91.23 

$`16P LOSS WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A8GI TCGA-EB-A5SG TCGA-EE-A20H 
        9.76        62.07        38.76        13.41        33.24       166.75 
TCGA-EE-A2GD TCGA-EE-A2MR TCGA-EE-A3JD TCGA-FR-A729 TCGA-WE-AAA3 TCGA-3N-A9WC 
      269.03       134.40        27.35       216.43         7.40        60.46 
TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       12.99        14.83         8.42        15.72        49.35       133.25 
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-A2JG TCGA-D3-A2JH TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CE 
      107.61        36.30        43.53        58.06       140.98        59.70 
TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F 
       24.53         9.34        90.21        23.67       173.85        30.67 
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-A5GU TCGA-D3-A8GC TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL 
      177.86       124.08        78.21       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-A1HY TCGA-DA-A1I1 TCGA-DA-A1I5 TCGA-DA-A1I7 
       22.85        76.34       138.67        68.68       110.53        60.10 
TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-DA-A95V 
       64.83        58.85        30.44       225.11         8.71        72.10 
TCGA-DA-A95W TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN 
        0.76        14.14        12.30         3.91        16.41        52.41 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20C 
       18.21        13.15        24.89         0.00        26.24        75.55 
TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H 
       79.20        75.22        76.14         0.26        44.28        47.41 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 
       27.16        61.12       346.49       115.43        30.02        77.98 
TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
       26.14        12.95        68.65        10.62        32.48        18.35 
TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 
       93.63         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-A2ML TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AA 
       63.25       104.78       227.01       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-A199 
       45.90         3.35       168.85        19.86        34.45         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       184.60       150.12 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S 
       99.06        59.84        42.51       120.76        49.71        47.18 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
      146.63        73.05        22.36        16.87        10.19        28.67 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A3YN 
      173.29        68.52        15.48        32.05        74.47         4.50 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FS-A1YW TCGA-FS-A1YY 
      174.21         4.14        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        43.92         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-A264 TCGA-GN-A265 
       19.30         9.90        18.25         1.91       117.93        96.92 
TCGA-GN-A26A TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-GN-A8LK TCGA-GN-A9SD TCGA-LH-A9QB 
        7.59        34.49        46.92        43.23        59.41        85.05 
TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 
        7.23         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        47.54 
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-AAA4 TCGA-XV-AB01 
       37.32        24.99         6.61 

  16P LOSS MUTATED 16P LOSS WILD-TYPE 
              4.47               0.00 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
            297.01             346.49 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
             55.59              43.92 
[1] "4.5 - 297.0 (55.6)" "0.0 - 346.5 (43.9)"
[1] "hr=" "1.2"
D69V2, survival
                    sevent
clus2                  0   1
  16P LOSS MUTATED    30  37
  16P LOSS WILD-TYPE 136 155
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                67                291 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                37                155 
$`16P LOSS MUTATED`
TCGA-EE-A180 TCGA-EE-A29L TCGA-EE-A2GO TCGA-ER-A193 TCGA-FW-A3R5 TCGA-QB-AA9O 
       94.98         2.60       126.81        31.40        36.95        18.05 
TCGA-WE-A8K5 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1QA TCGA-D3-A2JB TCGA-D3-A2JC 
       61.15       112.04       112.57        90.90       168.00        86.76 
TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A3BZ TCGA-D3-A3CC TCGA-D3-A51N 
      171.58        66.48        66.08       130.72        86.93        22.62 
TCGA-D3-A8GD TCGA-D3-A8GM TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HW TCGA-DA-A1I2 
       23.61       107.15        25.18        77.56        36.03       176.55 
TCGA-DA-A95X TCGA-EB-A44R TCGA-EB-A5UL TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A20I 
       73.94        10.36        29.29         8.65        33.73        13.55 
TCGA-EE-A29D TCGA-EE-A29M TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2GC 
       13.97        56.84       195.02        17.92        46.82        67.43 
TCGA-EE-A2GH TCGA-EE-A2M5 TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MQ TCGA-EE-A2MU 
      220.24        21.67       180.39       167.90        43.23        53.26 
TCGA-EE-A3AB TCGA-EE-A3J5 TCGA-EE-A3JA TCGA-EE-A3JI TCGA-ER-A197 TCGA-ER-A19E 
      122.73        36.95        53.19       152.81        13.94        13.02 
TCGA-ER-A19T TCGA-ER-A2ND TCGA-FR-A8YC TCGA-FS-A1Z0 TCGA-FS-A1ZT TCGA-FS-A1ZU 
        8.88        23.34        34.82       202.65        53.16        26.56 
TCGA-FS-A1ZW TCGA-FW-A3TU TCGA-GN-A262 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26D 
       49.48        55.59       139.89        64.44        62.79        48.00 
TCGA-GN-A4U3 TCGA-OD-A75X TCGA-WE-A8JZ TCGA-WE-A8ZQ TCGA-YG-AA3O TCGA-YG-AA3P 
      121.91       297.90        24.03        63.22        37.94        14.43 
TCGA-Z2-AA3S 
       96.99 

$`16P LOSS WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-D3-A8GI TCGA-EB-A5SG 
       27.65        62.07        46.32        13.87        58.52        68.25 
TCGA-EB-A5SH TCGA-EE-A184 TCGA-EE-A20H TCGA-EE-A2GD TCGA-EE-A2MR TCGA-EE-A3JD 
       54.02        68.15       168.26       340.14       134.40        27.35 
TCGA-ER-A198 TCGA-FR-A729 TCGA-FS-A1ZF TCGA-WE-AAA3 TCGA-3N-A9WB TCGA-3N-A9WC 
       50.76       220.80        15.45        21.40        17.03        66.48 
TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       12.99        14.93        16.57        16.67        71.80       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 
       28.08        31.59        95.74        43.43       103.10        65.49 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK 
       23.77       115.53        11.87       113.52        42.08        12.10 
TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3CF 
       59.57        58.06        46.98       166.52        60.23        24.53 
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-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GN 
       79.59        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-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-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-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA 
      222.51        35.93       135.02        88.87        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        43.36 
TCGA-DA-A95V TCGA-DA-A95W TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5KH 
       72.10        37.35        14.14        13.02        13.87        20.35 
TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A182 
       58.92         7.04        36.46        29.82        27.22        14.70 
TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29A 
       26.89         4.96       133.81       151.27        91.56        63.35 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29N 
       85.08        78.97        63.78        72.07        64.64        18.61 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V 
       56.42        66.74        14.47        61.28       369.93        25.87 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE 
      115.96        59.64        39.29        86.14        59.28       173.79 
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-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-A2ML TCGA-EE-A2MN 
      103.20        16.96       204.66        96.23       216.66        47.54 
TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AD 
      248.65       162.48        71.21       124.31        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-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A195 
       64.08        34.32       201.80        51.35       134.33        35.44 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19F 
        9.17        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 
      302.07       152.35         6.44       131.51        61.05        44.09 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
      162.08        50.89        49.48       148.18       105.07        43.82 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET 
       20.15        28.83        48.99        41.56       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-A69P TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YD TCGA-FR-A8YE 
       15.72        27.85        18.77        38.27        36.26       104.42 
TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 
      216.92        48.59       228.59        20.91        28.08         7.79 
TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG 
       27.72        48.85       357.37        53.52        46.45         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        17.46        13.51        19.30         9.90        19.43 
TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A26A 
        2.04        15.78       117.93        96.92        10.13        32.48 
TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A8LL 
       39.35        10.42        48.89        22.13        50.10        21.37 
TCGA-GN-A9SD TCGA-HR-A2OG TCGA-HR-A2OH TCGA-LH-A9QB TCGA-QB-A6FS TCGA-RP-A690 
       59.41         0.23        65.88       368.78         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-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-AAA4 TCGA-XV-AB01 TCGA-YD-A89C 
       49.51        12.16        40.41        24.99        13.25         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 
             55.59              50.14 
[1] "2.6 - 297.9 (55.6)" "0.2 - 369.9 (50.1)"
[1] "hr=" "1"  
D69V3, continuous
                    vv
clus                 I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  16P LOSS MUTATED          3       2       4        3        6        2
  16P LOSS WILD-TYPE       10       5      25       15       22       24
                    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        28         12
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  16P LOSS MUTATED            5          8        5
  16P LOSS WILD-TYPE         30         46       16
D69V4, multiclass
            clus
vv           16P LOSS MUTATED 16P LOSS WILD-TYPE
  I/II NOS                  3                 10
  STAGE 0                   2                  5
  STAGE I                   4                 25
  STAGE IA                  3                 15
  STAGE IB                  6                 22
  STAGE II                  2                 24
  STAGE IIA                 2                 12
  STAGE IIB                 8                 11
  STAGE IIC                 3                 12
  STAGE III                11                 28
  STAGE IIIA                3                 12
  STAGE IIIB                5                 30
  STAGE IIIC                8                 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
  16P LOSS MUTATED       9 15 12 18
  16P LOSS WILD-TYPE    55 58 69 49
D69V5, multiclass
       clus
vv      16P LOSS MUTATED 16P LOSS WILD-TYPE
  T0+T1                9                 55
  T2                  15                 58
  T3                  12                 69
  T4                  18                 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
  16P LOSS MUTATED    36  13   6   9
  16P LOSS WILD-TYPE 141  52  33  36
D69V6, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  N0               36                141
  N1               13                 52
  N2                6                 33
  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"
D69V7, binary
                    cls
clus                   0   1
  16P LOSS MUTATED    60   5
  16P LOSS WILD-TYPE 259  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED     60    5
  16P LOSS WILD-TYPE  259   17
   clus
vv  16P LOSS MUTATED 16P LOSS WILD-TYPE
  0               60                259
  1                5                 17
[1] 2 2
[1] FALSE
D69V8, binary
                    cls
clus                   0   1
  16P LOSS MUTATED    31  16
  16P LOSS WILD-TYPE 103  74
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED     31   16
  16P LOSS WILD-TYPE  103   74
     clus
vv    16P LOSS MUTATED 16P LOSS WILD-TYPE
  NO                31                103
  YES               16                 74
[1] 2 2
[1] FALSE
D69V9, binary
                    cls
clus                   0   1
  16P LOSS MUTATED     5  64
  16P LOSS WILD-TYPE  42 256
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      5   64
  16P LOSS WILD-TYPE   42  256
     clus
vv    16P LOSS MUTATED 16P LOSS WILD-TYPE
  NO                 5                 42
  YES               64                256
[1] 2 2
[1] FALSE
D69V10, continuous
D69V11, binary
                    cls
clus                   0   1
  16P LOSS MUTATED    29  40
  16P LOSS WILD-TYPE 109 189
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED     29   40
  16P LOSS WILD-TYPE  109  189
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  FEMALE               29                109
  MALE                 40                189
[1] 2 2
[1] FALSE
D69V12, binary
                    cls
clus                   0   1
  16P LOSS MUTATED    60   9
  16P LOSS WILD-TYPE 259  38
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED     60    9
  16P LOSS WILD-TYPE  259   38
     clus
vv    16P LOSS MUTATED 16P LOSS WILD-TYPE
  NO                60                259
  YES                9                 38
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16P LOSS MUTATED       1                         1    63
  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                                   63                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  65
  16P LOSS WILD-TYPE   4 287
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      3   65
  16P LOSS WILD-TYPE    4  287
                        clus
vv                       16P LOSS MUTATED 16P LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  4
  NOT HISPANIC OR LATINO               65                287
[1] 2 2
[1] FALSE

Clustering(70) Variable = 16Q LOSS MUTATION ANALYSIS
D70V1, survival
                    sevent
clus2                 0  1
  16Q LOSS MUTATED   34 33
  16Q LOSS WILD-TYPE 94 91
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                67                185 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                33                 91 
$`16Q LOSS MUTATED`
TCGA-D3-A2JF TCGA-D3-A8GI TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A2GO TCGA-ER-A193 
       62.07        13.41        33.24        31.96        52.90        19.04 
TCGA-FW-A3R5 TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q7 
       36.95        52.73         7.40        31.89       110.93       133.25 
TCGA-D3-A1QA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
       76.41       168.00        86.30       171.58        64.83        66.08 
TCGA-D3-A3CC TCGA-D3-A8GD TCGA-D3-A8GM TCGA-D9-A3Z3 TCGA-D9-A6EC TCGA-DA-A1I2 
       40.01        23.61        70.62        16.90        69.21       150.61 
TCGA-DA-A3F8 TCGA-DA-A95V TCGA-DA-A95X TCGA-EE-A181 TCGA-EE-A20C TCGA-EE-A29B 
        8.71        72.10        65.03        20.38        75.55        75.22 
TCGA-EE-A29D TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29W TCGA-EE-A2GH TCGA-EE-A2GP 
       12.99        47.74        27.16       185.19       201.60         0.76 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AE 
       63.25        89.26       145.45        53.26       122.73        54.51 
TCGA-EE-A3AF TCGA-EE-A3J4 TCGA-EE-A3JI TCGA-ER-A197 TCGA-ER-A19B TCGA-ER-A19N 
        6.28       111.85       135.98        10.49        53.29        42.51 
TCGA-ER-A19W TCGA-ER-A2ND TCGA-FR-A8YC TCGA-FS-A1Z0 TCGA-FS-A1ZT TCGA-FS-A1ZU 
      146.63         4.70        10.06       195.98        35.28         4.47 
TCGA-FS-A1ZW TCGA-FW-A3TU TCGA-GN-A262 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A4U3 
       23.21        55.59        53.29        17.06        42.48       120.53 
TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-W3-AA1R TCGA-WE-A8ZQ TCGA-YG-AA3O 
       85.05       297.01         7.23        79.99        62.89        28.21 
TCGA-Z2-AA3S 
       91.23 

$`16Q LOSS WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A3C8 TCGA-EE-A20H TCGA-EE-A2GD TCGA-EE-A2MR TCGA-EE-A3JD 
        9.76        38.76       166.75       269.03       134.40        27.35 
TCGA-FR-A729 TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q3 
      216.43        60.46        12.99        14.83         8.42        15.72 
TCGA-D3-A1Q6 TCGA-D3-A1Q8 TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 
       49.35        19.04        62.60        25.64        45.99        62.86 
TCGA-D3-A2JA TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CB 
       15.75       107.61        36.30        43.53        58.06       140.98 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E 
       59.70        24.53         9.34        90.21        23.67       173.85 
TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL 
       30.67       144.46        31.76        62.70        11.34        42.05 
TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D3-A8GC TCGA-D3-A8GJ TCGA-D3-A8GK 
       45.70       177.86       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-A4Z6 
       69.53       135.12        36.53        10.78        15.02        18.44 
TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I5 TCGA-DA-A1I7 
       22.85        76.34       138.67        68.68       110.53        60.10 
TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A95W TCGA-DA-A95Y 
       64.83        58.85        30.44       225.11         0.76        14.14 
TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X 
       12.30         3.91        16.41        52.41        18.21        13.15 
TCGA-EE-A17Y TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29E 
       24.89         0.00        26.24        79.20        76.14         0.26 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A2A1 TCGA-EE-A2A2 
       44.28        47.41        61.12       346.49       115.43        30.02 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
       77.98        26.14        12.95        68.65        10.62        32.48 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 
       18.35        93.63         0.20        71.31        81.99       103.13 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI 
       15.25         5.75        23.77       209.79        94.19       171.85 
TCGA-EE-A2ML TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AC 
      104.78       227.01       143.93        23.51       124.31        64.04 
TCGA-EE-A3AD TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH 
        4.41        67.89        45.90         3.35       168.85        19.86 
TCGA-ER-A195 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19G 
       34.45         7.82         4.54        39.81        11.47       184.60 
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-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES 
       73.05        22.36        16.87        10.19        28.67       173.29 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A 
       68.52        15.48        32.05        74.47         4.50       174.21 
TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z3 
        4.14        26.20         5.65       171.78        49.74         8.35 
TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ 
       27.62       312.07        32.78        43.92         7.82        36.33 
TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 
       78.61       130.95       136.27         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-A4EO TCGA-GF-A6C8 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A26A 
        9.90        18.25         1.91       117.93        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        47.54        65.42        12.69        21.90        10.95 
TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-XV-AB01 
       48.39         1.94        37.32        24.99         6.61 

  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 
             54.51              43.53 
[1] "0.8 - 297.0 (54.5)" "0.0 - 346.5 (43.5)"
[1] "hr=" "1.1"
D70V2, survival
                    sevent
clus2                  0   1
  16Q LOSS MUTATED    45  57
  16Q LOSS WILD-TYPE 121 135
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
               102                256 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                57                135 
$`16Q LOSS MUTATED`
TCGA-D3-A2JF TCGA-D3-A8GI TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A29L TCGA-EE-A2GO 
       62.07        58.52        68.25        94.98         2.60       126.81 
TCGA-ER-A193 TCGA-FS-A1ZF TCGA-FW-A3R5 TCGA-QB-AA9O TCGA-WE-A8K5 TCGA-WE-AAA3 
       31.40        15.45        36.95        18.05        61.15        21.40 
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-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A3BZ TCGA-D3-A3CC TCGA-D3-A51N 
      171.58        66.48        66.08       130.72        86.93        22.62 
TCGA-D3-A8GD TCGA-D3-A8GM TCGA-D3-A8GS TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A3Z3 
       23.61       107.15       117.17       151.53        54.67        22.29 
TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HW TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A3F8 
       25.18        77.56        36.03       176.55        35.93        43.36 
TCGA-DA-A95V TCGA-DA-A95X TCGA-EB-A44R TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A185 
       72.10        73.94        10.36         8.65        33.73         4.96 
TCGA-EE-A20C TCGA-EE-A20I TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29M TCGA-EE-A29P 
      151.27        13.55        85.08        13.97        56.84        56.42 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A5 TCGA-EE-A2GC TCGA-EE-A2GH 
      195.02        17.92        46.82        39.29        67.43       220.24 
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-A197 TCGA-ER-A19B TCGA-ER-A19E 
       36.95        53.19       152.81        13.94        98.40        13.02 
TCGA-ER-A19N TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A2ND TCGA-FR-A8YC TCGA-FS-A1Z0 
       44.09         8.88       148.18        23.34        34.82       202.65 
TCGA-FS-A1ZB TCGA-FS-A1ZP TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A4F2 
       48.85        74.73        53.16        26.56        49.48        50.14 
TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-GN-A262 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26D 
       17.46        55.59       139.89        64.44        62.79        48.00 
TCGA-GN-A4U3 TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-W3-AA1R TCGA-WE-A8JZ 
      121.91       368.78       297.90         7.23       111.09        24.03 
TCGA-WE-A8ZQ TCGA-WE-A8ZX TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-AA3S TCGA-Z2-AA3V 
       63.22        35.80        37.94        14.43        96.99        15.98 

$`16Q LOSS WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EB-A5SH TCGA-EE-A184 TCGA-EE-A20H 
       27.65        46.32        13.87        54.02        68.15       168.26 
TCGA-EE-A2GD TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A198 TCGA-FR-A729 TCGA-3N-A9WB 
      340.14       134.40        27.35        50.76       220.80        17.03 
TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q6 
       66.48        12.99        14.93        16.57        16.67        71.80 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 
       28.08        31.59        95.74        43.43       103.10        65.49 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK 
       23.77       115.53        11.87       113.52        42.08        12.10 
TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3CF 
       59.57        58.06        46.98       166.52        60.23        24.53 
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-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GN 
       79.59        26.43       241.38       170.20        89.13       161.00 
TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GV TCGA-D9-A1JW TCGA-D9-A1JX 
      152.75        29.06       129.63       167.70         3.65         7.10 
TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EG TCGA-DA-A1HV 
       18.12        15.39        18.44         9.90        22.95        76.57 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
      144.89        20.38       222.51       135.02        88.87        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-A95W TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UL 
       37.35        14.14        13.02        13.87        20.35        29.29 
TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A182 
       58.92         7.04        36.46        29.82        27.22        14.70 
TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29E 
       26.89       133.81        91.56        63.35        78.97        63.78 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
       72.07        64.64        18.61        66.74        14.47        61.28 
TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB 
      369.93        25.87       115.96        59.64        86.14        59.28 
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-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M6 
      102.12        42.77        81.21        44.88        94.82       129.27 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG 
       28.83        19.76        61.51       103.27       268.73       103.20 
TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2ML TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MS 
       16.96       204.66       216.66        47.54       248.65       162.48 
TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AG TCGA-EE-A3AH 
       71.21       124.31        64.04        28.77        41.59       138.81 
TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JE TCGA-EE-A3JH 
      172.18        64.08        34.32       201.80        51.35       134.33 
TCGA-ER-A195 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19F 
       35.44         9.17        77.75        48.89        12.59        26.37 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19P 
      302.07       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       105.07        43.82        20.15        28.83 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL 
       48.99        41.56       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-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        19.43 
TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A26A 
        2.04        15.78       117.93        96.92        10.13        32.48 
TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A8LL 
       39.35        10.42        48.89        22.13        50.10        21.37 
TCGA-GN-A9SD TCGA-HR-A2OG TCGA-HR-A2OH TCGA-RP-A690 TCGA-RP-A693 TCGA-RP-A694 
       59.41         0.23        65.88         0.20         0.33         0.69 
TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1Q TCGA-W3-AA1V 
      228.16        63.02       121.08         4.01        69.07        42.08 
TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN 
      219.16       105.04        49.05        17.95       101.33        58.98 
TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 
       70.52        11.80        49.51        12.16        40.41        24.99 
TCGA-XV-AB01 TCGA-YD-A89C TCGA-YD-A9TA TCGA-Z2-A8RT 
       13.25         6.90        49.18        27.58 

  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
               2.6                0.2 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
            368.78             369.93 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
            55.130             49.495 
[1] "2.6 - 368.8 (55.1)" "0.2 - 369.9 (49.5)"
[1] "hr=" "1"  
D70V3, continuous
                    vv
clus                 I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  16Q LOSS MUTATED          3       3       5        7        8        7
  16Q LOSS WILD-TYPE       10       4      24       11       20       19
                    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        28         12
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  16Q LOSS MUTATED            9         13        6
  16Q LOSS WILD-TYPE         26         41       15
D70V4, multiclass
            clus
vv           16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  I/II NOS                  3                 10
  STAGE 0                   3                  4
  STAGE I                   5                 24
  STAGE IA                  7                 11
  STAGE IB                  8                 20
  STAGE II                  7                 19
  STAGE IIA                 2                 12
  STAGE IIB                 9                 10
  STAGE IIC                 7                  8
  STAGE III                11                 28
  STAGE IIIA                3                 12
  STAGE IIIB                9                 26
  STAGE IIIC               13                 41
  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 17 20 26
  16Q LOSS WILD-TYPE    47 56 61 41
D70V5, multiclass
       clus
vv      16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  T0+T1               17                 47
  T2                  17                 56
  T3                  20                 61
  T4                  26                 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"
                    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 231  15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED     88    7
  16Q LOSS WILD-TYPE  231   15
   clus
vv  16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  0               88                231
  1                7                 15
[1] 2 2
[1] FALSE
D70V8, binary
                    cls
clus                  0  1
  16Q LOSS MUTATED   45 27
  16Q LOSS WILD-TYPE 89 63
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED     45   27
  16Q LOSS WILD-TYPE   89   63
     clus
vv    16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  NO                45                 89
  YES               27                 63
[1] 2 2
[1] FALSE
D70V9, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED    10  95
  16Q LOSS WILD-TYPE  37 225
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED     10   95
  16Q LOSS WILD-TYPE   37  225
     clus
vv    16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  NO                10                 37
  YES               95                225
[1] 2 2
[1] FALSE
D70V10, continuous
D70V11, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED    46  59
  16Q LOSS WILD-TYPE  92 170
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED     46   59
  16Q LOSS WILD-TYPE   92  170
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  FEMALE               46                 92
  MALE                 59                170
[1] 2 2
[1] FALSE
D70V12, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED    91  14
  16Q LOSS WILD-TYPE 228  33
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED     91   14
  16Q LOSS WILD-TYPE  228   33
     clus
vv    16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  NO                91                228
  YES               14                 33
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16Q LOSS MUTATED       1                         1    99
  16Q LOSS WILD-TYPE     4                         0   254
D70V13, multiclass
                           clus
vv                          16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  ASIAN                                    1                  4
  BLACK OR AFRICAN AMERICAN                1                  0
  WHITE                                   99                254
[1] 3 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     3 101
  16Q LOSS WILD-TYPE   4 251
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      3  101
  16Q LOSS WILD-TYPE    4  251
                        clus
vv                       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  4
  NOT HISPANIC OR LATINO              101                251
[1] 2 2
[1] FALSE

Clustering(71) Variable = 17P LOSS MUTATION ANALYSIS
D71V1, survival
                    sevent
clus2                 0  1
  17P LOSS MUTATED   39 39
  17P LOSS WILD-TYPE 89 85
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                78                174 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                39                 85 
$`17P LOSS MUTATED`
TCGA-D3-A8GI TCGA-EE-A180 TCGA-EE-A2MR TCGA-ER-A193 TCGA-FR-A729 TCGA-FW-A3R5 
       13.41        31.96       134.40        19.04       216.43        36.95 
TCGA-WE-AAA3 TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1QA TCGA-D3-A2J6 TCGA-D3-A2JB 
        7.40        60.46        12.99        76.41        25.64       168.00 
TCGA-D3-A2JG TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A3MO TCGA-D3-A51T 
      107.61       171.58        64.83        66.08         9.34        11.34 
TCGA-D3-A8GC TCGA-D3-A8GL TCGA-DA-A1HY TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A3F5 
       78.21        69.53       138.67       150.61       110.53       225.11 
TCGA-DA-A95X TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A20C TCGA-EE-A29C TCGA-EE-A29E 
       65.03        52.41        13.15        75.55        76.14         0.26 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29T TCGA-EE-A2A1 TCGA-EE-A2A2 
       44.28        47.41        47.74       346.49       115.43        30.02 
TCGA-EE-A2GJ TCGA-EE-A2GP TCGA-EE-A2M6 TCGA-EE-A2MC TCGA-EE-A2MG TCGA-EE-A2MP 
       68.65         0.76       103.13        23.77        94.19       227.01 
TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3J7 TCGA-EE-A3J8 
      143.93        53.26       124.31        64.04        45.90         3.35 
TCGA-EE-A3JB TCGA-EE-A3JH TCGA-ER-A195 TCGA-ER-A199 TCGA-ER-A19C TCGA-ER-A19S 
      168.85        19.86        34.45         7.82        39.81        47.18 
TCGA-ER-A2NG TCGA-ER-A3EV TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A8YC TCGA-FS-A1Z4 
       28.67        15.48         4.50       174.21        10.06        27.62 
TCGA-FS-A1ZJ TCGA-FS-A1ZQ TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY 
       36.33       130.95        35.28         4.47        23.21         5.29 
TCGA-FS-A4F9 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A4U3 TCGA-W3-AA1R 
       13.28        96.92        17.06        42.48       120.53        79.99 
TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-YG-AA3O 
       92.84        47.54        48.39         1.94        37.32        28.21 

$`17P LOSS WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A20H TCGA-EE-A2GD 
        9.76        62.07        38.76        33.24       166.75       269.03 
TCGA-EE-A2GO TCGA-EE-A3JD TCGA-WE-A8K5 TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q3 
       52.90        27.35        52.73        14.83         8.42        15.72 
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QB 
       31.89       110.93        49.35       133.25        19.04        62.60 
TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JH TCGA-D3-A2JP 
       45.99        62.86        15.75        86.30        36.30        43.53 
TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MR 
       58.06       140.98        40.01        59.70        24.53        90.21 
TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R 
       23.67       173.85        30.67       144.46        31.76        62.70 
TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D3-A8GD TCGA-D3-A8GJ 
       42.05        45.70       177.86       124.08        23.61       179.97 
TCGA-D3-A8GK TCGA-D3-A8GM TCGA-D3-A8GP TCGA-D3-A8GR TCGA-D9-A1X3 TCGA-D9-A3Z1 
      120.00        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        68.68 
TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F8 TCGA-DA-A95V 
       60.10        64.83        58.85        30.44         8.71        72.10 
TCGA-DA-A95W TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A6L9 
        0.76        14.14        12.30         3.91        16.41        18.21 
TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20F TCGA-EE-A29B 
       24.89        20.38         0.00        26.24        79.20        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-A2GE TCGA-EE-A2GH TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN 
       12.95       201.60        10.62        32.48        18.35        93.63 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MF 
        0.20        71.31        81.99        15.25         5.75       209.79 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MT 
      171.85        63.25        89.26       104.78       145.45        23.51 
TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 
      122.73         4.41        54.51         6.28        67.89       111.85 
TCGA-EE-A3JI TCGA-ER-A197 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19G 
      135.98        10.49         4.54        53.29        11.47       184.60 
TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
      150.12        99.06        59.84        42.51       120.76        49.71 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF 
      146.63        73.05        22.36         4.70        16.87        10.19 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A69P TCGA-FR-A7U8 
      173.29        68.52        32.05        74.47         4.14        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-A1ZG TCGA-FS-A1ZM TCGA-FS-A1ZS TCGA-FS-A1ZZ 
       32.78        43.92         7.82        78.61       136.27         3.06 
TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV 
       30.90        66.67       173.19        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        18.25         1.91        53.29       117.93 
TCGA-GN-A26A TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-GN-A8LK TCGA-GN-A9SD TCGA-LH-A9QB 
        7.59        34.49        46.92        43.23        59.41        85.05 
TCGA-OD-A75X TCGA-QB-A6FS TCGA-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-AA1V TCGA-W3-AA1W TCGA-WE-A8ZM TCGA-WE-A8ZN 
      120.07        44.05         8.09       185.13        65.42        12.69 
TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-AAA4 TCGA-XV-AB01 TCGA-Z2-AA3S 
       21.90        62.89        10.95        24.99         6.61        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 
            47.475             44.875 
[1] "0.3 - 346.5 (47.5)" "0.0 - 312.1 (44.9)"
[1] "hr=" "1"  
D71V2, survival
                    sevent
clus2                  0   1
  17P LOSS MUTATED    55  65
  17P LOSS WILD-TYPE 111 127
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               120                238 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                65                127 
$`17P LOSS MUTATED`
TCGA-D3-A3ML TCGA-D3-A8GI TCGA-EE-A180 TCGA-EE-A184 TCGA-EE-A29L TCGA-EE-A2MR 
       13.87        58.52        94.98        68.15         2.60       134.40 
TCGA-ER-A193 TCGA-FR-A729 TCGA-FW-A3R5 TCGA-QB-AA9O TCGA-WE-AAA3 TCGA-3N-A9WB 
       31.40       220.80        36.95        18.05        21.40        17.03 
TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1QA TCGA-D3-A2J6 TCGA-D3-A2JB TCGA-D3-A2JD 
       66.48        12.99        90.90        43.43       168.00        11.87 
TCGA-D3-A2JG TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A3MO TCGA-D3-A51N 
      113.52       171.58        66.48        66.08         9.34        22.62 
TCGA-D3-A51T TCGA-D3-A5GO TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GL TCGA-D3-A8GN 
       26.89       137.92        30.84        79.59        89.13       161.00 
TCGA-D9-A148 TCGA-D9-A1JW TCGA-D9-A6EA TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I2 
      151.53         3.65        25.18        36.03       144.89       176.55 
TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A95X TCGA-EB-A44R 
      135.02        53.92        10.49       225.96        73.94        10.36 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A29C 
       29.29        58.92        29.82         4.96       151.27        78.97 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29S TCGA-EE-A29T 
       63.78        72.07        64.64        56.84        61.28       369.93 
TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2GC 
       25.87        17.92       115.96        59.64        39.29        67.43 
TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GP TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2M6 
       48.72       107.38        13.91        44.88        21.67       129.27 
TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2MG TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ 
       61.51        47.28       103.20        47.54       248.65        43.23 
TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3J5 TCGA-EE-A3J7 
      162.48        53.26       124.31        64.04        36.95        64.08 
TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH TCGA-ER-A195 TCGA-ER-A199 TCGA-ER-A19C 
       34.32       201.80       134.33        35.44         9.17        48.89 
TCGA-ER-A19S TCGA-ER-A2NG TCGA-ER-A3EV TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A7U9 
       49.48        48.99        46.98        92.98       174.21        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-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A4U3 
       17.46        96.92        10.13        64.44        62.79       121.91 
TCGA-GN-A4U9 TCGA-HR-A2OG TCGA-W3-AA1R TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K1 
       22.13         0.23       111.09       105.04        24.03        49.05 
TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-YG-AA3O TCGA-Z2-AA3V 
       35.80        49.51        12.16        40.41        37.94        15.98 

$`17P LOSS WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A20H 
       27.65        62.07        46.32        68.25        54.02       168.26 
TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A3JD TCGA-ER-A198 TCGA-FS-A1ZF TCGA-WE-A8K5 
      340.14       126.81        27.35        50.76        15.45        61.15 
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-A2JH TCGA-D3-A2JK TCGA-D3-A2JP 
       23.77       115.53        86.76        42.08        12.10        59.57 
TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE 
      130.72        58.06        46.98       166.52        86.93        60.23 
TCGA-D3-A3CF TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F 
       24.53       103.59        39.75        45.30       174.84        55.73 
TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A5GL TCGA-D3-A5GN 
       56.35       145.12        32.94        63.81       125.79       135.75 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GJ 
      178.32        18.18       125.19        23.61        26.43       241.38 
TCGA-D3-A8GK TCGA-D3-A8GM TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS 
      170.20       107.15       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-A6E9 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1I0 
       18.44         9.90        77.56        22.95        76.57        20.38 
TCGA-DA-A1I1 TCGA-DA-A1I4 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
      222.51        35.93        88.87        65.92        40.60        68.09 
TCGA-DA-A3F2 TCGA-DA-A3F8 TCGA-DA-A95V TCGA-DA-A95W TCGA-DA-A95Y TCGA-DA-A95Z 
       33.93        43.36        72.10        37.35        14.14        13.02 
TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17Y TCGA-EE-A17Z 
       13.87        20.35         7.04        36.46        27.22         8.65 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20I 
       33.73        14.70        26.89       133.81        91.56        13.55 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
       63.35        85.08        13.97        18.61        56.42        66.74 
TCGA-EE-A29R TCGA-EE-A29W TCGA-EE-A2A0 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE 
       14.47       195.02        46.82        86.14        59.28       173.79 
TCGA-EE-A2GH TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GR 
      220.24        54.74        79.66        75.48       102.12        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-A3AE TCGA-EE-A3AF TCGA-EE-A3AG 
       71.21       122.73        28.77        54.51        13.81        41.59 
TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3JA TCGA-EE-A3JE TCGA-EE-A3JI 
      138.81       172.18       127.20        53.19        51.35       152.81 
TCGA-ER-A197 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F 
       13.94        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 
      302.07       152.35         6.44       131.51        61.05        44.09 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
      162.08        50.89         8.88       148.18       105.07        43.82 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET 
       23.34        20.15        28.83        41.56       247.04        93.01 
TCGA-ER-A3PL TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A7UA 
       33.21        12.95       149.03        15.72        27.85        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-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-A1ZG TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZS 
        9.70        23.93       101.26        74.73        11.41       148.80 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4FB 
       27.02        77.82        66.67        28.73       174.84        26.73 
TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
       54.41        80.68        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-A26A 
       19.43         2.04        15.78       139.89       117.93        32.48 
TCGA-GN-A26D TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A8LK TCGA-GN-A8LL 
       48.00        39.35        10.42        48.89        50.10        21.37 
TCGA-GN-A9SD TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 
       59.41        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-AA1V TCGA-W3-AA1W TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN 
       69.07        42.08       219.16        17.95       101.33        58.98 
TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-AAA4 TCGA-XV-AB01 TCGA-YD-A89C 
       70.52        63.22        11.80        24.99        13.25         6.90 
TCGA-YD-A9TA TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S 
       49.18        14.43        27.58        96.99 

  17P LOSS MUTATED 17P LOSS WILD-TYPE 
              0.23               0.20 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
            369.93             368.78 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
            49.480             54.215 
[1] "0.2 - 369.9 (49.5)" "0.2 - 368.8 (54.2)"
[1] "hr=" "1.1"
D71V3, continuous
                    vv
clus                 I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  17P LOSS MUTATED          5       3      15        9       10        5
  17P LOSS WILD-TYPE        8       4      14        9       18       21
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  17P LOSS MUTATED           4         6         4        14          7
  17P LOSS WILD-TYPE        10        13        11        25          8
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  17P LOSS MUTATED           10         18        4
  17P LOSS WILD-TYPE         25         36       17
D71V4, multiclass
            clus
vv           17P LOSS MUTATED 17P LOSS WILD-TYPE
  I/II NOS                  5                  8
  STAGE 0                   3                  4
  STAGE I                  15                 14
  STAGE IA                  9                  9
  STAGE IB                 10                 18
  STAGE II                  5                 21
  STAGE IIA                 4                 10
  STAGE IIB                 6                 13
  STAGE IIC                 4                 11
  STAGE III                14                 25
  STAGE IIIA                7                  8
  STAGE IIIB               10                 25
  STAGE IIIC               18                 36
  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      21 30 24 24
  17P LOSS WILD-TYPE    43 43 57 43
D71V5, multiclass
       clus
vv      17P LOSS MUTATED 17P LOSS WILD-TYPE
  T0+T1               21                 43
  T2                  30                 43
  T3                  24                 57
  T4                  24                 43
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  17P LOSS MUTATED    61  23  13  15
  17P LOSS WILD-TYPE 116  42  26  30
D71V6, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  N0               61                116
  N1               23                 42
  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"
D71V7, binary
                    cls
clus                   0   1
  17P LOSS MUTATED   113   5
  17P LOSS WILD-TYPE 206  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED    113    5
  17P LOSS WILD-TYPE  206   17
   clus
vv  17P LOSS MUTATED 17P LOSS WILD-TYPE
  0              113                206
  1                5                 17
[1] 2 2
[1] FALSE
D71V8, binary
                    cls
clus                  0  1
  17P LOSS MUTATED   55 31
  17P LOSS WILD-TYPE 79 59
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     55   31
  17P LOSS WILD-TYPE   79   59
     clus
vv    17P LOSS MUTATED 17P LOSS WILD-TYPE
  NO                55                 79
  YES               31                 59
[1] 2 2
[1] FALSE
D71V9, binary
                    cls
clus                   0   1
  17P LOSS MUTATED    13 111
  17P LOSS WILD-TYPE  34 209
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     13  111
  17P LOSS WILD-TYPE   34  209
     clus
vv    17P LOSS MUTATED 17P LOSS WILD-TYPE
  NO                13                 34
  YES              111                209
[1] 2 2
[1] FALSE
D71V10, continuous
D71V11, binary
                    cls
clus                   0   1
  17P LOSS MUTATED    37  87
  17P LOSS WILD-TYPE 101 142
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     37   87
  17P LOSS WILD-TYPE  101  142
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  FEMALE               37                101
  MALE                 87                142
[1] 2 2
[1] FALSE
D71V12, binary
                    cls
clus                   0   1
  17P LOSS MUTATED   112  12
  17P LOSS WILD-TYPE 207  35
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED    112   12
  17P LOSS WILD-TYPE  207   35
     clus
vv    17P LOSS MUTATED 17P LOSS WILD-TYPE
  NO               112                207
  YES               12                 35
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  17P LOSS MUTATED       1                         1   119
  17P LOSS WILD-TYPE     4                         0   234
D71V13, multiclass
                           clus
vv                          17P LOSS MUTATED 17P LOSS WILD-TYPE
  ASIAN                                    1                  4
  BLACK OR AFRICAN AMERICAN                1                  0
  WHITE                                  119                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"
D71V14, binary
                    cls
clus                   0   1
  17P LOSS MUTATED     1 120
  17P LOSS WILD-TYPE   6 232
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      1  120
  17P LOSS WILD-TYPE    6  232
                        clus
vv                       17P LOSS MUTATED 17P LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO              120                232
[1] 2 2
[1] FALSE

Clustering(72) Variable = 17Q LOSS MUTATION ANALYSIS
D72V1, survival
                    sevent
clus2                  0   1
  17Q LOSS MUTATED    17  22
  17Q LOSS WILD-TYPE 111 102
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                39                213 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                22                102 
$`17Q LOSS MUTATED`
TCGA-D3-A8GI TCGA-EE-A180 TCGA-ER-A193 TCGA-FR-A729 TCGA-FW-A3R5 TCGA-3N-A9WD 
       13.41        31.96        19.04       216.43        36.95        12.99 
TCGA-D3-A2J6 TCGA-D3-A2JG TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D9-A6EC TCGA-DA-A1I2 
       25.64       107.61        64.83        66.08        69.21       150.61 
TCGA-DA-A1I5 TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A2GP TCGA-EE-A2M6 TCGA-EE-A2MC 
      110.53        76.14         0.26         0.76       103.13        23.77 
TCGA-EE-A2MG TCGA-EE-A2MP TCGA-EE-A3AA TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB 
       94.19       227.01       124.31        45.90         3.35       168.85 
TCGA-EE-A3JH TCGA-ER-A19C TCGA-ER-A19L TCGA-ER-A19S TCGA-FR-A8YC TCGA-FS-A1Z4 
       19.86        39.81        99.06        47.18        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-WE-A8ZY TCGA-WE-AA9Y TCGA-YG-AA3O 
       48.39         1.94        28.21 

$`17Q LOSS WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A20H TCGA-EE-A2GD 
        9.76        62.07        38.76        33.24       166.75       269.03 
TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-3N-A9WC 
       52.90       134.40        27.35        52.73         7.40        60.46 
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-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-A2JH TCGA-D3-A2JL TCGA-D3-A2JP 
       15.75       168.00        86.30        36.30       171.58        43.53 
TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO 
       58.06       140.98        40.01        59.70        24.53         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K 
       90.21        23.67       173.85        30.67       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-A1I7 TCGA-DA-A1IA 
       22.85        76.34       138.67        68.68        60.10        64.83 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-DA-A95V TCGA-DA-A95W 
       58.85        30.44       225.11         8.71        72.10         0.76 
TCGA-DA-A95X TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN 
       65.03        14.14        12.30         3.91        16.41        52.41 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
       18.21        13.15        24.89        20.38         0.00        26.24 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29H 
       75.55        79.20        75.22        12.99        44.28        47.41 
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-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ 
       30.02        77.98        26.14        12.95       201.60        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        93.63         0.20        71.31 
TCGA-EE-A2GU TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MF TCGA-EE-A2MI TCGA-EE-A2MJ 
       81.99        15.25         5.75       209.79       171.85        63.25 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU 
       89.26       104.78       145.45       143.93        23.51        53.26 
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-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A 
      111.85       135.98        34.45        10.49         7.82         4.54 
TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19M TCGA-ER-A19N 
       53.29        11.47       184.60       150.12        59.84        42.51 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
      120.76        49.71       146.63        73.05        22.36         4.70 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
       16.87        10.19        28.67       173.29        68.52        15.48 
TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A7U8 
       32.05        74.47         4.50       174.21         4.14        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-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZS 
       32.78        43.92         7.82        36.33        78.61       136.27 
TCGA-FS-A1ZU TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4FD 
        4.47         3.06        30.90        66.67       173.19        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        18.25         1.91 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 
       53.29       117.93        96.92        42.48         7.59       120.53 
TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-GN-A8LK TCGA-GN-A9SD TCGA-LH-A9QB TCGA-OD-A75X 
       34.49        46.92        43.23        59.41        85.05       297.01 
TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 
        7.23         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        47.54 
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        37.32 
TCGA-WE-AAA4 TCGA-XV-AB01 TCGA-Z2-AA3S 
       24.99         6.61        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 
             36.95              47.54 
[1] "0.3 - 227.0 (37.0)" "0.0 - 346.5 (47.5)"
[1] "hr=" "1.3"
D72V2, survival
                    sevent
clus2                  0   1
  17Q LOSS MUTATED    25  33
  17Q LOSS WILD-TYPE 141 159
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                58                300 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                33                159 
$`17Q LOSS MUTATED`
TCGA-D3-A8GI TCGA-EE-A180 TCGA-ER-A193 TCGA-FR-A729 TCGA-FW-A3R5 TCGA-QB-AA9O 
       58.52        94.98        31.40       220.80        36.95        18.05 
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-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HW TCGA-DA-A1I2 
       66.08        22.62        25.18        77.56        36.03       176.55 
TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29X TCGA-EE-A2A5 
      135.02        53.92        78.97        63.78        17.92        39.29 
TCGA-EE-A2GI TCGA-EE-A2GP TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2MC 
       48.72        13.91        44.88        21.67       129.27        61.51 
TCGA-EE-A2MG TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A3AA TCGA-EE-A3J7 TCGA-EE-A3J8 
      103.20       248.65        43.23       124.31        64.08        34.32 
TCGA-EE-A3JB TCGA-EE-A3JH TCGA-ER-A19C TCGA-ER-A19L TCGA-ER-A19S TCGA-FR-A7U9 
      201.80       134.33        48.89       131.51        49.48        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-GN-A267 TCGA-WE-A8ZX 
       27.09        50.14        34.03        17.46        64.44        35.80 
TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-YG-AA3O TCGA-Z2-AA3V 
       49.51        12.16        37.94        15.98 

$`17Q LOSS WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EB-A5SG TCGA-EB-A5SH 
       27.65        62.07        46.32        13.87        68.25        54.02 
TCGA-EE-A184 TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR 
       68.15       168.26         2.60       340.14       126.81       134.40 
TCGA-EE-A3JD TCGA-ER-A198 TCGA-FS-A1ZF TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-3N-A9WC 
       27.35        50.76        15.45        61.15        21.40        66.48 
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-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-A2JH 
       65.49        23.77       115.53       168.00        86.76        42.08 
TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 
       12.10       171.58        59.57       130.72        58.06        46.98 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR 
      166.52        86.93        60.23        24.53         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-A8GD 
      178.32        18.18       125.19        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-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-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-A1I4 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
      222.51        35.93        88.87        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        43.36        72.10        37.35 
TCGA-DA-A95X TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH 
       73.94        14.14        13.02        13.87        10.36        20.35 
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-A185 TCGA-EE-A20B 
        8.65        33.73        14.70        26.89         4.96       133.81 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29D 
      151.27        91.56        13.55        63.35        85.08        13.97 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
       72.07        64.64        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-A2A0 
       14.47        61.28       369.93        25.87       195.02        46.82 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GE 
      115.96        59.64        86.14        59.28        67.43       173.79 
TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN 
      220.24       107.38        54.74        79.66        75.48       102.12 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MD 
       42.77        81.21        94.82        28.83        19.76        47.28 
TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK 
      103.27       268.73        16.96       204.66        96.23       180.39 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU 
      216.66       167.90        47.54       162.48        71.21        53.26 
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-A3JA TCGA-EE-A3JE 
      138.81       172.18       127.20        36.95        53.19        51.35 
TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B 
      152.81        35.44        13.94         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       302.07       152.35         6.44 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19T TCGA-ER-A19W 
       61.05        44.09       162.08        50.89         8.88       148.18 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
      105.07        43.82        23.34        20.15        28.83        48.99 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K 
       41.56       247.04        93.01        46.98        33.21        12.95 
TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A7UA 
      149.03        92.98       174.21        15.72        27.85        38.27 
TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
       36.26       104.42       216.92        48.59       228.59       202.65 
TCGA-FS-A1Z3 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD 
       20.91         7.79        27.72        48.85       357.37        53.52 
TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP 
       46.45         9.70        47.38        23.93       101.26        74.73 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 
       11.41       148.80        26.56        27.02        77.82        66.67 
TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3TU 
       28.73       174.84        26.73        54.41        80.68        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        19.43         2.04        15.78 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A268 TCGA-GN-A26A 
      139.89       117.93        96.92        10.13        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-A8K6 TCGA-WE-A8ZM 
      219.16       105.04        24.03        49.05        17.95       101.33 
TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-AAA0 TCGA-WE-AAA4 
       58.98        70.52        63.22        11.80        40.41        24.99 
TCGA-XV-AB01 TCGA-YD-A89C TCGA-YD-A9TA TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S 
       13.25         6.90        49.18        14.43        27.58        96.99 

  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
             11.87               0.20 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
            248.65             369.93 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
            48.805             54.460 
[1] "11.9 - 248.7 (48.8)" "0.2 - 369.9 (54.5)" 
[1] "hr=" "1.2"
D72V3, continuous
                    vv
clus                 I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  17Q LOSS MUTATED          3       1       9        4        4        0
  17Q LOSS WILD-TYPE       10       6      20       14       24       26
                    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        32          9
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  17Q LOSS MUTATED            5          7        4
  17Q LOSS WILD-TYPE         30         47       17
D72V4, multiclass
            clus
vv           17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  I/II NOS                  3                 10
  STAGE 0                   1                  6
  STAGE I                   9                 20
  STAGE IA                  4                 14
  STAGE IB                  4                 24
  STAGE II                  0                 26
  STAGE IIA                 2                 12
  STAGE IIB                 4                 15
  STAGE IIC                 2                 13
  STAGE III                 7                 32
  STAGE IIIA                6                  9
  STAGE IIIB                5                 30
  STAGE IIIC                7                 47
  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      12 15 13 10
  17Q LOSS WILD-TYPE    52 58 68 57
D72V5, multiclass
       clus
vv      17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  T0+T1               12                 52
  T2                  15                 58
  T3                  13                 68
  T4                  10                 57
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  17Q LOSS MUTATED    29  14   5   7
  17Q LOSS WILD-TYPE 148  51  34  38
D72V6, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  N0               29                148
  N1               14                 51
  N2                5                 34
  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"
D72V7, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED    54   4
  17Q LOSS WILD-TYPE 265  18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     54    4
  17Q LOSS WILD-TYPE  265   18
   clus
vv  17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  0               54                265
  1                4                 18
[1] 2 2
[1] FALSE
D72V8, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED    28  14
  17Q LOSS WILD-TYPE 106  76
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     28   14
  17Q LOSS WILD-TYPE  106   76
     clus
vv    17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  NO                28                106
  YES               14                 76
[1] 2 2
[1] FALSE
D72V9, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED     7  55
  17Q LOSS WILD-TYPE  40 265
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      7   55
  17Q LOSS WILD-TYPE   40  265
     clus
vv    17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  NO                 7                 40
  YES               55                265
[1] 2 2
[1] FALSE
D72V10, continuous
D72V11, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED    20  42
  17Q LOSS WILD-TYPE 118 187
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     20   42
  17Q LOSS WILD-TYPE  118  187
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  FEMALE               20                118
  MALE                 42                187
[1] 2 2
[1] FALSE
D72V12, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED    58   4
  17Q LOSS WILD-TYPE 261  43
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     58    4
  17Q LOSS WILD-TYPE  261   43
     clus
vv    17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  NO                58                261
  YES                4                 43
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  17Q LOSS MUTATED       0                         0    61
  17Q LOSS WILD-TYPE     5                         1   292
D72V13, multiclass
                           clus
vv                          17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  ASIAN                                    0                  5
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   61                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"
D72V14, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED     1  61
  17Q LOSS WILD-TYPE   6 291
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      1   61
  17Q LOSS WILD-TYPE    6  291
                        clus
vv                       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO               61                291
[1] 2 2
[1] FALSE

Clustering(73) Variable = 18P LOSS MUTATION ANALYSIS
D73V1, survival
                    sevent
clus2                 0  1
  18P LOSS MUTATED   38 37
  18P LOSS WILD-TYPE 90 87
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                75                177 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                37                 87 
$`18P LOSS MUTATED`
TCGA-D3-A2JF TCGA-D3-A8GI TCGA-EB-A5SG TCGA-EE-A2GD TCGA-ER-A193 TCGA-D3-A1Q1 
       62.07        13.41        33.24       269.03        19.04         8.42 
TCGA-D3-A1Q6 TCGA-D3-A2J7 TCGA-D3-A2JC TCGA-D3-A2JL TCGA-D3-A2JO TCGA-D3-A2JP 
       49.35        45.99        86.30       171.58        66.08        43.53 
TCGA-D3-A3C6 TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51J TCGA-D3-A5GL TCGA-D3-A5GR 
       58.06        90.21        23.67       144.46        42.05       177.86 
TCGA-D3-A5GU TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GR TCGA-D9-A1X3 TCGA-D9-A6EG 
      124.08        78.21        23.61        36.53        10.78        22.85 
TCGA-DA-A1HV TCGA-DA-A1I2 TCGA-DA-A1I7 TCGA-DA-A3F5 TCGA-EB-A5UN TCGA-EE-A20C 
       76.34       150.61        60.10       225.11        52.41        75.55 
TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29M TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2GE 
       12.99        44.28        47.74       346.49       185.19        12.95 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2MG TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MS 
        0.76         0.20        94.19        89.26       145.45       143.93 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3J3 
       53.26       124.31       122.73         4.41        54.51        67.89 
TCGA-EE-A3J8 TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19C 
        3.35        19.86       135.98         7.82        53.29        39.81 
TCGA-ER-A19H TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A42L TCGA-FR-A44A TCGA-FR-A69P 
      150.12        49.71        47.18        74.47       174.21         4.14 
TCGA-FR-A7U8 TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZW TCGA-FS-A1ZY 
       26.20        78.61       130.95       136.27        23.21         5.29 
TCGA-FW-A3TU TCGA-GN-A268 TCGA-GN-A8LK TCGA-GN-A9SD TCGA-W3-A825 TCGA-WE-A8K1 
       55.59        42.48        43.23        59.41         1.97        47.54 
TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-YG-AA3O 
       48.39         1.94        28.21 

$`18P LOSS WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A3C8 TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GO TCGA-EE-A2MR 
        9.76        38.76        31.96       166.75        52.90       134.40 
TCGA-EE-A3JD TCGA-FR-A729 TCGA-FW-A3R5 TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-3N-A9WC 
       27.35       216.43        36.95        52.73         7.40        60.46 
TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q7 
       12.99        14.83        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-A2JG TCGA-D3-A2JH TCGA-D3-A2JN TCGA-D3-A3CB TCGA-D3-A3CC 
      168.00       107.61        36.30        64.83       140.98        40.01 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51K 
       59.70        24.53         9.34       173.85        30.67        31.76 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL 
       62.70        11.34        45.70       179.97       120.00        69.53 
TCGA-D3-A8GM TCGA-D3-A8GP TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6EC 
       70.62       135.12        15.02        16.90        18.44        69.21 
TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I5 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 
      138.67        68.68       110.53        64.83        58.85        30.44 
TCGA-DA-A3F8 TCGA-DA-A95V TCGA-DA-A95W TCGA-DA-A95X TCGA-DA-A95Y TCGA-DA-A95Z 
        8.71        72.10         0.76        65.03        14.14        12.30 
TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A181 
        3.91        16.41        18.21        13.15        24.89        20.38 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E 
        0.00        26.24        79.20        75.22        76.14         0.26 
TCGA-EE-A29H TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 
       47.41        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-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 
       93.63        71.31        81.99       103.13        15.25         5.75 
TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MP 
       23.77       209.79       171.85        63.25       104.78       227.01 
TCGA-EE-A2MT TCGA-EE-A3AC TCGA-EE-A3AF TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3JB 
       23.51        64.04         6.28       111.85        45.90       168.85 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A19A TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19L 
       34.45        10.49         4.54        11.47       184.60        99.06 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
       59.84        42.51       120.76       146.63        73.05        22.36 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET 
        4.70        16.87        10.19        28.67       173.29        68.52 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FS-A1YW 
       15.48        32.05         4.50         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-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZZ 
       43.92         7.82        36.33        35.28         4.47         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-A262 TCGA-GN-A264 
       19.30         9.90        18.25         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-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-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-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        37.32 
TCGA-WE-AAA4 TCGA-XV-AB01 TCGA-Z2-AA3S 
       24.99         6.61        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 
             52.41              38.76 
[1] "0.2 - 346.5 (52.4)" "0.0 - 312.1 (38.8)"
[1] "hr=" "1.1"
D73V2, survival
                    sevent
clus2                  0   1
  18P LOSS MUTATED    45  55
  18P LOSS WILD-TYPE 121 137
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
               100                258 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                55                137 
$`18P LOSS MUTATED`
TCGA-D3-A2JF TCGA-D3-A8GI TCGA-EB-A5SG TCGA-EE-A2GD TCGA-ER-A193 TCGA-D3-A1Q1 
       62.07        58.52        68.25       340.14        31.40        16.57 
TCGA-D3-A1Q6 TCGA-D3-A2J7 TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JL TCGA-D3-A2JO 
       71.80       103.10        86.76        11.87       171.58        66.08 
TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51J 
       59.57        58.06        46.98       103.59        39.75       145.12 
TCGA-D3-A5GL TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GN 
      125.79       178.32       125.19        79.59        23.61       161.00 
TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A1JX TCGA-D9-A1X3 TCGA-D9-A6EG TCGA-DA-A1HV 
      129.63       117.17         7.10        18.12        22.95        76.57 
TCGA-DA-A1I2 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A3F5 TCGA-EB-A5UN TCGA-EE-A20B 
      176.55        88.87        53.92       225.96        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-A2GE TCGA-EE-A2GI 
       25.87       195.02        17.92        67.43       173.79        48.72 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2MG TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MQ 
       13.91        42.77       103.20       180.39       167.90        43.23 
TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE 
      162.48        53.26       124.31       122.73        28.77        54.51 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JH 
       41.59       138.81       172.18        34.32        53.19       134.33 
TCGA-EE-A3JI TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19E TCGA-ER-A19H 
      152.81         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-D3-A2JE TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EB-A5SH TCGA-EE-A180 TCGA-EE-A184 
       27.65        46.32        13.87        54.02        94.98        68.15 
TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A198 
      168.26         2.60       126.81       134.40        27.35        50.76 
TCGA-FR-A729 TCGA-FS-A1ZF TCGA-FW-A3R5 TCGA-QB-AA9O TCGA-WE-A8K5 TCGA-WE-AAA3 
      220.80        15.45        36.95        18.05        61.15        21.40 
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-A2JG 
       43.43        65.49        23.77       115.53       168.00       113.52 
TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JN TCGA-D3-A3BZ TCGA-D3-A3CB TCGA-D3-A3CC 
       42.08        12.10        66.48       130.72       166.52        86.93 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F 
       60.23        24.53         9.34        45.30       174.84        55.73 
TCGA-D3-A51H TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN 
       56.35        32.94        22.62        63.81        26.89       135.75 
TCGA-D3-A5GO TCGA-D3-A5GS TCGA-D3-A8GB TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GK 
      137.92        18.18        30.84        26.43       241.38       170.20 
TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GV TCGA-D9-A148 
       89.13       107.15       152.75        29.06       167.70       151.53 
TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 
       54.67         3.65        15.39        22.29        18.44         9.90 
TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 
       25.18        77.56        36.03       144.89        20.38       222.51 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
       35.93       135.02        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        43.36        72.10        37.35        73.94        14.14 
TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5UL TCGA-EB-A5VV 
       13.02        13.87        10.36        20.35        29.29         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-A185 TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29B TCGA-EE-A29C 
       26.89         4.96        91.56        13.55        85.08        78.97 
TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
       63.78        64.64        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-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 
      102.12        81.21        44.88        94.82        21.67       129.27 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF 
       28.83        19.76        61.51        47.28       103.27       268.73 
TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MN TCGA-EE-A2MP 
       16.96       204.66        96.23       216.66        47.54       248.65 
TCGA-EE-A2MT TCGA-EE-A3AC TCGA-EE-A3AF TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 
       71.21        64.04        13.81       127.20        36.95        64.08 
TCGA-EE-A3JB TCGA-EE-A3JE TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A19A TCGA-ER-A19D 
      201.80        51.35        35.44        13.94        77.75        12.59 
TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
       26.37       302.07         6.44       131.51        61.05        44.09 
TCGA-ER-A19P TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
      162.08       148.18       105.07        43.82        23.34        20.15 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
       28.83        48.99        41.56       247.04        93.01        46.98 
TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD 
       33.21        92.98        18.77        38.27        34.82        36.26 
TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
      104.42       216.92        48.59       228.59       202.65        20.91 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE 
       28.08         7.79        48.85       357.37        53.52        46.45 
TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZT 
        9.70        32.75        47.38        23.93        74.73        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        17.46 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 
       13.51        19.30         9.90        19.43         2.04        15.78 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A26A 
      139.89       117.93        96.92        10.13        64.44        32.48 
TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-HR-A2OG 
       48.00       121.91        39.35        10.42        48.89         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-A828 TCGA-W3-AA1O TCGA-W3-AA1Q TCGA-W3-AA1R 
        0.69       228.16       121.08         4.01        69.07       111.09 
TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN 
       42.08       219.16       105.04        17.95       101.33        58.98 
TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-AAA0 TCGA-WE-AAA4 
       70.52        63.22        11.80        35.80        40.41        24.99 
TCGA-XV-AB01 TCGA-YD-A89C TCGA-YD-A9TA TCGA-YG-AA3P TCGA-Z2-AA3S TCGA-Z2-AA3V 
       13.25         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             47.770 
[1] "7.1 - 369.9 (59.2)" "0.2 - 368.8 (47.8)"
[1] "hr=" "1.1"
D73V3, continuous
                    vv
clus                 I/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       18
                    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        26          9
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  18P LOSS MUTATED            6         16        2
  18P LOSS WILD-TYPE         29         38       19
D73V4, multiclass
            clus
vv           18P LOSS MUTATED 18P LOSS WILD-TYPE
  I/II NOS                  5                  8
  STAGE 0                   3                  4
  STAGE I                   8                 21
  STAGE IA                  6                 12
  STAGE IB                 10                 18
  STAGE II                  8                 18
  STAGE IIA                 1                 13
  STAGE IIB                 6                 13
  STAGE IIC                 3                 12
  STAGE III                13                 26
  STAGE IIIA                6                  9
  STAGE IIIB                6                 29
  STAGE IIIC               16                 38
  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 63 46
D73V5, multiclass
       clus
vv      18P LOSS MUTATED 18P LOSS WILD-TYPE
  T0+T1               23                 41
  T2                  21                 52
  T3                  18                 63
  T4                  21                 46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  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 225  20
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     94    2
  18P LOSS WILD-TYPE  225   20
   clus
vv  18P LOSS MUTATED 18P LOSS WILD-TYPE
  0               94                225
  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  31 232
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     16   88
  18P LOSS WILD-TYPE   31  232
     clus
vv    18P LOSS MUTATED 18P LOSS WILD-TYPE
  NO                16                 31
  YES               88                232
[1] 2 2
[1] FALSE
D73V10, continuous
D73V11, binary
                    cls
clus                   0   1
  18P LOSS MUTATED    40  64
  18P LOSS WILD-TYPE  98 165
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     40   64
  18P LOSS WILD-TYPE   98  165
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  FEMALE               40                 98
  MALE                 64                165
[1] 2 2
[1] FALSE
D73V12, binary
                    cls
clus                   0   1
  18P LOSS MUTATED    92  12
  18P LOSS WILD-TYPE 227  35
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     92   12
  18P LOSS WILD-TYPE  227   35
     clus
vv    18P LOSS MUTATED 18P LOSS WILD-TYPE
  NO                92                227
  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   251
D73V13, multiclass
                           clus
vv                          18P LOSS MUTATED 18P LOSS WILD-TYPE
  ASIAN                                    0                  5
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                  102                251
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V14, binary
                    cls
clus                   0   1
  18P LOSS MUTATED     2 100
  18P LOSS WILD-TYPE   5 252
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      2  100
  18P LOSS WILD-TYPE    5  252
                        clus
vv                       18P LOSS MUTATED 18P LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  5
  NOT HISPANIC OR LATINO              100                252
[1] 2 2
[1] FALSE

Clustering(74) Variable = 18Q LOSS MUTATION ANALYSIS
D74V1, survival
                    sevent
clus2                 0  1
  18Q LOSS MUTATED   38 39
  18Q LOSS WILD-TYPE 90 85
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                77                175 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                39                 85 
$`18Q LOSS MUTATED`
TCGA-D3-A2JF TCGA-D3-A8GI TCGA-EB-A5SG TCGA-EE-A2GD TCGA-ER-A193 TCGA-BF-AAP0 
       62.07        13.41        33.24       269.03        19.04        14.83 
TCGA-D3-A1Q1 TCGA-D3-A1Q6 TCGA-D3-A2J7 TCGA-D3-A2JC TCGA-D3-A2JL TCGA-D3-A2JO 
        8.42        49.35        45.99        86.30       171.58        66.08 
TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51J TCGA-D3-A5GR 
       58.06        59.70        90.21        23.67       144.46       177.86 
TCGA-D3-A5GU TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GR TCGA-D9-A1X3 TCGA-D9-A6EC 
      124.08        78.21        23.61        36.53        10.78        69.21 
TCGA-DA-A1HV TCGA-DA-A1I2 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A3F5 TCGA-DA-A95X 
       76.34       150.61        60.10        64.83       225.11        65.03 
TCGA-EB-A5UN TCGA-EE-A20C TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29M TCGA-EE-A29T 
       52.41        75.55        12.99        44.28        47.74       346.49 
TCGA-EE-A29W TCGA-EE-A2GE TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2MG TCGA-EE-A2MK 
      185.19        12.95         0.76         0.20        94.19        89.26 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3J3 
       53.26       124.31       122.73         4.41        54.51        67.89 
TCGA-EE-A3J8 TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19C 
        3.35        19.86       135.98         7.82        53.29        39.81 
TCGA-ER-A19H TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A3EV TCGA-ER-A42L TCGA-FR-A44A 
      150.12        47.18       146.63        15.48        74.47       174.21 
TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZW 
        4.14        26.20        78.61       130.95       136.27        23.21 
TCGA-FS-A1ZY TCGA-FW-A3TU TCGA-GN-A268 TCGA-GN-A8LK TCGA-GN-A9SD TCGA-W3-A825 
        5.29        55.59        42.48        43.23        59.41         1.97 
TCGA-W3-AA1V TCGA-WE-A8K1 TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-YG-AA3O 
        8.09        47.54        48.39         1.94        28.21 

$`18Q LOSS WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A3C8 TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GO TCGA-EE-A2MR 
        9.76        38.76        31.96       166.75        52.90       134.40 
TCGA-EE-A3JD TCGA-FR-A729 TCGA-FW-A3R5 TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-3N-A9WC 
       27.35       216.43        36.95        52.73         7.40        60.46 
TCGA-3N-A9WD TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       12.99        15.72        31.89       110.93       133.25        19.04 
TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JB 
       76.41        62.60        25.64        62.86        15.75       168.00 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3CB TCGA-D3-A3CC 
      107.61        36.30        64.83        43.53       140.98        40.01 
TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51K TCGA-D3-A51R 
       24.53         9.34       173.85        30.67        31.76        62.70 
TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL 
       11.34        42.05        45.70       179.97       120.00        69.53 
TCGA-D3-A8GM TCGA-D3-A8GP TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6EG 
       70.62       135.12        15.02        16.90        18.44        22.85 
TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I5 TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F8 
      138.67        68.68       110.53        58.85        30.44         8.71 
TCGA-DA-A95V TCGA-DA-A95W TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5KH 
       72.10         0.76        14.14        12.30         3.91        16.41 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
       18.21        13.15        24.89        20.38         0.00        26.24 
TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29P 
       79.20        75.22        76.14         0.26        47.41        27.16 
TCGA-EE-A29Q TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GH 
       61.12       115.43        30.02        77.98        26.14       201.60 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GS 
       68.65        10.62        32.48        18.35        93.63        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-A2ML TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MS 
      171.85        63.25       104.78       145.45       227.01       143.93 
TCGA-EE-A2MT TCGA-EE-A3AC TCGA-EE-A3AF TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3JB 
       23.51        64.04         6.28       111.85        45.90       168.85 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A19A TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19L 
       34.45        10.49         4.54        11.47       184.60        99.06 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A1A1 TCGA-ER-A2NC 
       59.84        42.51       120.76        49.71        73.05        22.36 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET 
        4.70        16.87        10.19        28.67       173.29        68.52 
TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FS-A1YW TCGA-FS-A1YY 
       32.05         4.50         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        43.92 
TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZZ TCGA-FS-A4F0 
        7.82        36.33        35.28         4.47         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-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        9.90        18.25         1.91        53.29       117.93        96.92 
TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-LH-A9QB 
       17.06         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-A828 
      297.01         7.23         0.20         0.33       174.12       120.07 
TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8ZM TCGA-WE-A8ZN 
       44.05        79.99       185.13        92.84        65.42        12.69 
TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-XV-AB01 
       21.90        62.89        10.95        37.32        24.99         6.61 
TCGA-Z2-AA3S 
       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 
             53.29              40.01 
[1] "0.2 - 346.5 (53.3)" "0.0 - 312.1 (40.0)"
[1] "hr=" "1.1"
D74V2, survival
                    sevent
clus2                  0   1
  18Q LOSS MUTATED    43  52
  18Q LOSS WILD-TYPE 123 140
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                95                263 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                52                140 
$`18Q LOSS MUTATED`
TCGA-D3-A2JF TCGA-D3-A8GI TCGA-EB-A5SG TCGA-EE-A2GD TCGA-ER-A193 TCGA-BF-AAP0 
       62.07        58.52        68.25       340.14        31.40        14.93 
TCGA-D3-A1Q1 TCGA-D3-A1Q6 TCGA-D3-A1Q9 TCGA-D3-A2J7 TCGA-D3-A2JC TCGA-D3-A2JD 
       16.57        71.80        31.59       103.10        86.76        11.87 
TCGA-D3-A2JL TCGA-D3-A2JO TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3MR TCGA-D3-A3MU 
      171.58        66.08        58.06        60.23       103.59        39.75 
TCGA-D3-A51J TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GN 
      145.12       178.32       125.19        79.59        23.61       161.00 
TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A148 TCGA-D9-A1X3 TCGA-D9-A6EC TCGA-DA-A1HV 
      129.63       117.17       151.53        18.12        77.56        76.57 
TCGA-DA-A1I2 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A3F5 TCGA-DA-A95X 
      176.55        88.87        53.92        65.92       225.96        73.94 
TCGA-EB-A5UN TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A29A TCGA-EE-A29D TCGA-EE-A29G 
       58.92       133.81       151.27        63.35        13.97        72.07 
TCGA-EE-A29M TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2GC 
       56.84       369.93        25.87       195.02        17.92        67.43 
TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2MG TCGA-EE-A2MK 
      173.79        48.72        13.91        42.77       103.20       180.39 
TCGA-EE-A2MQ TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE 
       43.23        53.26       124.31       122.73        28.77        54.51 
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-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-D3-A2JE TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EB-A5SH TCGA-EE-A180 TCGA-EE-A184 
       27.65        46.32        13.87        54.02        94.98        68.15 
TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A198 
      168.26         2.60       126.81       134.40        27.35        50.76 
TCGA-FR-A729 TCGA-FS-A1ZF TCGA-FW-A3R5 TCGA-QB-AA9O TCGA-WE-A8K5 TCGA-WE-AAA3 
      220.80        15.45        36.95        18.05        61.15        21.40 
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-A2JG TCGA-D3-A2JH TCGA-D3-A2JK 
       23.77       115.53       168.00       113.52        42.08        12.10 
TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CC 
       66.48        59.57       130.72        46.98       166.52        86.93 
TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
       24.53         9.34        45.30       174.84        55.73        56.35 
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-A5GS TCGA-D3-A8GB TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GK 
      137.92        18.18        30.84        26.43       241.38       170.20 
TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GV TCGA-D9-A149 
       89.13       107.15       152.75        29.06       167.70        54.67 
TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 
        3.65         7.10        15.39        22.29        18.44         9.90 
TCGA-D9-A6EA TCGA-D9-A6EG TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 
       25.18        22.95        36.03       144.89        20.38       222.51 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
       35.93       135.02        40.60        68.09        33.93        10.49 
TCGA-DA-A3F8 TCGA-DA-A95V TCGA-DA-A95W TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q 
       43.36        72.10        37.35        14.14        13.02        13.87 
TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5UL TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X 
       10.36        20.35        29.29         7.04        36.46        29.82 
TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 
       27.22         8.65        33.73        14.70        26.89         4.96 
TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H 
       91.56        13.55        85.08        78.97        63.78        64.64 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A2A0 
       18.61        56.42        66.74        14.47        61.28        46.82 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GH 
      115.96        59.64        39.29        86.14        59.28       220.24 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GS 
      107.38        54.74        79.66        75.48       102.12        81.21 
TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 
       44.88        94.82        21.67       129.27        28.83        19.76 
TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MH TCGA-EE-A2MI 
       61.51        47.28       103.27       268.73        16.96       204.66 
TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MS 
       96.23       216.66       167.90        47.54       248.65       162.48 
TCGA-EE-A2MT TCGA-EE-A3AC TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3J4 TCGA-EE-A3J5 
       71.21        64.04        13.81        41.59       127.20        36.95 
TCGA-EE-A3J7 TCGA-EE-A3JB TCGA-EE-A3JE TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A19A 
       64.08       201.80        51.35        35.44        13.94        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       302.07         6.44       131.51 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A1A1 TCGA-ER-A2NC 
       61.05        44.09       162.08        50.89       105.07        43.82 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES 
       23.34        20.15        28.83        48.99        41.56       247.04 
TCGA-ER-A3ET TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A7U9 TCGA-FR-A7UA 
       93.01        33.21        12.95        92.98        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-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ 
      357.37        53.52        46.45         9.70        32.75        47.38 
TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZZ 
       23.93        74.73        11.41        53.16        26.56        27.02 
TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 
       77.82        50.14        66.67        28.73       174.84        34.03 
TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TV TCGA-FW-A5DY 
       26.73        54.41        80.68        17.46        13.51        19.30 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 
        9.90        19.43         2.04        15.78       139.89       117.93 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U3 
       96.92        10.13        64.44        32.48        48.00       121.91 
TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-HR-A2OG TCGA-HR-A2OH TCGA-LH-A9QB 
       39.35        10.42        48.89         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-A828 TCGA-W3-AA1O TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1W TCGA-W3-AA21 
      121.08         4.01        69.07       111.09       219.16       105.04 
TCGA-WE-A8JZ TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ 
       24.03        17.95       101.33        58.98        70.52        63.22 
TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-XV-AB01 TCGA-YD-A89C 
       11.80        35.80        40.41        24.99        13.25         6.90 
TCGA-YD-A9TA TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
       49.18        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 
             63.02              46.98 
[1] "8.9 - 369.9 (63.0)" "0.2 - 368.8 (47.0)"
[1] "hr=" "1.2"
D74V3, continuous
                    vv
clus                 I/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       19
                    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        26          9
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  18Q LOSS MUTATED            6         14        3
  18Q LOSS WILD-TYPE         29         40       18
D74V4, multiclass
            clus
vv           18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  I/II NOS                  5                  8
  STAGE 0                   3                  4
  STAGE I                   7                 22
  STAGE IA                  6                 12
  STAGE IB                  9                 19
  STAGE II                  7                 19
  STAGE IIA                 1                 13
  STAGE IIB                 5                 14
  STAGE IIC                 3                 12
  STAGE III                13                 26
  STAGE IIIA                6                  9
  STAGE IIIB                6                 29
  STAGE IIIC               14                 40
  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 63 47
D74V5, multiclass
       clus
vv      18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  T0+T1               21                 43
  T2                  19                 54
  T3                  18                 63
  T4                  20                 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
  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 233  18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     86    4
  18Q LOSS WILD-TYPE  233   18
   clus
vv  18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  0               86                233
  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  33 234
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     14   86
  18Q LOSS WILD-TYPE   33  234
     clus
vv    18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  NO                14                 33
  YES               86                234
[1] 2 2
[1] FALSE
D74V10, continuous
D74V11, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED    37  63
  18Q LOSS WILD-TYPE 101 166
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     37   63
  18Q LOSS WILD-TYPE  101  166
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  FEMALE               37                101
  MALE                 63                166
[1] 2 2
[1] FALSE
D74V12, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED    87  13
  18Q LOSS WILD-TYPE 232  34
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     87   13
  18Q LOSS WILD-TYPE  232   34
     clus
vv    18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  NO                87                232
  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   254
D74V13, multiclass
                           clus
vv                          18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  ASIAN                                    0                  5
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   99                254
[1] 3 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   5 255
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      2   97
  18Q LOSS WILD-TYPE    5  255
                        clus
vv                       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  5
  NOT HISPANIC OR LATINO               97                255
[1] 2 2
[1] FALSE

Clustering(75) Variable = 19P LOSS MUTATION ANALYSIS
D75V1, survival
                    sevent
clus2                  0   1
  19P LOSS MUTATED    28  23
  19P LOSS WILD-TYPE 100 101
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                51                201 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                23                101 
$`19P LOSS MUTATED`
TCGA-EE-A20H TCGA-EE-A3JD TCGA-D3-A1Q1 TCGA-D3-A2JL TCGA-D3-A3CE TCGA-D3-A3MU 
      166.75        27.35         8.42       171.58        59.70        23.67 
TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A8GD TCGA-D3-A8GM TCGA-D3-A8GP 
       11.34        42.05        45.70        23.61        70.62       135.12 
TCGA-D9-A1X3 TCGA-D9-A3Z3 TCGA-DA-A1HV TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA 
       10.78        16.90        76.34       110.53        60.10        64.83 
TCGA-DA-A95Y TCGA-EE-A17X TCGA-EE-A29D TCGA-EE-A29H TCGA-EE-A2GM TCGA-EE-A2MG 
       14.14        13.15        12.99        47.41        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-FR-A69P TCGA-FS-A1ZJ 
       39.81        49.71        15.48       174.21         4.14        36.33 
TCGA-FS-A1ZQ TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A4FD TCGA-FW-A3TV TCGA-GF-A4EO 
      130.95        35.28        23.21        80.68        11.54        18.25 
TCGA-GN-A262 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-W3-A825 TCGA-W3-AA1R 
       53.29        42.48         7.59       120.53         1.97        79.99 
TCGA-W3-AA1V TCGA-WE-A8K1 TCGA-WE-A8ZM 
        8.09        47.54        65.42 

$`19P LOSS WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A8GI TCGA-EB-A5SG TCGA-EE-A180 
        9.76        62.07        38.76        13.41        33.24        31.96 
TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR TCGA-ER-A193 TCGA-FR-A729 TCGA-FW-A3R5 
      269.03        52.90       134.40        19.04       216.43        36.95 
TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q3 
       52.73         7.40        60.46        12.99        14.83        15.72 
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA 
       31.89       110.93        49.35       133.25        19.04        76.41 
TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JB 
       62.60        25.64        45.99        62.86        15.75       168.00 
TCGA-D3-A2JC TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP 
       86.30       107.61        36.30        64.83        66.08        43.53 
TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR 
       58.06       140.98        40.01        24.53         9.34        90.21 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A5GR 
      173.85        30.67       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        68.68 
TCGA-DA-A1I2 TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-DA-A95V 
      150.61        58.85        30.44       225.11         8.71        72.10 
TCGA-DA-A95W TCGA-DA-A95X TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN 
        0.76        65.03        12.30         3.91        16.41        52.41 
TCGA-EB-A6L9 TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20C 
       18.21        24.89        20.38         0.00        26.24        75.55 
TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29M 
       79.20        75.22        76.14         0.26        44.28        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-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK 
       77.98        26.14        12.95       201.60        68.65        10.62 
TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU 
       32.48        93.63         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-A2MI 
      103.13        15.25         5.75        23.77       209.79       171.85 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MU TCGA-EE-A3AA 
       63.25        89.26       104.78       145.45        53.26       124.31 
TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 
       64.04        54.51         6.28        67.89       111.85        45.90 
TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 
        3.35       168.85        19.86       135.98        34.45        10.49 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L 
        7.82         4.54        11.47       184.60       150.12        99.06 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 
       59.84        42.51       120.76        47.18       146.63        73.05 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES 
       22.36         4.70        16.87        10.19        28.67       173.29 
TCGA-ER-A3ET TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A7U8 TCGA-FR-A7UA 
       68.52        32.05        74.47         4.50        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-A1ZG TCGA-FS-A1ZM TCGA-FS-A1ZS 
      312.07        32.78        43.92         7.82        78.61       136.27 
TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 
        4.47         5.29         3.06        30.90        66.67       173.19 
TCGA-FS-A4F9 TCGA-FW-A3TU TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GN-A264 
       13.28        55.59        19.30         9.90         1.91       117.93 
TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-GN-A8LK TCGA-GN-A9SD 
       96.92        17.06        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-A828 TCGA-W3-AA1Q TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8ZN TCGA-WE-A8ZO 
      120.07        44.05       185.13        92.84        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        37.32        24.99 
TCGA-XV-AB01 TCGA-YG-AA3O TCGA-Z2-AA3S 
        6.61        28.21        91.23 

  19P LOSS MUTATED 19P LOSS WILD-TYPE 
              1.97               0.00 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
            227.01             346.49 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
             42.48              47.18 
[1] "2.0 - 227.0 (42.5)" "0.0 - 346.5 (47.2)"
[1] "hr=" "1"  
D75V2, survival
                    sevent
clus2                  0   1
  19P LOSS MUTATED    36  40
  19P LOSS WILD-TYPE 130 152
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                76                282 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                40                152 
$`19P LOSS MUTATED`
TCGA-EE-A20H TCGA-EE-A3JD TCGA-D3-A1Q1 TCGA-D3-A1Q9 TCGA-D3-A2JD TCGA-D3-A2JL 
      168.26        27.35        16.57        31.59        11.87       171.58 
TCGA-D3-A3CE TCGA-D3-A3MU TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A8GD 
       60.23        39.75        26.89       125.79       135.75        23.61 
TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GS TCGA-D3-A8GV TCGA-D9-A148 
      107.15       161.00       152.75       117.17       167.70       151.53 
TCGA-D9-A1X3 TCGA-D9-A3Z3 TCGA-D9-A6EA TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I0 
       18.12        22.29        25.18        76.57        36.03        20.38 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A95Y TCGA-EB-A44R 
      135.02        88.87        53.92        65.92        14.14        10.36 
TCGA-EB-A5UL TCGA-EE-A17X TCGA-EE-A20I TCGA-EE-A29D TCGA-EE-A29H TCGA-EE-A29X 
       29.29        29.82        13.55        13.97        64.64        17.92 
TCGA-EE-A2A0 TCGA-EE-A2GM TCGA-EE-A2MG TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MT 
       46.82        75.48       103.20       248.65       162.48        71.21 
TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3J5 TCGA-EE-A3JA TCGA-ER-A19B TCGA-ER-A19C 
      122.73        28.77        36.95        53.19        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        41.56        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        19.43       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-D3-A2JE TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-D3-A8GI TCGA-EB-A5SG 
       27.65        62.07        46.32        13.87        58.52        68.25 
TCGA-EB-A5SH TCGA-EE-A180 TCGA-EE-A184 TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2GO 
       54.02        94.98        68.15         2.60       340.14       126.81 
TCGA-EE-A2MR TCGA-ER-A193 TCGA-ER-A198 TCGA-FR-A729 TCGA-FS-A1ZF TCGA-FW-A3R5 
      134.40        31.40        50.76       220.80        15.45        36.95 
TCGA-QB-AA9O TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD 
       18.05        61.15        21.40        17.03        66.48        12.99 
TCGA-BF-AAP0 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       14.93        16.67       112.04       112.57        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-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JG TCGA-D3-A2JH 
       23.77       115.53       168.00        86.76       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-A3CB TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR 
       46.98       166.52        86.93        24.53         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-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU 
       22.62        63.81       137.92       178.32        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-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-A1HY TCGA-DA-A1I1 
       18.44         9.90        77.56        22.95       144.89       222.51 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
      176.55        35.93        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-A95Z 
      225.96        43.36        72.10        37.35        73.94        13.02 
TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17Y 
       13.87        20.35        58.92         7.04        36.46        27.22 
TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B 
        8.65        33.73        14.70        26.89         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-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
       72.07        56.84        18.61        56.42        66.74        14.47 
TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A2 
       61.28       369.93        25.87       195.02       115.96        59.64 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GH 
       39.29        86.14        59.28        67.43       173.79       220.24 
TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GP 
       48.72       107.38        54.74        79.66       102.12        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-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-A2MU TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AE 
       47.54        43.23        53.26       124.31        64.04        54.51 
TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 
       13.81        41.59       138.81       172.18       127.20        64.08 
TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 
       34.32       201.80        51.35       134.33       152.81        35.44 
TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F 
       13.94         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 
      302.07       152.35         6.44       131.51        61.05        44.09 
TCGA-ER-A19P TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
      162.08        49.48       148.18       105.07        43.82        23.34 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3PL 
       20.15        28.83        48.99       247.04        93.01        33.21 
TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA 
       12.95       149.03        92.98        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-A1ZG TCGA-FS-A1ZK TCGA-FS-A1ZM 
      357.37        53.52        46.45         9.70        23.93       101.26 
TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A1ZZ 
       74.73        11.41       148.80        26.56        27.09        27.02 
TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 
       77.82        50.14        66.67        28.73       174.84        34.03 
TCGA-FS-A4FC TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 
       54.41        17.46        55.59        19.30         9.90         2.04 
TCGA-GF-A6C9 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A26D 
       15.78       117.93        96.92        10.13        64.44        48.00 
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-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-A828 TCGA-W3-AA1O TCGA-W3-AA1Q 
        0.33         0.69       228.16       121.08         4.01        69.07 
TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K6 TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ 
      219.16       105.04        17.95        58.98        70.52        63.22 
TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 
       11.80        35.80        49.51        12.16        40.41        24.99 
TCGA-XV-AB01 TCGA-YD-A89C TCGA-YG-AA3O TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
       13.25         6.90        37.94        27.58        96.99        15.98 

  19P LOSS MUTATED 19P LOSS WILD-TYPE 
              8.88               0.20 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
            248.65             369.93 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
            49.115             54.215 
[1] "8.9 - 248.7 (49.1)" "0.2 - 369.9 (54.2)"
[1] "hr=" "1.1"
D75V3, continuous
                    vv
clus                 I/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       21
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  19P LOSS MUTATED           1         3         3        11          2
  19P LOSS WILD-TYPE        13        16        12        28         13
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  19P LOSS MUTATED           11         12        5
  19P LOSS WILD-TYPE         24         42       16
D75V4, multiclass
            clus
vv           19P LOSS MUTATED 19P LOSS WILD-TYPE
  I/II NOS                  5                  8
  STAGE 0                   0                  7
  STAGE I                   7                 22
  STAGE IA                  2                 16
  STAGE IB                  4                 24
  STAGE II                  5                 21
  STAGE IIA                 1                 13
  STAGE IIB                 3                 16
  STAGE IIC                 3                 12
  STAGE III                11                 28
  STAGE IIIA                2                 13
  STAGE IIIB               11                 24
  STAGE IIIC               12                 42
  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 15 16
  19P LOSS WILD-TYPE    50 56 66 51
D75V5, multiclass
       clus
vv      19P LOSS MUTATED 19P LOSS WILD-TYPE
  T0+T1               14                 50
  T2                  17                 56
  T3                  15                 66
  T4                  16                 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
  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 252  16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED     67    6
  19P LOSS WILD-TYPE  252   16
   clus
vv  19P LOSS MUTATED 19P LOSS WILD-TYPE
  0               67                252
  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  38 252
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      9   68
  19P LOSS WILD-TYPE   38  252
     clus
vv    19P LOSS MUTATED 19P LOSS WILD-TYPE
  NO                 9                 38
  YES               68                252
[1] 2 2
[1] FALSE
D75V10, continuous
D75V11, binary
                    cls
clus                   0   1
  19P LOSS MUTATED    33  44
  19P LOSS WILD-TYPE 105 185
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED     33   44
  19P LOSS WILD-TYPE  105  185
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  FEMALE               33                105
  MALE                 44                185
[1] 2 2
[1] FALSE
D75V12, binary
                    cls
clus                   0   1
  19P LOSS MUTATED    61  16
  19P LOSS WILD-TYPE 258  31
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED     61   16
  19P LOSS WILD-TYPE  258   31
     clus
vv    19P LOSS MUTATED 19P LOSS WILD-TYPE
  NO                61                258
  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   279
D75V13, multiclass
                           clus
vv                          19P LOSS MUTATED 19P LOSS WILD-TYPE
  ASIAN                                    1                  4
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   74                279
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V14, binary
                    cls
clus                   0   1
  19P LOSS MUTATED     1  74
  19P LOSS WILD-TYPE   6 278
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      1   74
  19P LOSS WILD-TYPE    6  278
                        clus
vv                       19P LOSS MUTATED 19P LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO               74                278
[1] 2 2
[1] FALSE

Clustering(76) Variable = 19Q LOSS MUTATION ANALYSIS
D76V1, survival
                    sevent
clus2                  0   1
  19Q LOSS MUTATED    29  20
  19Q LOSS WILD-TYPE  99 104
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                49                203 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                20                104 
$`19Q LOSS MUTATED`
TCGA-EE-A20H TCGA-EE-A2GO TCGA-EE-A3JD TCGA-WE-A8K5 TCGA-D3-A2JL TCGA-D3-A3MU 
      166.75        52.90        27.35        52.73       171.58        23.67 
TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A8GM TCGA-D3-A8GP TCGA-D9-A1X3 
       11.34        42.05        45.70        70.62       135.12        10.78 
TCGA-D9-A3Z3 TCGA-DA-A1HV TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A95X 
       16.90        76.34       110.53        60.10        64.83        65.03 
TCGA-DA-A95Y TCGA-EE-A17X TCGA-EE-A29D TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A2MG 
       14.14        13.15        12.99        47.41        47.74        94.19 
TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AB TCGA-EE-A3AD 
      145.45       227.01       143.93        23.51       122.73         4.41 
TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A3EV TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1ZJ 
       53.29        39.81        15.48       174.21         4.14        36.33 
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        18.25        53.29 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-W3-A825 TCGA-W3-AA21 TCGA-WE-A8K1 
       42.48         7.59       120.53         1.97        92.84        47.54 
TCGA-WE-A8ZM 
       65.42 

$`19Q LOSS WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A8GI TCGA-EB-A5SG TCGA-EE-A180 
        9.76        62.07        38.76        13.41        33.24        31.96 
TCGA-EE-A2GD TCGA-EE-A2MR TCGA-ER-A193 TCGA-FR-A729 TCGA-FW-A3R5 TCGA-WE-AAA3 
      269.03       134.40        19.04       216.43        36.95         7.40 
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-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-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR 
      140.98        40.01        59.70        24.53         9.34        90.21 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A5GR 
      173.85        30.67       144.46        31.76        62.70       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-A8GR TCGA-D9-A3Z1 TCGA-D9-A4Z6 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HY 
       36.53        15.02        18.44        69.21        22.85       138.67 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 
       68.68       150.61        58.85        30.44       225.11         8.71 
TCGA-DA-A95V TCGA-DA-A95W TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN 
       72.10         0.76        12.30         3.91        16.41        52.41 
TCGA-EB-A6L9 TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20C 
       18.21        24.89        20.38         0.00        26.24        75.55 
TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29P 
       79.20        75.22        76.14         0.26        44.28        27.16 
TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 
       61.12       346.49       185.19       115.43        30.02        77.98 
TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
       26.14        12.95       201.60        68.65        10.62        32.48 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU 
       18.35        93.63         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-A2MI 
      103.13        15.25         5.75        23.77       209.79       171.85 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AC 
       63.25        89.26       104.78        53.26       124.31        64.04 
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-A195 TCGA-ER-A197 TCGA-ER-A199 
      168.85        19.86       135.98        34.45        10.49         7.82 
TCGA-ER-A19A TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M 
        4.54        11.47       184.60       150.12        99.06        59.84 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 
       42.51       120.76        49.71        47.18       146.63        73.05 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES 
       22.36         4.70        16.87        10.19        28.67       173.29 
TCGA-ER-A3ET TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A7U8 TCGA-FR-A7UA 
       68.52        32.05        74.47         4.50        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-A1ZG TCGA-FS-A1ZM TCGA-FS-A1ZQ 
      312.07        32.78        43.92         7.82        78.61       130.95 
TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 
      136.27         4.47         5.29         3.06        30.90        66.67 
TCGA-FS-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-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-GN-A8LK 
      117.93        96.92        17.06        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-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-AAA4 TCGA-XV-AB01 TCGA-YG-AA3O TCGA-Z2-AA3S 
       37.32        24.99         6.61        28.21        91.23 

  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
              1.97               0.00 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
            227.01             346.49 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
             47.54              45.90 
[1] "2.0 - 227.0 (47.5)" "0.0 - 346.5 (45.9)"
[1] "hr=" "1.2"
D76V2, survival
                    sevent
clus2                  0   1
  19Q LOSS MUTATED    34  38
  19Q LOSS WILD-TYPE 132 154
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                72                286 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                38                154 
$`19Q LOSS MUTATED`
TCGA-EE-A20H TCGA-EE-A2GO TCGA-EE-A3JD TCGA-WE-A8K5 TCGA-D3-A1Q9 TCGA-D3-A2JD 
      168.26       126.81        27.35        61.15        31.59        11.87 
TCGA-D3-A2JL TCGA-D3-A3MU TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A8GM 
      171.58        39.75        26.89       125.79       135.75       107.15 
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-A1I0 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
       25.18        76.57        20.38       135.02        88.87        53.92 
TCGA-DA-A1IA TCGA-DA-A95X TCGA-DA-A95Y TCGA-EB-A44R TCGA-EE-A17X TCGA-EE-A20I 
       65.92        73.94        14.14        10.36        29.82        13.55 
TCGA-EE-A29D TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29S TCGA-EE-A29X TCGA-EE-A2MG 
       13.97        64.64        56.84        61.28        17.92       103.20 
TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AB TCGA-EE-A3AD 
      167.90       248.65       162.48        71.21       122.73        28.77 
TCGA-EE-A3AG TCGA-EE-A3JA TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19T TCGA-ER-A2NH 
       41.59        53.19        98.40        48.89         8.88        41.56 
TCGA-ER-A3EV TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZT 
       46.98       174.21        15.72        32.75        47.38        53.16 
TCGA-FS-A1ZW TCGA-FS-A4F2 TCGA-FS-A4FB TCGA-FS-A4FD TCGA-FW-A3TV TCGA-GF-A4EO 
       49.48        50.14        26.73        80.68        13.51        19.43 
TCGA-GN-A262 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A4U7 
      139.89        62.79        32.48        48.00       121.91        10.42 
TCGA-W3-A825 TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8ZM TCGA-YD-A9TA TCGA-YG-AA3P 
       63.02       105.04        49.05       101.33        49.18        14.43 

$`19Q LOSS WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-D3-A8GI TCGA-EB-A5SG 
       27.65        62.07        46.32        13.87        58.52        68.25 
TCGA-EB-A5SH TCGA-EE-A180 TCGA-EE-A184 TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2MR 
       54.02        94.98        68.15         2.60       340.14       134.40 
TCGA-ER-A193 TCGA-ER-A198 TCGA-FR-A729 TCGA-FS-A1ZF TCGA-FW-A3R5 TCGA-QB-AA9O 
       31.40        50.76       220.80        15.45        36.95        18.05 
TCGA-WE-AAA3 TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 
       21.40        17.03        66.48        12.99        14.93        16.57 
TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       16.67       112.04       112.57        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-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK 
      115.53       168.00        86.76       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-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR 
      166.52        86.93        60.23        24.53         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-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU 
       22.62        63.81       137.92       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-A8GN TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D9-A149 TCGA-D9-A1JW 
       89.13       161.00        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-A1HW TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1IB 
       36.03       144.89       222.51       176.55        35.93        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        43.36        72.10 
TCGA-DA-A95W TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UL TCGA-EB-A5UN 
       37.35        13.02        13.87        20.35        29.29        58.92 
TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 
        7.04        36.46        27.22         8.65        33.73        14.70 
TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29A 
       26.89         4.96       133.81       151.27        91.56        63.35 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29N TCGA-EE-A29P 
       85.08        78.97        63.78        72.07        18.61        56.42 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A2A0 
       66.74        14.47       369.93        25.87       195.02        46.82 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC 
      115.96        59.64        39.29        86.14        59.28        67.43 
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-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT 
       75.48       102.12        13.91        42.77        81.21        44.88 
TCGA-EE-A2GU TCGA-EE-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-A2MN TCGA-EE-A2MQ TCGA-EE-A2MU TCGA-EE-A3AA 
      180.39       216.66        47.54        43.23        53.26       124.31 
TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 
       64.04        54.51        13.81       138.81       172.18       127.20 
TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JE TCGA-EE-A3JH 
       36.95        64.08        34.32       201.80        51.35       134.33 
TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19D 
      152.81        35.44        13.94         9.17        77.75        12.59 
TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L 
       13.02        26.37       302.07       152.35         6.44       131.51 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W 
       61.05        44.09       162.08        50.89        49.48       148.18 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
      105.07        43.82        23.34        20.15        28.83        48.99 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3PL TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A3YN 
      247.04        93.01        33.21        12.95       149.03        92.98 
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-A1ZG TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR 
        9.70        23.93       101.26        74.73       133.55        11.41 
TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 
      148.80        26.56        27.09        27.02        77.82        66.67 
TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A3I3 TCGA-FW-A3TU 
       28.73       174.84        34.03        54.41        17.46        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-A4U4 TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK 
       10.13        64.44        39.35        48.89        22.13        50.10 
TCGA-GN-A8LL TCGA-GN-A9SD TCGA-HR-A2OG TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X 
       21.37        59.41         0.23        65.88       368.78       297.90 
TCGA-QB-A6FS TCGA-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-AA1O TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1V TCGA-W3-AA1W TCGA-WE-A8JZ 
        4.01        69.07       111.09        42.08       219.16        24.03 
TCGA-WE-A8K6 TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX 
       17.95        58.98        70.52        63.22        11.80        35.80 
TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-XV-AB01 TCGA-YD-A89C 
       49.51        12.16        40.41        24.99        13.25         6.90 
TCGA-YG-AA3O TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
       37.94        27.58        96.99        15.98 

  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
              8.88               0.20 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
            248.65             369.93 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
            53.175             51.120 
[1] "8.9 - 248.7 (53.2)" "0.2 - 369.9 (51.1)"
[1] "hr=" "1"  
D76V3, continuous
                    vv
clus                 I/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       22
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  19Q LOSS MUTATED           1         3         4         9          2
  19Q LOSS WILD-TYPE        13        16        11        30         13
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  19Q LOSS MUTATED            9         10        6
  19Q LOSS WILD-TYPE         26         44       15
D76V4, multiclass
            clus
vv           19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  I/II NOS                  3                 10
  STAGE 0                   0                  7
  STAGE I                   9                 20
  STAGE IA                  2                 16
  STAGE IB                  6                 22
  STAGE II                  4                 22
  STAGE IIA                 1                 13
  STAGE IIB                 3                 16
  STAGE IIC                 4                 11
  STAGE III                 9                 30
  STAGE IIIA                2                 13
  STAGE IIIB                9                 26
  STAGE IIIC               10                 44
  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 14 14
  19Q LOSS WILD-TYPE    52 51 67 53
D76V5, multiclass
       clus
vv      19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  T0+T1               12                 52
  T2                  22                 51
  T3                  14                 67
  T4                  14                 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
  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 258  15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED     61    7
  19Q LOSS WILD-TYPE  258   15
   clus
vv  19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  0               61                258
  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  39 255
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      8   65
  19Q LOSS WILD-TYPE   39  255
     clus
vv    19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  NO                 8                 39
  YES               65                255
[1] 2 2
[1] FALSE
D76V10, continuous
D76V11, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED    30  43
  19Q LOSS WILD-TYPE 108 186
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED     30   43
  19Q LOSS WILD-TYPE  108  186
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  FEMALE               30                108
  MALE                 43                186
[1] 2 2
[1] FALSE
D76V12, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED    59  14
  19Q LOSS WILD-TYPE 260  33
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED     59   14
  19Q LOSS WILD-TYPE  260   33
     clus
vv    19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  NO                59                260
  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   282
D76V13, multiclass
                           clus
vv                          19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  ASIAN                                    1                  4
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   71                282
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V14, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED     1  71
  19Q LOSS WILD-TYPE   6 281
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      1   71
  19Q LOSS WILD-TYPE    6  281
                        clus
vv                       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO               71                281
[1] 2 2
[1] FALSE

Clustering(77) Variable = 20P LOSS MUTATION ANALYSIS
D77V1, survival
                    sevent
clus2                  0   1
  20P LOSS MUTATED     8  11
  20P LOSS WILD-TYPE 120 113
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                19                233 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                11                113 
$`20P LOSS MUTATED`
TCGA-WE-A8K5 TCGA-D3-A2JC TCGA-D3-A3CF TCGA-D3-A8GK TCGA-DA-A1HV TCGA-DA-A1I1 
       52.73        86.30        24.53       120.00        76.34        68.68 
TCGA-DA-A95Y TCGA-EE-A29E TCGA-EE-A29G TCGA-ER-A19C TCGA-ER-A19H TCGA-ER-A19W 
       14.14         0.26        44.28        39.81       150.12       146.63 
TCGA-ER-A2NG TCGA-ER-A3PL TCGA-FS-A1ZE TCGA-FS-A4F4 TCGA-GN-A4U3 TCGA-W3-AA1W 
       28.67        32.05        43.92        66.67       120.53       185.13 
TCGA-YG-AA3O 
       28.21 

$`20P LOSS WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A8GI TCGA-EB-A5SG TCGA-EE-A180 
        9.76        62.07        38.76        13.41        33.24        31.96 
TCGA-EE-A20H TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 
      166.75       269.03        52.90       134.40        27.35        19.04 
TCGA-FR-A729 TCGA-FW-A3R5 TCGA-WE-AAA3 TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 
      216.43        36.95         7.40        60.46        12.99        14.83 
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
        8.42        15.72        31.89       110.93        49.35       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-A2JA TCGA-D3-A2JB TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN 
       15.75       168.00       107.61        36.30       171.58        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-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51J 
        9.34        90.21        23.67       173.85        30.67       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       110.53        60.10 
TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-DA-A95V 
       64.83        58.85        30.44       225.11         8.71        72.10 
TCGA-DA-A95W TCGA-DA-A95X TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN 
        0.76        65.03        12.30         3.91        16.41        52.41 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
       18.21        13.15        24.89        20.38         0.00        26.24 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29H 
       75.55        79.20        75.22        76.14        12.99        47.41 
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-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ 
       30.02        77.98        26.14        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        93.63         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-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA 
      145.45       227.01       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-EE-A3JI 
      111.85        45.90         3.35       168.85        19.86       135.98 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19D 
       34.45        10.49         7.82         4.54        53.29        11.47 
TCGA-ER-A19G TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
      184.60        99.06        59.84        42.51       120.76        49.71 
TCGA-ER-A19S TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF 
       47.18        73.05        22.36         4.70        16.87        10.19 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A 
      173.29        68.52        15.48        74.47         4.50       174.21 
TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FS-A1YW TCGA-FS-A1YY 
        4.14        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-A1ZG 
      195.98         8.35        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-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F8 TCGA-FS-A4F9 
       23.21         5.29         3.06        30.90       173.19        13.28 
TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
       80.68        55.59        11.54        19.30         9.90        18.25 
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-A4U4 TCGA-GN-A4U8 TCGA-GN-A8LK TCGA-GN-A9SD TCGA-LH-A9QB 
        7.59        34.49        46.92        43.23        59.41        85.05 
TCGA-OD-A75X TCGA-QB-A6FS TCGA-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-AA21 TCGA-WE-A8K1 
      120.07        44.05        79.99         8.09        92.84        47.54 
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-XV-AB01 TCGA-Z2-AA3S 
        1.94        37.32        24.99         6.61        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 
             52.73              45.99 
[1] "0.3 - 185.1 (52.7)" "0.0 - 346.5 (46.0)"
[1] "hr=" "1.1"
D77V2, survival
                    sevent
clus2                  0   1
  20P LOSS MUTATED     9  15
  20P LOSS WILD-TYPE 157 177
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                24                334 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                15                177 
$`20P LOSS MUTATED`
TCGA-WE-A8K5 TCGA-3N-A9WB TCGA-D3-A2JC TCGA-D3-A3CF TCGA-D3-A8GK TCGA-DA-A1HV 
       61.15        17.03        86.76        24.53       170.20        76.57 
TCGA-DA-A1I1 TCGA-DA-A95Y TCGA-EE-A29E TCGA-EE-A29G TCGA-ER-A19C TCGA-ER-A19E 
      222.51        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        48.99        33.21        46.45        11.41 
TCGA-FS-A4F4 TCGA-GN-A4U3 TCGA-GN-A4U7 TCGA-W3-AA1W TCGA-YG-AA3O TCGA-YG-AA3P 
       66.67       121.91        10.42       219.16        37.94        14.43 

$`20P LOSS WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-D3-A8GI TCGA-EB-A5SG 
       27.65        62.07        46.32        13.87        58.52        68.25 
TCGA-EB-A5SH TCGA-EE-A180 TCGA-EE-A184 TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GD 
       54.02        94.98        68.15       168.26         2.60       340.14 
TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 TCGA-ER-A198 TCGA-FR-A729 
      126.81       134.40        27.35        31.40        50.76       220.80 
TCGA-FS-A1ZF TCGA-FW-A3R5 TCGA-QB-AA9O TCGA-WE-AAA3 TCGA-3N-A9WC TCGA-3N-A9WD 
       15.45        36.95        18.05        21.40        66.48        12.99 
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-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-A2JD 
      103.10        65.49        23.77       115.53       168.00        11.87 
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-A3CB TCGA-D3-A3CC 
       59.57       130.72        58.06        46.98       166.52        86.93 
TCGA-D3-A3CE TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E 
       60.23         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-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       135.02        88.87        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        43.36        72.10 
TCGA-DA-A95W TCGA-DA-A95X TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH 
       37.35        73.94        13.02        13.87        10.36        20.35 
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-A185 TCGA-EE-A20B 
        8.65        33.73        14.70        26.89         4.96       133.81 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C 
      151.27        91.56        13.55        63.35        85.08        78.97 
TCGA-EE-A29D TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
       13.97        64.64        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-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
       67.43       173.79       220.24        48.72       107.38        54.74 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
       79.66        75.48       102.12        13.91        42.77        81.21 
TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 
       44.88        94.82        21.67       129.27        28.83        19.76 
TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-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-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA 
      248.65        43.23       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-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 
       53.19       201.80        51.35       134.33       152.81        35.44 
TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19F 
       13.94         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 
      302.07         6.44       131.51        61.05        44.09       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       105.07        43.82        23.34 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
       20.15        28.83        41.56       247.04        93.01        46.98 
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-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW 
       18.77        38.27        34.82        36.26       104.42       216.92 
TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 
       48.59       228.59       202.65        20.91        28.08         7.79 
TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZG TCGA-FS-A1ZH 
       27.72        48.85       357.37        53.52         9.70        32.75 
TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZS 
       47.38        23.93       101.26        74.73       133.55       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-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC 
       50.14        28.73       174.84        34.03        26.73        54.41 
TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
       80.68        17.46        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 
       19.43         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-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-AA21 TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K6 
      111.09        42.08       105.04        24.03        49.05        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-XV-AB01 TCGA-YD-A89C 
       49.51        12.16        40.41        24.99        13.25         6.90 
TCGA-YD-A9TA TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
       49.18        27.58        96.99        15.98 

  20P LOSS MUTATED 20P LOSS WILD-TYPE 
             10.42               0.20 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
            222.51             369.93 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
            55.070             52.255 
[1] "10.4 - 222.5 (55.1)" "0.2 - 369.9 (52.3)" 
[1] "hr=" "1.2"
D77V3, continuous
                    vv
clus                 I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  20P LOSS MUTATED          0       0       1        1        1        3
  20P LOSS WILD-TYPE       13       7      28       17       27       23
                    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        36         14
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  20P LOSS MUTATED            2          3        3
  20P LOSS WILD-TYPE         33         51       18
D77V4, multiclass
            clus
vv           20P LOSS MUTATED 20P LOSS WILD-TYPE
  I/II NOS                  0                 13
  STAGE 0                   0                  7
  STAGE I                   1                 28
  STAGE IA                  1                 17
  STAGE IB                  1                 27
  STAGE II                  3                 23
  STAGE IIA                 1                 13
  STAGE IIB                 1                 18
  STAGE IIC                 2                 13
  STAGE III                 3                 36
  STAGE IIIA                1                 14
  STAGE IIIB                2                 33
  STAGE IIIC                3                 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
  20P LOSS MUTATED       4  5  7  5
  20P LOSS WILD-TYPE    60 68 74 62
D77V5, multiclass
       clus
vv      20P LOSS MUTATED 20P LOSS WILD-TYPE
  T0+T1                4                 60
  T2                   5                 68
  T3                   7                 74
  T4                   5                 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
  20P LOSS MUTATED    10   2   4   4
  20P LOSS WILD-TYPE 167  63  35  41
D77V6, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  N0               10                167
  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    20   3
  20P LOSS WILD-TYPE 299  19
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED     20    3
  20P LOSS WILD-TYPE  299   19
   clus
vv  20P LOSS MUTATED 20P LOSS WILD-TYPE
  0               20                299
  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  22
  20P LOSS WILD-TYPE  44 298
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      3   22
  20P LOSS WILD-TYPE   44  298
     clus
vv    20P LOSS MUTATED 20P LOSS WILD-TYPE
  NO                 3                 44
  YES               22                298
[1] 2 2
[1] FALSE
D77V10, continuous
D77V11, binary
                    cls
clus                   0   1
  20P LOSS MUTATED     8  17
  20P LOSS WILD-TYPE 130 212
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      8   17
  20P LOSS WILD-TYPE  130  212
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  FEMALE                8                130
  MALE                 17                212
[1] 2 2
[1] FALSE
D77V12, binary
                    cls
clus                   0   1
  20P LOSS MUTATED    22   3
  20P LOSS WILD-TYPE 297  44
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED     22    3
  20P LOSS WILD-TYPE  297   44
     clus
vv    20P LOSS MUTATED 20P LOSS WILD-TYPE
  NO                22                297
  YES                3                 44
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  20P LOSS MUTATED       0                         0    23
  20P LOSS WILD-TYPE     5                         1   330
D77V13, multiclass
                           clus
vv                          20P LOSS MUTATED 20P LOSS WILD-TYPE
  ASIAN                                    0                  5
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   23                330
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V14, binary
                    cls
clus                   0   1
  20P LOSS MUTATED     2  22
  20P LOSS WILD-TYPE   5 330
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      2   22
  20P LOSS WILD-TYPE    5  330
                        clus
vv                       20P LOSS MUTATED 20P LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  5
  NOT HISPANIC OR LATINO               22                330
[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 126 120
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 6                246 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 4                120 
$`20Q LOSS MUTATED`
TCGA-WE-A8K5 TCGA-DA-A1I1 TCGA-EE-A29G TCGA-ER-A19C TCGA-FS-A1ZE TCGA-GN-A4U3 
       52.73        68.68        44.28        39.81        43.92       120.53 

$`20Q LOSS WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A8GI TCGA-EB-A5SG TCGA-EE-A180 
        9.76        62.07        38.76        13.41        33.24        31.96 
TCGA-EE-A20H TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 
      166.75       269.03        52.90       134.40        27.35        19.04 
TCGA-FR-A729 TCGA-FW-A3R5 TCGA-WE-AAA3 TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 
      216.43        36.95         7.40        60.46        12.99        14.83 
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
        8.42        15.72        31.89       110.93        49.35       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-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL 
       15.75       168.00        86.30       107.61        36.30       171.58 
TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CC 
       64.83        66.08        43.53        58.06       140.98        40.01 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E 
       59.70        24.53         9.34        90.21        23.67       173.85 
TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL 
       30.67       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       110.53        60.10        64.83        58.85 
TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-DA-A95V TCGA-DA-A95W TCGA-DA-A95X 
       30.44       225.11         8.71        72.10         0.76        65.03 
TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A6L9 
       14.14        12.30         3.91        16.41        52.41        18.21 
TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20C 
       13.15        24.89        20.38         0.00        26.24        75.55 
TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H 
       79.20        75.22        76.14        12.99         0.26        47.41 
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-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ 
       30.02        77.98        26.14        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        93.63         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-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA 
      145.45       227.01       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-EE-A3JI 
      111.85        45.90         3.35       168.85        19.86       135.98 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19D 
       34.45        10.49         7.82         4.54        53.29        11.47 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P 
      184.60       150.12        99.06        59.84        42.51       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        73.05        22.36         4.70 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
       16.87        10.19        28.67       173.29        68.52        15.48 
TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A7U8 
       32.05        74.47         4.50       174.21         4.14        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-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM 
       27.62       312.07        32.78         7.82        36.33        78.61 
TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-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        18.25         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-A4U4 TCGA-GN-A4U8 TCGA-GN-A8LK TCGA-GN-A9SD TCGA-LH-A9QB TCGA-OD-A75X 
       34.49        46.92        43.23        59.41        85.05       297.01 
TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 
        7.23         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        47.54 
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-XV-AB01 TCGA-YG-AA3O TCGA-Z2-AA3S 
        1.94        37.32        24.99         6.61        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 
            48.505             46.455 
[1] "39.8 - 120.5 (48.5)" "0.0 - 346.5 (46.5)" 
[1] "hr=" "1.4"
D78V2, survival
                    sevent
clus2                  0   1
  20Q LOSS MUTATED     3   5
  20Q LOSS WILD-TYPE 163 187
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 8                350 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 5                187 
$`20Q LOSS MUTATED`
TCGA-WE-A8K5 TCGA-DA-A1I1 TCGA-EE-A29G TCGA-ER-A19C TCGA-FS-A1ZE TCGA-GN-A4U3 
       61.15       222.51        72.07        48.89        46.45       121.91 
TCGA-GN-A4U7 TCGA-YG-AA3P 
       10.42        14.43 

$`20Q LOSS WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-D3-A8GI TCGA-EB-A5SG 
       27.65        62.07        46.32        13.87        58.52        68.25 
TCGA-EB-A5SH TCGA-EE-A180 TCGA-EE-A184 TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GD 
       54.02        94.98        68.15       168.26         2.60       340.14 
TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 TCGA-ER-A198 TCGA-FR-A729 
      126.81       134.40        27.35        31.40        50.76       220.80 
TCGA-FS-A1ZF TCGA-FW-A3R5 TCGA-QB-AA9O TCGA-WE-AAA3 TCGA-3N-A9WB TCGA-3N-A9WC 
       15.45        36.95        18.05        21.40        17.03        66.48 
TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 
       12.99        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-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-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-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-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR 
      166.52        86.93        60.23        24.53         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-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM 
       23.61        26.43       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-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-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 
      135.02        88.87        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        43.36        72.10        37.35 
TCGA-DA-A95X TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH 
       73.94        14.14        13.02        13.87        10.36        20.35 
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-A185 TCGA-EE-A20B 
        8.65        33.73        14.70        26.89         4.96       133.81 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C 
      151.27        91.56        13.55        63.35        85.08        78.97 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P 
       13.97        63.78        64.64        56.84        18.61        56.42 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W 
       66.74        14.47        61.28       369.93        25.87       195.02 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
       17.92        46.82       115.96        59.64        39.29        86.14 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       59.28        67.43       173.79       220.24        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-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-A2MS TCGA-EE-A2MT TCGA-EE-A2MU 
       47.54       248.65        43.23       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-A3JB TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI 
       34.32        53.19       201.80        51.35       134.33       152.81 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19D 
       35.44        13.94         9.17        77.75        98.40        12.59 
TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L 
       13.02        26.37       302.07       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        44.09       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       105.07        43.82        23.34        20.15        28.83 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL 
       48.99        41.56       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-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW 
       18.77        38.27        34.82        36.26       104.42       216.92 
TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 
       48.59       228.59       202.65        20.91        28.08         7.79 
TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZG TCGA-FS-A1ZH 
       27.72        48.85       357.37        53.52         9.70        32.75 
TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR 
       47.38        23.93       101.26        74.73       133.55        11.41 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ 
      148.80        53.16        26.56        49.48        27.09        27.02 
TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 
       77.82        50.14        66.67        28.73       174.84        34.03 
TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV 
       26.73        54.41        80.68        17.46        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        19.43         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-A4U4 TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A8LL 
       48.00        39.35        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-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-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO 
       24.03        49.05        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-AAA4 TCGA-XV-AB01 TCGA-YD-A89C TCGA-YD-A9TA TCGA-YG-AA3O TCGA-Z2-A8RT 
       24.99        13.25         6.90        49.18        37.94        27.58 
TCGA-Z2-AA3S TCGA-Z2-AA3V 
       96.99        15.98 

  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
             10.42               0.20 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
            222.51             369.93 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
            55.020             52.255 
[1] "10.4 - 222.5 (55.0)" "0.2 - 369.9 (52.3)" 
[1] "hr=" "1.1"
D78V3, continuous
                    vv
clus                 I/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       26
                    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        37         14
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  20Q LOSS MUTATED            0          1        2
  20Q LOSS WILD-TYPE         35         53       19
D78V4, multiclass
            clus
vv           20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  I/II NOS                  0                 13
  STAGE 0                   0                  7
  STAGE I                   1                 28
  STAGE IA                  0                 18
  STAGE IB                  0                 28
  STAGE II                  0                 26
  STAGE IIA                 0                 14
  STAGE IIB                 1                 18
  STAGE IIC                 1                 14
  STAGE III                 2                 37
  STAGE IIIA                1                 14
  STAGE IIIB                0                 35
  STAGE IIIC                1                 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
  20Q LOSS MUTATED       1  3  1  3
  20Q LOSS WILD-TYPE    63 70 80 64
D78V5, multiclass
       clus
vv      20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  T0+T1                1                 63
  T2                   3                 70
  T3                   1                 80
  T4                   3                 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
  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 312  20
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      7    2
  20Q LOSS WILD-TYPE  312   20
   clus
vv  20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  0                7                312
  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  46 312
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      1    8
  20Q LOSS WILD-TYPE   46  312
     clus
vv    20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  NO                 1                 46
  YES                8                312
[1] 2 2
[1] FALSE
D78V10, continuous
D78V11, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     2   7
  20Q LOSS WILD-TYPE 136 222
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      2    7
  20Q LOSS WILD-TYPE  136  222
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  FEMALE                2                136
  MALE                  7                222
[1] 2 2
[1] FALSE
D78V12, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     8   1
  20Q LOSS WILD-TYPE 311  46
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      8    1
  20Q LOSS WILD-TYPE  311   46
     clus
vv    20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  NO                 8                311
  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   345
D78V13, multiclass
                           clus
vv                          20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  ASIAN                                    0                  5
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                    8                345
[1] 3 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   6 344
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      1    8
  20Q LOSS WILD-TYPE    6  344
                        clus
vv                       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO                8                344
[1] 2 2
[1] FALSE

Clustering(79) Variable = 21Q LOSS MUTATION ANALYSIS
D79V1, survival
                    sevent
clus2                  0   1
  21Q LOSS MUTATED    25  18
  21Q LOSS WILD-TYPE 103 106
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                43                209 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                18                106 
$`21Q LOSS MUTATED`
TCGA-D3-A3C8 TCGA-EE-A180 TCGA-EE-A2GO TCGA-3N-A9WD TCGA-D3-A1Q5 TCGA-D3-A2JB 
       38.76        31.96        52.90        12.99       110.93       168.00 
TCGA-D3-A2JC TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A51T 
       86.30        36.30       171.58        64.83        66.08        11.34 
TCGA-DA-A95V TCGA-DA-A95Z TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A29G TCGA-EE-A29H 
       72.10        12.30        24.89        20.38        44.28        47.41 
TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2M6 
      346.49       185.19        30.02        77.98        26.14       103.13 
TCGA-EE-A2MK TCGA-EE-A2MS TCGA-ER-A197 TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZM 
       89.26       143.93        10.49        43.92         7.82        78.61 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FW-A5DY TCGA-GN-A262 TCGA-GN-A268 
       35.28         4.47        23.21        19.30        53.29        42.48 
TCGA-GN-A4U3 TCGA-GN-A9SD TCGA-OD-A75X TCGA-W3-AA1R TCGA-WE-A8ZQ TCGA-WE-A8ZY 
      120.53        59.41       297.01        79.99        62.89        48.39 
TCGA-YG-AA3O 
       28.21 

$`21Q LOSS WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A8GI TCGA-EB-A5SG TCGA-EE-A20H TCGA-EE-A2GD 
        9.76        62.07        13.41        33.24       166.75       269.03 
TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 TCGA-FR-A729 TCGA-FW-A3R5 TCGA-WE-A8K5 
      134.40        27.35        19.04       216.43        36.95        52.73 
TCGA-WE-AAA3 TCGA-3N-A9WC TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
        7.40        60.46        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-A2JA TCGA-D3-A2JG TCGA-D3-A2JP TCGA-D3-A3C6 
       45.99        62.86        15.75       107.61        43.53        58.06 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR 
      140.98        40.01        59.70        24.53         9.34        90.21 
TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R 
       23.67       173.85        30.67       144.46        31.76        62.70 
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        68.68       150.61       110.53        60.10 
TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-DA-A95W 
       64.83        58.85        30.44       225.11         8.71         0.76 
TCGA-DA-A95X TCGA-DA-A95Y TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A6L9 
       65.03        14.14         3.91        16.41        52.41        18.21 
TCGA-EE-A17X TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29B 
       13.15         0.00        26.24        75.55        79.20        75.22 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29Q 
       76.14        12.99         0.26        47.74        27.16        61.12 
TCGA-EE-A2A1 TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
      115.43        12.95       201.60        68.65        10.62        32.48 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU 
       18.35        93.63         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-A2MJ TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MT TCGA-EE-A2MU 
       63.25       104.78       145.45       227.01        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       168.85        19.86 
TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C 
      135.98        34.45         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       184.60       150.12        99.06        59.84        42.51 
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        73.05        22.36 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET 
        4.70        16.87        10.19        28.67       173.29        68.52 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       15.48        32.05        74.47         4.50       174.21         4.14 
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-A1ZJ TCGA-FS-A1ZQ 
        8.35        27.62       312.07        32.78        36.33       130.95 
TCGA-FS-A1ZS TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 
      136.27         5.29         3.06        30.90        66.67       173.19 
TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV TCGA-GF-A3OT TCGA-GF-A4EO 
       13.28        80.68        55.59        11.54         9.90        18.25 
TCGA-GF-A6C8 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A4U4 
        1.91       117.93        96.92        17.06         7.59        34.49 
TCGA-GN-A4U8 TCGA-GN-A8LK TCGA-LH-A9QB TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 
       46.92        43.23        85.05         7.23         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        47.54        65.42        12.69        21.90        10.95 
TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-XV-AB01 TCGA-Z2-AA3S 
        1.94        37.32        24.99         6.61        91.23 

  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
              4.47               0.00 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
            346.49             312.07 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
             48.39              45.90 
[1] "4.5 - 346.5 (48.4)" "0.0 - 312.1 (45.9)"
[1] "hr=" "1.4"
D79V2, survival
                    sevent
clus2                  0   1
  21Q LOSS MUTATED    34  35
  21Q LOSS WILD-TYPE 132 157
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                69                289 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                35                157 
$`21Q LOSS MUTATED`
TCGA-D3-A3C8 TCGA-EE-A180 TCGA-EE-A2GO TCGA-QB-AA9O TCGA-3N-A9WD TCGA-D3-A1Q5 
       46.32        94.98       126.81        18.05        12.99       112.57 
TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
      168.00        86.76        42.08       171.58        66.48        66.08 
TCGA-D3-A51T TCGA-D3-A5GS TCGA-D3-A8GN TCGA-D9-A1JX TCGA-D9-A6E9 TCGA-D9-A6EA 
       26.89        18.18       161.00         7.10         9.90        25.18 
TCGA-DA-A1I0 TCGA-DA-A95V TCGA-DA-A95Z TCGA-EB-A44R TCGA-EE-A17Y TCGA-EE-A181 
       20.38        72.10        13.02        10.36        27.22        33.73 
TCGA-EE-A20B TCGA-EE-A20I TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29T TCGA-EE-A29V 
      133.81        13.55        72.07        64.64       369.93        25.87 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC 
      195.02        17.92        59.64        86.14        59.28        67.43 
TCGA-EE-A2GI TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2MK TCGA-EE-A2MN TCGA-EE-A2MS 
       48.72        21.67       129.27       180.39        47.54       162.48 
TCGA-EE-A3AH TCGA-EE-A3J5 TCGA-EE-A3JA TCGA-ER-A197 TCGA-ER-A19E TCGA-FS-A1ZA 
      138.81        36.95        53.19        13.94        13.02        27.72 
TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZM TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW 
       46.45         9.70       101.26        53.16        26.56        49.48 
TCGA-FW-A5DY TCGA-GN-A262 TCGA-GN-A266 TCGA-GN-A268 TCGA-GN-A4U3 TCGA-GN-A4U9 
       19.30       139.89        10.13        62.79       121.91        22.13 
TCGA-GN-A9SD TCGA-OD-A75X TCGA-RP-A694 TCGA-W3-AA1O TCGA-W3-AA1R TCGA-WE-A8ZQ 
       59.41       297.90         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-D3-A2JE TCGA-D3-A2JF TCGA-D3-A3ML TCGA-D3-A8GI TCGA-EB-A5SG TCGA-EB-A5SH 
       27.65        62.07        13.87        58.52        68.25        54.02 
TCGA-EE-A184 TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2MR TCGA-EE-A3JD 
       68.15       168.26         2.60       340.14       134.40        27.35 
TCGA-ER-A193 TCGA-ER-A198 TCGA-FR-A729 TCGA-FS-A1ZF TCGA-FW-A3R5 TCGA-WE-A8K5 
       31.40        50.76       220.80        15.45        36.95        61.15 
TCGA-WE-AAA3 TCGA-3N-A9WB TCGA-3N-A9WC TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q3 
       21.40        17.03        66.48        14.93        16.57        16.67 
TCGA-D3-A1Q4 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA 
      112.04        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-A2JD TCGA-D3-A2JG TCGA-D3-A2JK TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 
       11.87       113.52        12.10        59.57       130.72        58.06 
TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO 
       46.98       166.52        86.93        60.23        24.53         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-A5GL TCGA-D3-A5GN 
      145.12        32.94        22.62        63.81       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-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-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-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6EC 
        3.65        18.12        15.39        22.29        18.44        77.56 
TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 
       22.95        76.57        36.03       144.89       222.51       176.55 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB 
       35.93       135.02        88.87        53.92        65.92        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        43.36        37.35 
TCGA-DA-A95X TCGA-DA-A95Y TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UL TCGA-EB-A5UN 
       73.94        14.14        13.87        20.35        29.29        58.92 
TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A182 TCGA-EE-A183 
        7.04        36.46        29.82         8.65        14.70        26.89 
TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C 
        4.96       151.27        91.56        63.35        85.08        78.97 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
       13.97        63.78        56.84        18.61        56.42        66.74 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-EE-A2GE 
       14.47        61.28        46.82       115.96        39.29       173.79 
TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN 
      220.24       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-A2M7 
       13.91        42.77        81.21        44.88        94.82        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-A2ML TCGA-EE-A2MM TCGA-EE-A2MP 
       16.96       204.66        96.23       216.66       167.90       248.65 
TCGA-EE-A2MQ TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC 
       43.23        71.21        53.26       124.31       122.73        64.04 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3J4 
       28.77        54.51        13.81        41.59       172.18       127.20 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI 
       64.08        34.32       201.80        51.35       134.33       152.81 
TCGA-ER-A195 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D 
       35.44         9.17        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       302.07       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 
       44.09       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 
      105.07        43.82        23.34        20.15        28.83        48.99 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K 
       41.56       247.04        93.01        46.98        33.21        12.95 
TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A7U9 
      149.03        92.98       174.21        15.72        27.85        18.77 
TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-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-A1ZB 
      228.59       202.65        20.91        28.08         7.79        48.85 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZP 
      357.37        53.52        32.75        47.38        23.93        74.73 
TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 
      133.55        11.41       148.80        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-A3TU TCGA-FW-A3TV TCGA-GF-A3OT 
       54.41        80.68        17.46        55.59        13.51         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 
       19.43         2.04        15.78       117.93        96.92        64.44 
TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A8LK 
       32.48        48.00        39.35        10.42        48.89        50.10 
TCGA-GN-A8LL TCGA-HR-A2OG TCGA-HR-A2OH TCGA-LH-A9QB TCGA-QB-A6FS TCGA-RP-A690 
       21.37         0.23        65.88       368.78         7.23         0.20 
TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1Q TCGA-W3-AA1V 
        0.33       228.16        63.02       121.08        69.07        42.08 
TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K6 TCGA-WE-A8ZM 
      219.16       105.04        24.03        49.05        17.95       101.33 
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-AAA4 TCGA-XV-AB01 TCGA-YD-A9TA TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S 
       24.99        13.25        49.18        14.43        27.58        96.99 
TCGA-Z2-AA3V 
       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              53.52 
[1] "0.7 - 369.9 (49.5)" "0.2 - 368.8 (53.5)"
[1] "hr=" "1"  
D79V3, continuous
                    vv
clus                 I/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       20
                    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        29         12
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  21Q LOSS MUTATED            6          9        5
  21Q LOSS WILD-TYPE         29         45       16
D79V4, multiclass
            clus
vv           21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  I/II NOS                  3                 10
  STAGE 0                   3                  4
  STAGE I                   3                 26
  STAGE IA                  5                 13
  STAGE IB                  4                 24
  STAGE II                  6                 20
  STAGE IIA                 2                 12
  STAGE IIB                 2                 17
  STAGE IIC                 3                 12
  STAGE III                10                 29
  STAGE IIIA                3                 12
  STAGE IIIB                6                 29
  STAGE IIIC                9                 45
  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 67 52
D79V5, multiclass
       clus
vv      21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  T0+T1               10                 54
  T2                  11                 62
  T3                  14                 67
  T4                  15                 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
  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 259  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     60    5
  21Q LOSS WILD-TYPE  259   17
   clus
vv  21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  0               60                259
  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  39 258
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      8   62
  21Q LOSS WILD-TYPE   39  258
     clus
vv    21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  NO                 8                 39
  YES               62                258
[1] 2 2
[1] FALSE
D79V10, continuous
D79V11, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED    28  42
  21Q LOSS WILD-TYPE 110 187
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     28   42
  21Q LOSS WILD-TYPE  110  187
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  FEMALE               28                110
  MALE                 42                187
[1] 2 2
[1] FALSE
D79V12, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED    62   8
  21Q LOSS WILD-TYPE 257  39
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     62    8
  21Q LOSS WILD-TYPE  257   39
     clus
vv    21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  NO                62                257
  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   288
D79V13, multiclass
                           clus
vv                          21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  ASIAN                                    2                  3
  BLACK OR AFRICAN AMERICAN                1                  0
  WHITE                                   65                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"
D79V14, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED     1  68
  21Q LOSS WILD-TYPE   6 284
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      1   68
  21Q LOSS WILD-TYPE    6  284
                        clus
vv                       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO               68                284
[1] 2 2
[1] FALSE

Clustering(80) Variable = 22Q LOSS MUTATION ANALYSIS
D80V1, survival
                    sevent
clus2                  0   1
  22Q LOSS MUTATED    10  14
  22Q LOSS WILD-TYPE 118 110
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                24                228 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                14                110 
$`22Q LOSS MUTATED`
TCGA-D3-A2JF TCGA-D3-A1Q8 TCGA-D3-A2JB TCGA-D3-A2JL TCGA-DA-A1I2 TCGA-DA-A95X 
       62.07        19.04       168.00       171.58       150.61        65.03 
TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A2A6 TCGA-EE-A2GP TCGA-EE-A2MG TCGA-EE-A2MM 
       76.14         0.26        77.98         0.76        94.19       145.45 
TCGA-ER-A19D TCGA-ER-A19H TCGA-ER-A19P TCGA-FS-A1YW TCGA-FS-A1ZJ TCGA-FS-A1ZY 
       11.47       150.12       120.76       171.78        36.33         5.29 
TCGA-FS-A4F0 TCGA-GF-A4EO TCGA-GN-A4U3 TCGA-RP-A693 TCGA-W3-A825 TCGA-WE-A8ZQ 
       30.90        18.25       120.53         0.33         1.97        62.89 

$`22Q LOSS WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A3C8 TCGA-D3-A8GI TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A20H 
        9.76        38.76        13.41        33.24        31.96       166.75 
TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 TCGA-FR-A729 
      269.03        52.90       134.40        27.35        19.04       216.43 
TCGA-FW-A3R5 TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 
       36.95        52.73         7.40        60.46        12.99        14.83 
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
        8.42        15.72        31.89       110.93        49.35       133.25 
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-A2JC TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP 
       86.30       107.61        36.30        64.83        66.08        43.53 
TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO 
       58.06       140.98        40.01        59.70        24.53         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K 
       90.21        23.67       173.85        30.67       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-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I5 
       69.21        22.85        76.34       138.67        68.68       110.53 
TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 
       60.10        64.83        58.85        30.44       225.11         8.71 
TCGA-DA-A95V TCGA-DA-A95W TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5KH 
       72.10         0.76        14.14        12.30         3.91        16.41 
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-A183 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29G 
       26.24        75.55        79.20        75.22        12.99        44.28 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W 
       47.41        47.74        27.16        61.12       346.49       185.19 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ 
      115.43        30.02        26.14        12.95       201.60        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        93.63         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-A2MS 
      171.85        63.25        89.26       104.78       227.01       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-A195 TCGA-ER-A197 TCGA-ER-A199 
      168.85        19.86       135.98        34.45        10.49         7.82 
TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19G TCGA-ER-A19L TCGA-ER-A19M 
        4.54        53.29        39.81       184.60        99.06        59.84 
TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
       42.51        49.71        47.18       146.63        73.05        22.36 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET 
        4.70        16.87        10.19        28.67       173.29        68.52 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       15.48        32.05        74.47         4.50       174.21         4.14 
TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
       26.20         5.65        10.06        49.74       195.98         8.35 
TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZM 
       27.62       312.07        32.78        43.92         7.82        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-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV 
       66.67       173.19        13.28        80.68        55.59        11.54 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
       19.30         9.90         1.91        53.29       117.93        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-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 TCGA-W3-A824 
       59.41        85.05       297.01         7.23         0.20       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-A8K1 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-A8ZY 
       47.54        65.42        12.69        21.90        10.95        48.39 
TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-XV-AB01 TCGA-YG-AA3O TCGA-Z2-AA3S 
        1.94        37.32        24.99         6.61        28.21        91.23 

  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
              0.26               0.00 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
            171.78             346.49 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
             63.96              45.80 
[1] "0.3 - 171.8 (64.0)" "0.0 - 346.5 (45.8)"
[1] "hr=" "1.1"
D80V2, survival
                    sevent
clus2                  0   1
  22Q LOSS MUTATED    14  24
  22Q LOSS WILD-TYPE 152 168
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                38                320 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                24                168 
$`22Q LOSS MUTATED`
TCGA-D3-A2JF TCGA-EE-A184 TCGA-D3-A1Q8 TCGA-D3-A2JB TCGA-D3-A2JL TCGA-D3-A5GO 
       62.07        68.15        28.08       168.00       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        73.94        10.36 
TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A2A6 TCGA-EE-A2GP TCGA-EE-A2MG TCGA-EE-A2MM 
       78.97        63.78        86.14        13.91       103.20       167.90 
TCGA-EE-A3JA TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19H TCGA-ER-A19P TCGA-ER-A19T 
       53.19        12.59        13.02       152.35       162.08         8.88 
TCGA-FR-A8YD TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1ZJ TCGA-FS-A1ZY TCGA-FS-A4F0 
       36.26       216.92        48.59        47.38        27.09        77.82 
TCGA-GF-A4EO TCGA-GN-A266 TCGA-GN-A4U3 TCGA-GN-A4U9 TCGA-RP-A693 TCGA-W3-A825 
       19.43        10.13       121.91        22.13         0.33        63.02 
TCGA-WE-A8JZ TCGA-WE-A8ZQ 
       24.03        63.22 

$`22Q LOSS WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-D3-A8GI TCGA-EB-A5SG TCGA-EB-A5SH 
       27.65        46.32        13.87        58.52        68.25        54.02 
TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR 
       94.98       168.26         2.60       340.14       126.81       134.40 
TCGA-EE-A3JD TCGA-ER-A193 TCGA-ER-A198 TCGA-FR-A729 TCGA-FS-A1ZF TCGA-FW-A3R5 
       27.35        31.40        50.76       220.80        15.45        36.95 
TCGA-QB-AA9O TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD 
       18.05        61.15        21.40        17.03        66.48        12.99 
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-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
      133.25        31.59        90.90        95.74        43.43       103.10 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG 
       65.49        23.77       115.53        86.76        11.87       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-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF 
       58.06        46.98       166.52        86.93        60.23        24.53 
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-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-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-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       222.51        35.93       135.02        88.87 
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        43.36        72.10        37.35        14.14        13.02 
TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 
       13.87        20.35        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-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-A29D TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N 
       85.08        13.97        72.07        64.64        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-A2GB TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       59.28        67.43       173.79       220.24        48.72       107.38 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GR TCGA-EE-A2GS 
       54.74        79.66        75.48       102.12        42.77        81.21 
TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 
       44.88        94.82        21.67       129.27        28.83        19.76 
TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MH TCGA-EE-A2MI 
       61.51        47.28       103.27       268.73        16.96       204.66 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ 
       96.23       180.39       216.66        47.54       248.65        43.23 
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-A3JE 
      127.20        36.95        64.08        34.32       201.80        51.35 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A 
      134.33       152.81        35.44        13.94         9.17        77.75 
TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19J TCGA-ER-A19L 
       98.40        48.89        26.37       302.07         6.44       131.51 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 
       61.05        44.09        50.89        49.48       148.18       105.07 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH 
       43.82        23.34        20.15        28.83        48.99        41.56 
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-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-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ 
        9.70        32.75        23.93       101.26        74.73       133.55 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZZ 
       11.41       148.80        53.16        26.56        49.48        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-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
       54.41        80.68        17.46        55.59        13.51        19.30 
TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        9.90         2.04        15.78       139.89       117.93        96.92 
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-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-RP-A690 TCGA-RP-A694 TCGA-W3-A824 
      368.78       297.90         7.23         0.20         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-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-A8ZX TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 
       11.80        35.80        49.51        12.16        40.41        24.99 
TCGA-XV-AB01 TCGA-YD-A89C TCGA-YD-A9TA TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-A8RT 
       13.25         6.90        49.18        37.94        14.43        27.58 
TCGA-Z2-AA3S TCGA-Z2-AA3V 
       96.99        15.98 

  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
              0.33               0.20 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
            216.92             369.93 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
            62.545             50.450 
[1] "0.3 - 216.9 (62.5)" "0.2 - 369.9 (50.5)"
[1] "hr=" "1.2"
D80V3, continuous
                    vv
clus                 I/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       24
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  22Q LOSS MUTATED           1         2         1         2          0
  22Q LOSS WILD-TYPE        13        17        14        37         15
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  22Q LOSS MUTATED            5          2        3
  22Q LOSS WILD-TYPE         30         52       18
D80V4, multiclass
            clus
vv           22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  I/II NOS                  3                 10
  STAGE 0                   1                  6
  STAGE I                   4                 25
  STAGE IA                  2                 16
  STAGE IB                  7                 21
  STAGE II                  2                 24
  STAGE IIA                 1                 13
  STAGE IIB                 2                 17
  STAGE IIC                 1                 14
  STAGE III                 2                 37
  STAGE IIIA                0                 15
  STAGE IIIB                5                 30
  STAGE IIIC                2                 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
  22Q LOSS MUTATED       5 12  6  7
  22Q LOSS WILD-TYPE    59 61 75 60
D80V5, multiclass
       clus
vv      22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  T0+T1                5                 59
  T2                  12                 61
  T3                   6                 75
  T4                   7                 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
  22Q LOSS MUTATED    25   6   2   4
  22Q LOSS WILD-TYPE 152  59  37  41
D80V6, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  N0               25                152
  N1                6                 59
  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 284  19
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     35    3
  22Q LOSS WILD-TYPE  284   19
   clus
vv  22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  0               35                284
  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  42 286
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      5   34
  22Q LOSS WILD-TYPE   42  286
     clus
vv    22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  NO                 5                 42
  YES               34                286
[1] 2 2
[1] FALSE
D80V10, continuous
D80V11, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED    15  24
  22Q LOSS WILD-TYPE 123 205
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     15   24
  22Q LOSS WILD-TYPE  123  205
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  FEMALE               15                123
  MALE                 24                205
[1] 2 2
[1] FALSE
D80V12, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED    34   5
  22Q LOSS WILD-TYPE 285  42
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     34    5
  22Q LOSS WILD-TYPE  285   42
     clus
vv    22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  NO                34                285
  YES                5                 42
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  22Q LOSS MUTATED       1                         1    35
  22Q LOSS WILD-TYPE     4                         0   318
D80V13, multiclass
                           clus
vv                          22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  ASIAN                                    1                  4
  BLACK OR AFRICAN AMERICAN                1                  0
  WHITE                                   35                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"
D80V14, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED     1  37
  22Q LOSS WILD-TYPE   6 315
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      1   37
  22Q LOSS WILD-TYPE    6  315
                        clus
vv                       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO               37                315
[1] 2 2
[1] FALSE

Clustering(81) Variable = XP LOSS MUTATION ANALYSIS
D81V1, survival
                   sevent
clus2                0  1
  XP LOSS MUTATED   30 40
  XP LOSS WILD-TYPE 98 84
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               70               182 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               40                84 
$`XP LOSS MUTATED`
TCGA-ER-A193 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q8 TCGA-D3-A2J6 TCGA-D3-A2JC 
       19.04        31.89       110.93        19.04        25.64        86.30 
TCGA-D3-A2JG TCGA-D3-A2JL TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A51T TCGA-D3-A5GL 
      107.61       171.58        58.06        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       110.53 
TCGA-DA-A95X TCGA-EE-A17Y TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29D 
       65.03        24.89        75.55        79.20        76.14        12.99 
TCGA-EE-A29H TCGA-EE-A29Q TCGA-EE-A2A2 TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2MF 
       47.41        61.12        30.02         0.20        71.31       209.79 
TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MS TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3J8 
       89.26       145.45       143.93         4.41         6.28         3.35 
TCGA-EE-A3JH TCGA-ER-A19G TCGA-ER-A19L TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF 
       19.86       184.60        99.06         4.70        16.87        10.19 
TCGA-ER-A3ET TCGA-FR-A7U8 TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1ZG TCGA-FS-A1ZJ 
       68.52        26.20       171.78        49.74         7.82        36.33 
TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F9 
      130.95       136.27         3.06        30.90        66.67        13.28 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A268 TCGA-GN-A4U3 
       55.59        11.54         1.91        53.29        42.48       120.53 
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-D3-A2JE TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A8GI TCGA-EB-A5SG TCGA-EE-A180 
        9.76        62.07        38.76        13.41        33.24        31.96 
TCGA-EE-A20H TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-FR-A729 
      166.75       269.03        52.90       134.40        27.35       216.43 
TCGA-FW-A3R5 TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 
       36.95        52.73         7.40        60.46        12.99        14.83 
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1QA TCGA-D3-A1QB 
        8.42        15.72        49.35       133.25        76.41        62.60 
TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JH TCGA-D3-A2JN 
       45.99        62.86        15.75       168.00        36.30        64.83 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO 
       66.08        43.53       140.98        59.70        24.53         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K 
       90.21        23.67       173.85        30.67       144.46        31.76 
TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D3-A8GD TCGA-D3-A8GJ 
       62.70        45.70       177.86       124.08        23.61       179.97 
TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GP TCGA-D9-A3Z1 TCGA-D9-A6EC 
      120.00        69.53        70.62       135.12        15.02        69.21 
TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I7 
       22.85        76.34       138.67        68.68       150.61        60.10 
TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-DA-A95V 
       64.83        58.85        30.44       225.11         8.71        72.10 
TCGA-DA-A95W TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN 
        0.76        14.14        12.30         3.91        16.41        52.41 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A29B 
       18.21        13.15        20.38         0.00        26.24        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-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ 
      115.43        77.98        26.14        12.95       201.60        68.65 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GU 
       10.62        32.48        18.35        93.63         0.76        81.99 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MG TCGA-EE-A2MI 
      103.13        15.25         5.75        23.77        94.19       171.85 
TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MP TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA 
       63.25       104.78       227.01        23.51        53.26       124.31 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 
      122.73        64.04        54.51        67.89       111.85        45.90 
TCGA-EE-A3JB TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A 
      168.85       135.98        34.45        10.49         7.82         4.54 
TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19H TCGA-ER-A19M TCGA-ER-A19N 
       53.29        39.81        11.47       150.12        59.84        42.51 
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        73.05        22.36 
TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A3YN 
       28.67       173.29        15.48        32.05        74.47         4.50 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FS-A1Z0 TCGA-FS-A1Z3 
      174.21         4.14         5.65        10.06       195.98         8.35 
TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZM TCGA-FS-A1ZT 
       27.62       312.07        32.78        43.92        78.61        35.28 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F8 TCGA-FS-A4FD TCGA-FW-A5DY 
        4.47        23.21         5.29       173.19        80.68        19.30 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A26A 
        9.90        18.25       117.93        96.92        17.06         7.59 
TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-GN-A9SD TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 
       34.49        46.92        59.41         7.23         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-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-AAA0 TCGA-WE-AAA4 
       47.54        12.69        21.90        62.89        37.32        24.99 
TCGA-XV-AB01 TCGA-YG-AA3O 
        6.61        28.21 

  XP LOSS MUTATED XP LOSS WILD-TYPE 
              0.2               0.0 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
           297.01            346.49 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
           45.320            46.455 
[1] "0.2 - 297.0 (45.3)" "0.0 - 346.5 (46.5)"
[1] "hr=" "1.4"
D81V2, survival
                   sevent
clus2                 0   1
  XP LOSS MUTATED    41  53
  XP LOSS WILD-TYPE 125 139
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               94               264 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               53               139 
$`XP LOSS MUTATED`
TCGA-ER-A193 TCGA-FS-A1ZF TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q8 TCGA-D3-A2J6 
       31.40        15.45       112.04       112.57        28.08        43.43 
TCGA-D3-A2JC TCGA-D3-A2JG TCGA-D3-A2JL TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CC 
       86.76       113.52       171.58        58.06        46.98        86.93 
TCGA-D3-A51N TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GO TCGA-D3-A8GC TCGA-D3-A8GR 
       22.62        26.89       125.79       137.92        79.59       129.63 
TCGA-D9-A148 TCGA-D9-A1X3 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-DA-A1HW TCGA-DA-A1I5 
      151.53        18.12        22.29        18.44        36.03       135.02 
TCGA-DA-A1I8 TCGA-DA-A95X TCGA-EE-A17Y TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A20F 
       53.92        73.94        27.22         4.96       151.27        91.56 
TCGA-EE-A20I TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29H TCGA-EE-A29Q TCGA-EE-A29V 
       13.55        78.97        13.97        64.64        66.74        25.87 
TCGA-EE-A29X TCGA-EE-A2A2 TCGA-EE-A2GC TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2MF 
       17.92        59.64        67.43        42.77        81.21       268.73 
TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MS TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AH 
      180.39       167.90       162.48        28.77        13.81       138.81 
TCGA-EE-A3J8 TCGA-EE-A3JH TCGA-ER-A19E TCGA-ER-A19G TCGA-ER-A19L TCGA-ER-A2ND 
       34.32       134.33        13.02       302.07       131.51        23.34 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NH TCGA-ER-A3ET TCGA-FR-A7U8 TCGA-FS-A1YW 
       20.15        28.83        41.56        93.01        27.85       216.92 
TCGA-FS-A1YY TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZQ TCGA-FS-A1ZR 
      228.59         9.70        32.75        47.38       133.55        11.41 
TCGA-FS-A1ZS TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F9 TCGA-FS-A4FB 
      148.80        27.02        77.82        66.67        34.03        26.73 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A268 
       55.59        13.51         2.04        15.78       139.89        62.79 
TCGA-GN-A4U3 TCGA-GN-A8LK TCGA-GN-A8LL TCGA-LH-A9QB TCGA-OD-A75X TCGA-W3-AA1R 
      121.91        50.10        21.37       368.78       297.90       111.09 
TCGA-W3-AA1V TCGA-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-D3-A2JE TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-D3-A8GI TCGA-EB-A5SG 
       27.65        62.07        46.32        13.87        58.52        68.25 
TCGA-EB-A5SH TCGA-EE-A180 TCGA-EE-A184 TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GD 
       54.02        94.98        68.15       168.26         2.60       340.14 
TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A198 TCGA-FR-A729 TCGA-FW-A3R5 
      126.81       134.40        27.35        50.76       220.80        36.95 
TCGA-QB-AA9O TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD 
       18.05        61.15        21.40        17.03        66.48        12.99 
TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q9 
       14.93        16.57        16.67        71.80       133.25        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-A2JD TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JN TCGA-D3-A2JO 
      168.00        11.87        42.08        12.10        66.48        66.08 
TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO 
       59.57       130.72       166.52        60.23        24.53         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-A5GN TCGA-D3-A5GR TCGA-D3-A5GS 
      145.12        32.94        63.81       135.75       178.32        18.18 
TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GK 
      125.19        30.84        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-A8GS 
       89.13       107.15       161.00       152.75        29.06       117.17 
TCGA-D3-A8GV TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A6E9 
      167.70        54.67         3.65         7.10        15.39         9.90 
TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I0 
       25.18        77.56        22.95        76.57       144.89        20.38 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IB 
      222.51       176.55        35.93        88.87        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        43.36        72.10 
TCGA-DA-A95W TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH 
       37.35        14.14        13.02        13.87        10.36        20.35 
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-A20B TCGA-EE-A29A TCGA-EE-A29B 
       33.73        14.70        26.89       133.81        63.35        85.08 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29R 
       63.78        72.07        56.84        18.61        56.42        14.47 
TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A5 
       61.28       369.93       195.02        46.82       115.96        39.29 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       86.14        59.28       173.79       220.24        48.72       107.38 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GT 
       54.74        79.66        75.48       102.12        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-A2MT TCGA-EE-A2MU 
      216.66        47.54       248.65        43.23        71.21        53.26 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3AG TCGA-EE-A3J3 
      124.31       122.73        64.04        54.51        41.59       172.18 
TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JE 
      127.20        36.95        64.08        53.19       201.80        51.35 
TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B 
      152.81        35.44        13.94         9.17        77.75        98.40 
TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19M 
       48.89        12.59        26.37       152.35         6.44        61.05 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W 
       44.09       162.08        50.89        49.48         8.88       148.18 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3EV TCGA-ER-A3PL 
      105.07        43.82        48.99       247.04        46.98        33.21 
TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A7U9 
       12.95       149.03        92.98       174.21        15.72        18.77 
TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YX TCGA-FS-A1Z0 
       38.27        34.82        36.26       104.42        48.59       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-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZT 
       53.52        46.45        23.93       101.26        74.73        53.16 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F2 TCGA-FS-A4F5 TCGA-FS-A4F8 
       26.56        49.48        27.09        50.14        28.73       174.84 
TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
       54.41        80.68        17.46        19.30         9.90        19.43 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A26D 
      117.93        96.92        10.13        64.44        32.48        48.00 
TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A9SD TCGA-HR-A2OG 
       39.35        10.42        48.89        22.13        59.41         0.23 
TCGA-HR-A2OH TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 
       65.88         7.23         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-A8K1 TCGA-WE-A8K6 TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZX 
       49.05        17.95        58.98        70.52        63.22        35.80 
TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-XV-AB01 TCGA-YD-A89C TCGA-YG-AA3O TCGA-Z2-AA3V 
       40.41        24.99        13.25         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 
           52.010            52.255 
[1] "2.0 - 368.8 (52.0)" "0.2 - 369.9 (52.3)"
[1] "hr=" "1"  
D81V3, continuous
                   vv
clus                I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  XP LOSS MUTATED          4       3       5        2       10        8
  XP LOSS WILD-TYPE        9       4      24       16       18       18
                   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        33         12
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  XP LOSS MUTATED            8         15        7
  XP LOSS WILD-TYPE         27         39       14
D81V4, multiclass
            clus
vv           XP LOSS MUTATED XP LOSS WILD-TYPE
  I/II NOS                 4                 9
  STAGE 0                  3                 4
  STAGE I                  5                24
  STAGE IA                 2                16
  STAGE IB                10                18
  STAGE II                 8                18
  STAGE IIA                2                12
  STAGE IIB               10                 9
  STAGE IIC                4                11
  STAGE III                6                33
  STAGE IIIA               3                12
  STAGE IIIB               8                27
  STAGE IIIC              15                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 26 18
  XP LOSS WILD-TYPE    49 57 55 49
D81V5, multiclass
       clus
vv      XP LOSS MUTATED XP LOSS WILD-TYPE
  T0+T1              15                49
  T2                 16                57
  T3                 26                55
  T4                 18                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
  XP LOSS MUTATED    48  19   5  12
  XP LOSS WILD-TYPE 129  46  34  33
D81V6, multiclass
    clus
vv   XP LOSS MUTATED XP LOSS WILD-TYPE
  N0              48               129
  N1              19                46
  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 239  14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED     80    8
  XP LOSS WILD-TYPE  239   14
   clus
vv  XP LOSS MUTATED XP LOSS WILD-TYPE
  0              80               239
  1               8                14
[1] 2 2
[1] FALSE
D81V8, binary
                   cls
clus                  0   1
  XP LOSS MUTATED    33  26
  XP LOSS WILD-TYPE 101  64
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED     33   26
  XP LOSS WILD-TYPE  101   64
     clus
vv    XP LOSS MUTATED XP LOSS WILD-TYPE
  NO               33               101
  YES              26                64
[1] 2 2
[1] FALSE
D81V9, binary
                   cls
clus                  0   1
  XP LOSS MUTATED     9  87
  XP LOSS WILD-TYPE  38 233
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED      9   87
  XP LOSS WILD-TYPE   38  233
     clus
vv    XP LOSS MUTATED XP LOSS WILD-TYPE
  NO                9                38
  YES              87               233
[1] 2 2
[1] FALSE
D81V10, continuous
D81V11, binary
                   cls
clus                  0   1
  XP LOSS MUTATED    45  51
  XP LOSS WILD-TYPE  93 178
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED     45   51
  XP LOSS WILD-TYPE   93  178
        clus
vv       XP LOSS MUTATED XP LOSS WILD-TYPE
  FEMALE              45                93
  MALE                51               178
[1] 2 2
[1] FALSE
D81V12, binary
                   cls
clus                  0   1
  XP LOSS MUTATED    79  17
  XP LOSS WILD-TYPE 240  30
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED     79   17
  XP LOSS WILD-TYPE  240   30
     clus
vv    XP LOSS MUTATED XP LOSS WILD-TYPE
  NO               79               240
  YES              17                30
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  XP LOSS MUTATED       1                         0    93
  XP LOSS WILD-TYPE     4                         1   260
D81V13, multiclass
                           clus
vv                          XP LOSS MUTATED XP LOSS WILD-TYPE
  ASIAN                                   1                 4
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  93               260
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D81V14, binary
                   cls
clus                  0   1
  XP LOSS MUTATED     2  91
  XP LOSS WILD-TYPE   5 261
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED      2   91
  XP LOSS WILD-TYPE    5  261
                        clus
vv                       XP LOSS MUTATED XP LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                 5
  NOT HISPANIC OR LATINO              91               261
[1] 2 2
[1] FALSE

Clustering(82) Variable = XQ LOSS MUTATION ANALYSIS
D82V1, survival
                   sevent
clus2                 0   1
  XQ LOSS MUTATED    27  37
  XQ LOSS WILD-TYPE 101  87
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               64               188 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               37                87 
$`XQ LOSS MUTATED`
TCGA-ER-A193 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q8 TCGA-D3-A2J6 TCGA-D3-A2JC 
       19.04        31.89       110.93        19.04        25.64        86.30 
TCGA-D3-A2JL TCGA-D3-A3C6 TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A8GC TCGA-D3-A8GR 
      171.58        58.06        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       110.53        65.03        24.89 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29H TCGA-EE-A29Q 
       75.55        79.20        76.14        12.99        47.41        61.12 
TCGA-EE-A2A2 TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2MF TCGA-EE-A2MK TCGA-EE-A2MM 
       30.02         0.20        71.31       209.79        89.26       145.45 
TCGA-EE-A2MS TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3J8 TCGA-ER-A19G TCGA-ER-A19L 
      143.93         4.41         6.28         3.35       184.60        99.06 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ET TCGA-FR-A7U8 TCGA-FS-A1YW 
       16.87        10.19        28.67        68.52        26.20       171.78 
TCGA-FS-A1YY TCGA-FS-A1ZJ TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZZ TCGA-FS-A4F0 
       49.74        36.33       130.95       136.27         3.06        30.90 
TCGA-FS-A4F4 TCGA-FS-A4F9 TCGA-FW-A3TU TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A4U3 
       66.67        13.28        55.59         1.91        53.29       120.53 
TCGA-GN-A8LK TCGA-LH-A9QB TCGA-OD-A75X TCGA-W3-AA1R TCGA-W3-AA1V TCGA-W3-AA1W 
       43.23        85.05       297.01        79.99         8.09       185.13 
TCGA-WE-A8ZM TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-Z2-AA3S 
       65.42        48.39         1.94        91.23 

$`XQ LOSS WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A8GI TCGA-EB-A5SG TCGA-EE-A180 
        9.76        62.07        38.76        13.41        33.24        31.96 
TCGA-EE-A20H TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-FR-A729 
      166.75       269.03        52.90       134.40        27.35       216.43 
TCGA-FW-A3R5 TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 
       36.95        52.73         7.40        60.46        12.99        14.83 
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1QA TCGA-D3-A1QB 
        8.42        15.72        49.35       133.25        76.41        62.60 
TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JG TCGA-D3-A2JH 
       45.99        62.86        15.75       168.00       107.61        36.30 
TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE 
       64.83        66.08        43.53       140.98        40.01        59.70 
TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F 
       24.53         9.34        90.21        23.67       173.85        30.67 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GU 
      144.46        31.76        62.70        45.70       177.86       124.08 
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-D9-A3Z1 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 
       15.02        69.21        22.85        76.34       138.67        68.68 
TCGA-DA-A1I2 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 
      150.61        60.10        64.83        58.85        30.44       225.11 
TCGA-DA-A3F8 TCGA-DA-A95V TCGA-DA-A95W TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q 
        8.71        72.10         0.76        14.14        12.30         3.91 
TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A182 
       16.41        52.41        18.21        13.15        20.38         0.00 
TCGA-EE-A183 TCGA-EE-A29B TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29M TCGA-EE-A29P 
       26.24        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-A2GE 
      346.49       185.19       115.43        77.98        26.14        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        93.63 
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-A2MT 
       94.19       171.85        63.25       104.78       227.01        23.51 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3J3 
       53.26       124.31       122.73        64.04        54.51        67.89 
TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 
      111.85        45.90       168.85        19.86       135.98        34.45 
TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D 
       10.49         7.82         4.54        53.29        39.81        11.47 
TCGA-ER-A19H TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S 
      150.12        59.84        42.51       120.76        49.71        47.18 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A3ES TCGA-ER-A3EV 
      146.63        73.05        22.36         4.70       173.29        15.48 
TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A7UA 
       32.05        74.47         4.50       174.21         4.14         5.65 
TCGA-FR-A8YC TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD 
       10.06       195.98         8.35        27.62       312.07        32.78 
TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZM TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW 
       43.92         7.82        78.61        35.28         4.47        23.21 
TCGA-FS-A1ZY TCGA-FS-A4F8 TCGA-FS-A4FD TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
        5.29       173.19        80.68        11.54        19.30         9.90 
TCGA-GF-A4EO TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
       18.25       117.93        96.92        17.06        42.48         7.59 
TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-GN-A9SD TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 
       34.49        46.92        59.41         7.23         0.20         0.33 
TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1Q TCGA-W3-AA21 TCGA-WE-A8K1 
      174.12         1.97       120.07        44.05        92.84        47.54 
TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-AAA0 TCGA-WE-AAA4 
       12.69        21.90        62.89        10.95        37.32        24.99 
TCGA-XV-AB01 TCGA-YG-AA3O 
        6.61        28.21 

  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
              0.2               0.0 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
           297.01            346.49 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
           51.515            44.990 
[1] "0.2 - 297.0 (51.5)" "0.0 - 346.5 (45.0)"
[1] "hr=" "1.2"
D82V2, survival
                   sevent
clus2                 0   1
  XQ LOSS MUTATED    37  51
  XQ LOSS WILD-TYPE 129 141
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               88               270 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               51               141 
$`XQ LOSS MUTATED`
TCGA-ER-A193 TCGA-FS-A1ZF TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q8 TCGA-D3-A2J6 
       31.40        15.45       112.04       112.57        28.08        43.43 
TCGA-D3-A2JC TCGA-D3-A2JL TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A51N TCGA-D3-A51T 
       86.76       171.58        58.06        46.98        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       135.02        53.92        73.94 
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-ER-A19E 
      162.48        28.77        13.81       138.81        34.32        13.02 
TCGA-ER-A19G TCGA-ER-A19L TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH 
      302.07       131.51        20.15        28.83        48.99        41.56 
TCGA-ER-A3ET TCGA-FR-A7U8 TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1ZA TCGA-FS-A1ZH 
       93.01        27.85       216.92       228.59        27.72        32.75 
TCGA-FS-A1ZJ TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZZ TCGA-FS-A4F0 
       47.38       133.55        11.41       148.80        27.02        77.82 
TCGA-FS-A4F4 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FW-A3TU TCGA-GF-A6C8 TCGA-GN-A262 
       66.67        34.03        26.73        55.59         2.04       139.89 
TCGA-GN-A4U3 TCGA-GN-A8LK TCGA-GN-A8LL TCGA-LH-A9QB TCGA-OD-A75X TCGA-W3-AA1R 
      121.91        50.10        21.37       368.78       297.90       111.09 
TCGA-W3-AA1V TCGA-W3-AA1W TCGA-WE-A8JZ TCGA-WE-A8ZM TCGA-WE-A8ZY TCGA-WE-AA9Y 
       42.08       219.16        24.03       101.33        49.51        12.16 
TCGA-YD-A9TA TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S 
       49.18        14.43        27.58        96.99 

$`XQ LOSS WILD-TYPE`
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-D3-A8GI TCGA-EB-A5SG 
       27.65        62.07        46.32        13.87        58.52        68.25 
TCGA-EB-A5SH TCGA-EE-A180 TCGA-EE-A184 TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GD 
       54.02        94.98        68.15       168.26         2.60       340.14 
TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A198 TCGA-FR-A729 TCGA-FW-A3R5 
      126.81       134.40        27.35        50.76       220.80        36.95 
TCGA-QB-AA9O TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD 
       18.05        61.15        21.40        17.03        66.48        12.99 
TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q9 
       14.93        16.57        16.67        71.80       133.25        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-A2JD TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JN 
      168.00        11.87       113.52        42.08        12.10        66.48 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE 
       66.08        59.57       130.72       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-A51R TCGA-D3-A5GN 
       55.73        56.35       145.12        32.94        63.81       135.75 
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-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       222.51       176.55        35.93        88.87 
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 
       43.36        72.10        37.35        14.14        13.02        13.87 
TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 
       10.36        20.35        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-A20B 
       29.82         8.65        33.73        14.70        26.89       133.81 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29M TCGA-EE-A29N 
       63.35        85.08        63.78        72.07        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-A2GE TCGA-EE-A2GH 
      115.96        39.29        86.14        59.28       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-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 
       13.91        44.88        94.82        21.67       129.27        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-A2ML TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ 
      204.66        96.23       216.66        47.54       248.65        43.23 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AE 
       71.21        53.26       124.31       122.73        64.04        54.51 
TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3JA 
       41.59       172.18       127.20        36.95        64.08        53.19 
TCGA-EE-A3JB TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 
      201.80        51.35       134.33       152.81        35.44        13.94 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19F 
        9.17        77.75        98.40        48.89        12.59        26.37 
TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
      152.35         6.44        61.05        44.09       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       105.07        43.82        23.34 
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-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD 
      174.21        15.72        18.77        38.27        34.82        36.26 
TCGA-FR-A8YE TCGA-FS-A1YX TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 
      104.42        48.59       202.65        20.91        28.08         7.79 
TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZK 
       48.85       357.37        53.52        46.45         9.70        23.93 
TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY 
      101.26        74.73        53.16        26.56        49.48        27.09 
TCGA-FS-A4F2 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 
       50.14        28.73       174.84        54.41        80.68        17.46 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C9 TCGA-GN-A264 
       13.51        19.30         9.90        19.43        15.78       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-A9SD TCGA-HR-A2OG 
       39.35        10.42        48.89        22.13        59.41         0.23 
TCGA-HR-A2OH TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 
       65.88         7.23         0.20         0.33         0.69       228.16 
TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1Q TCGA-W3-AA21 TCGA-WE-A8K1 
       63.02       121.08         4.01        69.07       105.04        49.05 
TCGA-WE-A8K6 TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX 
       17.95        58.98        70.52        63.22        11.80        35.80 
TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-XV-AB01 TCGA-YD-A89C TCGA-YG-AA3O TCGA-Z2-AA3V 
       40.41        24.99        13.25         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 
           52.010            52.255 
[1] "2.0 - 368.8 (52.0)" "0.2 - 369.9 (52.3)"
[1] "hr=" "1"  
D82V3, continuous
                   vv
clus                I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  XQ LOSS MUTATED          5       3       5        2        9        9
  XQ LOSS WILD-TYPE        8       4      24       16       19       17
                   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        33         13
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  XQ LOSS MUTATED            7         14        6
  XQ LOSS WILD-TYPE         28         40       15
D82V4, multiclass
            clus
vv           XQ LOSS MUTATED XQ LOSS WILD-TYPE
  I/II NOS                 5                 8
  STAGE 0                  3                 4
  STAGE I                  5                24
  STAGE IA                 2                16
  STAGE IB                 9                19
  STAGE II                 9                17
  STAGE IIA                2                12
  STAGE IIB                9                10
  STAGE IIC                3                12
  STAGE III                6                33
  STAGE IIIA               2                13
  STAGE IIIB               7                28
  STAGE IIIC              14                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 26 16
  XQ LOSS WILD-TYPE    51 58 55 51
D82V5, multiclass
       clus
vv      XQ LOSS MUTATED XQ LOSS WILD-TYPE
  T0+T1              13                51
  T2                 15                58
  T3                 26                55
  T4                 16                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
  XQ LOSS MUTATED    47  17   4  12
  XQ LOSS WILD-TYPE 130  48  35  33
D82V6, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  N0              47               130
  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    77   7
  XQ LOSS WILD-TYPE 242  15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     77    7
  XQ LOSS WILD-TYPE  242   15
   clus
vv  XQ LOSS MUTATED XQ LOSS WILD-TYPE
  0              77               242
  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  84
  XQ LOSS WILD-TYPE  39 236
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      8   84
  XQ LOSS WILD-TYPE   39  236
     clus
vv    XQ LOSS MUTATED XQ LOSS WILD-TYPE
  NO                8                39
  YES              84               236
[1] 2 2
[1] FALSE
D82V10, continuous
D82V11, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED    42  50
  XQ LOSS WILD-TYPE  96 179
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     42   50
  XQ LOSS WILD-TYPE   96  179
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  FEMALE              42                96
  MALE                50               179
[1] 2 2
[1] FALSE
D82V12, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED    75  17
  XQ LOSS WILD-TYPE 244  30
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     75   17
  XQ LOSS WILD-TYPE  244   30
     clus
vv    XQ LOSS MUTATED XQ LOSS WILD-TYPE
  NO               75               244
  YES              17                30
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  XQ LOSS MUTATED       1                         0    89
  XQ LOSS WILD-TYPE     4                         1   264
D82V13, multiclass
                           clus
vv                          XQ LOSS MUTATED XQ LOSS WILD-TYPE
  ASIAN                                   1                 4
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  89               264
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D82V14, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED     2  87
  XQ LOSS WILD-TYPE   5 265
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      2   87
  XQ LOSS WILD-TYPE    5  265
                        clus
vv                       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                 5
  NOT HISPANIC OR LATINO              87               265
[1] 2 2
[1] FALSE
