[1] "ofn"        "-oTBLCA-TP"
[1] "opt"       "-OPMUTSIG"
[1] "tl" ""  
[1] "dx" ""  
[1] "opt"    "MUTSIG"
[1] "dx" ""  
[1] "cfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/BLCA-TP/15076720/BLCA-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/BLCA-TP/15082909/transformed.cor.cli.txt"

nPatients in clinical file=393, in cluster file=408, common to both=389
[1]  82 389
[1] "1P GAIN MUTATION ANALYSIS"
[1] 3
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               88               301 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               88               301 
[1] "1Q GAIN MUTATION ANALYSIS"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              122               267 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              122               267 
[1] "2P GAIN MUTATION ANALYSIS"
[1] 3
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
              104               285 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
              104               285 
[1] "2Q GAIN MUTATION ANALYSIS"
[1] 3
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               53               336 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               53               336 
[1] "3P GAIN MUTATION ANALYSIS"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
              134               255 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
              134               255 
[1] "3Q GAIN MUTATION ANALYSIS"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
              169               220 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
              169               220 
[1] "4P GAIN MUTATION ANALYSIS"
[1] 3
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               35               354 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               35               354 
[1] "4Q GAIN MUTATION ANALYSIS"
[1] 3
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               26               363 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               26               363 
[1] "5P GAIN MUTATION ANALYSIS"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
              155               234 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
              155               234 
[1] "5Q GAIN MUTATION ANALYSIS"
[1] 3
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               51               338 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               51               338 
[1] "6P GAIN MUTATION ANALYSIS"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               74               315 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               74               315 
[1] "6Q GAIN MUTATION ANALYSIS"
[1] 3
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               39               350 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               39               350 
[1] "7P GAIN MUTATION ANALYSIS"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              162               227 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              162               227 
[1] "7Q GAIN MUTATION ANALYSIS"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              142               247 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              142               247 
[1] "8P GAIN MUTATION ANALYSIS"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               85               304 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               85               304 
[1] "8Q GAIN MUTATION ANALYSIS"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              193               196 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              193               196 
[1] "9P GAIN MUTATION ANALYSIS"
[1] 3
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               65               324 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               65               324 
[1] "9Q GAIN MUTATION ANALYSIS"
[1] 3
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               54               335 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               54               335 
[1] "10P GAIN MUTATION ANALYSIS"
[1] 3
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
               109                280 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
               109                280 
[1] "10Q GAIN MUTATION ANALYSIS"
[1] 3
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                41                348 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                41                348 
[1] "11P GAIN MUTATION ANALYSIS"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                27                362 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                27                362 
[1] "11Q GAIN MUTATION ANALYSIS"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                47                342 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                47                342 
[1] "12P GAIN MUTATION ANALYSIS"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
               111                278 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
               111                278 
[1] "12Q GAIN MUTATION ANALYSIS"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                89                300 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                89                300 
[1] "13Q GAIN MUTATION ANALYSIS"
[1] 3
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                95                294 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                95                294 
[1] "14Q GAIN MUTATION ANALYSIS"
[1] 3
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                55                334 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                55                334 
[1] "15Q GAIN MUTATION ANALYSIS"
[1] 3
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                33                356 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                33                356 
[1] "16P GAIN MUTATION ANALYSIS"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                68                321 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                68                321 
[1] "16Q GAIN MUTATION ANALYSIS"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                77                312 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                77                312 
[1] "17P GAIN MUTATION ANALYSIS"
[1] 3
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                57                332 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                57                332 
[1] "17Q GAIN MUTATION ANALYSIS"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
               131                258 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
               131                258 
[1] "18P GAIN MUTATION ANALYSIS"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
               108                281 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
               108                281 
[1] "18Q GAIN MUTATION ANALYSIS"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                59                330 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                59                330 
[1] "19P GAIN MUTATION ANALYSIS"
[1] 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                81                308 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                81                308 
[1] "19Q GAIN MUTATION ANALYSIS"
[1] 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
               124                265 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
               124                265 
[1] "20P GAIN MUTATION ANALYSIS"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               190                199 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               190                199 
[1] "20Q GAIN MUTATION ANALYSIS"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               217                172 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               217                172 
[1] "21Q GAIN MUTATION ANALYSIS"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
               105                284 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
               105                284 
[1] "22Q GAIN MUTATION ANALYSIS"
[1] 3
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                46                343 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                46                343 
[1] "XP GAIN MUTATION ANALYSIS"
[1] 3
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               66               323 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               66               323 
[1] "XQ GAIN MUTATION ANALYSIS"
[1] 3
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               46               343 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               46               343 
[1] "1P LOSS MUTATION ANALYSIS"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               32               357 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               32               357 
[1] "1Q LOSS MUTATION ANALYSIS"
[1] 3
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               33               356 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               33               356 
[1] "2P LOSS MUTATION ANALYSIS"
[1] 3
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               43               346 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               43               346 
[1] "2Q LOSS MUTATION ANALYSIS"
[1] 3
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               85               304 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               85               304 
[1] "3P LOSS MUTATION ANALYSIS"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               51               338 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               51               338 
[1] "3Q LOSS MUTATION ANALYSIS"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               23               366 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               23               366 
[1] "4P LOSS MUTATION ANALYSIS"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
              136               253 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
              136               253 
[1] "4Q LOSS MUTATION ANALYSIS"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
              129               260 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
              129               260 
[1] "5P LOSS MUTATION ANALYSIS"
[1] 3
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               53               336 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               53               336 
[1] "5Q LOSS MUTATION ANALYSIS"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
              149               240 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
              149               240 
[1] "6P LOSS MUTATION ANALYSIS"
[1] 3
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               94               295 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               94               295 
[1] "6Q LOSS MUTATION ANALYSIS"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
              148               241 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
              148               241 
[1] "7P LOSS MUTATION ANALYSIS"
[1] 3
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               20               369 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               20               369 
[1] "7Q LOSS MUTATION ANALYSIS"
[1] 3
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               25               364 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               25               364 
[1] "8P LOSS MUTATION ANALYSIS"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
              177               212 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
              177               212 
[1] "8Q LOSS MUTATION ANALYSIS"
[1] 3
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               34               355 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               34               355 
[1] "9P LOSS MUTATION ANALYSIS"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              164               225 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              164               225 
[1] "9Q LOSS MUTATION ANALYSIS"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
              160               229 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
              160               229 
[1] "10P LOSS MUTATION ANALYSIS"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                71                318 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                71                318 
[1] "10Q LOSS MUTATION ANALYSIS"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
               121                268 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
               121                268 
[1] "11P LOSS MUTATION ANALYSIS"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
               169                220 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
               169                220 
[1] "11Q LOSS MUTATION ANALYSIS"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
               121                268 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
               121                268 
[1] "12P LOSS MUTATION ANALYSIS"
[1] 3
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                51                338 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                51                338 
[1] "12Q LOSS MUTATION ANALYSIS"
[1] 3
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                54                335 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                54                335 
[1] "13Q LOSS MUTATION ANALYSIS"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                81                308 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                81                308 
[1] "14Q LOSS MUTATION ANALYSIS"
[1] 3
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               115                274 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               115                274 
[1] "15Q LOSS MUTATION ANALYSIS"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
               134                255 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
               134                255 
[1] "16P LOSS MUTATION ANALYSIS"
[1] 3
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
               100                289 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
               100                289 
[1] "16Q LOSS MUTATION ANALYSIS"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                95                294 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                95                294 
[1] "17P LOSS MUTATION ANALYSIS"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               168                221 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               168                221 
[1] "17Q LOSS MUTATION ANALYSIS"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                42                347 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                42                347 
[1] "18P LOSS MUTATION ANALYSIS"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                97                292 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                97                292 
[1] "18Q LOSS MUTATION ANALYSIS"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               138                251 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               138                251 
[1] "19P LOSS MUTATION ANALYSIS"
[1] 3
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                90                299 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                90                299 
[1] "19Q LOSS MUTATION ANALYSIS"
[1] 3
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                54                335 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                54                335 
[1] "20P LOSS MUTATION ANALYSIS"
[1] 3
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                32                357 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                32                357 
[1] "20Q LOSS MUTATION ANALYSIS"
[1] 3
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                13                376 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                13                376 
[1] "21Q LOSS MUTATION ANALYSIS"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                76                313 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                76                313 
[1] "22Q LOSS MUTATION ANALYSIS"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
               152                237 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
               152                237 
[1] "XP LOSS MUTATION ANALYSIS"
[1] 3
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               67               322 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               67               322 
[1] "XQ LOSS MUTATION ANALYSIS"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               78               311 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               78               311 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                        
 [2] "VITAL_STATUS"                          
 [3] "DAYS_TO_DEATH"                         
 [4] "DAYS_TO_LAST_FOLLOWUP"                 
 [5] "PRIMARY_SITE_OF_DISEASE"               
 [6] "NEOPLASM_DISEASESTAGE"                 
 [7] "PATHOLOGY_T_STAGE"                     
 [8] "PATHOLOGY_N_STAGE"                     
 [9] "PATHOLOGY_M_STAGE"                     
[10] "DCC_UPLOAD_DATE"                       
[11] "GENDER"                                
[12] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"  
[13] "DAYS_TO_LAST_KNOWN_ALIVE"              
[14] "RADIATION_THERAPY"                     
[15] "KARNOFSKY_PERFORMANCE_SCORE"           
[16] "HISTOLOGICAL_TYPE"                     
[17] "RADIATIONS_RADIATION_REGIMENINDICATION"
[18] "NUMBER_PACK_YEARS_SMOKED"              
[19] "NUMBER_OF_LYMPH_NODES"                 
[20] "RACE"                                  
[21] "ETHNICITY"                             
[22] "BATCH_NUMBER"                          

Input Data has 22 rows and 389 columns.

[1] "Batch" "22"   
[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=51,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=136,	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=254,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'PRIMARY_SITE_OF_DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PRIMARY_SITE_OF_DISEASE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'NEOPLASM_DISEASESTAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY_T_STAGE':	nDistinctValues=11,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY_N_STAGE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY_M_STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'DCC_UPLOAD_DATE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 11:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=15,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 13:'DAYS_TO_LAST_KNOWN_ALIVE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "DAYS_TO_LAST_KNOWN_ALIVE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 14:'RADIATION_THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATION_THERAPY is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 15:'KARNOFSKY_PERFORMANCE_SCORE':	nDistinctValues=8,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 16:'HISTOLOGICAL_TYPE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "HISTOLOGICAL_TYPE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 17:'RADIATIONS_RADIATION_REGIMENINDICATION':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATIONS_RADIATION_REGIMENINDICATION is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 18:'NUMBER_PACK_YEARS_SMOKED':	nDistinctValues=71,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 19:'NUMBER_OF_LYMPH_NODES':	nDistinctValues=22,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 20:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 21:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 22:'BATCH_NUMBER':	nDistinctValues=29,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] NA
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "PATHOLOGY_T_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_N_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_M_STAGE is converted to rank data using modified categoies"
[1] "****** SUMMARY ***** "
Output Data has 389 columns, 1 survival variables, and 11 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
 [1] "YEARS_TO_BIRTH"              "NEOPLASM_DISEASESTAGE"      
 [3] "PATHOLOGY_T_STAGE"           "PATHOLOGY_N_STAGE"          
 [5] "PATHOLOGY_M_STAGE"           "GENDER"                     
 [7] "KARNOFSKY_PERFORMANCE_SCORE" "NUMBER_PACK_YEARS_SMOKED"   
 [9] "NUMBER_OF_LYMPH_NODES"       "RACE"                       
[11] "ETHNICITY"                  
YEARS_TO_BIRTH, nv=51, binary=FALSE, numeric=TRUE
NEOPLASM_DISEASESTAGE, nv=4, binary=FALSE, numeric=FALSE
PATHOLOGY_T_STAGE, nv=5, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T0  T1  T2  T3  T4 
  2   3 116 184  53 
[1] "table(vv)"
vv
T0+T1+T2       T3       T4 
     121      184       53 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T0  T1  T2  T3  T4 
  2   3 116 184  53 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


T0+T1+T2       T3       T4 
     121      184       53 
PATHOLOGY_N_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2  N3 
224  42  75   8 
[1] "table(vv)"
vv
 N0  N1  N2  N3 
224  42  75   8 
$ClinVariableName
[1] "PATHOLOGY_N_STAGE"

$Table
vv
 N0  N1  N2  N3 
224  42  75   8 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 N0  N1  N2  N3 
224  42  75   8 
PATHOLOGY_M_STAGE, nv=2, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
KARNOFSKY_PERFORMANCE_SCORE, nv=8, binary=FALSE, numeric=TRUE
NUMBER_PACK_YEARS_SMOKED, nv=71, binary=FALSE, numeric=TRUE
NUMBER_OF_LYMPH_NODES, nv=22, binary=FALSE, numeric=TRUE
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    51  36
  1P GAIN WILD-TYPE 179 117
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               87               296 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               36               117 
$`1P GAIN MUTATED`
TCGA-2F-A9KR TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-BT-A20R TCGA-BT-A2LA TCGA-BT-A3PJ 
      103.50        10.22        47.80         5.06        17.16        12.82 
TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-CU-A0YN TCGA-CU-A5W6 TCGA-DK-A2I1 TCGA-DK-A2I2 
        8.98         1.94        12.92         1.84        10.59         7.79 
TCGA-DK-A2I4 TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IU TCGA-DK-A3X2 
      123.85        13.58         7.82         8.22        23.21        17.98 
TCGA-DK-A6AV TCGA-DK-AA6L TCGA-DK-AA6P TCGA-DK-AA6S TCGA-DK-AA6U TCGA-DK-AA77 
       64.18        38.24        15.02       166.03        10.49        10.62 
TCGA-E5-A4U1 TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A97Q TCGA-FD-A3B5 TCGA-FD-A3B7 
       38.83        17.39         0.56         8.09         8.94         4.01 
TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SO TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N 
       60.66        24.30         5.52        19.79        12.85        22.98 
TCGA-FD-A5BU TCGA-FD-A5C0 TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3ZF 
       19.33        18.08         3.06         9.67        31.07        17.23 
TCGA-FT-A3EE TCGA-G2-A3IE TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3OO TCGA-GC-A3RB 
        3.25        20.12        19.46        21.40        15.81         4.50 
TCGA-GC-A3YS TCGA-GC-A4ZW TCGA-GD-A3OS TCGA-GD-A76B TCGA-GU-A42P TCGA-GV-A3JV 
       24.92         0.49        20.98         7.36        10.92        14.27 
TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QI TCGA-GV-A6ZA TCGA-K4-A5RH TCGA-K4-A5RI 
       19.82        20.28        10.59        22.72         9.07        11.70 
TCGA-K4-AAQO TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-SY-A9G5 TCGA-UY-A78M 
       11.80        15.32        15.58        13.48        31.56        22.68 
TCGA-UY-A8OC TCGA-UY-A9PB TCGA-UY-A9PE TCGA-XF-A8HD TCGA-XF-A9SG TCGA-XF-A9T5 
        3.58        29.56         4.54        97.45        48.62        66.64 
TCGA-XF-AAMT TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN3 TCGA-XF-AAN7 TCGA-YF-AA3M 
        2.96        98.99        44.32        86.30        18.81        13.64 
TCGA-ZF-A9R7 TCGA-ZF-A9RE TCGA-ZF-A9RN TCGA-ZF-AA4T TCGA-ZF-AA4X TCGA-ZF-AA51 
       21.86         3.48        20.22        19.69        63.02        38.73 
TCGA-ZF-AA52 TCGA-ZF-AA58 TCGA-ZF-AA5H 
       35.41        47.15        19.17 

$`1P GAIN WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KT TCGA-2F-A9KW TCGA-4Z-AA7M 
       22.29        11.97        91.63       105.70         8.35        16.27 
TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W 
       44.94        16.83        16.77        17.16        34.98        27.62 
TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA84 
       49.12         0.62        41.75        51.16        66.54        15.12 
TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ 
       33.83        40.08         7.33         2.66         6.74        12.39 
TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P 
        6.58        13.15        19.04        32.84        12.16        17.88 
TCGA-BT-A20Q TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X 
       19.50        14.89        14.96         5.06         8.35         8.25 
TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C 
       16.18        20.48         4.67         9.96        17.56        28.70 
TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C 
       24.26        28.41        23.01         0.46         0.43         0.69 
TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y 
       10.95        12.66        12.46        12.10        12.62        12.26 
TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A8HY TCGA-CF-A9FF 
       13.12        12.00        12.10        11.34        11.34        11.87 
TCGA-CF-A9FM TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL 
       13.08         4.90         7.20         5.46         5.19        16.31 
TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA 
       13.58        21.86         2.14        66.41        18.41        19.00 
TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG 
       16.70       130.88       112.44        16.14        17.62        15.62 
TCGA-DK-A2HX TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT 
        1.81        87.32         2.20        17.72        50.27        21.30 
TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A6AW 
        9.67        20.81        10.55       140.81        48.00        41.56 
TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6Q 
       76.60        67.36        15.68        41.06        30.67        13.58 
TCGA-DK-AA6T TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA76 
       12.36         8.65         7.53        13.64        43.50        12.03 
TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ 
       43.59        15.35        24.66         0.10         0.49         2.24 
TCGA-E7-A519 TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF 
       16.70         0.66        14.56        13.97        12.99        14.33 
TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A8O7 
        0.92         1.22        13.68        14.07        12.95        15.32 
TCGA-E7-A97P TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B6 TCGA-FD-A3B8 TCGA-FD-A3N5 
       14.37        32.02        16.77        33.04        12.62        22.52 
TCGA-FD-A3N6 TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SP TCGA-FD-A3SQ 
       27.98        23.41        17.98        29.16        25.74        46.78 
TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR 
       27.35        14.96        20.91         3.62        15.58        26.73 
TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ 
       53.88        11.01         5.36         5.69         8.25        27.45 
TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA 
       58.92         2.70         7.10         6.28        13.35        62.86 
TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TH 
       18.81         6.15        12.69        12.36         2.27         4.31 
TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-FT-A61P TCGA-G2-A2EF 
       10.85         7.13        10.65         8.94         6.48        61.94 
TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB 
       30.61        15.95        26.93        35.24        33.01         7.23 
TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3D TCGA-GC-A3I6 TCGA-GC-A3RC 
       17.62        66.02         6.94        64.44         2.24        15.91 
TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP 
       14.07        17.75         8.94        13.91         7.73         2.10 
TCGA-GD-A3OQ TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 
        3.12         2.20        11.31        11.31         7.63        27.09 
TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATP TCGA-GU-AATQ 
       20.05         5.62         4.73        10.65        32.98         7.00 
TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QH TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G 
       21.34        19.10         8.48        27.35         8.58        19.07 
TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE 
        1.51        19.40        38.60         3.06         9.01         8.22 
TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R 
       25.02         3.45        21.24         2.76         9.14        27.68 
TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-LT-A8JT TCGA-PQ-A6FI 
        1.74         1.81        15.42         6.38        21.07        12.23 
TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-UY-A78K 
       16.67        14.24         1.84         3.75        12.43        17.62 
TCGA-UY-A78L TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OB TCGA-UY-A8OD 
       37.05        86.83        76.01        67.79        65.75       112.83 
TCGA-UY-A9PA TCGA-UY-A9PD TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HE 
       35.24        17.82         1.64        45.04         6.58       125.49 
TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SI 
       97.12        15.35         1.87        17.88        64.80        79.66 
TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY 
        3.22        66.41        12.76        11.90        23.64        21.04 
TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T6 
       28.24        26.27        18.90         2.24        16.27         2.10 
TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAMJ 
       13.74        92.98        10.82       110.60        11.31        54.90 
TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 
        7.63        71.57        91.73         8.32         6.77        56.48 
TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN8 TCGA-YC-A89H 
       30.94        61.45        27.06        75.39         3.88        18.84 
TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R2 
        9.63         0.66        11.97        18.64         7.36        21.11 
TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RD 
       24.13        30.28        27.19        28.41        74.56        13.41 
TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-AA4N TCGA-ZF-AA4R 
       52.73        52.60        82.49        47.84         2.89        34.06 
TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 
        8.61        59.38        60.16        57.90        19.40         8.52 
TCGA-ZF-AA5N TCGA-ZF-AA5P 
        5.52        10.13 

  1P GAIN MUTATED 1P GAIN WILD-TYPE 
             0.49              0.10 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
           166.03            140.81 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
            17.23             15.50 
[1] "0.5 - 166.0 (17.2)" "0.1 - 140.8 (15.5)"
[1] "hr=" "1"  
D1V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  1P GAIN MUTATED         1       25        27       34
  1P GAIN WILD-TYPE       3       99       100       95
D1V3, multiclass
           clus
vv          1P GAIN MUTATED 1P GAIN WILD-TYPE
  STAGE I                 1                 3
  STAGE II               25                99
  STAGE III              27               100
  STAGE IV               34                95
[1] 4 2
[1] TRUE
[1] "dimension of contingency 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         23  43  14
  1P GAIN WILD-TYPE       98 141  39
D1V4, multiclass
          clus
vv         1P GAIN MUTATED 1P GAIN WILD-TYPE
  T0+T1+T2              23                98
  T3                    43               141
  T4                    14                39
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  1P GAIN MUTATED    42  14  17   5
  1P GAIN WILD-TYPE 182  28  58   3
D1V5, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  N0              42               182
  N1              14                28
  N2              17                58
  N3               5                 3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V6, binary
                   cls
clus                  0   1
  1P GAIN MUTATED    39   1
  1P GAIN WILD-TYPE 146   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     39    1
  1P GAIN WILD-TYPE  146    9
   clus
vv  1P GAIN MUTATED 1P GAIN WILD-TYPE
  0              39               146
  1               1                 9
[1] 2 2
[1] FALSE
D1V7, binary
                   cls
clus                  0   1
  1P GAIN MUTATED    25  63
  1P GAIN WILD-TYPE  76 225
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     25   63
  1P GAIN WILD-TYPE   76  225
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  FEMALE              25                76
  MALE                63               225
[1] 2 2
[1] FALSE
D1V8, continuous
D1V9, continuous
D1V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  1P GAIN MUTATED       4                         5    73
  1P GAIN WILD-TYPE    38                        16   238
D1V11, multiclass
                           clus
vv                          1P GAIN MUTATED 1P GAIN WILD-TYPE
  ASIAN                                   4                38
  BLACK OR AFRICAN AMERICAN               5                16
  WHITE                                  73               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"
D1V12, binary
                   cls
clus                  0   1
  1P GAIN MUTATED     2  81
  1P GAIN WILD-TYPE   7 271
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      2   81
  1P GAIN WILD-TYPE    7  271
                        clus
vv                       1P GAIN MUTATED 1P GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 7
  NOT HISPANIC OR LATINO              81               271
[1] 2 2
[1] FALSE

Clustering(2) Variable = 1Q GAIN MUTATION ANALYSIS
D2V1, survival
                   sevent
clus2                 0   1
  1Q GAIN MUTATED    72  49
  1Q GAIN WILD-TYPE 158 104
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              121               262 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               49               104 
$`1Q GAIN MUTATED`
TCGA-2F-A9KP TCGA-2F-A9KR TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA86 TCGA-4Z-AA87 
       11.97       103.50        41.75        51.16        10.22        47.80 
TCGA-BL-A3JM TCGA-BT-A20V TCGA-BT-A2LA TCGA-BT-A2LD TCGA-BT-A42C TCGA-BT-A42F 
        6.74         5.06        17.16        20.48        28.70        28.41 
TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-CF-A47V TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CU-A0YN 
        8.98         1.94        12.46        11.34        11.87        12.92 
TCGA-CU-A3KJ TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1AD TCGA-DK-A2I1 TCGA-DK-A2I2 
        5.46         1.84        21.86       112.44        10.59         7.79 
TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6B1 
       13.58         7.82         8.22        17.98        64.18        67.36 
TCGA-DK-AA6L TCGA-DK-AA6P TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA71 
       38.24        15.02       166.03        12.36        10.49        13.64 
TCGA-DK-AA77 TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A541 TCGA-E7-A5KF 
       10.62        38.83        24.66         0.10        17.39         0.66 
TCGA-E7-A7PW TCGA-E7-A97Q TCGA-FD-A3B5 TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SJ 
       13.68         8.09         8.94         4.01        60.66        24.30 
TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SO TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N 
       23.41        17.98         5.52        19.79        12.85        22.98 
TCGA-FD-A43X TCGA-FD-A5BU TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A6TG TCGA-FD-A6TI 
        3.62        19.33        18.08        58.92         3.06         9.67 
TCGA-FJ-A3ZE TCGA-FT-A3EE TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3OO TCGA-GC-A3RB 
       10.65         3.25        19.46        21.40        15.81         4.50 
TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A4ZW TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OS 
       17.75        24.92         0.49         7.73         2.10        20.98 
TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-AATO TCGA-GV-A3JV TCGA-GV-A3JX TCGA-GV-A3JZ 
        7.36        10.92        10.65        14.27        19.10        19.82 
TCGA-GV-A3QI TCGA-GV-A6ZA TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-K4-A3WS TCGA-K4-A5RH 
       10.59        22.72        38.60         3.06        25.02         9.07 
TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-AAQO TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V 
       11.70         1.74        11.80        15.32        15.58        13.48 
TCGA-PQ-A6FI TCGA-SY-A9G5 TCGA-UY-A78M TCGA-UY-A8OC TCGA-UY-A9PB TCGA-UY-A9PE 
       12.23        31.56        22.68         3.58        29.56         4.54 
TCGA-XF-A8HD TCGA-XF-A8HG TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SJ TCGA-XF-A9SW 
       97.45        15.35        17.88        48.62         3.22        11.90 
TCGA-XF-A9T5 TCGA-XF-AAMT TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN3 
       66.64         2.96        98.99        44.32        56.48        86.30 
TCGA-XF-AAN7 TCGA-YC-A9TC TCGA-YF-AA3M TCGA-ZF-A9R7 TCGA-ZF-A9RC TCGA-ZF-A9RD 
       18.81         0.66        13.64        21.86        74.56        13.41 
TCGA-ZF-A9RE TCGA-ZF-A9RN TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA58 
        3.48        20.22        63.02        38.73        35.41        47.15 
TCGA-ZF-AA5H 
       19.17 

$`1Q GAIN WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KQ TCGA-2F-A9KT TCGA-2F-A9KW TCGA-4Z-AA7M TCGA-4Z-AA7N 
       22.29        91.63       105.70         8.35        16.27        44.94 
TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA7Y 
       16.83        16.77        17.16        34.98        27.62        49.12 
TCGA-4Z-AA80 TCGA-4Z-AA83 TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I 
        0.62        66.54        15.12        33.83        40.08         7.33 
TCGA-BL-A13J TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N 
        2.66        12.39         6.58        13.15        19.04        32.84 
TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U 
       12.16        17.88        19.50         5.06        14.89        14.96 
TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK 
        8.35         8.25        16.18         4.67        12.82         9.96 
TCGA-BT-A42B TCGA-BT-A42E TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C 
       17.56        24.26        23.01         0.46         0.43         0.69 
TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 
       10.95        12.66        12.10        12.62        12.26        13.12 
TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A9FM TCGA-CU-A0YO TCGA-CU-A0YR 
       12.00        12.10        11.34        13.08         4.90         7.20 
TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 
        5.19        16.31        13.58         2.14        66.41        18.41 
TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG 
       19.00        16.70       130.88        16.14        17.62        15.62 
TCGA-DK-A2HX TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IQ TCGA-DK-A3IS 
        1.81       123.85        87.32         2.20        17.72        50.27 
TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY 
       21.30        23.21         9.67        20.81        10.55       140.81 
TCGA-DK-A3X1 TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 
       48.00        41.56        76.60        15.68        41.06        30.67 
TCGA-DK-AA6Q TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA74 TCGA-DK-AA76 TCGA-E5-A2PC 
       13.58         8.65         7.53        43.50        12.03        43.59 
TCGA-E5-A4TZ TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KE TCGA-E7-A677 
       15.35         0.49         2.24        16.70         0.56        14.56 
TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7XN 
       13.97        12.99        14.33         0.92         1.22        14.07 
TCGA-E7-A85H TCGA-E7-A8O7 TCGA-E7-A97P TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B6 
       12.95        15.32        14.37        32.02        16.77        33.04 
TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SN TCGA-FD-A3SP TCGA-FD-A3SQ 
       12.62        22.52        27.98        29.16        25.74        46.78 
TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS 
       27.35        14.96        20.91        15.58        26.73        53.88 
TCGA-FD-A5BT TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A62N 
       11.01         5.36         5.69         8.25        27.45         2.70 
TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC 
        7.10         6.28        13.35        62.86        18.81         6.15 
TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TH TCGA-FD-A6TK TCGA-FJ-A3Z7 
       12.69        12.36         2.27         4.31        10.85        31.07 
TCGA-FJ-A3Z9 TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ 
        7.13        17.23         8.94         6.48        61.94        30.61 
TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE 
       15.95        26.93        35.24        33.01         7.23        20.12 
TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3D TCGA-GC-A3I6 TCGA-GC-A3RC 
       17.62        66.02         6.94        64.44         2.24        15.91 
TCGA-GC-A3RD TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A3OQ TCGA-GD-A6C6 TCGA-GU-A42Q 
       14.07         8.94        13.91         3.12         2.20        11.31 
TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 
       11.31         7.63        27.09        20.05         5.62         4.73 
TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JW TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QK 
       32.98         7.00        21.34        20.28         8.48        27.35 
TCGA-GV-A40E TCGA-GV-A40G TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A5ND TCGA-HQ-A5NE 
        8.58        19.07         1.51        19.40         9.01         8.22 
TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A6FZ 
        3.45        21.24         2.76         9.14        27.68         1.81 
TCGA-K4-A6MB TCGA-K4-A83P TCGA-LT-A8JT TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX 
       15.42         6.38        21.07        16.67        14.24         1.84 
TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78N TCGA-UY-A78O 
        3.75        12.43        17.62        37.05        86.83        76.01 
TCGA-UY-A78P TCGA-UY-A8OB TCGA-UY-A8OD TCGA-UY-A9PA TCGA-UY-A9PD TCGA-UY-A9PF 
       67.79        65.75       112.83        35.24        17.82         1.64 
TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HH TCGA-XF-A9SH 
       45.04         6.58       125.49        97.12         1.87        64.80 
TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ 
       79.66        66.41        12.76        23.64        21.04        28.24 
TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T6 TCGA-XF-A9T8 
       26.27        18.90         2.24        16.27         2.10        13.74 
TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML 
       92.98        10.82       110.60        11.31        54.90         7.63 
TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN1 TCGA-XF-AAN2 
       71.57        91.73         8.32         6.77        30.94        61.45 
TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YF-AA3L 
       27.06        75.39         3.88        18.84         9.63        11.97 
TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 
       18.64         7.36        21.11        24.13        30.28        27.19 
TCGA-ZF-A9R9 TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-AA4N 
       28.41        52.73        52.60        82.49        47.84         2.89 
TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA53 
       34.06        19.69         8.61        59.38        60.16        57.90 
TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA5N TCGA-ZF-AA5P 
       19.40         8.52         5.52        10.13 

  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
             0.10              0.43 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
           166.03            140.81 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
           15.320            16.045 
[1] "0.1 - 166.0 (15.3)" "0.4 - 140.8 (16.0)"
[1] "hr=" "1.1"
D2V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  1Q GAIN MUTATED         1       35        34       50
  1Q GAIN WILD-TYPE       3       89        93       79
D2V3, multiclass
           clus
vv          1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  STAGE I                 1                 3
  STAGE II               35                89
  STAGE III              34                93
  STAGE IV               50                79
[1] 4 2
[1] TRUE
[1] "dimension of contingency 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         35  58  18
  1Q GAIN WILD-TYPE       86 126  35
D2V4, multiclass
          clus
vv         1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  T0+T1+T2              35                86
  T3                    58               126
  T4                    18                35
[1] 3 2
[1] TRUE
[1] "dimension of 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    60  16  29   5
  1Q GAIN WILD-TYPE 164  26  46   3
D2V5, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  N0              60               164
  N1              16                26
  N2              29                46
  N3               5                 3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V6, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED    54   5
  1Q GAIN WILD-TYPE 131   5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     54    5
  1Q GAIN WILD-TYPE  131    5
   clus
vv  1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  0              54               131
  1               5                 5
[1] 2 2
[1] FALSE
D2V7, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED    32  90
  1Q GAIN WILD-TYPE  69 198
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     32   90
  1Q GAIN WILD-TYPE   69  198
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  FEMALE              32                69
  MALE                90               198
[1] 2 2
[1] FALSE
D2V8, continuous
D2V9, continuous
D2V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  1Q GAIN MUTATED       8                         7    99
  1Q GAIN WILD-TYPE    34                        14   212
D2V11, multiclass
                           clus
vv                          1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  ASIAN                                   8                34
  BLACK OR AFRICAN AMERICAN               7                14
  WHITE                                  99               212
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V12, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED     2 110
  1Q GAIN WILD-TYPE   7 242
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      2  110
  1Q GAIN WILD-TYPE    7  242
                        clus
vv                       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 7
  NOT HISPANIC OR LATINO             110               242
[1] 2 2
[1] FALSE

Clustering(3) Variable = 2P GAIN MUTATION ANALYSIS
D3V1, survival
                   sevent
clus2                 0   1
  2P GAIN MUTATED    64  39
  2P GAIN WILD-TYPE 166 114
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
              103               280 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               39               114 
$`2P GAIN MUTATED`
TCGA-4Z-AA7Q TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA84 TCGA-BL-A5ZZ 
       16.77         0.62        41.75        51.16        15.12        12.39 
TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A2LB TCGA-BT-A2LD 
       13.15        19.04         5.06         8.35        16.18        20.48 
TCGA-BT-A3PJ TCGA-BT-A42C TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F6 TCGA-CF-A1HS 
       12.82        28.70        28.41         8.98        23.01         0.43 
TCGA-CF-A47X TCGA-CF-A8HY TCGA-CU-A0YR TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 
       12.62        11.34         7.20        21.86        66.41        18.41 
TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I6 TCGA-DK-A3IK 
      130.88       112.44        10.59         7.79        87.32         2.20 
TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6B1 
        7.82         8.22        48.00        17.98        64.18        67.36 
TCGA-DK-A6B2 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6P TCGA-DK-AA6S TCGA-DK-AA6T 
       15.68        30.67        38.24        15.02       166.03        12.36 
TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E7-A541 
       10.49         8.65        12.03        10.62        43.59        17.39 
TCGA-E7-A6ME TCGA-E7-A97Q TCGA-FD-A3NA TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A43P 
       12.99         8.09        60.66        46.78        19.79        27.35 
TCGA-FD-A43U TCGA-FD-A5BZ TCGA-FD-A62O TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG 
       20.91        27.45         7.10        12.36         2.27         3.06 
TCGA-FD-A6TH TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A3VY TCGA-GC-A3RD 
        4.31        17.23         3.25         6.48        17.62        14.07 
TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OS TCGA-GU-A764 TCGA-GU-AATP 
       13.91         7.73         2.10        20.98        20.05        32.98 
TCGA-GU-AATQ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QK TCGA-H4-A2HQ TCGA-HQ-A2OE 
        7.00        20.28         8.48        27.35        19.40        38.60 
TCGA-K4-A3WS TCGA-K4-A3WV TCGA-K4-A5RI TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-UY-A78K 
       25.02        21.24        11.70         1.81        15.42        17.62 
TCGA-UY-A78M TCGA-UY-A8OB TCGA-UY-A8OD TCGA-UY-A9PB TCGA-UY-A9PE TCGA-XF-A8HD 
       22.68        65.75       112.83        29.56         4.54        97.45 
TCGA-XF-A8HG TCGA-XF-AAMG TCGA-XF-AAMZ TCGA-ZF-A9R0 TCGA-ZF-A9R3 TCGA-ZF-A9RC 
       15.35       110.60        44.32        18.64        24.13        74.56 
TCGA-ZF-A9RN TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4V TCGA-ZF-AA51 TCGA-ZF-AA54 
       20.22        34.06        19.69        59.38        38.73        19.40 
TCGA-ZF-AA56 
        8.52 

$`2P GAIN WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        91.63       103.50       105.70         8.35 
TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W 
       16.27        44.94        16.83        17.16        34.98        27.62 
TCGA-4Z-AA7Y TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A0C8 
       49.12        66.54        10.22        47.80        33.83        40.08 
TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A20N TCGA-BT-A20O 
        7.33         2.66         6.74         6.58        32.84        12.16 
TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20X 
       17.88        19.50         5.06        14.89        14.96         8.25 
TCGA-BT-A2LA TCGA-BT-A3PH TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42E TCGA-C4-A0F0 
       17.16         4.67         9.96        17.56        24.26         1.94 
TCGA-CF-A1HR TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W 
        0.46         0.69        10.95        12.66        12.46        12.10 
TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A9FF 
       12.26        13.12        12.00        12.10        11.34        11.87 
TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL 
       13.08        12.92         4.90         5.46         5.19        16.31 
TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AE 
        1.84        13.58         2.14        19.00        16.70        16.14 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I4 TCGA-DK-A3IL TCGA-DK-A3IQ 
       17.62        15.62         1.81       123.85        13.58        17.72 
TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX 
       50.27        21.30        23.21         9.67        20.81        10.55 
TCGA-DK-A3WY TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B5 TCGA-DK-AA6Q TCGA-DK-AA6X 
      140.81        41.56        76.60        41.06        13.58         7.53 
TCGA-DK-AA71 TCGA-DK-AA74 TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 
       13.64        43.50        15.35        38.83        24.66         0.10 
TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 
        0.49         2.24        16.70         0.56         0.66        14.56 
TCGA-E7-A678 TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A7XN 
       13.97        14.33         0.92         1.22        13.68        14.07 
TCGA-E7-A85H TCGA-E7-A8O7 TCGA-E7-A97P TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 
       12.95        15.32        14.37        32.02        16.77         8.94 
TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SJ 
       33.04         4.01        12.62        22.52        27.98        24.30 
TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SS 
       23.41        17.98        29.16         5.52        25.74        12.85 
TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS 
       22.98        14.96         3.62        15.58        26.73        53.88 
TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C0 
       11.01        19.33         5.36         5.69         8.25        18.08 
TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB 
       58.92         2.70         6.28        13.35        62.86        18.81 
TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 
        6.15        12.69         9.67        10.85        31.07         7.13 
TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL 
       10.65         8.94        61.94        30.61        15.95        26.93 
TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3C 
       35.24        33.01         7.23        20.12        66.02         6.94 
TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB 
       64.44        19.46        21.40         2.24        15.81         4.50 
TCGA-GC-A3RC TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GD-A3OQ 
       15.91        17.75        24.92         0.49         8.94         3.12 
TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 
        2.20         7.36        10.92        11.31        11.31         7.63 
TCGA-GU-A763 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO TCGA-GV-A3JV TCGA-GV-A3JW 
       27.09         5.62         4.73        10.65        14.27        21.34 
TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QI TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA 
       19.10        19.82        10.59         8.58        19.07        22.72 
TCGA-H4-A2HO TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WU TCGA-K4-A4AB 
        1.51         3.06         9.01         8.22         3.45         2.76 
TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RJ TCGA-K4-A83P TCGA-K4-AAQO 
        9.14        27.68         9.07         1.74         6.38        11.80 
TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN 
       15.32        15.58        21.07        13.48        12.23        16.67 
TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78L 
       14.24         1.84         3.75        12.43        31.56        37.05 
TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OC TCGA-UY-A9PA TCGA-UY-A9PD 
       86.83        76.01        67.79         3.58        35.24        17.82 
TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HH 
        1.64        45.04         6.58       125.49        97.12         1.87 
TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SL 
       17.88        48.62        64.80        79.66         3.22        66.41 
TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 
       12.76        11.90        23.64        21.04        28.24        26.27 
TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 
       18.90         2.24        16.27        66.64         2.10        13.74 
TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ 
       92.98        10.82        11.31        54.90         7.63        71.57 
TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAN0 
       91.73         2.96         8.32         6.77        98.99        56.48 
TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 
       30.94        61.45        86.30        27.06        75.39        18.81 
TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M 
        3.88        18.84         9.63         0.66        11.97        13.64 
TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 
        7.36        21.11        30.28        27.19        21.86        28.41 
TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM 
       13.41         3.48        52.73        52.60        82.49        47.84 
TCGA-ZF-AA4N TCGA-ZF-AA4U TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA52 TCGA-ZF-AA53 
        2.89         8.61        60.16        63.02        35.41        57.90 
TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
       47.15        19.17         5.52        10.13 

  2P GAIN MUTATED 2P GAIN WILD-TYPE 
             0.43              0.10 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
           166.03            140.81 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
            17.98             14.96 
[1] "0.4 - 166.0 (18.0)" "0.1 - 140.8 (15.0)"
[1] "hr=" "1.2"
D3V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  2P GAIN MUTATED         1       28        28       44
  2P GAIN WILD-TYPE       3       96        99       85
D3V3, multiclass
           clus
vv          2P GAIN MUTATED 2P GAIN WILD-TYPE
  STAGE I                 1                 3
  STAGE II               28                96
  STAGE III              28                99
  STAGE IV               44                85
[1] 4 2
[1] TRUE
[1] "dimension of contingency 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         30  49  13
  2P GAIN WILD-TYPE       91 135  40
D3V4, multiclass
          clus
vv         2P GAIN MUTATED 2P GAIN WILD-TYPE
  T0+T1+T2              30                91
  T3                    49               135
  T4                    13                40
[1] 3 2
[1] TRUE
[1] "dimension of 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    47  14  28   3
  2P GAIN WILD-TYPE 177  28  47   5
D3V5, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  N0              47               177
  N1              14                28
  N2              28                47
  N3               3                 5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V6, binary
                   cls
clus                  0   1
  2P GAIN MUTATED    49   4
  2P GAIN WILD-TYPE 136   6
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     49    4
  2P GAIN WILD-TYPE  136    6
   clus
vv  2P GAIN MUTATED 2P GAIN WILD-TYPE
  0              49               136
  1               4                 6
[1] 2 2
[1] FALSE
D3V7, binary
                   cls
clus                  0   1
  2P GAIN MUTATED    37  67
  2P GAIN WILD-TYPE  64 221
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     37   67
  2P GAIN WILD-TYPE   64  221
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  FEMALE              37                64
  MALE                67               221
[1] 2 2
[1] FALSE
D3V8, continuous
D3V9, continuous
D3V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  2P GAIN MUTATED       8                         6    87
  2P GAIN WILD-TYPE    34                        15   224
D3V11, multiclass
                           clus
vv                          2P GAIN MUTATED 2P GAIN WILD-TYPE
  ASIAN                                   8                34
  BLACK OR AFRICAN AMERICAN               6                15
  WHITE                                  87               224
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V12, binary
                   cls
clus                  0   1
  2P GAIN MUTATED     3  90
  2P GAIN WILD-TYPE   6 262
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      3   90
  2P GAIN WILD-TYPE    6  262
                        clus
vv                       2P GAIN MUTATED 2P GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                 6
  NOT HISPANIC OR LATINO              90               262
[1] 2 2
[1] FALSE

Clustering(4) Variable = 2Q GAIN MUTATION ANALYSIS
D4V1, survival
                   sevent
clus2                 0   1
  2Q GAIN MUTATED    33  19
  2Q GAIN WILD-TYPE 197 134
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               52               331 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               19               134 
$`2Q GAIN MUTATED`
TCGA-4Z-AA82 TCGA-4Z-AA84 TCGA-BL-A5ZZ TCGA-BT-A20J TCGA-BT-A2LB TCGA-BT-A42B 
       51.16        15.12        12.39        19.04        16.18        17.56 
TCGA-BT-A42C TCGA-BT-A42F TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CU-A0YR TCGA-DK-A1A6 
       28.70        28.41        11.34        11.87         7.20        66.41 
TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A3IN TCGA-DK-AA6L 
      130.88       112.44        10.59         7.79         8.22        38.24 
TCGA-DK-AA6P TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA76 TCGA-E5-A2PC TCGA-FD-A3NA 
       15.02        10.49         8.65        12.03        43.59        60.66 
TCGA-FD-A3SQ TCGA-FD-A62O TCGA-FD-A6TG TCGA-FJ-A3ZF TCGA-G2-A3VY TCGA-GD-A3OS 
       46.78         7.10         3.06        17.23        17.62        20.98 
TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A40G TCGA-H4-A2HQ 
       32.98         7.00        20.28         8.48        19.07        19.40 
TCGA-HQ-A2OF TCGA-K4-A3WS TCGA-K4-A3WV TCGA-K4-A5RI TCGA-K4-A6FZ TCGA-UY-A78K 
        3.06        25.02        21.24        11.70         1.81        17.62 
TCGA-UY-A78M TCGA-UY-A8OD TCGA-UY-A9PB TCGA-XF-A8HD TCGA-ZF-A9R0 TCGA-ZF-A9RC 
       22.68       112.83        29.56        97.45        18.64        74.56 
TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA51 TCGA-ZF-AA56 
       34.06        19.69        38.73         8.52 

$`2Q GAIN WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        91.63       103.50       105.70         8.35 
TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S 
       16.27        44.94        16.83        16.77        17.16        34.98 
TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA83 TCGA-4Z-AA86 
       27.62        49.12         0.62        41.75        66.54        10.22 
TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM 
       47.80        33.83        40.08         7.33         2.66         6.74 
TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q 
        6.58        13.15        32.84        12.16        17.88        19.50 
TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X 
        5.06        14.89        14.96         5.06         8.35         8.25 
TCGA-BT-A2LA TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42E 
       17.16        20.48         4.67        12.82         9.96        24.26 
TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C 
        8.98         1.94        23.01         0.46         0.43         0.69 
TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y 
       10.95        12.66        12.46        12.10        12.62        12.26 
TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A9FM TCGA-CU-A0YN 
       13.12        12.00        12.10        11.34        13.08        12.92 
TCGA-CU-A0YO TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E 
        4.90         5.46         5.19        16.31         1.84        13.58 
TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AE 
       21.86         2.14        18.41        19.00        16.70        16.14 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK 
       17.62        15.62         1.81       123.85        87.32         2.20 
TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU 
       13.58         7.82        17.72        50.27        21.30        23.21 
TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 
        9.67        20.81        10.55       140.81        48.00        17.98 
TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 
       64.18        41.56        76.60        67.36        15.68        41.06 
TCGA-DK-A6B6 TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6X TCGA-DK-AA71 
       30.67        13.58       166.03        12.36         7.53        13.64 
TCGA-DK-AA74 TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 
       43.50        10.62        15.35        38.83        24.66         0.10 
TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF 
        0.49         2.24        16.70        17.39         0.56         0.66 
TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV 
       14.56        13.97        12.99        14.33         0.92         1.22 
TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A8O7 TCGA-E7-A97P TCGA-E7-A97Q 
       13.68        14.07        12.95        15.32        14.37         8.09 
TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 
       32.02        16.77         8.94        33.04         4.01        12.62 
TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN 
       22.52        27.98        24.30        23.41        17.98        29.16 
TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P 
        5.52        25.74        19.79        12.85        22.98        27.35 
TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS 
       14.96        20.91         3.62        15.58        26.73        53.88 
TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ 
       11.01        19.33         5.36         5.69         8.25        27.45 
TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA 
       18.08        58.92         2.70         6.28        13.35        62.86 
TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TH 
       18.81         6.15        12.69        12.36         2.27         4.31 
TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 
        9.67        10.85        31.07         7.13        10.65         8.94 
TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL 
        3.25         6.48        61.94        30.61        15.95        26.93 
TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3C 
       35.24        33.01         7.23        20.12        66.02         6.94 
TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB 
       64.44        19.46        21.40         2.24        15.81         4.50 
TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A4ZW TCGA-GC-A6I1 
       15.91        14.07        17.75        24.92         0.49         8.94 
TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A6C6 TCGA-GD-A76B 
       13.91         7.73         2.10         3.12         2.20         7.36 
TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 
       10.92        11.31        11.31         7.63        27.09        20.05 
TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX 
        5.62         4.73        10.65        14.27        21.34        19.10 
TCGA-GV-A3JZ TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A6ZA TCGA-H4-A2HO 
       19.82        10.59        27.35         8.58        22.72         1.51 
TCGA-HQ-A2OE TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A4AC 
       38.60         9.01         8.22         3.45         2.76         9.14 
TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RJ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO 
       27.68         9.07         1.74        15.42         6.38        11.80 
TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN 
       15.32        15.58        21.07        13.48        12.23        16.67 
TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78L 
       14.24         1.84         3.75        12.43        31.56        37.05 
TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A9PA 
       86.83        76.01        67.79        65.75         3.58        35.24 
TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HE 
       17.82         4.54         1.64        45.04         6.58       125.49 
TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH 
       97.12        15.35         1.87        17.88        48.62        64.80 
TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX 
       79.66         3.22        66.41        12.76        11.90        23.64 
TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 
       21.04        28.24        26.27        18.90         2.24        16.27 
TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMG 
       66.64         2.10        13.74        92.98        10.82       110.60 
TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMT 
       11.31        54.90         7.63        71.57        91.73         2.96 
TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN1 
        8.32         6.77        98.99        44.32        56.48        30.94 
TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-XF-AAN8 
       61.45        86.30        27.06        75.39        18.81         3.88 
TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R1 
       18.84         9.63         0.66        11.97        13.64         7.36 
TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 
       21.11        24.13        30.28        27.19        21.86        28.41 
TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM 
       13.41         3.48        52.73        52.60        82.49        47.84 
TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X 
       20.22         2.89         8.61        59.38        60.16        63.02 
TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N 
       35.41        57.90        19.40        47.15        19.17         5.52 
TCGA-ZF-AA5P 
       10.13 

  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
             1.81              0.10 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
           130.88            166.03 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
            18.84             15.35 
[1] "1.8 - 130.9 (18.8)" "0.1 - 166.0 (15.3)"
[1] "hr=" "1.3"
D4V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  2Q GAIN MUTATED         1       17        15       19
  2Q GAIN WILD-TYPE       3      107       112      110
D4V3, multiclass
           clus
vv          2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  STAGE I                 1                 3
  STAGE II               17               107
  STAGE III              15               112
  STAGE IV               19               110
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1+T2  T3  T4
  2Q GAIN MUTATED         17  21   5
  2Q GAIN WILD-TYPE      104 163  48
D4V4, multiclass
          clus
vv         2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  T0+T1+T2              17               104
  T3                    21               163
  T4                     5                48
[1] 3 2
[1] TRUE
[1] "dimension of 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    28   7  11   1
  2Q GAIN WILD-TYPE 196  35  64   7
D4V5, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  N0              28               196
  N1               7                35
  N2              11                64
  N3               1                 7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V6, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED    21   2
  2Q GAIN WILD-TYPE 164   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     21    2
  2Q GAIN WILD-TYPE  164    8
   clus
vv  2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  0              21               164
  1               2                 8
[1] 2 2
[1] FALSE
D4V7, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED    17  36
  2Q GAIN WILD-TYPE  84 252
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     17   36
  2Q GAIN WILD-TYPE   84  252
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  FEMALE              17                84
  MALE                36               252
[1] 2 2
[1] FALSE
D4V8, continuous
D4V9, continuous
D4V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  2Q GAIN MUTATED       5                         3    44
  2Q GAIN WILD-TYPE    37                        18   267
D4V11, multiclass
                           clus
vv                          2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  ASIAN                                   5                37
  BLACK OR AFRICAN AMERICAN               3                18
  WHITE                                  44               267
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V12, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED     1  46
  2Q GAIN WILD-TYPE   8 306
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      1   46
  2Q GAIN WILD-TYPE    8  306
                        clus
vv                       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 8
  NOT HISPANIC OR LATINO              46               306
[1] 2 2
[1] FALSE

Clustering(5) Variable = 3P GAIN MUTATION ANALYSIS
D5V1, survival
                   sevent
clus2                 0   1
  3P GAIN MUTATED    75  56
  3P GAIN WILD-TYPE 155  97
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
              131               252 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               56                97 
$`3P GAIN MUTATED`
TCGA-2F-A9KO TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA84 
       22.29        16.27        16.77        34.98        27.62        15.12 
TCGA-4Z-AA87 TCGA-BL-A13I TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A20J TCGA-BT-A20W 
       47.80         7.33         6.74        12.39        19.04         8.35 
TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PK TCGA-CF-A1HR TCGA-CU-A0YO TCGA-CU-A0YR 
       20.48         4.67         9.96         0.46         4.90         7.20 
TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1AD TCGA-DK-A2HX 
       16.31         1.84        21.86         2.14       112.44         1.81 
TCGA-DK-A2I1 TCGA-DK-A2I6 TCGA-DK-A3IN TCGA-DK-A3IS TCGA-DK-A3IU TCGA-DK-A3X2 
       10.59        87.32         8.22        50.27        23.21        17.98 
TCGA-DK-A6AV TCGA-DK-A6B6 TCGA-DK-AA6S TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA71 
       64.18        30.67       166.03        10.49         8.65        13.64 
TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3Y1 TCGA-E7-A5KE 
       12.03        43.59        15.35        38.83         0.10         0.56 
TCGA-E7-A6ME TCGA-E7-A7PW TCGA-E7-A97Q TCGA-FD-A43U TCGA-FD-A5C0 TCGA-FD-A62O 
       12.99        13.68         8.09        20.91        18.08         7.10 
TCGA-FD-A62P TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI 
        6.28        12.36         2.27         3.06         4.31         9.67 
TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ 
       10.65        17.23         3.25         6.48        61.94        30.61 
TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3VY TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3OO 
       35.24        33.01        17.62        19.46         2.24        15.81 
TCGA-GC-A4ZW TCGA-GC-A6I3 TCGA-GD-A3OP TCGA-GD-A3OS TCGA-GD-A76B TCGA-GU-A42P 
        0.49        13.91         2.10        20.98         7.36        10.92 
TCGA-GU-A762 TCGA-GU-AATO TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3QF 
        7.63        10.65         7.00        14.27        21.34        20.28 
TCGA-GV-A3QH TCGA-GV-A3QK TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HQ TCGA-HQ-A2OE 
        8.48        27.35        19.07        22.72        19.40        38.60 
TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A5RH TCGA-K4-A6MB 
        9.01        25.02         3.45        21.24         9.07        15.42 
TCGA-K4-AAQO TCGA-PQ-A6FI TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-SY-A9G5 
       11.80        12.23        14.24         1.84        12.43        31.56 
TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78N TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A9PB 
       17.62        37.05        86.83        65.75         3.58        29.56 
TCGA-UY-A9PD TCGA-XF-A8HC TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A8HI 
       17.82         6.58        97.12        15.35         1.87        17.88 
TCGA-XF-A9SG TCGA-XF-A9SI TCGA-XF-A9SV TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAML 
       48.62        79.66        12.76        13.74        10.82         7.63 
TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-ZF-A9R0 TCGA-ZF-A9R4 TCGA-ZF-A9RC 
        6.77        98.99        44.32        18.64        30.28        74.56 
TCGA-ZF-A9RD TCGA-ZF-A9RM TCGA-ZF-AA4N TCGA-ZF-AA4T TCGA-ZF-AA4V TCGA-ZF-AA4X 
       13.41        47.84         2.89        19.69        59.38        63.02 
TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA58 
       38.73        35.41        57.90        19.40        47.15 

$`3P GAIN WILD-TYPE`
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW TCGA-4Z-AA7N 
       11.97        91.63       103.50       105.70         8.35        44.94 
TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 
       16.83        17.16        49.12         0.62        41.75        51.16 
TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BT-A0S7 
       66.54        10.22        33.83        40.08         2.66         6.58 
TCGA-BT-A0YX TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R 
       13.15        32.84        12.16        17.88        19.50         5.06 
TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB 
       14.89        14.96         5.06         8.25        17.16        16.18 
TCGA-BT-A3PJ TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ 
       12.82        17.56        28.70        24.26        28.41         8.98 
TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T 
        1.94        23.01         0.43         0.69        10.95        12.66 
TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA 
       12.46        12.10        12.62        12.26        13.12        12.00 
TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YN 
       12.10        11.34        11.34        11.87        13.08        12.92 
TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A72E TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA 
        5.46         5.19        13.58        66.41        18.41        19.00 
TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I2 
       16.70       130.88        16.14        17.62        15.62         7.79 
TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IQ TCGA-DK-A3IT 
      123.85         2.20        13.58         7.82        17.72        21.30 
TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A6AW 
        9.67        20.81        10.55       140.81        48.00        41.56 
TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-AA6L TCGA-DK-AA6P 
       76.60        67.36        15.68        41.06        38.24        15.02 
TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6X TCGA-DK-AA74 TCGA-DK-AA77 TCGA-E7-A3X6 
       13.58        12.36         7.53        43.50        10.62        24.66 
TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KF TCGA-E7-A677 
        0.49         2.24        16.70        17.39         0.66        14.56 
TCGA-E7-A678 TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7XN TCGA-E7-A85H 
       13.97        14.33         0.92         1.22        14.07        12.95 
TCGA-E7-A8O7 TCGA-E7-A97P TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 
       15.32        14.37        32.02        16.77         8.94        33.04 
TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ 
        4.01        12.62        22.52        27.98        60.66        24.30 
TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ 
       23.41        17.98        29.16         5.52        25.74        46.78 
TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43X 
       19.79        12.85        22.98        27.35        14.96         3.62 
TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV 
       15.58        26.73        53.88        11.01        19.33         5.36 
TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62S 
        5.69         8.25        27.45        58.92         2.70        13.35 
TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TK TCGA-FJ-A3Z7 
       62.86        18.81         6.15        12.69        10.85        31.07 
TCGA-FJ-A3Z9 TCGA-FJ-A871 TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A3IB TCGA-G2-A3IE 
        7.13         8.94        15.95        26.93         7.23        20.12 
TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3D TCGA-GC-A3BM TCGA-GC-A3RB TCGA-GC-A3RC 
       66.02         6.94        64.44        21.40         4.50        15.91 
TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OQ 
       14.07        17.75        24.92         8.94         7.73         3.12 
TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 
        2.20        11.31        11.31        27.09        20.05         5.62 
TCGA-GU-A767 TCGA-GU-AATP TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QI TCGA-GV-A40E 
        4.73        32.98        19.10        19.82        10.59         8.58 
TCGA-H4-A2HO TCGA-HQ-A2OF TCGA-HQ-A5NE TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R 
        1.51         3.06         8.22         2.76         9.14        27.68 
TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A83P TCGA-LC-A66R TCGA-LT-A5Z6 
       11.70         1.74         1.81         6.38        15.32        15.58 
TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-UY-A78M TCGA-UY-A78O 
       21.07        13.48        16.67         3.75        22.68        76.01 
TCGA-UY-A78P TCGA-UY-A8OD TCGA-UY-A9PA TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HB 
       67.79       112.83        35.24         4.54         1.64        45.04 
TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A9SH TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SW 
       97.45       125.49        64.80         3.22        66.41        11.90 
TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 
       23.64        21.04        28.24        26.27        18.90         2.24 
TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-AAME TCGA-XF-AAMG TCGA-XF-AAMH 
       16.27        66.64         2.10        92.98       110.60        11.31 
TCGA-XF-AAMJ TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAN0 
       54.90        71.57        91.73         2.96         8.32        56.48 
TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 
       30.94        61.45        86.30        27.06        75.39        18.81 
TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M 
        3.88        18.84         9.63         0.66        11.97        13.64 
TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 
        7.36        21.11        24.13        27.19        21.86        28.41 
TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RN TCGA-ZF-AA4R 
        3.48        52.73        52.60        82.49        20.22        34.06 
TCGA-ZF-AA4U TCGA-ZF-AA4W TCGA-ZF-AA56 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
        8.61        60.16         8.52        19.17         5.52        10.13 

  3P GAIN MUTATED 3P GAIN WILD-TYPE 
             0.10              0.43 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
           166.03            140.81 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
           15.420            15.795 
[1] "0.1 - 166.0 (15.4)" "0.4 - 140.8 (15.8)"
[1] "hr=" "1.2"
D5V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  3P GAIN MUTATED         1       41        37       53
  3P GAIN WILD-TYPE       3       83        90       76
D5V3, multiclass
           clus
vv          3P GAIN MUTATED 3P GAIN WILD-TYPE
  STAGE I                 1                 3
  STAGE II               41                83
  STAGE III              37                90
  STAGE IV               53                76
[1] 4 2
[1] TRUE
[1] "dimension of contingency 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         37  59  23
  3P GAIN WILD-TYPE       84 125  30
D5V4, multiclass
          clus
vv         3P GAIN MUTATED 3P GAIN WILD-TYPE
  T0+T1+T2              37                84
  T3                    59               125
  T4                    23                30
[1] 3 2
[1] TRUE
[1] "dimension of 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    64  16  34   3
  3P GAIN WILD-TYPE 160  26  41   5
D5V5, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  N0              64               160
  N1              16                26
  N2              34                41
  N3               3                 5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V6, binary
                   cls
clus                  0   1
  3P GAIN MUTATED    60   5
  3P GAIN WILD-TYPE 125   5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     60    5
  3P GAIN WILD-TYPE  125    5
   clus
vv  3P GAIN MUTATED 3P GAIN WILD-TYPE
  0              60               125
  1               5                 5
[1] 2 2
[1] FALSE
D5V7, binary
                   cls
clus                  0   1
  3P GAIN MUTATED    28 106
  3P GAIN WILD-TYPE  73 182
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     28  106
  3P GAIN WILD-TYPE   73  182
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  FEMALE              28                73
  MALE               106               182
[1] 2 2
[1] FALSE
D5V8, continuous
D5V9, continuous
D5V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3P GAIN MUTATED      10                         5   115
  3P GAIN WILD-TYPE    32                        16   196
D5V11, multiclass
                           clus
vv                          3P GAIN MUTATED 3P GAIN WILD-TYPE
  ASIAN                                  10                32
  BLACK OR AFRICAN AMERICAN               5                16
  WHITE                                 115               196
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V12, binary
                   cls
clus                  0   1
  3P GAIN MUTATED     3 122
  3P GAIN WILD-TYPE   6 230
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      3  122
  3P GAIN WILD-TYPE    6  230
                        clus
vv                       3P GAIN MUTATED 3P GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                 6
  NOT HISPANIC OR LATINO             122               230
[1] 2 2
[1] FALSE

Clustering(6) Variable = 3Q GAIN MUTATION ANALYSIS
D6V1, survival
                   sevent
clus2                 0   1
  3Q GAIN MUTATED    97  69
  3Q GAIN WILD-TYPE 133  84
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
              166               217 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               69                84 
$`3Q GAIN MUTATED`
TCGA-2F-A9KO TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA84 
       22.29        16.27        16.77        34.98        27.62        15.12 
TCGA-4Z-AA87 TCGA-BL-A13I TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0YX TCGA-BT-A20J 
       47.80         7.33         6.74        12.39        13.15        19.04 
TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LD TCGA-BT-A3PH 
        5.06         8.35         8.25        17.16        20.48         4.67 
TCGA-BT-A3PK TCGA-BT-A42C TCGA-BT-A42E TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CU-A0YO 
        9.96        28.70        24.26         0.46         0.43         4.90 
TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A6 
        7.20         5.46        16.31         1.84        21.86        66.41 
TCGA-DK-A1A7 TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I6 
       18.41       130.88       112.44         1.81        10.59        87.32 
TCGA-DK-A3IK TCGA-DK-A3IN TCGA-DK-A3IS TCGA-DK-A3IU TCGA-DK-A3X2 TCGA-DK-A6AV 
        2.20         8.22        50.27        23.21        17.98        64.18 
TCGA-DK-A6B2 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6S TCGA-DK-AA6U TCGA-DK-AA6W 
       15.68        30.67        38.24       166.03        10.49         8.65 
TCGA-DK-AA71 TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E7-A3Y1 
       13.64        12.03        10.62        43.59        15.35         0.10 
TCGA-E7-A4IJ TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A6ME TCGA-E7-A7PW TCGA-E7-A85H 
        0.49        17.39         0.56        12.99        13.68        12.95 
TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B6 TCGA-FD-A3N5 TCGA-FD-A3SJ TCGA-FD-A3SL 
        8.09        32.02        33.04        22.52        24.30        23.41 
TCGA-FD-A43P TCGA-FD-A43U TCGA-FD-A5C0 TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A6TC 
       27.35        20.91        18.08         7.10         6.28         6.15 
TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3ZE 
       12.36         2.27         3.06         4.31         9.67        10.65 
TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EO TCGA-G2-A2ES 
       17.23         6.48        61.94        30.61        35.24        33.01 
TCGA-G2-A3IB TCGA-G2-A3VY TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RD 
        7.23        17.62        19.46         2.24        15.81        14.07 
TCGA-GC-A3WC TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A3OP TCGA-GD-A3OS 
       17.75         0.49         8.94        13.91         2.10        20.98 
TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A762 TCGA-GU-AATO TCGA-GU-AATQ TCGA-GV-A3JV 
        7.36        10.92         7.63        10.65         7.00        14.27 
TCGA-GV-A3JW TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QK TCGA-GV-A40G TCGA-GV-A6ZA 
       21.34        20.28         8.48        27.35        19.07        22.72 
TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV 
       19.40        38.60         9.01        25.02         3.45        21.24 
TCGA-K4-A5RH TCGA-K4-A6MB TCGA-K4-AAQO TCGA-PQ-A6FI TCGA-R3-A69X TCGA-S5-A6DX 
        9.07        15.42        11.80        12.23        14.24         1.84 
TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78N TCGA-UY-A8OB 
       12.43        31.56        17.62        37.05        86.83        65.75 
TCGA-UY-A8OC TCGA-UY-A9PB TCGA-UY-A9PD TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HF 
        3.58        29.56        17.82        45.04         6.58        97.12 
TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SV 
       15.35         1.87        17.88        79.66         3.22        12.76 
TCGA-XF-A9SZ TCGA-XF-A9T5 TCGA-XF-A9T8 TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMT 
       28.24        66.64        13.74         7.63        71.57         2.96 
TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN3 TCGA-YF-AA3M TCGA-ZF-A9R0 
        6.77        98.99        44.32        86.30        13.64        18.64 
TCGA-ZF-A9R2 TCGA-ZF-A9R4 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RM 
       21.11        30.28        74.56        13.41         3.48        47.84 
TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4T TCGA-ZF-AA4V TCGA-ZF-AA4X TCGA-ZF-AA51 
       20.22         2.89        19.69        59.38        63.02        38.73 
TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA58 
       35.41        57.90        19.40        47.15 

$`3Q GAIN WILD-TYPE`
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW TCGA-4Z-AA7N 
       11.97        91.63       103.50       105.70         8.35        44.94 
TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 
       16.83        17.16        49.12         0.62        41.75        51.16 
TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BT-A0S7 
       66.54        10.22        33.83        40.08         2.66         6.58 
TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T 
       32.84        12.16        17.88        19.50         5.06        14.89 
TCGA-BT-A20U TCGA-BT-A2LB TCGA-BT-A3PJ TCGA-BT-A42B TCGA-BT-A42F TCGA-C4-A0EZ 
       14.96        16.18        12.82        17.56        28.41         8.98 
TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V 
        1.94        23.01         0.69        10.95        12.66        12.46 
TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 
       12.10        12.62        12.26        13.12        12.00        12.10 
TCGA-CF-A8HX TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A3QU 
       11.34        11.34        11.87        13.08        12.92         5.19 
TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AE TCGA-DK-A1AF 
       13.58         2.14        19.00        16.70        16.14        17.62 
TCGA-DK-A1AG TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IQ 
       15.62         7.79       123.85        13.58         7.82        17.72 
TCGA-DK-A3IT TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 
       21.30         9.67        20.81        10.55       140.81        48.00 
TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B5 TCGA-DK-AA6P TCGA-DK-AA6Q 
       41.56        76.60        67.36        41.06        15.02        13.58 
TCGA-DK-AA6T TCGA-DK-AA6X TCGA-DK-AA74 TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A4XJ 
       12.36         7.53        43.50        38.83        24.66         2.24 
TCGA-E7-A519 TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MF TCGA-E7-A7DU 
       16.70         0.66        14.56        13.97        14.33         0.92 
TCGA-E7-A7DV TCGA-E7-A7XN TCGA-E7-A8O7 TCGA-E7-A97P TCGA-FD-A3B4 TCGA-FD-A3B5 
        1.22        14.07        15.32        14.37        16.77         8.94 
TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SM TCGA-FD-A3SN 
        4.01        12.62        27.98        60.66        17.98        29.16 
TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N 
        5.52        25.74        46.78        19.79        12.85        22.98 
TCGA-FD-A43S TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT 
       14.96         3.62        15.58        26.73        53.88        11.01 
TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C1 
       19.33         5.36         5.69         8.25        27.45        58.92 
TCGA-FD-A62N TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TD TCGA-FD-A6TK 
        2.70        13.35        62.86        18.81        12.69        10.85 
TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EK TCGA-G2-A2EL 
       31.07         7.13         8.94         3.25        15.95        26.93 
TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3D TCGA-GC-A3BM TCGA-GC-A3RB 
       20.12        66.02         6.94        64.44        21.40         4.50 
TCGA-GC-A3RC TCGA-GC-A3YS TCGA-GD-A2C5 TCGA-GD-A3OQ TCGA-GD-A6C6 TCGA-GU-A42Q 
       15.91        24.92         7.73         3.12         2.20        11.31 
TCGA-GU-A42R TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATP 
       11.31        27.09        20.05         5.62         4.73        32.98 
TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QI TCGA-GV-A40E TCGA-H4-A2HO TCGA-HQ-A2OF 
       19.10        19.82        10.59         8.58         1.51         3.06 
TCGA-HQ-A5NE TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RI TCGA-K4-A5RJ 
        8.22         2.76         9.14        27.68        11.70         1.74 
TCGA-K4-A6FZ TCGA-K4-A83P TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-MV-A51V 
        1.81         6.38        15.32        15.58        21.07        13.48 
TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-UY-A78M TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OD 
       16.67         3.75        22.68        76.01        67.79       112.83 
TCGA-UY-A9PA TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A9SG 
       35.24         4.54         1.64        97.45       125.49        48.62 
TCGA-XF-A9SH TCGA-XF-A9SL TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9T0 
       64.80        66.41        11.90        23.64        21.04        26.27 
TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T6 TCGA-XF-AAME TCGA-XF-AAMF 
       18.90         2.24        16.27         2.10        92.98        10.82 
TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAMR TCGA-XF-AAMW TCGA-XF-AAN0 
      110.60        11.31        54.90        91.73         8.32        56.48 
TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-XF-AAN8 
       30.94        61.45        27.06        75.39        18.81         3.88 
TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R1 TCGA-ZF-A9R3 
       18.84         9.63         0.66        11.97         7.36        24.13 
TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL 
       27.19        21.86        28.41        52.73        52.60        82.49 
TCGA-ZF-AA4R TCGA-ZF-AA4U TCGA-ZF-AA4W TCGA-ZF-AA56 TCGA-ZF-AA5H TCGA-ZF-AA5N 
       34.06         8.61        60.16         8.52        19.17         5.52 
TCGA-ZF-AA5P 
       10.13 

  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
             0.10              0.62 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
           166.03            140.81 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
            16.29             15.58 
[1] "0.1 - 166.0 (16.3)" "0.6 - 140.8 (15.6)"
[1] "hr=" "1.1"
D6V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  3Q GAIN MUTATED         1       52        47       65
  3Q GAIN WILD-TYPE       3       72        80       64
D6V3, multiclass
           clus
vv          3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  STAGE I                 1                 3
  STAGE II               52                72
  STAGE III              47                80
  STAGE IV               65                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                T0+T1+T2  T3  T4
  3Q GAIN MUTATED         47  79  25
  3Q GAIN WILD-TYPE       74 105  28
D6V4, multiclass
          clus
vv         3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  T0+T1+T2              47                74
  T3                    79               105
  T4                    25                28
[1] 3 2
[1] TRUE
[1] "dimension of 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    81  20  43   3
  3Q GAIN WILD-TYPE 143  22  32   5
D6V5, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  N0              81               143
  N1              20                22
  N2              43                32
  N3               3                 5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V6, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED    77   6
  3Q GAIN WILD-TYPE 108   4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     77    6
  3Q GAIN WILD-TYPE  108    4
   clus
vv  3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  0              77               108
  1               6                 4
[1] 2 2
[1] FALSE
D6V7, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED    42 127
  3Q GAIN WILD-TYPE  59 161
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     42  127
  3Q GAIN WILD-TYPE   59  161
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  FEMALE              42                59
  MALE               127               161
[1] 2 2
[1] FALSE
D6V8, continuous
D6V9, continuous
D6V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3Q GAIN MUTATED      13                         9   143
  3Q GAIN WILD-TYPE    29                        12   168
D6V11, multiclass
                           clus
vv                          3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  ASIAN                                  13                29
  BLACK OR AFRICAN AMERICAN               9                12
  WHITE                                 143               168
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V12, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED     4 154
  3Q GAIN WILD-TYPE   5 198
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      4  154
  3Q GAIN WILD-TYPE    5  198
                        clus
vv                       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   4                 5
  NOT HISPANIC OR LATINO             154               198
[1] 2 2
[1] FALSE

Clustering(7) Variable = 4P GAIN MUTATION ANALYSIS
D7V1, survival
                   sevent
clus2                 0   1
  4P GAIN MUTATED    28   7
  4P GAIN WILD-TYPE 202 146
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               35               348 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                7               146 
$`4P GAIN MUTATED`
TCGA-4Z-AA87 TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A47X TCGA-CF-A5UA TCGA-CF-A8HY 
       47.80         1.94        23.01        12.62        12.00        11.34 
TCGA-CF-A9FF TCGA-CU-A3KJ TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1AC TCGA-DK-A2I2 
       11.87         5.46         2.14        66.41       130.88         7.79 
TCGA-DK-A3X1 TCGA-DK-A6AV TCGA-DK-A6B1 TCGA-E5-A4U1 TCGA-E7-A541 TCGA-E7-A7DU 
       48.00        64.18        67.36        38.83        17.39         0.92 
TCGA-FD-A3NA TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A6TC TCGA-FD-A6TE TCGA-GD-A76B 
       60.66         5.36        27.45         6.15        12.36         7.36 
TCGA-GU-A42P TCGA-GV-A6ZA TCGA-HQ-A5ND TCGA-K4-A6FZ TCGA-MV-A51V TCGA-UY-A78N 
       10.92        22.72         9.01         1.81        13.48        86.83 
TCGA-UY-A78O TCGA-XF-A9T3 TCGA-YF-AA3L TCGA-ZF-A9R2 TCGA-ZF-AA5H 
       76.01         2.24        11.97        21.11        19.17 

$`4P GAIN WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        91.63       103.50       105.70         8.35 
TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S 
       16.27        44.94        16.83        16.77        17.16        34.98 
TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 
       27.62        49.12         0.62        41.75        51.16        66.54 
TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J 
       15.12        10.22        33.83        40.08         7.33         2.66 
TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N 
        6.74        12.39         6.58        13.15        19.04        32.84 
TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U 
       12.16        17.88        19.50         5.06        14.89        14.96 
TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD 
        5.06         8.35         8.25        17.16        16.18        20.48 
TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E 
        4.67        12.82         9.96        17.56        28.70        24.26 
TCGA-BT-A42F TCGA-C4-A0EZ TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S 
       28.41         8.98         0.46         0.43         0.69        10.95 
TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A7I0 
       12.66        12.46        12.10        12.26        13.12        12.10 
TCGA-CF-A8HX TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3QU 
       11.34        13.08        12.92         4.90         7.20         5.19 
TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A7 TCGA-DK-A1AA 
       16.31         1.84        13.58        21.86        18.41        19.00 
TCGA-DK-A1AB TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX 
       16.70       112.44        16.14        17.62        15.62         1.81 
TCGA-DK-A2I1 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM 
       10.59       123.85        87.32         2.20        13.58         7.82 
TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV 
        8.22        17.72        50.27        21.30        23.21         9.67 
TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X2 TCGA-DK-A6AW TCGA-DK-A6B0 
       20.81        10.55       140.81        17.98        41.56        76.60 
TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6P TCGA-DK-AA6Q 
       15.68        41.06        30.67        38.24        15.02        13.58 
TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 
      166.03        12.36        10.49         8.65         7.53        13.64 
TCGA-DK-AA74 TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E7-A3X6 
       43.50        12.03        10.62        43.59        15.35        24.66 
TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KE TCGA-E7-A5KF 
        0.10         0.49         2.24        16.70         0.56         0.66 
TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DV TCGA-E7-A7PW 
       14.56        13.97        12.99        14.33         1.22        13.68 
TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A8O7 TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 
       14.07        12.95        15.32        14.37         8.09        32.02 
TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 
       16.77         8.94        33.04         4.01        12.62        22.52 
TCGA-FD-A3N6 TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO 
       27.98        24.30        23.41        17.98        29.16         5.52 
TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P 
       25.74        46.78        19.79        12.85        22.98        27.35 
TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS 
       14.96        20.91         3.62        15.58        26.73        53.88 
TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A5C1 
       11.01        19.33         5.69         8.25        18.08        58.92 
TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB 
        2.70         7.10         6.28        13.35        62.86        18.81 
TCGA-FD-A6TD TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK 
       12.69         2.27         3.06         4.31         9.67        10.85 
TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A3EE 
       31.07         7.13        10.65        17.23         8.94         3.25 
TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO 
        6.48        61.94        30.61        15.95        26.93        35.24 
TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C 
       33.01         7.23        20.12        17.62        66.02         6.94 
TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB 
       64.44        19.46        21.40         2.24        15.81         4.50 
TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A4ZW TCGA-GC-A6I1 
       15.91        14.07        17.75        24.92         0.49         8.94 
TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 
       13.91         7.73         2.10         3.12        20.98         2.20 
TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 
       11.31        11.31         7.63        27.09        20.05         5.62 
TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW 
        4.73        10.65        32.98         7.00        14.27        21.34 
TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK 
       19.10        19.82        20.28         8.48        10.59        27.35 
TCGA-GV-A40E TCGA-GV-A40G TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF 
        8.58        19.07         1.51        19.40        38.60         3.06 
TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC 
        8.22        25.02         3.45        21.24         2.76         9.14 
TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6MB TCGA-K4-A83P 
       27.68         9.07        11.70         1.74        15.42         6.38 
TCGA-K4-AAQO TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-PQ-A6FI TCGA-PQ-A6FN 
       11.80        15.32        15.58        21.07        12.23        16.67 
TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78K 
       14.24         1.84         3.75        12.43        31.56        17.62 
TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78P TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A8OD 
       37.05        22.68        67.79        65.75         3.58       112.83 
TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HB 
       35.24        29.56        17.82         4.54         1.64        45.04 
TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A8HH 
        6.58        97.45       125.49        97.12        15.35         1.87 
TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SL 
       17.88        48.62        64.80        79.66         3.22        66.41 
TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 
       12.76        11.90        23.64        21.04        28.24        26.27 
TCGA-XF-A9T2 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME 
       18.90        16.27        66.64         2.10        13.74        92.98 
TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ 
       10.82       110.60        11.31        54.90         7.63        71.57 
TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ 
       91.73         2.96         8.32         6.77        98.99        44.32 
TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 
       56.48        30.94        61.45        86.30        27.06        75.39 
TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3M 
       18.81         3.88        18.84         9.63         0.66        13.64 
TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 
       18.64         7.36        24.13        30.28        27.19        21.86 
TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG 
       28.41        74.56        13.41         3.48        52.73        52.60 
TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4T 
       82.49        47.84        20.22         2.89        34.06        19.69 
TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 
        8.61        59.38        60.16        63.02        38.73        35.41 
TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5N TCGA-ZF-AA5P 
       57.90        19.40         8.52        47.15         5.52        10.13 

  4P GAIN MUTATED 4P GAIN WILD-TYPE 
             0.92              0.10 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
           130.88            166.03 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
            12.62             15.86 
[1] "0.9 - 130.9 (12.6)" "0.1 - 166.0 (15.9)"
[1] "hr=" "2.2"
D7V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  4P GAIN MUTATED         0       16        10        9
  4P GAIN WILD-TYPE       4      108       117      120
D7V3, multiclass
           clus
vv          4P GAIN MUTATED 4P GAIN WILD-TYPE
  STAGE I                 0                 4
  STAGE II               16               108
  STAGE III              10               117
  STAGE IV                9               120
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1+T2  T3  T4
  4P GAIN MUTATED         18  15   2
  4P GAIN WILD-TYPE      103 169  51
D7V4, multiclass
          clus
vv         4P GAIN MUTATED 4P GAIN WILD-TYPE
  T0+T1+T2              18               103
  T3                    15               169
  T4                     2                51
[1] 3 2
[1] TRUE
[1] "dimension of 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    26   5   3   1
  4P GAIN WILD-TYPE 198  37  72   7
D7V5, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  N0              26               198
  N1               5                37
  N2               3                72
  N3               1                 7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V6, binary
                   cls
clus                  0   1
  4P GAIN MUTATED    22   0
  4P GAIN WILD-TYPE 163  10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED     22    0
  4P GAIN WILD-TYPE  163   10
   clus
vv  4P GAIN MUTATED 4P GAIN WILD-TYPE
  0              22               163
  1               0                10
[1] 2 2
[1] FALSE
D7V7, binary
                   cls
clus                  0   1
  4P GAIN MUTATED    13  22
  4P GAIN WILD-TYPE  88 266
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED     13   22
  4P GAIN WILD-TYPE   88  266
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  FEMALE              13                88
  MALE                22               266
[1] 2 2
[1] FALSE
D7V8, continuous
D7V9, continuous
D7V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  4P GAIN MUTATED       5                         1    24
  4P GAIN WILD-TYPE    37                        20   287
D7V11, multiclass
                           clus
vv                          4P GAIN MUTATED 4P GAIN WILD-TYPE
  ASIAN                                   5                37
  BLACK OR AFRICAN AMERICAN               1                20
  WHITE                                  24               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"
D7V12, binary
                   cls
clus                  0   1
  4P GAIN MUTATED     1  28
  4P GAIN WILD-TYPE   8 324
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      1   28
  4P GAIN WILD-TYPE    8  324
                        clus
vv                       4P GAIN MUTATED 4P GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 8
  NOT HISPANIC OR LATINO              28               324
[1] 2 2
[1] FALSE

Clustering(8) Variable = 4Q GAIN MUTATION ANALYSIS
D8V1, survival
                   sevent
clus2                 0   1
  4Q GAIN MUTATED    19   7
  4Q GAIN WILD-TYPE 211 146
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               26               357 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                7               146 
$`4Q GAIN MUTATED`
TCGA-4Z-AA7M TCGA-4Z-AA7W TCGA-C4-A0F6 TCGA-CF-A47X TCGA-CF-A8HY TCGA-CF-A9FF 
       16.27        27.62        23.01        12.62        11.34        11.87 
TCGA-CU-A3KJ TCGA-DK-A1A5 TCGA-DK-A3X1 TCGA-DK-A6B1 TCGA-E5-A4U1 TCGA-FD-A3NA 
        5.46         2.14        48.00        67.36        38.83        60.66 
TCGA-FD-A5BV TCGA-FD-A5C0 TCGA-FD-A6TE TCGA-GD-A76B TCGA-GU-A42P TCGA-GV-A6ZA 
        5.36        18.08        12.36         7.36        10.92        22.72 
TCGA-HQ-A5ND TCGA-UY-A78O TCGA-XF-AAN7 TCGA-YF-AA3L TCGA-ZF-A9R2 TCGA-ZF-A9RN 
        9.01        76.01        18.81        11.97        21.11        20.22 
TCGA-ZF-AA4W TCGA-ZF-AA5H 
       60.16        19.17 

$`4Q GAIN WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        91.63       103.50       105.70         8.35 
TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7Y 
       44.94        16.83        16.77        17.16        34.98        49.12 
TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA84 TCGA-4Z-AA86 
        0.62        41.75        51.16        66.54        15.12        10.22 
TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM 
       47.80        33.83        40.08         7.33         2.66         6.74 
TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O 
       12.39         6.58        13.15        19.04        32.84        12.16 
TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V 
       17.88        19.50         5.06        14.89        14.96         5.06 
TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH 
        8.35         8.25        17.16        16.18        20.48         4.67 
TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F 
       12.82         9.96        17.56        28.70        24.26        28.41 
TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S 
        8.98         1.94         0.46         0.43         0.69        10.95 
TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA 
       12.66        12.46        12.10        12.26        13.12        12.00 
TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR 
       12.10        11.34        13.08        12.92         4.90         7.20 
TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A6 
        5.19        16.31         1.84        13.58        21.86        66.41 
TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE 
       18.41        19.00        16.70       130.88       112.44        16.14 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 
       17.62        15.62         1.81        10.59         7.79       123.85 
TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ 
       87.32         2.20        13.58         7.82         8.22        17.72 
TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX 
       50.27        21.30        23.21         9.67        20.81        10.55 
TCGA-DK-A3WY TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B2 
      140.81        17.98        64.18        41.56        76.60        15.68 
TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6S 
       41.06        30.67        38.24        15.02        13.58       166.03 
TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 
       12.36        10.49         8.65         7.53        13.64        43.50 
TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E7-A3X6 TCGA-E7-A3Y1 
       12.03        10.62        43.59        15.35        24.66         0.10 
TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF 
        0.49         2.24        16.70        17.39         0.56         0.66 
TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV 
       14.56        13.97        12.99        14.33         0.92         1.22 
TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A8O7 TCGA-E7-A97P TCGA-E7-A97Q 
       13.68        14.07        12.95        15.32        14.37         8.09 
TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 
       32.02        16.77         8.94        33.04         4.01        12.62 
TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN 
       22.52        27.98        24.30        23.41        17.98        29.16 
TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N 
        5.52        25.74        46.78        19.79        12.85        22.98 
TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR 
       27.35        14.96        20.91         3.62        15.58        26.73 
TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ 
       53.88        11.01        19.33         5.69         8.25        27.45 
TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA 
       58.92         2.70         7.10         6.28        13.35        62.86 
TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH 
       18.81         6.15        12.69         2.27         3.06         4.31 
TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF 
        9.67        10.85        31.07         7.13        10.65        17.23 
TCGA-FJ-A871 TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK 
        8.94         3.25         6.48        61.94        30.61        15.95 
TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY 
       26.93        35.24        33.01         7.23        20.12        17.62 
TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 
       66.02         6.94        64.44        19.46        21.40         2.24 
TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS 
       15.81         4.50        15.91        14.07        17.75        24.92 
TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ 
        0.49         8.94        13.91         7.73         2.10         3.12 
TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 
       20.98         2.20        11.31        11.31         7.63        27.09 
TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATP TCGA-GU-AATQ 
       20.05         5.62         4.73        10.65        32.98         7.00 
TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH 
       14.27        21.34        19.10        19.82        20.28         8.48 
TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-H4-A2HO TCGA-H4-A2HQ 
       10.59        27.35         8.58        19.07         1.51        19.40 
TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV 
       38.60         3.06         8.22        25.02         3.45        21.24 
TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ 
        2.76         9.14        27.68         9.07        11.70         1.74 
TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-LC-A66R TCGA-LT-A5Z6 
        1.81        15.42         6.38        11.80        15.32        15.58 
TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX 
       21.07        13.48        12.23        16.67        14.24         1.84 
TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M 
        3.75        12.43        31.56        17.62        37.05        22.68 
TCGA-UY-A78N TCGA-UY-A78P TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A8OD TCGA-UY-A9PA 
       86.83        67.79        65.75         3.58       112.83        35.24 
TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HC 
       29.56        17.82         4.54         1.64        45.04         6.58 
TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A8HI 
       97.45       125.49        97.12        15.35         1.87        17.88 
TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SV 
       48.62        64.80        79.66         3.22        66.41        12.76 
TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 
       11.90        23.64        21.04        28.24        26.27        18.90 
TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME 
        2.24        16.27        66.64         2.10        13.74        92.98 
TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ 
       10.82       110.60        11.31        54.90         7.63        71.57 
TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ 
       91.73         2.96         8.32         6.77        98.99        44.32 
TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 
       56.48        30.94        61.45        86.30        27.06        75.39 
TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3M TCGA-ZF-A9R0 
        3.88        18.84         9.63         0.66        13.64        18.64 
TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 
        7.36        24.13        30.28        27.19        21.86        28.41 
TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL 
       74.56        13.41         3.48        52.73        52.60        82.49 
TCGA-ZF-A9RM TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4V 
       47.84         2.89        34.06        19.69         8.61        59.38 
TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 
       63.02        38.73        35.41        57.90        19.40         8.52 
TCGA-ZF-AA58 TCGA-ZF-AA5N TCGA-ZF-AA5P 
       47.15         5.52        10.13 

  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
             2.14              0.10 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
            76.01            166.03 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
           18.445            15.580 
[1] "2.1 - 76.0 (18.4)"  "0.1 - 166.0 (15.6)"
[1] "hr=" "1.6"
D8V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  4Q GAIN MUTATED         0       13         7        6
  4Q GAIN WILD-TYPE       4      111       120      123
D8V3, multiclass
           clus
vv          4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  STAGE I                 0                 4
  STAGE II               13               111
  STAGE III               7               120
  STAGE IV                6               123
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1+T2  T3  T4
  4Q GAIN MUTATED         13  13   0
  4Q GAIN WILD-TYPE      108 171  53
D8V4, multiclass
          clus
vv         4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  T0+T1+T2              13               108
  T3                    13               171
  T4                     0                53
[1] 3 2
[1] TRUE
[1] "dimension of 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    19   3   3   0
  4Q GAIN WILD-TYPE 205  39  72   8
D8V5, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  N0              19               205
  N1               3                39
  N2               3                72
  N3               0                 8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V6, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED    16   0
  4Q GAIN WILD-TYPE 169  10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED     16    0
  4Q GAIN WILD-TYPE  169   10
   clus
vv  4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  0              16               169
  1               0                10
[1] 2 2
[1] FALSE
D8V7, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     8  18
  4Q GAIN WILD-TYPE  93 270
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      8   18
  4Q GAIN WILD-TYPE   93  270
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  FEMALE               8                93
  MALE                18               270
[1] 2 2
[1] FALSE
D8V8, continuous
D8V9, continuous
D8V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  4Q GAIN MUTATED       3                         0    19
  4Q GAIN WILD-TYPE    39                        21   292
D8V11, multiclass
                           clus
vv                          4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  ASIAN                                   3                39
  BLACK OR AFRICAN AMERICAN               0                21
  WHITE                                  19               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"
D8V12, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     1  21
  4Q GAIN WILD-TYPE   8 331
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      1   21
  4Q GAIN WILD-TYPE    8  331
                        clus
vv                       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 8
  NOT HISPANIC OR LATINO              21               331
[1] 2 2
[1] FALSE

Clustering(9) Variable = 5P GAIN MUTATION ANALYSIS
D9V1, survival
                   sevent
clus2                 0   1
  5P GAIN MUTATED    89  63
  5P GAIN WILD-TYPE 141  90
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
              152               231 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               63                90 
$`5P GAIN MUTATED`
TCGA-2F-A9KT TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA86 
      105.70        27.62        49.12         0.62        41.75        10.22 
TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A20V TCGA-BT-A20W 
        6.74        12.39        32.84        14.89         5.06         8.35 
TCGA-BT-A2LA TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42C TCGA-CF-A1HS TCGA-CF-A47S 
       17.16        12.82         9.96        28.70         0.43        10.95 
TCGA-CF-A5UA TCGA-CU-A0YN TCGA-CU-A0YR TCGA-CU-A3QU TCGA-DK-A1A3 TCGA-DK-A2I4 
       12.00        12.92         7.20         5.19        21.86       123.85 
TCGA-DK-A2I6 TCGA-DK-A3IN TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WX TCGA-DK-A6AV 
       87.32         8.22        23.21         9.67        10.55        64.18 
TCGA-DK-A6B1 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6P TCGA-DK-AA6Q 
       67.36        41.06        30.67        38.24        15.02        13.58 
TCGA-DK-AA6S TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 
      166.03        10.49         8.65         7.53        13.64        43.50 
TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A4IJ TCGA-E7-A541 TCGA-E7-A7DV 
       15.35        38.83        24.66         0.49        17.39         1.22 
TCGA-E7-A85H TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3N5 
       12.95         8.09        32.02        16.77         8.94        22.52 
TCGA-FD-A3NA TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SR TCGA-FD-A43Y TCGA-FD-A5BR 
       60.66         5.52        25.74        19.79        15.58        26.73 
TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BY TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O 
       19.33         5.36         8.25        58.92         2.70         7.10 
TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TE TCGA-FD-A6TG 
        6.28        13.35        18.81         6.15        12.36         3.06 
TCGA-FD-A6TH TCGA-FD-A6TK TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EO 
        4.31        10.85        17.23         3.25         6.48        35.24 
TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3I6 
        7.23        20.12        66.02        64.44        19.46         2.24 
TCGA-GC-A3OO TCGA-GC-A3YS TCGA-GC-A4ZW TCGA-GC-A6I3 TCGA-GD-A3OP TCGA-GD-A3OS 
       15.81        24.92         0.49        13.91         2.10        20.98 
TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A762 TCGA-GU-A766 TCGA-GU-AATO TCGA-GU-AATQ 
        7.36        10.92         7.63         5.62        10.65         7.00 
TCGA-GV-A3JV TCGA-GV-A3JX TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A40E 
       14.27        19.10        20.28         8.48        10.59         8.58 
TCGA-GV-A40G TCGA-H4-A2HQ TCGA-HQ-A5NE TCGA-K4-A4AC TCGA-K4-A5RH TCGA-K4-A5RI 
       19.07        19.40         8.22         9.14         9.07        11.70 
TCGA-K4-A6FZ TCGA-LC-A66R TCGA-MV-A51V TCGA-PQ-A6FN TCGA-S5-A6DX TCGA-SY-A9G5 
        1.81        15.32        13.48        16.67         1.84        31.56 
TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78N TCGA-UY-A8OB TCGA-UY-A9PB TCGA-UY-A9PE 
       17.62        37.05        86.83        65.75        29.56         4.54 
TCGA-XF-A8HF TCGA-XF-A9SG TCGA-XF-A9SJ TCGA-XF-A9T3 TCGA-XF-A9T5 TCGA-XF-AAME 
       97.12        48.62         3.22         2.24        66.64        92.98 
TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMT TCGA-XF-AAN7 TCGA-YF-AA3M TCGA-ZF-A9R3 
       54.90         7.63         2.96        18.81        13.64        24.13 
TCGA-ZF-A9R4 TCGA-ZF-A9R7 TCGA-ZF-A9RC TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL 
       30.28        21.86        74.56        52.73        52.60        82.49 
TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4V 
       47.84        20.22         2.89        34.06        19.69        59.38 
TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 
       63.02        38.73        35.41        57.90        19.40         8.52 
TCGA-ZF-AA58 TCGA-ZF-AA5H 
       47.15        19.17 

$`5P GAIN WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7M 
       22.29        11.97        91.63       103.50         8.35        16.27 
TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA82 
       44.94        16.83        16.77        17.16        34.98        51.16 
TCGA-4Z-AA83 TCGA-4Z-AA84 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I 
       66.54        15.12        47.80        33.83        40.08         7.33 
TCGA-BL-A13J TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P 
        2.66         6.58        13.15        19.04        12.16        17.88 
TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20X TCGA-BT-A2LB TCGA-BT-A2LD 
       19.50         5.06        14.96         8.25        16.18        20.48 
TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 
        4.67        17.56        24.26        28.41         8.98         1.94 
TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A27C TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W 
       23.01         0.46         0.69        12.66        12.46        12.10 
TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A8HY 
       12.62        12.26        13.12        12.10        11.34        11.34 
TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YO TCGA-CU-A3KJ TCGA-CU-A3YL TCGA-CU-A5W6 
       11.87        13.08         4.90         5.46        16.31         1.84 
TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB 
       13.58         2.14        66.41        18.41        19.00        16.70 
TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX 
      130.88       112.44        16.14        17.62        15.62         1.81 
TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IQ 
       10.59         7.79         2.20        13.58         7.82        17.72 
TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3WW TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 
       50.27        21.30        20.81       140.81        48.00        17.98 
TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B2 TCGA-DK-AA6T TCGA-DK-AA76 TCGA-DK-AA77 
       41.56        76.60        15.68        12.36        12.03        10.62 
TCGA-E5-A2PC TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KE TCGA-E7-A5KF 
       43.59         0.10         2.24        16.70         0.56         0.66 
TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7PW 
       14.56        13.97        12.99        14.33         0.92        13.68 
TCGA-E7-A7XN TCGA-E7-A8O7 TCGA-E7-A97P TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 
       14.07        15.32        14.37        33.04         4.01        12.62 
TCGA-FD-A3N6 TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SQ 
       27.98        24.30        23.41        17.98        29.16        46.78 
TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X 
       12.85        22.98        27.35        14.96        20.91         3.62 
TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A6TA 
       53.88        11.01         5.69        27.45        18.08        62.86 
TCGA-FD-A6TD TCGA-FD-A6TF TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE 
       12.69         2.27         9.67        31.07         7.13        10.65 
TCGA-FJ-A871 TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2ES 
        8.94        61.94        30.61        15.95        26.93        33.01 
TCGA-G2-A3VY TCGA-G2-AA3C TCGA-GC-A3BM TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD 
       17.62         6.94        21.40         4.50        15.91        14.07 
TCGA-GC-A3WC TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OQ TCGA-GD-A6C6 TCGA-GU-A42Q 
       17.75         8.94         7.73         3.12         2.20        11.31 
TCGA-GU-A42R TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A767 TCGA-GU-AATP TCGA-GV-A3JW 
       11.31        27.09        20.05         4.73        32.98        21.34 
TCGA-GV-A3JZ TCGA-GV-A3QK TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-HQ-A2OE TCGA-HQ-A2OF 
       19.82        27.35        22.72         1.51        38.60         3.06 
TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A54R 
        9.01        25.02         3.45        21.24         2.76        27.68 
TCGA-K4-A5RJ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-LT-A5Z6 TCGA-LT-A8JT 
        1.74        15.42         6.38        11.80        15.58        21.07 
TCGA-PQ-A6FI TCGA-R3-A69X TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-UY-A78M TCGA-UY-A78O 
       12.23        14.24         3.75        12.43        22.68        76.01 
TCGA-UY-A78P TCGA-UY-A8OC TCGA-UY-A8OD TCGA-UY-A9PA TCGA-UY-A9PD TCGA-UY-A9PF 
       67.79         3.58       112.83        35.24        17.82         1.64 
TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HG TCGA-XF-A8HH 
       45.04         6.58        97.45       125.49        15.35         1.87 
TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SW 
       17.88        64.80        79.66        66.41        12.76        11.90 
TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T4 
       23.64        21.04        28.24        26.27        18.90        16.27 
TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAMQ 
        2.10        13.74        10.82       110.60        11.31        71.57 
TCGA-XF-AAMR TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN0 
       91.73         8.32         6.77        98.99        44.32        56.48 
TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN8 
       30.94        61.45        86.30        27.06        75.39         3.88 
TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R1 
       18.84         9.63         0.66        11.97        18.64         7.36 
TCGA-ZF-A9R2 TCGA-ZF-A9R5 TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-AA4U 
       21.11        27.19        28.41        13.41         3.48         8.61 
TCGA-ZF-AA4W TCGA-ZF-AA5N TCGA-ZF-AA5P 
       60.16         5.52        10.13 

  5P GAIN MUTATED 5P GAIN WILD-TYPE 
             0.43              0.10 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
           166.03            140.81 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
           15.695            15.680 
[1] "0.4 - 166.0 (15.7)" "0.1 - 140.8 (15.7)"
[1] "hr=" "1"  
D9V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  5P GAIN MUTATED         1       55        50       47
  5P GAIN WILD-TYPE       3       69        77       82
D9V3, multiclass
           clus
vv          5P GAIN MUTATED 5P GAIN WILD-TYPE
  STAGE I                 1                 3
  STAGE II               55                69
  STAGE III              50                77
  STAGE IV               47                82
[1] 4 2
[1] TRUE
[1] "dimension of contingency 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         48  69  20
  5P GAIN WILD-TYPE       73 115  33
D9V4, multiclass
          clus
vv         5P GAIN MUTATED 5P GAIN WILD-TYPE
  T0+T1+T2              48                73
  T3                    69               115
  T4                    20                33
[1] 3 2
[1] TRUE
[1] "dimension of 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    84  19  26   3
  5P GAIN WILD-TYPE 140  23  49   5
D9V5, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  N0              84               140
  N1              19                23
  N2              26                49
  N3               3                 5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V6, binary
                   cls
clus                  0   1
  5P GAIN MUTATED    68   1
  5P GAIN WILD-TYPE 117   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     68    1
  5P GAIN WILD-TYPE  117    9
   clus
vv  5P GAIN MUTATED 5P GAIN WILD-TYPE
  0              68               117
  1               1                 9
[1] 2 2
[1] FALSE
D9V7, binary
                   cls
clus                  0   1
  5P GAIN MUTATED    38 117
  5P GAIN WILD-TYPE  63 171
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     38  117
  5P GAIN WILD-TYPE   63  171
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  FEMALE              38                63
  MALE               117               171
[1] 2 2
[1] FALSE
D9V8, continuous
D9V9, continuous
D9V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  5P GAIN MUTATED      11                        10   129
  5P GAIN WILD-TYPE    31                        11   182
D9V11, multiclass
                           clus
vv                          5P GAIN MUTATED 5P GAIN WILD-TYPE
  ASIAN                                  11                31
  BLACK OR AFRICAN AMERICAN              10                11
  WHITE                                 129               182
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V12, binary
                   cls
clus                  0   1
  5P GAIN MUTATED     3 145
  5P GAIN WILD-TYPE   6 207
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      3  145
  5P GAIN WILD-TYPE    6  207
                        clus
vv                       5P GAIN MUTATED 5P GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                 6
  NOT HISPANIC OR LATINO             145               207
[1] 2 2
[1] FALSE

Clustering(10) Variable = 5Q GAIN MUTATION ANALYSIS
D10V1, survival
                   sevent
clus2                 0   1
  5Q GAIN MUTATED    30  19
  5Q GAIN WILD-TYPE 200 134
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               49               334 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               19               134 
$`5Q GAIN MUTATED`
TCGA-BL-A3JM TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A42C TCGA-CF-A1HS TCGA-DK-A2I4 
        6.74        32.84        14.89        28.70         0.43       123.85 
TCGA-DK-A2I6 TCGA-DK-A6AV TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA71 TCGA-DK-AA74 
       87.32        64.18        30.67        38.24        13.64        43.50 
TCGA-E7-A541 TCGA-E7-A85H TCGA-FD-A5BU TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A6TE 
       17.39        12.95        19.33        58.92         6.28        12.36 
TCGA-FD-A6TH TCGA-FT-A3EE TCGA-G2-A2EO TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3OO 
        4.31         3.25        35.24        19.46         2.24        15.81 
TCGA-GC-A3YS TCGA-GD-A76B TCGA-GU-A762 TCGA-GV-A3JV TCGA-GV-A3QH TCGA-GV-A3QI 
       24.92         7.36         7.63        14.27         8.48        10.59 
TCGA-GV-A40E TCGA-K4-A4AC TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A6FZ TCGA-LC-A66R 
        8.58         9.14         9.07        11.70         1.81        15.32 
TCGA-MV-A51V TCGA-S5-A6DX TCGA-UY-A78L TCGA-UY-A78N TCGA-UY-A9PE TCGA-XF-A9SG 
       13.48         1.84        37.05        86.83         4.54        48.62 
TCGA-XF-A9T5 TCGA-XF-AAMJ TCGA-XF-AAMZ TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 
       66.64        54.90        44.32        57.90        19.40         8.52 
TCGA-ZF-AA58 
       47.15 

$`5Q GAIN WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        91.63       103.50       105.70         8.35 
TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S 
       16.27        44.94        16.83        16.77        17.16        34.98 
TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 
       27.62        49.12         0.62        41.75        51.16        66.54 
TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I 
       15.12        10.22        47.80        33.83        40.08         7.33 
TCGA-BL-A13J TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O 
        2.66        12.39         6.58        13.15        19.04        12.16 
TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W 
       17.88        19.50         5.06        14.96         5.06         8.35 
TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ 
        8.25        17.16        16.18        20.48         4.67        12.82 
TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 
        9.96        17.56        24.26        28.41         8.98         1.94 
TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V 
       23.01         0.46         0.69        10.95        12.66        12.46 
TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 
       12.10        12.62        12.26        13.12        12.00        12.10 
TCGA-CF-A8HX TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO 
       11.34        11.34        11.87        13.08        12.92         4.90 
TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E 
        7.20         5.46         5.19        16.31         1.84        13.58 
TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB 
       21.86         2.14        66.41        18.41        19.00        16.70 
TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX 
      130.88       112.44        16.14        17.62        15.62         1.81 
TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN 
       10.59         7.79         2.20        13.58         7.82         8.22 
TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW 
       17.72        50.27        21.30        23.21         9.67        20.81 
TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AW TCGA-DK-A6B0 
       10.55       140.81        48.00        17.98        41.56        76.60 
TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6S 
       67.36        15.68        41.06        15.02        13.58       166.03 
TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA76 TCGA-DK-AA77 
       12.36        10.49         8.65         7.53        12.03        10.62 
TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ 
       43.59        15.35        38.83        24.66         0.10         0.49 
TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 
        2.24        16.70         0.56         0.66        14.56        13.97 
TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A7XN 
       12.99        14.33         0.92         1.22        13.68        14.07 
TCGA-E7-A8O7 TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 
       15.32        14.37         8.09        32.02        16.77         8.94 
TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA 
       33.04         4.01        12.62        22.52        27.98        60.66 
TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP 
       24.30        23.41        17.98        29.16         5.52        25.74 
TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S 
       46.78        19.79        12.85        22.98        27.35        14.96 
TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT 
       20.91         3.62        15.58        26.73        53.88        11.01 
TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A62N 
        5.36         5.69         8.25        27.45        18.08         2.70 
TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD 
        7.10        13.35        62.86        18.81         6.15        12.69 
TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 
        2.27         3.06         9.67        10.85        31.07         7.13 
TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ 
       10.65        17.23         8.94         6.48        61.94        30.61 
TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY 
       15.95        26.93        33.01         7.23        20.12        17.62 
TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3D TCGA-GC-A3BM TCGA-GC-A3RB TCGA-GC-A3RC 
       66.02         6.94        64.44        21.40         4.50        15.91 
TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 
       14.07        17.75         0.49         8.94        13.91         7.73 
TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42P TCGA-GU-A42Q 
        2.10         3.12        20.98         2.20        10.92        11.31 
TCGA-GU-A42R TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO 
       11.31        27.09        20.05         5.62         4.73        10.65 
TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF 
       32.98         7.00        21.34        19.10        19.82        20.28 
TCGA-GV-A3QK TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE 
       27.35        19.07        22.72         1.51        19.40        38.60 
TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV 
        3.06         9.01         8.22        25.02         3.45        21.24 
TCGA-K4-A4AB TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO 
        2.76        27.68         1.74        15.42         6.38        11.80 
TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-AA26 
       15.58        21.07        12.23        16.67        14.24         3.75 
TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78M TCGA-UY-A78O TCGA-UY-A78P 
       12.43        31.56        17.62        22.68        76.01        67.79 
TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A8OD TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD 
       65.75         3.58       112.83        35.24        29.56        17.82 
TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF 
        1.64        45.04         6.58        97.45       125.49        97.12 
TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ 
       15.35         1.87        17.88        64.80        79.66         3.22 
TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ 
       66.41        12.76        11.90        23.64        21.04        28.24 
TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T6 TCGA-XF-A9T8 
       26.27        18.90         2.24        16.27         2.10        13.74 
TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAML TCGA-XF-AAMQ 
       92.98        10.82       110.60        11.31         7.63        71.57 
TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAN0 
       91.73         2.96         8.32         6.77        98.99        56.48 
TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 
       30.94        61.45        86.30        27.06        75.39        18.81 
TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M 
        3.88        18.84         9.63         0.66        11.97        13.64 
TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 
       18.64         7.36        21.11        24.13        30.28        27.19 
TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF 
       21.86        28.41        74.56        13.41         3.48        52.73 
TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4R 
       52.60        82.49        47.84        20.22         2.89        34.06 
TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 
       19.69         8.61        59.38        60.16        63.02        38.73 
TCGA-ZF-AA52 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
       35.41        19.17         5.52        10.13 

  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
             0.43              0.10 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
           123.85            166.03 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
           15.320            15.795 
[1] "0.4 - 123.8 (15.3)" "0.1 - 166.0 (15.8)"
[1] "hr=" "1.1"
D10V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  5Q GAIN MUTATED         0       15        18       16
  5Q GAIN WILD-TYPE       4      109       109      113
D10V3, multiclass
           clus
vv          5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  STAGE I                 0                 4
  STAGE II               15               109
  STAGE III              18               109
  STAGE IV               16               113
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1+T2  T3  T4
  5Q GAIN MUTATED         14  27   5
  5Q GAIN WILD-TYPE      107 157  48
D10V4, multiclass
          clus
vv         5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  T0+T1+T2              14               107
  T3                    27               157
  T4                     5                48
[1] 3 2
[1] TRUE
[1] "dimension of 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   9   8   0
  5Q GAIN WILD-TYPE 195  33  67   8
D10V5, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  N0              29               195
  N1               9                33
  N2               8                67
  N3               0                 8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V6, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED    19   0
  5Q GAIN WILD-TYPE 166  10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     19    0
  5Q GAIN WILD-TYPE  166   10
   clus
vv  5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  0              19               166
  1               0                10
[1] 2 2
[1] FALSE
D10V7, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED    12  39
  5Q GAIN WILD-TYPE  89 249
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     12   39
  5Q GAIN WILD-TYPE   89  249
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  FEMALE              12                89
  MALE                39               249
[1] 2 2
[1] FALSE
D10V8, continuous
D10V9, continuous
D10V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  5Q GAIN MUTATED       6                         1    42
  5Q GAIN WILD-TYPE    36                        20   269
D10V11, multiclass
                           clus
vv                          5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  ASIAN                                   6                36
  BLACK OR AFRICAN AMERICAN               1                20
  WHITE                                  42               269
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V12, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED     1  49
  5Q GAIN WILD-TYPE   8 303
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      1   49
  5Q GAIN WILD-TYPE    8  303
                        clus
vv                       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 8
  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    47  27
  6P GAIN WILD-TYPE 183 126
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               74               309 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               27               126 
$`6P GAIN MUTATED`
TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-BT-A0S7 TCGA-CF-A47V 
       16.27        16.77         0.62        41.75         6.58        12.46 
TCGA-CF-A47X TCGA-CF-A5UA TCGA-DK-A1AC TCGA-DK-A2I6 TCGA-DK-A3IM TCGA-DK-A3WX 
       12.62        12.00       130.88        87.32         7.82        10.55 
TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-AA74 TCGA-E7-A541 TCGA-E7-A6ME TCGA-FD-A3B7 
       67.36        15.68        43.50        17.39        12.99         4.01 
TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A5BU TCGA-FD-A5C1 TCGA-FD-A6TC TCGA-FD-A6TF 
       19.79        12.85        19.33        58.92         6.15         2.27 
TCGA-FD-A6TG TCGA-FJ-A3ZE TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-AA3B TCGA-GC-A3BM 
        3.06        10.65         3.25         6.48        66.02        21.40 
TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A3YS TCGA-GC-A4ZW TCGA-GD-A2C5 
        2.24        15.81        15.91        24.92         0.49         7.73 
TCGA-GU-A42P TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-AATO TCGA-GU-AATP TCGA-GV-A6ZA 
       10.92        11.31         7.63        10.65        32.98        22.72 
TCGA-HQ-A5NE TCGA-K4-A4AC TCGA-K4-A5RH TCGA-K4-AAQO TCGA-LC-A66R TCGA-LT-A5Z6 
        8.22         9.14         9.07        11.80        15.32        15.58 
TCGA-SY-A9G0 TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A8OB 
       12.43        37.05        22.68        86.83        76.01        65.75 
TCGA-UY-A8OC TCGA-UY-A9PB TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HC TCGA-XF-A8HD 
        3.58        29.56         4.54         1.64         6.58        97.45 
TCGA-XF-A9T5 TCGA-XF-AAMG TCGA-XF-AAML TCGA-XF-AAMQ TCGA-ZF-A9R4 TCGA-ZF-A9RG 
       66.64       110.60         7.63        71.57        30.28        52.60 
TCGA-ZF-A9RN TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4V TCGA-ZF-AA4X TCGA-ZF-AA54 
       20.22        34.06        19.69        59.38        63.02        19.40 
TCGA-ZF-AA58 TCGA-ZF-AA5H 
       47.15        19.17 

$`6P GAIN WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        91.63       103.50       105.70         8.35 
TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA7Y 
       44.94        16.83        17.16        34.98        27.62        49.12 
TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 
       51.16        66.54        15.12        10.22        47.80        33.83 
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0YX 
       40.08         7.33         2.66         6.74        12.39        13.15 
TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R 
       19.04        32.84        12.16        17.88        19.50         5.06 
TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA 
       14.89        14.96         5.06         8.35         8.25        17.16 
TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B 
       16.18        20.48         4.67        12.82         9.96        17.56 
TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F6 
       28.70        24.26        28.41         8.98         1.94        23.01 
TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47W 
        0.46         0.43         0.69        10.95        12.66        12.10 
TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A8HY TCGA-CF-A9FF 
       12.26        13.12        12.10        11.34        11.34        11.87 
TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU 
       13.08        12.92         4.90         7.20         5.46         5.19 
TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 
       16.31         1.84        13.58        21.86         2.14        66.41 
TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF 
       18.41        19.00        16.70       112.44        16.14        17.62 
TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IK 
       15.62         1.81        10.59         7.79       123.85         2.20 
TCGA-DK-A3IL TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU 
       13.58         8.22        17.72        50.27        21.30        23.21 
TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV 
        9.67        20.81       140.81        48.00        17.98        64.18 
TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6P 
       41.56        76.60        41.06        30.67        38.24        15.02 
TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X 
       13.58       166.03        12.36        10.49         8.65         7.53 
TCGA-DK-AA71 TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 
       13.64        12.03        10.62        43.59        15.35        38.83 
TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KE 
       24.66         0.10         0.49         2.24        16.70         0.56 
TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV 
        0.66        14.56        13.97        14.33         0.92         1.22 
TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A8O7 TCGA-E7-A97P TCGA-E7-A97Q 
       13.68        14.07        12.95        15.32        14.37         8.09 
TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B8 TCGA-FD-A3N5 
       32.02        16.77         8.94        33.04        12.62        22.52 
TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN 
       27.98        60.66        24.30        23.41        17.98        29.16 
TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S 
        5.52        25.74        46.78        22.98        27.35        14.96 
TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT 
       20.91         3.62        15.58        26.73        53.88        11.01 
TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A62N 
        5.36         5.69         8.25        27.45        18.08         2.70 
TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TD 
        7.10         6.28        13.35        62.86        18.81        12.69 
TCGA-FD-A6TE TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 
       12.36         4.31         9.67        10.85        31.07         7.13 
TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL 
       17.23         8.94        61.94        30.61        15.95        26.93 
TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3C 
       35.24        33.01         7.23        20.12        17.62         6.94 
TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3RB TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A6I1 
       64.44        19.46         4.50        14.07        17.75         8.94 
TCGA-GC-A6I3 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B 
       13.91         2.10         3.12        20.98         2.20         7.36 
TCGA-GU-A42Q TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATQ 
       11.31        27.09        20.05         5.62         4.73         7.00 
TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH 
       14.27        21.34        19.10        19.82        20.28         8.48 
TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-H4-A2HO TCGA-H4-A2HQ 
       10.59        27.35         8.58        19.07         1.51        19.40 
TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV 
       38.60         3.06         9.01        25.02         3.45        21.24 
TCGA-K4-A4AB TCGA-K4-A54R TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB 
        2.76        27.68        11.70         1.74         1.81        15.42 
TCGA-K4-A83P TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X 
        6.38        21.07        13.48        12.23        16.67        14.24 
TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78P TCGA-UY-A8OD 
        1.84         3.75        31.56        17.62        67.79       112.83 
TCGA-UY-A9PA TCGA-UY-A9PD TCGA-XF-A8HB TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG 
       35.24        17.82        45.04       125.49        97.12        15.35 
TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ 
        1.87        17.88        48.62        64.80        79.66         3.22 
TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ 
       66.41        12.76        11.90        23.64        21.04        28.24 
TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T6 TCGA-XF-A9T8 
       26.27        18.90         2.24        16.27         2.10        13.74 
TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAMR TCGA-XF-AAMT 
       92.98        10.82        11.31        54.90        91.73         2.96 
TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN1 
        8.32         6.77        98.99        44.32        56.48        30.94 
TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-XF-AAN8 
       61.45        86.30        27.06        75.39        18.81         3.88 
TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R0 
       18.84         9.63         0.66        11.97        13.64        18.64 
TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 
        7.36        21.11        24.13        27.19        21.86        28.41 
TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RL TCGA-ZF-A9RM 
       74.56        13.41         3.48        52.73        82.49        47.84 
TCGA-ZF-AA4N TCGA-ZF-AA4U TCGA-ZF-AA4W TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA53 
        2.89         8.61        60.16        38.73        35.41        57.90 
TCGA-ZF-AA56 TCGA-ZF-AA5N TCGA-ZF-AA5P 
        8.52         5.52        10.13 

  6P GAIN MUTATED 6P GAIN WILD-TYPE 
             0.49              0.10 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
           130.88            166.03 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
            15.86             15.58 
[1] "0.5 - 130.9 (15.9)" "0.1 - 166.0 (15.6)"
[1] "hr=" "1.2"
D11V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  6P GAIN MUTATED         0       21        23       30
  6P GAIN WILD-TYPE       4      103       104       99
D11V3, multiclass
           clus
vv          6P GAIN MUTATED 6P GAIN WILD-TYPE
  STAGE I                 0                 4
  STAGE II               21               103
  STAGE III              23               104
  STAGE IV               30                99
[1] 4 2
[1] TRUE
[1] "dimension of contingency 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         25  33  13
  6P GAIN WILD-TYPE       96 151  40
D11V4, multiclass
          clus
vv         6P GAIN MUTATED 6P GAIN WILD-TYPE
  T0+T1+T2              25                96
  T3                    33               151
  T4                    13                40
[1] 3 2
[1] TRUE
[1] "dimension of 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    37  11  17   2
  6P GAIN WILD-TYPE 187  31  58   6
D11V5, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  N0              37               187
  N1              11                31
  N2              17                58
  N3               2                 6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V6, binary
                   cls
clus                  0   1
  6P GAIN MUTATED    29   2
  6P GAIN WILD-TYPE 156   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     29    2
  6P GAIN WILD-TYPE  156    8
   clus
vv  6P GAIN MUTATED 6P GAIN WILD-TYPE
  0              29               156
  1               2                 8
[1] 2 2
[1] FALSE
D11V7, binary
                   cls
clus                  0   1
  6P GAIN MUTATED    16  58
  6P GAIN WILD-TYPE  85 230
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     16   58
  6P GAIN WILD-TYPE   85  230
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  FEMALE              16                85
  MALE                58               230
[1] 2 2
[1] FALSE
D11V8, continuous
D11V9, continuous
D11V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  6P GAIN MUTATED       6                         2    65
  6P GAIN WILD-TYPE    36                        19   246
D11V11, multiclass
                           clus
vv                          6P GAIN MUTATED 6P GAIN WILD-TYPE
  ASIAN                                   6                36
  BLACK OR AFRICAN AMERICAN               2                19
  WHITE                                  65               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"
D11V12, binary
                   cls
clus                  0   1
  6P GAIN MUTATED     2  66
  6P GAIN WILD-TYPE   7 286
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      2   66
  6P GAIN WILD-TYPE    7  286
                        clus
vv                       6P GAIN MUTATED 6P GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 7
  NOT HISPANIC OR LATINO              66               286
[1] 2 2
[1] FALSE

Clustering(12) Variable = 6Q GAIN MUTATION ANALYSIS
D12V1, survival
                   sevent
clus2                 0   1
  6Q GAIN MUTATED    25  14
  6Q GAIN WILD-TYPE 205 139
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               39               344 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               14               139 
$`6Q GAIN MUTATED`
TCGA-4Z-AA7Q TCGA-4Z-AA80 TCGA-BT-A0S7 TCGA-BT-A2LA TCGA-CF-A47V TCGA-CF-A47X 
       16.77         0.62         6.58        17.16        12.46        12.62 
TCGA-CF-A5UA TCGA-DK-A1AC TCGA-DK-A2I6 TCGA-DK-A3IM TCGA-DK-A3WX TCGA-DK-A6B1 
       12.00       130.88        87.32         7.82        10.55        67.36 
TCGA-E7-A6ME TCGA-FD-A3SS TCGA-FD-A5C1 TCGA-FJ-A3ZE TCGA-GC-A3BM TCGA-GC-A3OO 
       12.99        12.85        58.92        10.65        21.40        15.81 
TCGA-GC-A3YS TCGA-GC-A4ZW TCGA-GU-A42P TCGA-GU-AATO TCGA-K4-A4AC TCGA-K4-A5RH 
       24.92         0.49        10.92        10.65         9.14         9.07 
TCGA-K4-AAQO TCGA-LC-A66R TCGA-UY-A78L TCGA-UY-A78N TCGA-XF-A8HC TCGA-XF-A8HD 
       11.80        15.32        37.05        86.83         6.58        97.45 
TCGA-XF-A9T5 TCGA-XF-AAMG TCGA-XF-AAMQ TCGA-ZF-A9R4 TCGA-ZF-A9RG TCGA-ZF-A9RN 
       66.64       110.60        71.57        30.28        52.60        20.22 
TCGA-ZF-AA4T TCGA-ZF-AA4V TCGA-ZF-AA4X 
       19.69        59.38        63.02 

$`6Q GAIN WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        91.63       103.50       105.70         8.35 
TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W 
       16.27        44.94        16.83        17.16        34.98        27.62 
TCGA-4Z-AA7Y TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA84 TCGA-4Z-AA86 
       49.12        41.75        51.16        66.54        15.12        10.22 
TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM 
       47.80        33.83        40.08         7.33         2.66         6.74 
TCGA-BL-A5ZZ TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P 
       12.39        13.15        19.04        32.84        12.16        17.88 
TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W 
       19.50         5.06        14.89        14.96         5.06         8.35 
TCGA-BT-A20X TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK 
        8.25        16.18        20.48         4.67        12.82         9.96 
TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 
       17.56        28.70        24.26        28.41         8.98         1.94 
TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T 
       23.01         0.46         0.43         0.69        10.95        12.66 
TCGA-CF-A47W TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A8HY 
       12.10        12.26        13.12        12.10        11.34        11.34 
TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ 
       11.87        13.08        12.92         4.90         7.20         5.46 
TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 
        5.19        16.31         1.84        13.58        21.86         2.14 
TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AD TCGA-DK-A1AE 
       66.41        18.41        19.00        16.70       112.44        16.14 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 
       17.62        15.62         1.81        10.59         7.79       123.85 
TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT 
        2.20        13.58         8.22        17.72        50.27        21.30 
TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 
       23.21         9.67        20.81       140.81        48.00        17.98 
TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 
       64.18        41.56        76.60        15.68        41.06        30.67 
TCGA-DK-AA6L TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U 
       38.24        15.02        13.58       166.03        12.36        10.49 
TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA76 TCGA-DK-AA77 
        8.65         7.53        13.64        43.50        12.03        10.62 
TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ 
       43.59        15.35        38.83        24.66         0.10         0.49 
TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 
        2.24        16.70        17.39         0.56         0.66        14.56 
TCGA-E7-A678 TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A7XN 
       13.97        14.33         0.92         1.22        13.68        14.07 
TCGA-E7-A85H TCGA-E7-A8O7 TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 
       12.95        15.32        14.37         8.09        32.02        16.77 
TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 
        8.94        33.04         4.01        12.62        22.52        27.98 
TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO 
       60.66        24.30        23.41        17.98        29.16         5.52 
TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S 
       25.74        46.78        19.79        22.98        27.35        14.96 
TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT 
       20.91         3.62        15.58        26.73        53.88        11.01 
TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 
       19.33         5.36         5.69         8.25        27.45        18.08 
TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB 
        2.70         7.10         6.28        13.35        62.86        18.81 
TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH 
        6.15        12.69        12.36         2.27         3.06         4.31 
TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZF TCGA-FJ-A871 
        9.67        10.85        31.07         7.13        17.23         8.94 
TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL 
        3.25         6.48        61.94        30.61        15.95        26.93 
TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B 
       35.24        33.01         7.23        20.12        17.62        66.02 
TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3RB TCGA-GC-A3RC 
        6.94        64.44        19.46         2.24         4.50        15.91 
TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP 
       14.07        17.75         8.94        13.91         7.73         2.10 
TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42Q TCGA-GU-A42R 
        3.12        20.98         2.20         7.36        11.31        11.31 
TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATP 
        7.63        27.09        20.05         5.62         4.73        32.98 
TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF 
        7.00        14.27        21.34        19.10        19.82        20.28 
TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA 
        8.48        10.59        27.35         8.58        19.07        22.72 
TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE 
        1.51        19.40        38.60         3.06         9.01         8.22 
TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A54R TCGA-K4-A5RI 
       25.02         3.45        21.24         2.76        27.68        11.70 
TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-LT-A5Z6 TCGA-LT-A8JT 
        1.74         1.81        15.42         6.38        15.58        21.07 
TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 
       13.48        12.23        16.67        14.24         1.84         3.75 
TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78M TCGA-UY-A78O TCGA-UY-A78P 
       12.43        31.56        17.62        22.68        76.01        67.79 
TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A8OD TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD 
       65.75         3.58       112.83        35.24        29.56        17.82 
TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG 
        4.54         1.64        45.04       125.49        97.12        15.35 
TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ 
        1.87        17.88        48.62        64.80        79.66         3.22 
TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ 
       66.41        12.76        11.90        23.64        21.04        28.24 
TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T6 TCGA-XF-A9T8 
       26.27        18.90         2.24        16.27         2.10        13.74 
TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMR 
       92.98        10.82        11.31        54.90         7.63        91.73 
TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN0 
        2.96         8.32         6.77        98.99        44.32        56.48 
TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 
       30.94        61.45        86.30        27.06        75.39        18.81 
TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M 
        3.88        18.84         9.63         0.66        11.97        13.64 
TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 
       18.64         7.36        21.11        24.13        27.19        21.86 
TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RL 
       28.41        74.56        13.41         3.48        52.73        82.49 
TCGA-ZF-A9RM TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4U TCGA-ZF-AA4W TCGA-ZF-AA51 
       47.84         2.89        34.06         8.61        60.16        38.73 
TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H 
       35.41        57.90        19.40         8.52        47.15        19.17 
TCGA-ZF-AA5N TCGA-ZF-AA5P 
        5.52        10.13 

  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
             0.49              0.10 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
           130.88            166.03 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
            16.77             15.60 
[1] "0.5 - 130.9 (16.8)" "0.1 - 166.0 (15.6)"
[1] "hr=" "1.4"
D12V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  6Q GAIN MUTATED         0       12        15       12
  6Q GAIN WILD-TYPE       4      112       112      117
D12V3, multiclass
           clus
vv          6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  STAGE I                 0                 4
  STAGE II               12               112
  STAGE III              15               112
  STAGE IV               12               117
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1+T2  T3  T4
  6Q GAIN MUTATED         14  17   6
  6Q GAIN WILD-TYPE      107 167  47
D12V4, multiclass
          clus
vv         6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  T0+T1+T2              14               107
  T3                    17               167
  T4                     6                47
[1] 3 2
[1] TRUE
[1] "dimension of 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    22   6   4   2
  6Q GAIN WILD-TYPE 202  36  71   6
D12V5, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  N0              22               202
  N1               6                36
  N2               4                71
  N3               2                 6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V6, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED    20   1
  6Q GAIN WILD-TYPE 165   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED     20    1
  6Q GAIN WILD-TYPE  165    9
   clus
vv  6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  0              20               165
  1               1                 9
[1] 2 2
[1] FALSE
D12V7, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED     6  33
  6Q GAIN WILD-TYPE  95 255
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      6   33
  6Q GAIN WILD-TYPE   95  255
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  FEMALE               6                95
  MALE                33               255
[1] 2 2
[1] FALSE
D12V8, continuous
D12V9, continuous
D12V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  6Q GAIN MUTATED       5                         0    34
  6Q GAIN WILD-TYPE    37                        21   277
D12V11, multiclass
                           clus
vv                          6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  ASIAN                                   5                37
  BLACK OR AFRICAN AMERICAN               0                21
  WHITE                                  34               277
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V12, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED     1  35
  6Q GAIN WILD-TYPE   8 317
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      1   35
  6Q GAIN WILD-TYPE    8  317
                        clus
vv                       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 8
  NOT HISPANIC OR LATINO              35               317
[1] 2 2
[1] FALSE

Clustering(13) Variable = 7P GAIN MUTATION ANALYSIS
D13V1, survival
                   sevent
clus2                 0   1
  7P GAIN MUTATED    97  63
  7P GAIN WILD-TYPE 133  90
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              160               223 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               63                90 
$`7P GAIN MUTATED`
TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7W TCGA-4Z-AA80 TCGA-4Z-AA81 
       16.27        16.77        17.16        27.62         0.62        41.75 
TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A5ZZ TCGA-BT-A0S7 
       15.12        10.22        47.80        33.83        12.39         6.58 
TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD 
       32.84        12.16         8.25        17.16        16.18        20.48 
TCGA-BT-A3PJ TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F6 TCGA-CF-A1HR 
       12.82        28.70        24.26        28.41        23.01         0.46 
TCGA-CF-A5U8 TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A3KJ TCGA-CU-A72E TCGA-DK-A1A3 
       13.12        12.92         4.90         5.46        13.58        21.86 
TCGA-DK-A1AC TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK 
      130.88        10.59         7.79       123.85        87.32         2.20 
TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IS TCGA-DK-A3IU TCGA-DK-A3X1 
       13.58         7.82         8.22        50.27        23.21        48.00 
TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6B1 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6P 
       17.98        64.18        67.36        30.67        38.24        15.02 
TCGA-DK-AA6S TCGA-DK-AA6U TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E7-A4IJ TCGA-E7-A541 
      166.03        10.49        43.59        15.35         0.49        17.39 
TCGA-E7-A6ME TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A97Q TCGA-FD-A3B3 
       12.99         0.92         1.22        13.68         8.09        32.02 
TCGA-FD-A3B5 TCGA-FD-A3B7 TCGA-FD-A3N5 TCGA-FD-A3SQ TCGA-FD-A3SS TCGA-FD-A43N 
        8.94         4.01        22.52        46.78        12.85        22.98 
TCGA-FD-A43P TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BV TCGA-FD-A5BZ 
       27.35        20.91         3.62        26.73         5.36        27.45 
TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A6TC TCGA-FD-A6TD 
       18.08        58.92         7.10         6.28         6.15        12.69 
TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3ZE 
       12.36         2.27         3.06         9.67        31.07        10.65 
TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EO TCGA-G2-A3VY TCGA-G2-AA3B 
       17.23         3.25         6.48        35.24        17.62        66.02 
TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3RC TCGA-GC-A3RD 
       64.44        19.46        21.40         2.24        15.91        14.07 
TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42P TCGA-GU-A42Q 
       13.91         7.73        20.98         2.20        10.92        11.31 
TCGA-GU-A766 TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JZ TCGA-GV-A3QK TCGA-GV-A40E 
        5.62        32.98         7.00        19.82        27.35         8.58 
TCGA-GV-A6ZA TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A5RH 
       22.72        19.40        38.60         9.01         8.22         9.07 
TCGA-K4-A5RI TCGA-K4-A6FZ TCGA-K4-A83P TCGA-LC-A66R TCGA-MV-A51V TCGA-S5-A6DX 
       11.70         1.81         6.38        15.32        13.48         1.84 
TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A8OB 
       12.43        31.56        22.68        86.83        76.01        65.75 
TCGA-UY-A8OC TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PE TCGA-XF-A8HD TCGA-XF-A8HF 
        3.58        35.24        29.56         4.54        97.45        97.12 
TCGA-XF-A8HG TCGA-XF-A9SG TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SY TCGA-XF-A9T3 
       15.35        48.62        79.66         3.22        21.04         2.24 
TCGA-XF-A9T5 TCGA-XF-AAMG TCGA-XF-AAMQ TCGA-XF-AAMT TCGA-XF-AAMX TCGA-XF-AAMY 
       66.64       110.60        71.57         2.96         6.77        98.99 
TCGA-XF-AAN0 TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R3 
       56.48        75.39        18.81        13.64        18.64        24.13 
TCGA-ZF-A9RD TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4R 
       13.41        52.73        52.60        20.22         2.89        34.06 
TCGA-ZF-AA4V TCGA-ZF-AA4X TCGA-ZF-AA56 TCGA-ZF-AA5H 
       59.38        63.02         8.52        19.17 

$`7P GAIN WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        91.63       103.50       105.70         8.35 
TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7S TCGA-4Z-AA7Y TCGA-4Z-AA82 TCGA-4Z-AA83 
       44.94        16.83        34.98        49.12        51.16        66.54 
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0YX TCGA-BT-A20J 
       40.08         7.33         2.66         6.74        13.15        19.04 
TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V 
       17.88        19.50         5.06        14.89        14.96         5.06 
TCGA-BT-A20W TCGA-BT-A3PH TCGA-BT-A3PK TCGA-BT-A42B TCGA-C4-A0EZ TCGA-C4-A0F0 
        8.35         4.67         9.96        17.56         8.98         1.94 
TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W 
        0.43         0.69        10.95        12.66        12.46        12.10 
TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A8HY 
       12.62        12.26        12.00        12.10        11.34        11.34 
TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YR TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 
       11.87        13.08         7.20         5.19        16.31         1.84 
TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AD 
        2.14        66.41        18.41        19.00        16.70       112.44 
TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A3IQ TCGA-DK-A3IT 
       16.14        17.62        15.62         1.81        17.72        21.30 
TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A6AW TCGA-DK-A6B0 
        9.67        20.81        10.55       140.81        41.56        76.60 
TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6W TCGA-DK-AA6X 
       15.68        41.06        13.58        12.36         8.65         7.53 
TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A4U1 TCGA-E7-A3X6 
       13.64        43.50        12.03        10.62        38.83        24.66 
TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 
        0.10         2.24        16.70         0.56         0.66        14.56 
TCGA-E7-A678 TCGA-E7-A6MF TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A8O7 TCGA-E7-A97P 
       13.97        14.33        14.07        12.95        15.32        14.37 
TCGA-FD-A3B4 TCGA-FD-A3B6 TCGA-FD-A3B8 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ 
       16.77        33.04        12.62        27.98        60.66        24.30 
TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SR 
       23.41        17.98        29.16         5.52        25.74        19.79 
TCGA-FD-A43S TCGA-FD-A43Y TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BX 
       14.96        15.58        53.88        11.01        19.33         5.69 
TCGA-FD-A5BY TCGA-FD-A62N TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TH 
        8.25         2.70        13.35        62.86        18.81         4.31 
TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A871 TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK 
       10.85         7.13         8.94        61.94        30.61        15.95 
TCGA-G2-A2EL TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3C TCGA-GC-A3OO 
       26.93        33.01         7.23        20.12         6.94        15.81 
TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GD-A3OP 
        4.50        17.75        24.92         0.49         8.94         2.10 
TCGA-GD-A3OQ TCGA-GD-A76B TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 
        3.12         7.36        11.31         7.63        27.09        20.05 
TCGA-GU-A767 TCGA-GU-AATO TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QF 
        4.73        10.65        14.27        21.34        19.10        20.28 
TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A40G TCGA-H4-A2HO TCGA-HQ-A2OF TCGA-K4-A3WS 
        8.48        10.59        19.07         1.51         3.06        25.02 
TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RJ 
        3.45        21.24         2.76         9.14        27.68         1.74 
TCGA-K4-A6MB TCGA-K4-AAQO TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-PQ-A6FI TCGA-PQ-A6FN 
       15.42        11.80        15.58        21.07        12.23        16.67 
TCGA-R3-A69X TCGA-S5-AA26 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78P TCGA-UY-A8OD 
       14.24         3.75        17.62        37.05        67.79       112.83 
TCGA-UY-A9PD TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HE TCGA-XF-A8HH 
       17.82         1.64        45.04         6.58       125.49         1.87 
TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX 
       17.88        64.80        66.41        12.76        11.90        23.64 
TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T4 TCGA-XF-A9T6 TCGA-XF-A9T8 
       28.24        26.27        18.90        16.27         2.10        13.74 
TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMR 
       92.98        10.82        11.31        54.90         7.63        91.73 
TCGA-XF-AAMW TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN4 
        8.32        44.32        30.94        61.45        86.30        27.06 
TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R1 
        3.88        18.84         9.63         0.66        11.97         7.36 
TCGA-ZF-A9R2 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RC 
       21.11        30.28        27.19        21.86        28.41        74.56 
TCGA-ZF-A9RE TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4W 
        3.48        82.49        47.84        19.69         8.61        60.16 
TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA58 TCGA-ZF-AA5N 
       38.73        35.41        57.90        19.40        47.15         5.52 
TCGA-ZF-AA5P 
       10.13 

  7P GAIN MUTATED 7P GAIN WILD-TYPE 
             0.46              0.10 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
           166.03            140.81 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
           16.965            15.420 
[1] "0.5 - 166.0 (17.0)" "0.1 - 140.8 (15.4)"
[1] "hr=" "1.1"
D13V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  7P GAIN MUTATED         1       39        57       62
  7P GAIN WILD-TYPE       3       85        70       67
D13V3, multiclass
           clus
vv          7P GAIN MUTATED 7P GAIN WILD-TYPE
  STAGE I                 1                 3
  STAGE II               39                85
  STAGE III              57                70
  STAGE IV               62                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                T0+T1+T2  T3  T4
  7P GAIN MUTATED         40  83  28
  7P GAIN WILD-TYPE       81 101  25
D13V4, multiclass
          clus
vv         7P GAIN MUTATED 7P GAIN WILD-TYPE
  T0+T1+T2              40                81
  T3                    83               101
  T4                    28                25
[1] 3 2
[1] TRUE
[1] "dimension of 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    84  21  34   7
  7P GAIN WILD-TYPE 140  21  41   1
D13V5, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  N0              84               140
  N1              21                21
  N2              34                41
  N3               7                 1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V6, binary
                   cls
clus                  0   1
  7P GAIN MUTATED    73   4
  7P GAIN WILD-TYPE 112   6
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     73    4
  7P GAIN WILD-TYPE  112    6
   clus
vv  7P GAIN MUTATED 7P GAIN WILD-TYPE
  0              73               112
  1               4                 6
[1] 2 2
[1] FALSE
D13V7, binary
                   cls
clus                  0   1
  7P GAIN MUTATED    44 118
  7P GAIN WILD-TYPE  57 170
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     44  118
  7P GAIN WILD-TYPE   57  170
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  FEMALE              44                57
  MALE               118               170
[1] 2 2
[1] FALSE
D13V8, continuous
D13V9, continuous
D13V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  7P GAIN MUTATED      11                        10   134
  7P GAIN WILD-TYPE    31                        11   177
D13V11, multiclass
                           clus
vv                          7P GAIN MUTATED 7P GAIN WILD-TYPE
  ASIAN                                  11                31
  BLACK OR AFRICAN AMERICAN              10                11
  WHITE                                 134               177
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V12, binary
                   cls
clus                  0   1
  7P GAIN MUTATED     4 142
  7P GAIN WILD-TYPE   5 210
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      4  142
  7P GAIN WILD-TYPE    5  210
                        clus
vv                       7P GAIN MUTATED 7P GAIN WILD-TYPE
  HISPANIC OR LATINO                   4                 5
  NOT HISPANIC OR LATINO             142               210
[1] 2 2
[1] FALSE

Clustering(14) Variable = 7Q GAIN MUTATION ANALYSIS
D14V1, survival
                   sevent
clus2                 0   1
  7Q GAIN MUTATED    85  55
  7Q GAIN WILD-TYPE 145  98
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              140               243 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               55                98 
$`7Q GAIN MUTATED`
TCGA-4Z-AA7Q TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA84 
       16.77        34.98        27.62         0.62        41.75        15.12 
TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A20N TCGA-BT-A20X 
       47.80        33.83        12.39         6.58        32.84         8.25 
TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A42E TCGA-BT-A42F 
       17.16        16.18        20.48        12.82        24.26        28.41 
TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A5U8 TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A3KJ 
       23.01         0.46        13.12        12.92         4.90         5.46 
TCGA-CU-A72E TCGA-DK-A1AD TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I6 
       13.58       112.44         1.81        10.59         7.79        87.32 
TCGA-DK-A3IL TCGA-DK-A3IN TCGA-DK-A3IS TCGA-DK-A3IU TCGA-DK-A3X2 TCGA-DK-A6B1 
       13.58         8.22        50.27        23.21        17.98        67.36 
TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W 
       30.67        38.24       166.03        12.36        10.49         8.65 
TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E7-A4IJ TCGA-E7-A541 TCGA-E7-A7DU 
       10.62        43.59        15.35         0.49        17.39         0.92 
TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A97Q TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B7 
        1.22        13.68         8.09        16.77         8.94         4.01 
TCGA-FD-A3N5 TCGA-FD-A3SQ TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43U 
       22.52        46.78        12.85        22.98        27.35        20.91 
TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A5C1 TCGA-FD-A62O 
        3.62        26.73         5.36        27.45        58.92         7.10 
TCGA-FD-A62P TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TF TCGA-FD-A6TH TCGA-FD-A6TI 
        6.28         6.15        12.69         2.27         4.31         9.67 
TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EO TCGA-G2-A3VY 
       10.65        17.23         3.25         6.48        35.24        17.62 
TCGA-G2-AA3B TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3RC 
       66.02        64.44        19.46        21.40         2.24        15.91 
TCGA-GC-A3RD TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OS TCGA-GU-A764 TCGA-GU-AATP 
       14.07        13.91         7.73        20.98        20.05        32.98 
TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA 
       19.82        20.28        27.35         8.58        19.07        22.72 
TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A5ND TCGA-K4-A3WV TCGA-K4-A5RH TCGA-K4-A5RI 
       19.40        38.60         9.01        21.24         9.07        11.70 
TCGA-K4-A6FZ TCGA-K4-A83P TCGA-LC-A66R TCGA-MV-A51V TCGA-S5-A6DX TCGA-SY-A9G0 
        1.81         6.38        15.32        13.48         1.84        12.43 
TCGA-SY-A9G5 TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A8OC TCGA-UY-A9PB 
       31.56        22.68        86.83        76.01         3.58        29.56 
TCGA-UY-A9PE TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG 
        4.54         6.58        97.45       125.49        97.12        15.35 
TCGA-XF-A9SG TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9T5 TCGA-XF-AAMG TCGA-XF-AAMQ 
       48.62        79.66         3.22        66.64       110.60        71.57 
TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAN0 TCGA-XF-AAN5 TCGA-ZF-A9R0 TCGA-ZF-A9R3 
        6.77        98.99        56.48        75.39        18.64        24.13 
TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RG TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4R 
       28.41        13.41        52.60        20.22         2.89        34.06 
TCGA-ZF-AA4X TCGA-ZF-AA5H 
       63.02        19.17 

$`7Q GAIN WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        91.63       103.50       105.70         8.35 
TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA7Y TCGA-4Z-AA82 
       16.27        44.94        16.83        17.16        49.12        51.16 
TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM 
       66.54        10.22        40.08         7.33         2.66         6.74 
TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R 
       13.15        19.04        12.16        17.88        19.50         5.06 
TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A3PH TCGA-BT-A3PK 
       14.89        14.96         5.06         8.35         4.67         9.96 
TCGA-BT-A42B TCGA-BT-A42C TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-CF-A1HS TCGA-CF-A27C 
       17.56        28.70         8.98         1.94         0.43         0.69 
TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y 
       10.95        12.66        12.46        12.10        12.62        12.26 
TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CF-A9FM 
       12.00        12.10        11.34        11.34        11.87        13.08 
TCGA-CU-A0YR TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A5 
        7.20         5.19        16.31         1.84        21.86         2.14 
TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AE 
       66.41        18.41        19.00        16.70       130.88        16.14 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IM TCGA-DK-A3IQ 
       17.62        15.62       123.85         2.20         7.82        17.72 
TCGA-DK-A3IT TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 
       21.30         9.67        20.81        10.55       140.81        48.00 
TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-AA6P 
       64.18        41.56        76.60        15.68        41.06        15.02 
TCGA-DK-AA6Q TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA76 TCGA-E5-A4U1 
       13.58         7.53        13.64        43.50        12.03        38.83 
TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KE TCGA-E7-A5KF 
       24.66         0.10         2.24        16.70         0.56         0.66 
TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7XN TCGA-E7-A85H 
       14.56        13.97        12.99        14.33        14.07        12.95 
TCGA-E7-A8O7 TCGA-E7-A97P TCGA-FD-A3B3 TCGA-FD-A3B6 TCGA-FD-A3B8 TCGA-FD-A3N6 
       15.32        14.37        32.02        33.04        12.62        27.98 
TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO 
       60.66        24.30        23.41        17.98        29.16         5.52 
TCGA-FD-A3SP TCGA-FD-A3SR TCGA-FD-A43S TCGA-FD-A43Y TCGA-FD-A5BS TCGA-FD-A5BT 
       25.74        19.79        14.96        15.58        53.88        11.01 
TCGA-FD-A5BU TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A62N TCGA-FD-A62S 
       19.33         5.69         8.25        18.08         2.70        13.35 
TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TK TCGA-FJ-A3Z7 
       62.86        18.81        12.36         3.06        10.85        31.07 
TCGA-FJ-A3Z9 TCGA-FJ-A871 TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL 
        7.13         8.94        61.94        30.61        15.95        26.93 
TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3C TCGA-GC-A3OO TCGA-GC-A3RB 
       33.01         7.23        20.12         6.94        15.81         4.50 
TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GD-A3OP TCGA-GD-A3OQ 
       17.75        24.92         0.49         8.94         2.10         3.12 
TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 
        2.20         7.36        10.92        11.31        11.31         7.63 
TCGA-GU-A763 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATQ TCGA-GV-A3JV 
       27.09         5.62         4.73        10.65         7.00        14.27 
TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QH TCGA-GV-A3QI TCGA-H4-A2HO TCGA-HQ-A2OF 
       21.34        19.10         8.48        10.59         1.51         3.06 
TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R 
        8.22        25.02         3.45         2.76         9.14        27.68 
TCGA-K4-A5RJ TCGA-K4-A6MB TCGA-K4-AAQO TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-PQ-A6FI 
        1.74        15.42        11.80        15.58        21.07        12.23 
TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-AA26 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78P 
       16.67        14.24         3.75        17.62        37.05        67.79 
TCGA-UY-A8OB TCGA-UY-A8OD TCGA-UY-A9PA TCGA-UY-A9PD TCGA-UY-A9PF TCGA-XF-A8HB 
       65.75       112.83        35.24        17.82         1.64        45.04 
TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SW 
        1.87        17.88        64.80        66.41        12.76        11.90 
TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 
       23.64        21.04        28.24        26.27        18.90         2.24 
TCGA-XF-A9T4 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMH 
       16.27         2.10        13.74        92.98        10.82        11.31 
TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMZ 
       54.90         7.63        91.73         2.96         8.32        44.32 
TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN7 TCGA-XF-AAN8 
       30.94        61.45        86.30        27.06        18.81         3.88 
TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R1 
       18.84         9.63         0.66        11.97        13.64         7.36 
TCGA-ZF-A9R2 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9RC TCGA-ZF-A9RE 
       21.11        30.28        27.19        21.86        74.56         3.48 
TCGA-ZF-A9RF TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4V 
       52.73        82.49        47.84        19.69         8.61        59.38 
TCGA-ZF-AA4W TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 
       60.16        38.73        35.41        57.90        19.40         8.52 
TCGA-ZF-AA58 TCGA-ZF-AA5N TCGA-ZF-AA5P 
       47.15         5.52        10.13 

  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
             0.46              0.10 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
           166.03            140.81 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
            17.31             15.02 
[1] "0.5 - 166.0 (17.3)" "0.1 - 140.8 (15.0)"
[1] "hr=" "1.1"
D14V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  7Q GAIN MUTATED         1       36        46       56
  7Q GAIN WILD-TYPE       3       88        81       73
D14V3, multiclass
           clus
vv          7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  STAGE I                 1                 3
  STAGE II               36                88
  STAGE III              46                81
  STAGE IV               56                73
[1] 4 2
[1] TRUE
[1] "dimension of contingency 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         39  66  27
  7Q GAIN WILD-TYPE       82 118  26
D14V4, multiclass
          clus
vv         7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  T0+T1+T2              39                82
  T3                    66               118
  T4                    27                26
[1] 3 2
[1] TRUE
[1] "dimension of 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    73  17  31   8
  7Q GAIN WILD-TYPE 151  25  44   0
D14V5, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  N0              73               151
  N1              17                25
  N2              31                44
  N3               8                 0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V6, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED    60   4
  7Q GAIN WILD-TYPE 125   6
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     60    4
  7Q GAIN WILD-TYPE  125    6
   clus
vv  7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  0              60               125
  1               4                 6
[1] 2 2
[1] FALSE
D14V7, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED    39 103
  7Q GAIN WILD-TYPE  62 185
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     39  103
  7Q GAIN WILD-TYPE   62  185
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  FEMALE              39                62
  MALE               103               185
[1] 2 2
[1] FALSE
D14V8, continuous
D14V9, continuous
D14V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  7Q GAIN MUTATED       9                        10   118
  7Q GAIN WILD-TYPE    33                        11   193
D14V11, multiclass
                           clus
vv                          7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  ASIAN                                   9                33
  BLACK OR AFRICAN AMERICAN              10                11
  WHITE                                 118               193
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V12, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED     3 126
  7Q GAIN WILD-TYPE   6 226
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      3  126
  7Q GAIN WILD-TYPE    6  226
                        clus
vv                       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                 6
  NOT HISPANIC OR LATINO             126               226
[1] 2 2
[1] FALSE

Clustering(15) Variable = 8P GAIN MUTATION ANALYSIS
D15V1, survival
                   sevent
clus2                 0   1
  8P GAIN MUTATED    52  32
  8P GAIN WILD-TYPE 178 121
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               84               299 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               32               121 
$`8P GAIN MUTATED`
TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA84 TCGA-4Z-AA87 
       16.27        44.94        41.75        51.16        15.12        47.80 
TCGA-4Z-AA89 TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20V 
       33.83         6.74        12.39        19.04        32.84         5.06 
TCGA-BT-A2LA TCGA-BT-A42E TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A27C TCGA-CF-A5UA 
       17.16        24.26         1.94        23.01         0.69        12.00 
TCGA-CU-A72E TCGA-DK-A1A6 TCGA-DK-A1AE TCGA-DK-A2I1 TCGA-DK-A3IQ TCGA-DK-A3IS 
       13.58        66.41        16.14        10.59        17.72        50.27 
TCGA-DK-A3WX TCGA-DK-A3X2 TCGA-DK-A6B6 TCGA-DK-AA6U TCGA-DK-AA71 TCGA-DK-AA74 
       10.55        17.98        30.67        10.49        13.64        43.50 
TCGA-E5-A2PC TCGA-E7-A4IJ TCGA-E7-A6ME TCGA-E7-A85H TCGA-E7-A97P TCGA-FD-A3N6 
       43.59         0.49        12.99        12.95        14.37        27.98 
TCGA-FD-A3NA TCGA-FD-A43U TCGA-FD-A5BS TCGA-FD-A5BX TCGA-FD-A5C1 TCGA-FD-A62O 
       60.66        20.91        53.88         5.69        58.92         7.10 
TCGA-FD-A6TI TCGA-FJ-A3ZE TCGA-G2-A2ES TCGA-G2-A3VY TCGA-G2-AA3B TCGA-GC-A3BM 
        9.67        10.65        33.01        17.62        66.02        21.40 
TCGA-GC-A3I6 TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3QI TCGA-GV-A6ZA TCGA-HQ-A2OE 
        2.24         7.00        14.27        10.59        22.72        38.60 
TCGA-HQ-A2OF TCGA-K4-A5RI TCGA-K4-A83P TCGA-MV-A51V TCGA-PQ-A6FN TCGA-S5-A6DX 
        3.06        11.70         6.38        13.48        16.67         1.84 
TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A8OC TCGA-UY-A9PE 
       12.43        31.56        22.68        86.83         3.58         4.54 
TCGA-UY-A9PF TCGA-XF-A8HD TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A9SG TCGA-XF-A9SH 
        1.64        97.45        97.12        15.35        48.62        64.80 
TCGA-XF-A9SY TCGA-XF-A9T6 TCGA-XF-AAMY TCGA-XF-AAN7 TCGA-YF-AA3M TCGA-ZF-A9R2 
       21.04         2.10        98.99        18.81        13.64        21.11 
TCGA-ZF-A9R3 TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 
       24.13        20.22         2.89        63.02        38.73        35.41 

$`8P GAIN WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        91.63       103.50       105.70         8.35 
TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA7Y 
       16.83        16.77        17.16        34.98        27.62        49.12 
TCGA-4Z-AA80 TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J 
        0.62        66.54        10.22        40.08         7.33         2.66 
TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R 
        6.58        13.15        12.16        17.88        19.50         5.06 
TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LB TCGA-BT-A2LD 
       14.89        14.96         8.35         8.25        16.18        20.48 
TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42F 
        4.67        12.82         9.96        17.56        28.70        28.41 
TCGA-C4-A0EZ TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V 
        8.98         0.46         0.43        10.95        12.66        12.46 
TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A7I0 TCGA-CF-A8HX 
       12.10        12.62        12.26        13.12        12.10        11.34 
TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR 
       11.34        11.87        13.08        12.92         4.90         7.20 
TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A5 
        5.46         5.19        16.31         1.84        21.86         2.14 
TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AF 
       18.41        19.00        16.70       130.88       112.44        17.62 
TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK 
       15.62         1.81         7.79       123.85        87.32         2.20 
TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV 
       13.58         7.82         8.22        21.30        23.21         9.67 
TCGA-DK-A3WW TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 
       20.81       140.81        48.00        64.18        41.56        76.60 
TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-AA6L TCGA-DK-AA6P TCGA-DK-AA6Q 
       67.36        15.68        41.06        38.24        15.02        13.58 
TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA76 TCGA-DK-AA77 
      166.03        12.36         8.65         7.53        12.03        10.62 
TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A519 
       15.35        38.83        24.66         0.10         2.24        16.70 
TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MF 
       17.39         0.56         0.66        14.56        13.97        14.33 
TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A8O7 TCGA-E7-A97Q 
        0.92         1.22        13.68        14.07        15.32         8.09 
TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 
       32.02        16.77         8.94        33.04         4.01        12.62 
TCGA-FD-A3N5 TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO 
       22.52        24.30        23.41        17.98        29.16         5.52 
TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P 
       25.74        46.78        19.79        12.85        22.98        27.35 
TCGA-FD-A43S TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BT TCGA-FD-A5BU 
       14.96         3.62        15.58        26.73        11.01        19.33 
TCGA-FD-A5BV TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A62N TCGA-FD-A62P 
        5.36         8.25        27.45        18.08         2.70         6.28 
TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE 
       13.35        62.86        18.81         6.15        12.69        12.36 
TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 
        2.27         3.06         4.31        10.85        31.07         7.13 
TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ 
       17.23         8.94         3.25         6.48        61.94        30.61 
TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3C 
       15.95        26.93        35.24         7.23        20.12         6.94 
TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD 
       64.44        19.46        15.81         4.50        15.91        14.07 
TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 
       17.75        24.92         0.49         8.94        13.91         7.73 
TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P 
        2.10         3.12        20.98         2.20         7.36        10.92 
TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 
       11.31        11.31         7.63        27.09        20.05         5.62 
TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATP TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ 
        4.73        10.65        32.98        21.34        19.10        19.82 
TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-H4-A2HO 
       20.28         8.48        27.35         8.58        19.07         1.51 
TCGA-H4-A2HQ TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV 
       19.40         9.01         8.22        25.02         3.45        21.24 
TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RJ TCGA-K4-A6FZ 
        2.76         9.14        27.68         9.07         1.74         1.81 
TCGA-K4-A6MB TCGA-K4-AAQO TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-PQ-A6FI 
       15.42        11.80        15.32        15.58        21.07        12.23 
TCGA-R3-A69X TCGA-S5-AA26 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78O TCGA-UY-A78P 
       14.24         3.75        17.62        37.05        76.01        67.79 
TCGA-UY-A8OB TCGA-UY-A8OD TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-XF-A8HB 
       65.75       112.83        35.24        29.56        17.82        45.04 
TCGA-XF-A8HC TCGA-XF-A8HE TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SI TCGA-XF-A9SJ 
        6.58       125.49         1.87        17.88        79.66         3.22 
TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T0 
       66.41        12.76        11.90        23.64        28.24        26.27 
TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T8 TCGA-XF-AAME 
       18.90         2.24        16.27        66.64        13.74        92.98 
TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ 
       10.82       110.60        11.31        54.90         7.63        71.57 
TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMZ TCGA-XF-AAN0 
       91.73         2.96         8.32         6.77        44.32        56.48 
TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN8 
       30.94        61.45        86.30        27.06        75.39         3.88 
TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R1 
       18.84         9.63         0.66        11.97        18.64         7.36 
TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RD 
       30.28        27.19        21.86        28.41        74.56        13.41 
TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-AA4R 
        3.48        52.73        52.60        82.49        47.84        34.06 
TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA53 TCGA-ZF-AA54 
       19.69         8.61        59.38        60.16        57.90        19.40 
TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
        8.52        47.15        19.17         5.52        10.13 

  8P GAIN MUTATED 8P GAIN WILD-TYPE 
             0.49              0.10 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
            98.99            166.03 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
            17.67             15.35 
[1] "0.5 - 99.0 (17.7)"  "0.1 - 166.0 (15.3)"
[1] "hr=" "1.2"
D15V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  8P GAIN MUTATED         1       27        31       24
  8P GAIN WILD-TYPE       3       97        96      105
D15V3, multiclass
           clus
vv          8P GAIN MUTATED 8P GAIN WILD-TYPE
  STAGE I                 1                 3
  STAGE II               27                97
  STAGE III              31                96
  STAGE IV               24               105
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1+T2  T3  T4
  8P GAIN MUTATED         30  39  11
  8P GAIN WILD-TYPE       91 145  42
D15V4, multiclass
          clus
vv         8P GAIN MUTATED 8P GAIN WILD-TYPE
  T0+T1+T2              30                91
  T3                    39               145
  T4                    11                42
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  8P GAIN MUTATED    49  11  12   1
  8P GAIN WILD-TYPE 175  31  63   7
D15V5, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  N0              49               175
  N1              11                31
  N2              12                63
  N3               1                 7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V6, binary
                   cls
clus                  0   1
  8P GAIN MUTATED    45   2
  8P GAIN WILD-TYPE 140   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     45    2
  8P GAIN WILD-TYPE  140    8
   clus
vv  8P GAIN MUTATED 8P GAIN WILD-TYPE
  0              45               140
  1               2                 8
[1] 2 2
[1] FALSE
D15V7, binary
                   cls
clus                  0   1
  8P GAIN MUTATED    19  66
  8P GAIN WILD-TYPE  82 222
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     19   66
  8P GAIN WILD-TYPE   82  222
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  FEMALE              19                82
  MALE                66               222
[1] 2 2
[1] FALSE
D15V8, continuous
D15V9, continuous
D15V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  8P GAIN MUTATED      10                         4    64
  8P GAIN WILD-TYPE    32                        17   247
D15V11, multiclass
                           clus
vv                          8P GAIN MUTATED 8P GAIN WILD-TYPE
  ASIAN                                  10                32
  BLACK OR AFRICAN AMERICAN               4                17
  WHITE                                  64               247
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V12, binary
                   cls
clus                  0   1
  8P GAIN MUTATED     2  70
  8P GAIN WILD-TYPE   7 282
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      2   70
  8P GAIN WILD-TYPE    7  282
                        clus
vv                       8P GAIN MUTATED 8P GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 7
  NOT HISPANIC OR LATINO              70               282
[1] 2 2
[1] FALSE

Clustering(16) Variable = 8Q GAIN MUTATION ANALYSIS
D16V1, survival
                   sevent
clus2                 0   1
  8Q GAIN MUTATED   117  74
  8Q GAIN WILD-TYPE 113  79
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              191               192 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               74                79 
$`8Q GAIN MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KR TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA80 
       22.29        11.97       103.50        16.27        44.94         0.62 
TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 
       41.75        51.16        15.12        10.22        47.80        33.83 
TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20V TCGA-BT-A20W 
        6.74        12.39        19.04        32.84         5.06         8.35 
TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ 
        8.25        17.16        16.18        24.26        28.41         8.98 
TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47X TCGA-CF-A5UA 
        1.94        23.01         0.69        10.95        12.62        12.00 
TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CU-A0YN TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A5W6 
       11.34        11.87        12.92         5.46         5.19         1.84 
TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AC TCGA-DK-A1AD 
       13.58        21.86        66.41        18.41       130.88       112.44 
TCGA-DK-A1AE TCGA-DK-A2I1 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IN TCGA-DK-A3IQ 
       16.14        10.59       123.85        87.32         8.22        17.72 
TCGA-DK-A3IS TCGA-DK-A3IU TCGA-DK-A3WX TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6B2 
       50.27        23.21        10.55        48.00        17.98        15.68 
TCGA-DK-A6B6 TCGA-DK-AA6P TCGA-DK-AA6S TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA71 
       30.67        15.02       166.03        10.49         8.65        13.64 
TCGA-DK-AA74 TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A4IJ TCGA-E7-A541 TCGA-E7-A6ME 
       43.50        43.59        38.83         0.49        17.39        12.99 
TCGA-E7-A7DU TCGA-E7-A7PW TCGA-E7-A85H TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B6 
        0.92        13.68        12.95        14.37         8.09        33.04 
TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SQ TCGA-FD-A43N TCGA-FD-A43U TCGA-FD-A5BR 
       27.98        60.66        46.78        22.98        20.91        26.73 
TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5C0 TCGA-FD-A5C1 
       53.88        11.01         5.36         5.69        18.08        58.92 
TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TH 
        7.10         6.28        13.35        12.69        12.36         4.31 
TCGA-FD-A6TI TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FT-A3EE TCGA-G2-A2EK TCGA-G2-A2ES 
        9.67         7.13        10.65         3.25        15.95        33.01 
TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3D TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3RB 
       17.62        66.02        64.44        21.40         2.24         4.50 
TCGA-GC-A3WC TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A76B TCGA-GU-AATP 
       17.75         2.10         3.12        20.98         7.36        32.98 
TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF 
        7.00        14.27        21.34        19.10        19.82        20.28 
TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A6ZA TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND 
        8.48        10.59        22.72        38.60         3.06         9.01 
TCGA-HQ-A5NE TCGA-K4-A4AB TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A6FZ TCGA-K4-A6MB 
        8.22         2.76         9.07        11.70         1.81        15.42 
TCGA-K4-A83P TCGA-LC-A66R TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN 
        6.38        15.32        21.07        13.48        12.23        16.67 
TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78M 
       14.24         1.84        12.43        31.56        17.62        22.68 
TCGA-UY-A78N TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A8OD TCGA-UY-A9PB TCGA-UY-A9PE 
       86.83        65.75         3.58       112.83        29.56         4.54 
TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HD TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A9SG 
        1.64        45.04        97.45        97.12        15.35        48.62 
TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SV TCGA-XF-A9SY TCGA-XF-A9T0 
       64.80        79.66         3.22        12.76        21.04        26.27 
TCGA-XF-A9T3 TCGA-XF-A9T6 TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML 
        2.24         2.10       110.60        11.31        54.90         7.63 
TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMY TCGA-XF-AAN2 TCGA-XF-AAN5 TCGA-XF-AAN7 
        2.96         8.32        98.99        61.45        75.39        18.81 
TCGA-YC-A89H TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 
       18.84        13.64        18.64         7.36        21.11        24.13 
TCGA-ZF-A9R4 TCGA-ZF-A9R9 TCGA-ZF-A9RE TCGA-ZF-A9RG TCGA-ZF-A9RN TCGA-ZF-AA4N 
       30.28        28.41         3.48        52.60        20.22         2.89 
TCGA-ZF-AA4U TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA53 
        8.61        60.16        63.02        38.73        35.41        57.90 
TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N 
       19.40         8.52        47.15        19.17         5.52 

$`8Q GAIN WILD-TYPE`
TCGA-2F-A9KQ TCGA-2F-A9KT TCGA-2F-A9KW TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R 
       91.63       105.70         8.35        16.83        16.77        17.16 
TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA83 TCGA-BL-A0C8 TCGA-BL-A13I 
       34.98        27.62        49.12        66.54        40.08         7.33 
TCGA-BL-A13J TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q 
        2.66         6.58        13.15        12.16        17.88        19.50 
TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ 
        5.06        14.89        14.96        20.48         4.67        12.82 
TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A47T 
        9.96        17.56        28.70         0.46         0.43        12.66 
TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A7I0 TCGA-CF-A8HX 
       12.46        12.10        12.26        13.12        12.10        11.34 
TCGA-CF-A9FM TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3YL TCGA-DK-A1A5 TCGA-DK-A1AA 
       13.08         4.90         7.20        16.31         2.14        19.00 
TCGA-DK-A1AB TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I2 TCGA-DK-A3IK 
       16.70        17.62        15.62         1.81         7.79         2.20 
TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IT TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WY 
       13.58         7.82        21.30         9.67        20.81       140.81 
TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B5 TCGA-DK-AA6L 
       64.18        41.56        76.60        67.36        41.06        38.24 
TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6X TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A4TZ 
       13.58        12.36         7.53        12.03        10.62        15.35 
TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KE TCGA-E7-A5KF 
       24.66         0.10         2.24        16.70         0.56         0.66 
TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MF TCGA-E7-A7DV TCGA-E7-A7XN TCGA-E7-A8O7 
       14.56        13.97        14.33         1.22        14.07        15.32 
TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 
       32.02        16.77         8.94         4.01        12.62        22.52 
TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP 
       24.30        23.41        17.98        29.16         5.52        25.74 
TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43X TCGA-FD-A43Y 
       19.79        12.85        27.35        14.96         3.62        15.58 
TCGA-FD-A5BU TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A62N TCGA-FD-A6TA TCGA-FD-A6TB 
       19.33         8.25        27.45         2.70        62.86        18.81 
TCGA-FD-A6TC TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3ZF 
        6.15         2.27         3.06        10.85        31.07        17.23 
TCGA-FJ-A871 TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EL TCGA-G2-A2EO 
        8.94         6.48        61.94        30.61        26.93        35.24 
TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3OO TCGA-GC-A3RC 
        7.23        20.12         6.94        19.46        15.81        15.91 
TCGA-GC-A3RD TCGA-GC-A3YS TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 
       14.07        24.92         0.49         8.94        13.91         7.73 
TCGA-GD-A6C6 TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 
        2.20        10.92        11.31        11.31         7.63        27.09 
TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO TCGA-GV-A3QK TCGA-GV-A40E 
       20.05         5.62         4.73        10.65        27.35         8.58 
TCGA-GV-A40G TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV 
       19.07         1.51        19.40        25.02         3.45        21.24 
TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-AAQO TCGA-LT-A5Z6 TCGA-S5-AA26 
        9.14        27.68         1.74        11.80        15.58         3.75 
TCGA-UY-A78L TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A9PA TCGA-UY-A9PD TCGA-XF-A8HC 
       37.05        76.01        67.79        35.24        17.82         6.58 
TCGA-XF-A8HE TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SL TCGA-XF-A9SW TCGA-XF-A9SX 
      125.49         1.87        17.88        66.41        11.90        23.64 
TCGA-XF-A9SZ TCGA-XF-A9T2 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T8 TCGA-XF-AAME 
       28.24        18.90        16.27        66.64        13.74        92.98 
TCGA-XF-AAMF TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMX TCGA-XF-AAMZ TCGA-XF-AAN0 
       10.82        71.57        91.73         6.77        44.32        56.48 
TCGA-XF-AAN1 TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YC-A9TC 
       30.94        86.30        27.06         3.88         9.63         0.66 
TCGA-YF-AA3L TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RF 
       11.97        27.19        21.86        74.56        13.41        52.73 
TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4V TCGA-ZF-AA5P 
       82.49        47.84        34.06        19.69        59.38        10.13 

  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
             0.49              0.10 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
           166.03            140.81 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
           16.180            15.465 
[1] "0.5 - 166.0 (16.2)" "0.1 - 140.8 (15.5)"
[1] "hr=" "1.2"
D16V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  8Q GAIN MUTATED         2       58        68       63
  8Q GAIN WILD-TYPE       2       66        59       66
D16V3, multiclass
           clus
vv          8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  STAGE I                 2                 2
  STAGE II               58                66
  STAGE III              68                59
  STAGE IV               63                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                T0+T1+T2 T3 T4
  8Q GAIN MUTATED         61 94 26
  8Q GAIN WILD-TYPE       60 90 27
D16V4, multiclass
          clus
vv         8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  T0+T1+T2              61                60
  T3                    94                90
  T4                    26                27
[1] 3 2
[1] TRUE
[1] "dimension of 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   108  24  34   3
  8Q GAIN WILD-TYPE 116  18  41   5
D16V5, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  N0             108               116
  N1              24                18
  N2              34                41
  N3               3                 5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V6, binary
                   cls
clus                 0  1
  8Q GAIN MUTATED   91  5
  8Q GAIN WILD-TYPE 94  5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     91    5
  8Q GAIN WILD-TYPE   94    5
   clus
vv  8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  0              91                94
  1               5                 5
[1] 2 2
[1] FALSE
D16V7, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED    49 144
  8Q GAIN WILD-TYPE  52 144
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     49  144
  8Q GAIN WILD-TYPE   52  144
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  FEMALE              49                52
  MALE               144               144
[1] 2 2
[1] FALSE
D16V8, continuous
D16V9, continuous
D16V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  8Q GAIN MUTATED      18                         7   155
  8Q GAIN WILD-TYPE    24                        14   156
D16V11, multiclass
                           clus
vv                          8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  ASIAN                                  18                24
  BLACK OR AFRICAN AMERICAN               7                14
  WHITE                                 155               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"
D16V12, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED     5 167
  8Q GAIN WILD-TYPE   4 185
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      5  167
  8Q GAIN WILD-TYPE    4  185
                        clus
vv                       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   5                 4
  NOT HISPANIC OR LATINO             167               185
[1] 2 2
[1] FALSE

Clustering(17) Variable = 9P GAIN MUTATION ANALYSIS
D17V1, survival
                   sevent
clus2                 0   1
  9P GAIN MUTATED    46  19
  9P GAIN WILD-TYPE 184 134
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               65               318 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               19               134 
$`9P GAIN MUTATED`
TCGA-2F-A9KO TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-BL-A3JM TCGA-BT-A2LA TCGA-BT-A3PJ 
       22.29        16.77        17.16         6.74        17.16        12.82 
TCGA-C4-A0F0 TCGA-CU-A0YN TCGA-CU-A0YR TCGA-CU-A3QU TCGA-DK-A1AC TCGA-DK-A1AD 
        1.94        12.92         7.20         5.19       130.88       112.44 
TCGA-DK-A2I1 TCGA-DK-A2I6 TCGA-DK-A3IM TCGA-DK-A6B6 TCGA-FD-A3B3 TCGA-FD-A3B6 
       10.59        87.32         7.82        30.67        32.02        33.04 
TCGA-FD-A3N5 TCGA-FD-A3SL TCGA-FD-A43P TCGA-FD-A5BT TCGA-FD-A62N TCGA-FD-A6TF 
       22.52        23.41        27.35        11.01         2.70         2.27 
TCGA-FD-A6TH TCGA-FJ-A3ZE TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-AA3D TCGA-GC-A3I6 
        4.31        10.65        61.94        30.61        64.44         2.24 
TCGA-GC-A3RC TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GU-A763 TCGA-GV-A3JZ TCGA-GV-A3QI 
       15.91         7.73         2.10        27.09        19.82        10.59 
TCGA-GV-A40G TCGA-HQ-A5NE TCGA-K4-A6FZ TCGA-LC-A66R TCGA-SY-A9G0 TCGA-UY-A78K 
       19.07         8.22         1.81        15.32        12.43        17.62 
TCGA-UY-A78P TCGA-UY-A9PB TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HG TCGA-XF-A9SG 
       67.79        29.56         6.58        97.45        15.35        48.62 
TCGA-XF-A9SY TCGA-XF-A9T3 TCGA-XF-AAML TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-YF-AA3M 
       21.04         2.24         7.63        27.06        75.39        13.64 
TCGA-ZF-A9R0 TCGA-ZF-A9R4 TCGA-ZF-A9R7 TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RM 
       18.64        30.28        21.86        52.73        52.60        47.84 
TCGA-ZF-AA4N TCGA-ZF-AA4T TCGA-ZF-AA4V TCGA-ZF-AA4X TCGA-ZF-AA58 
        2.89        19.69        59.38        63.02        47.15 

$`9P GAIN WILD-TYPE`
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW TCGA-4Z-AA7M 
       11.97        91.63       103.50       105.70         8.35        16.27 
TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 
       44.94        16.83        34.98        27.62        49.12         0.62 
TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-4Z-AA87 
       41.75        51.16        66.54        15.12        10.22        47.80 
TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A5ZZ TCGA-BT-A0S7 
       33.83        40.08         7.33         2.66        12.39         6.58 
TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q 
       13.15        19.04        32.84        12.16        17.88        19.50 
TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X 
        5.06        14.89        14.96         5.06         8.35         8.25 
TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C 
       16.18        20.48         4.67         9.96        17.56        28.70 
TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS 
       24.26        28.41         8.98        23.01         0.46         0.43 
TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X 
        0.69        10.95        12.66        12.46        12.10        12.62 
TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A8HY 
       12.26        13.12        12.00        12.10        11.34        11.34 
TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YO TCGA-CU-A3KJ TCGA-CU-A3YL TCGA-CU-A5W6 
       11.87        13.08         4.90         5.46        16.31         1.84 
TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA 
       13.58        21.86         2.14        66.41        18.41        19.00 
TCGA-DK-A1AB TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I2 
       16.70        16.14        17.62        15.62         1.81         7.79 
TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS 
      123.85         2.20        13.58         8.22        17.72        50.27 
TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY 
       21.30        23.21         9.67        20.81        10.55       140.81 
TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 
       48.00        17.98        64.18        41.56        76.60        67.36 
TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-AA6L TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6S 
       15.68        41.06        38.24        15.02        13.58       166.03 
TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 
       12.36        10.49         8.65         7.53        13.64        43.50 
TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 
       12.03        10.62        43.59        15.35        38.83        24.66 
TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE 
        0.10         0.49         2.24        16.70        17.39         0.56 
TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU 
        0.66        14.56        13.97        12.99        14.33         0.92 
TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A8O7 TCGA-E7-A97P 
        1.22        13.68        14.07        12.95        15.32        14.37 
TCGA-E7-A97Q TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N6 
        8.09        16.77         8.94         4.01        12.62        27.98 
TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP 
       60.66        24.30        17.98        29.16         5.52        25.74 
TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43U 
       46.78        19.79        12.85        22.98        14.96        20.91 
TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BU TCGA-FD-A5BV 
        3.62        15.58        26.73        53.88        19.33         5.36 
TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62O 
        5.69         8.25        27.45        18.08        58.92         7.10 
TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD 
        6.28        13.35        62.86        18.81         6.15        12.69 
TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 
       12.36         3.06         9.67        10.85        31.07         7.13 
TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EK TCGA-G2-A2EL 
       17.23         8.94         3.25         6.48        15.95        26.93 
TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B 
       35.24        33.01         7.23        20.12        17.62        66.02 
TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RD 
        6.94        19.46        21.40        15.81         4.50        14.07 
TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A3OQ 
       17.75        24.92         0.49         8.94        13.91         3.12 
TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R 
       20.98         2.20         7.36        10.92        11.31        11.31 
TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATP 
        7.63        20.05         5.62         4.73        10.65        32.98 
TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QF TCGA-GV-A3QH 
        7.00        14.27        21.34        19.10        20.28         8.48 
TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE 
       27.35         8.58        22.72         1.51        19.40        38.60 
TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB 
        3.06         9.01        25.02         3.45        21.24         2.76 
TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6MB 
        9.14        27.68         9.07        11.70         1.74        15.42 
TCGA-K4-A83P TCGA-K4-AAQO TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FI 
        6.38        11.80        15.58        21.07        13.48        12.23 
TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G5 TCGA-UY-A78L 
       16.67        14.24         1.84         3.75        31.56        37.05 
TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A8OD 
       22.68        86.83        76.01        65.75         3.58       112.83 
TCGA-UY-A9PA TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HE 
       35.24        17.82         4.54         1.64        45.04       125.49 
TCGA-XF-A8HF TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ 
       97.12         1.87        17.88        64.80        79.66         3.22 
TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T0 
       66.41        12.76        11.90        23.64        28.24        26.27 
TCGA-XF-A9T2 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME 
       18.90        16.27        66.64         2.10        13.74        92.98 
TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAMQ TCGA-XF-AAMR 
       10.82       110.60        11.31        54.90        71.57        91.73 
TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN0 
        2.96         8.32         6.77        98.99        44.32        56.48 
TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A89H 
       30.94        61.45        86.30        18.81         3.88        18.84 
TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 
        9.63         0.66        11.97         7.36        21.11        24.13 
TCGA-ZF-A9R5 TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RL 
       27.19        28.41        74.56        13.41         3.48        82.49 
TCGA-ZF-A9RN TCGA-ZF-AA4R TCGA-ZF-AA4U TCGA-ZF-AA4W TCGA-ZF-AA51 TCGA-ZF-AA52 
       20.22        34.06         8.61        60.16        38.73        35.41 
TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
       57.90        19.40         8.52        19.17         5.52        10.13 

  9P GAIN MUTATED 9P GAIN WILD-TYPE 
             1.81              0.10 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
           130.88            166.03 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
           18.640            15.335 
[1] "1.8 - 130.9 (18.6)" "0.1 - 166.0 (15.3)"
[1] "hr=" "1.6"
D17V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  9P GAIN MUTATED         0       20        23       22
  9P GAIN WILD-TYPE       4      104       104      107
D17V3, multiclass
           clus
vv          9P GAIN MUTATED 9P GAIN WILD-TYPE
  STAGE I                 0                 4
  STAGE II               20               104
  STAGE III              23               104
  STAGE IV               22               107
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1+T2  T3  T4
  9P GAIN MUTATED         18  32   8
  9P GAIN WILD-TYPE      103 152  45
D17V4, multiclass
          clus
vv         9P GAIN MUTATED 9P GAIN WILD-TYPE
  T0+T1+T2              18               103
  T3                    32               152
  T4                     8                45
[1] 3 2
[1] TRUE
[1] "dimension of 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    34   4  15   3
  9P GAIN WILD-TYPE 190  38  60   5
D17V5, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  N0              34               190
  N1               4                38
  N2              15                60
  N3               3                 5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V6, binary
                   cls
clus                  0   1
  9P GAIN MUTATED    29   3
  9P GAIN WILD-TYPE 156   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED     29    3
  9P GAIN WILD-TYPE  156    7
   clus
vv  9P GAIN MUTATED 9P GAIN WILD-TYPE
  0              29               156
  1               3                 7
[1] 2 2
[1] FALSE
D17V7, binary
                   cls
clus                  0   1
  9P GAIN MUTATED    15  50
  9P GAIN WILD-TYPE  86 238
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED     15   50
  9P GAIN WILD-TYPE   86  238
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  FEMALE              15                86
  MALE                50               238
[1] 2 2
[1] FALSE
D17V8, continuous
D17V9, continuous
D17V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  9P GAIN MUTATED       2                         3    56
  9P GAIN WILD-TYPE    40                        18   255
D17V11, multiclass
                           clus
vv                          9P GAIN MUTATED 9P GAIN WILD-TYPE
  ASIAN                                   2                40
  BLACK OR AFRICAN AMERICAN               3                18
  WHITE                                  56               255
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V12, binary
                   cls
clus                  0   1
  9P GAIN MUTATED     2  57
  9P GAIN WILD-TYPE   7 295
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      2   57
  9P GAIN WILD-TYPE    7  295
                        clus
vv                       9P GAIN MUTATED 9P GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 7
  NOT HISPANIC OR LATINO              57               295
[1] 2 2
[1] FALSE

Clustering(18) Variable = 9Q GAIN MUTATION ANALYSIS
D18V1, survival
                   sevent
clus2                 0   1
  9Q GAIN MUTATED    34  20
  9Q GAIN WILD-TYPE 196 133
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               54               329 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               20               133 
$`9Q GAIN MUTATED`
TCGA-4Z-AA7R TCGA-4Z-AA82 TCGA-4Z-AA84 TCGA-BL-A3JM TCGA-BT-A2LA TCGA-C4-A0F0 
       17.16        51.16        15.12         6.74        17.16         1.94 
TCGA-CU-A0YN TCGA-DK-A1AC TCGA-DK-A2I1 TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A6B6 
       12.92       130.88        10.59         7.82         8.22        30.67 
TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3SL TCGA-FD-A5BT TCGA-FD-A5BV TCGA-FD-A62N 
       32.02        16.77        23.41        11.01         5.36         2.70 
TCGA-FD-A6TD TCGA-FD-A6TH TCGA-FD-A6TK TCGA-FJ-A3ZE TCGA-G2-A2EF TCGA-G2-A2EJ 
       12.69         4.31        10.85        10.65        61.94        30.61 
TCGA-G2-AA3D TCGA-GC-A3I6 TCGA-GC-A3RC TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GD-A76B 
       64.44         2.24        15.91        17.75        24.92         7.36 
TCGA-H4-A2HQ TCGA-HQ-A5NE TCGA-K4-A6FZ TCGA-LC-A66R TCGA-UY-A78K TCGA-UY-A78P 
       19.40         8.22         1.81        15.32        17.62        67.79 
TCGA-UY-A8OB TCGA-UY-A9PB TCGA-UY-A9PE TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HG 
       65.75        29.56         4.54         6.58        97.45        15.35 
TCGA-XF-A9SG TCGA-XF-A9T3 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-ZF-A9R4 TCGA-ZF-A9R7 
       48.62         2.24        27.06        75.39        30.28        21.86 
TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-AA4N TCGA-ZF-AA4T TCGA-ZF-AA4V TCGA-ZF-AA58 
       52.60        47.84         2.89        19.69        59.38        47.15 

$`9Q GAIN WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        91.63       103.50       105.70         8.35 
TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7S TCGA-4Z-AA7W 
       16.27        44.94        16.83        16.77        34.98        27.62 
TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-4Z-AA87 
       49.12         0.62        41.75        66.54        10.22        47.80 
TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A5ZZ TCGA-BT-A0S7 
       33.83        40.08         7.33         2.66        12.39         6.58 
TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q 
       13.15        19.04        32.84        12.16        17.88        19.50 
TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X 
        5.06        14.89        14.96         5.06         8.35         8.25 
TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B 
       16.18        20.48         4.67        12.82         9.96        17.56 
TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F6 TCGA-CF-A1HR 
       28.70        24.26        28.41         8.98        23.01         0.46 
TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W 
        0.43         0.69        10.95        12.66        12.46        12.10 
TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A8HX 
       12.62        12.26        13.12        12.00        12.10        11.34 
TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ 
       11.34        11.87        13.08         4.90         7.20         5.46 
TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 
        5.19        16.31         1.84        13.58        21.86         2.14 
TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AD TCGA-DK-A1AE 
       66.41        18.41        19.00        16.70       112.44        16.14 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 
       17.62        15.62         1.81         7.79       123.85        87.32 
TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU 
        2.20        13.58        17.72        50.27        21.30        23.21 
TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 
        9.67        20.81        10.55       140.81        48.00        17.98 
TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 
       64.18        41.56        76.60        67.36        15.68        41.06 
TCGA-DK-AA6L TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U 
       38.24        15.02        13.58       166.03        12.36        10.49 
TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA76 TCGA-DK-AA77 
        8.65         7.53        13.64        43.50        12.03        10.62 
TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ 
       43.59        15.35        38.83        24.66         0.10         0.49 
TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 
        2.24        16.70        17.39         0.56         0.66        14.56 
TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW 
       13.97        12.99        14.33         0.92         1.22        13.68 
TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A8O7 TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B5 
       14.07        12.95        15.32        14.37         8.09         8.94 
TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA 
       33.04         4.01        12.62        22.52        27.98        60.66 
TCGA-FD-A3SJ TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ 
       24.30        17.98        29.16         5.52        25.74        46.78 
TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U 
       19.79        12.85        22.98        27.35        14.96        20.91 
TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BU TCGA-FD-A5BX 
        3.62        15.58        26.73        53.88        19.33         5.69 
TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62O TCGA-FD-A62P 
        8.25        27.45        18.08        58.92         7.10         6.28 
TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TE TCGA-FD-A6TF 
       13.35        62.86        18.81         6.15        12.36         2.27 
TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZF TCGA-FJ-A871 
        3.06         9.67        31.07         7.13        17.23         8.94 
TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES 
        3.25         6.48        15.95        26.93        35.24        33.01 
TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3F 
        7.23        20.12        17.62        66.02         6.94        19.46 
TCGA-GC-A3BM TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RD TCGA-GC-A4ZW TCGA-GC-A6I1 
       21.40        15.81         4.50        14.07         0.49         8.94 
TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 
       13.91         7.73         2.10         3.12        20.98         2.20 
TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 
       10.92        11.31        11.31         7.63        27.09        20.05 
TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JV 
        5.62         4.73        10.65        32.98         7.00        14.27 
TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI 
       21.34        19.10        19.82        20.28         8.48        10.59 
TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-HQ-A2OE 
       27.35         8.58        19.07        22.72         1.51        38.60 
TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB 
        3.06         9.01        25.02         3.45        21.24         2.76 
TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6MB 
        9.14        27.68         9.07        11.70         1.74        15.42 
TCGA-K4-A83P TCGA-K4-AAQO TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FI 
        6.38        11.80        15.58        21.07        13.48        12.23 
TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-SY-A9G5 
       16.67        14.24         1.84         3.75        12.43        31.56 
TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A8OC TCGA-UY-A8OD 
       37.05        22.68        86.83        76.01         3.58       112.83 
TCGA-UY-A9PA TCGA-UY-A9PD TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HE TCGA-XF-A8HF 
       35.24        17.82         1.64        45.04       125.49        97.12 
TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SL 
        1.87        17.88        64.80        79.66         3.22        66.41 
TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 
       12.76        11.90        23.64        21.04        28.24        26.27 
TCGA-XF-A9T2 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME 
       18.90        16.27        66.64         2.10        13.74        92.98 
TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ 
       10.82       110.60        11.31        54.90         7.63        71.57 
TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ 
       91.73         2.96         8.32         6.77        98.99        44.32 
TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN7 TCGA-XF-AAN8 
       56.48        30.94        61.45        86.30        18.81         3.88 
TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R0 
       18.84         9.63         0.66        11.97        13.64        18.64 
TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R9 TCGA-ZF-A9RC 
        7.36        21.11        24.13        27.19        28.41        74.56 
TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RL TCGA-ZF-A9RN TCGA-ZF-AA4R 
       13.41         3.48        52.73        82.49        20.22        34.06 
TCGA-ZF-AA4U TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA53 
        8.61        60.16        63.02        38.73        35.41        57.90 
TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
       19.40         8.52        19.17         5.52        10.13 

  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
             1.81              0.10 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
           130.88            166.03 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
            17.16             15.58 
[1] "1.8 - 130.9 (17.2)" "0.1 - 166.0 (15.6)"
[1] "hr=" "1.2"
D18V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  9Q GAIN MUTATED         0       13        24       17
  9Q GAIN WILD-TYPE       4      111       103      112
D18V3, multiclass
           clus
vv          9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  STAGE I                 0                 4
  STAGE II               13               111
  STAGE III              24               103
  STAGE IV               17               112
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1+T2  T3  T4
  9Q GAIN MUTATED         10  30   6
  9Q GAIN WILD-TYPE      111 154  47
D18V4, multiclass
          clus
vv         9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  T0+T1+T2              10               111
  T3                    30               154
  T4                     6                47
[1] 3 2
[1] TRUE
[1] "dimension of 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    34   3  11   1
  9Q GAIN WILD-TYPE 190  39  64   7
D18V5, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  N0              34               190
  N1               3                39
  N2              11                64
  N3               1                 7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V6, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED    19   4
  9Q GAIN WILD-TYPE 166   6
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     19    4
  9Q GAIN WILD-TYPE  166    6
   clus
vv  9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  0              19               166
  1               4                 6
[1] 2 2
[1] FALSE
D18V7, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED    16  38
  9Q GAIN WILD-TYPE  85 250
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     16   38
  9Q GAIN WILD-TYPE   85  250
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  FEMALE              16                85
  MALE                38               250
[1] 2 2
[1] FALSE
D18V8, continuous
D18V9, continuous
D18V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  9Q GAIN MUTATED       2                         4    45
  9Q GAIN WILD-TYPE    40                        17   266
D18V11, multiclass
                           clus
vv                          9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  ASIAN                                   2                40
  BLACK OR AFRICAN AMERICAN               4                17
  WHITE                                  45               266
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V12, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED     2  46
  9Q GAIN WILD-TYPE   7 306
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      2   46
  9Q GAIN WILD-TYPE    7  306
                        clus
vv                       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 7
  NOT HISPANIC OR LATINO              46               306
[1] 2 2
[1] FALSE

Clustering(19) Variable = 10P GAIN MUTATION ANALYSIS
D19V1, survival
                    sevent
clus2                  0   1
  10P GAIN MUTATED    53  53
  10P GAIN WILD-TYPE 177 100
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
               106                277 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                53                100 
$`10P GAIN MUTATED`
TCGA-2F-A9KO TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA80 TCGA-4Z-AA81 
       22.29        16.27        16.77        17.16         0.62        41.75 
TCGA-4Z-AA84 TCGA-BT-A0S7 TCGA-BT-A20N TCGA-BT-A20R TCGA-BT-A20V TCGA-BT-A20W 
       15.12         6.58        32.84         5.06         5.06         8.35 
TCGA-BT-A2LB TCGA-BT-A3PJ TCGA-BT-A42E TCGA-CF-A1HS TCGA-CF-A5UA TCGA-CU-A0YN 
       16.18        12.82        24.26         0.43        12.00        12.92 
TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1AD TCGA-DK-A2I6 TCGA-DK-A3IL 
       21.86         2.14        66.41       112.44        87.32        13.58 
TCGA-DK-A3IN TCGA-DK-A3X1 TCGA-DK-A6B2 TCGA-DK-A6B6 TCGA-DK-AA6P TCGA-DK-AA6S 
        8.22        48.00        15.68        30.67        15.02       166.03 
TCGA-E5-A4U1 TCGA-E7-A7PW TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B6 TCGA-FD-A3NA 
       38.83        13.68        14.37         8.09        33.04        60.66 
TCGA-FD-A3SJ TCGA-FD-A3SS TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BZ TCGA-FD-A5C0 
       24.30        12.85        26.73        53.88        27.45        18.08 
TCGA-FD-A5C1 TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FT-A3EE 
       58.92        12.36         2.27         3.06         9.67         3.25 
TCGA-FT-A61P TCGA-G2-A2ES TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3F TCGA-GC-A3RB 
        6.48        33.01        20.12        66.02        19.46         4.50 
TCGA-GC-A4ZW TCGA-GD-A2C5 TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42P TCGA-GU-A767 
        0.49         7.73        20.98         2.20        10.92         4.73 
TCGA-GU-AATO TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JW TCGA-GV-A3JZ TCGA-GV-A3QF 
       10.65        32.98         7.00        21.34        19.82        20.28 
TCGA-GV-A3QH TCGA-GV-A40E TCGA-GV-A6ZA TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND 
        8.48         8.58        22.72        38.60         3.06         9.01 
TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6FZ 
        8.22        25.02         9.14        27.68         1.74         1.81 
TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A8OB 
       31.56        17.62        37.05        22.68        86.83        65.75 
TCGA-UY-A9PA TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A9SH TCGA-XF-A9SJ TCGA-XF-A9SX 
       35.24        97.12        15.35        64.80         3.22        23.64 
TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAML TCGA-XF-AAMT TCGA-YF-AA3M TCGA-ZF-A9R0 
      110.60        11.31         7.63         2.96        13.64        18.64 
TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RF TCGA-ZF-AA4R 
       24.13        30.28        28.41        74.56        52.73        34.06 
TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA54 
       38.73        35.41        57.90        19.40 

$`10P GAIN WILD-TYPE`
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW TCGA-4Z-AA7N 
       11.97        91.63       103.50       105.70         8.35        44.94 
TCGA-4Z-AA7O TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA82 TCGA-4Z-AA83 
       16.83        34.98        27.62        49.12        51.16        66.54 
TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J 
       10.22        47.80        33.83        40.08         7.33         2.66 
TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P 
        6.74        12.39        13.15        19.04        12.16        17.88 
TCGA-BT-A20Q TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LD 
       19.50        14.89        14.96         8.25        17.16        20.48 
TCGA-BT-A3PH TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42F TCGA-C4-A0EZ 
        4.67         9.96        17.56        28.70        28.41         8.98 
TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T 
        1.94        23.01         0.46         0.69        10.95        12.66 
TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A7I0 
       12.46        12.10        12.62        12.26        13.12        12.10 
TCGA-CF-A8HX TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YO TCGA-CU-A0YR 
       11.34        11.34        11.87        13.08         4.90         7.20 
TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A7 
        5.46         5.19        16.31         1.84        13.58        18.41 
TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG 
       19.00        16.70       130.88        16.14        17.62        15.62 
TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IM 
        1.81        10.59         7.79       123.85         2.20         7.82 
TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW 
       17.72        50.27        21.30        23.21         9.67        20.81 
TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 
       10.55       140.81        17.98        64.18        41.56        76.60 
TCGA-DK-A6B1 TCGA-DK-A6B5 TCGA-DK-AA6L TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6U 
       67.36        41.06        38.24        13.58        12.36        10.49 
TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA76 TCGA-DK-AA77 
        8.65         7.53        13.64        43.50        12.03        10.62 
TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ 
       43.59        15.35        24.66         0.10         0.49         2.24 
TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 
       16.70        17.39         0.56         0.66        14.56        13.97 
TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7XN TCGA-E7-A85H 
       12.99        14.33         0.92         1.22        14.07        12.95 
TCGA-E7-A8O7 TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B7 TCGA-FD-A3B8 
       15.32        32.02        16.77         8.94         4.01        12.62 
TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO 
       22.52        27.98        23.41        17.98        29.16         5.52 
TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S 
       25.74        46.78        19.79        22.98        27.35        14.96 
TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV 
       20.91         3.62        15.58        11.01        19.33         5.36 
TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S 
        5.69         8.25         2.70         7.10         6.28        13.35 
TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TH TCGA-FD-A6TK 
       62.86        18.81         6.15        12.69         4.31        10.85 
TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-G2-A2EF 
       31.07         7.13        10.65        17.23         8.94        61.94 
TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A3IB TCGA-G2-A3VY 
       30.61        15.95        26.93        35.24         7.23        17.62 
TCGA-G2-AA3C TCGA-G2-AA3D TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RC 
        6.94        64.44        21.40         2.24        15.81        15.91 
TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A3OP 
       14.07        17.75        24.92         8.94        13.91         2.10 
TCGA-GD-A3OQ TCGA-GD-A76B TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 
        3.12         7.36        11.31        11.31         7.63        27.09 
TCGA-GU-A764 TCGA-GU-A766 TCGA-GV-A3JV TCGA-GV-A3JX TCGA-GV-A3QI TCGA-GV-A3QK 
       20.05         5.62        14.27        19.10        10.59        27.35 
TCGA-GV-A40G TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB 
       19.07         1.51        19.40         3.45        21.24         2.76 
TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-LC-A66R 
        9.07        11.70        15.42         6.38        11.80        15.32 
TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X 
       15.58        21.07        13.48        12.23        16.67        14.24 
TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OC 
        1.84         3.75        12.43        76.01        67.79         3.58 
TCGA-UY-A8OD TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HB 
      112.83        29.56        17.82         4.54         1.64        45.04 
TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG 
        6.58        97.45       125.49         1.87        17.88        48.62 
TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9SZ 
       79.66        66.41        12.76        11.90        21.04        28.24 
TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 
       26.27        18.90         2.24        16.27        66.64         2.10 
TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMJ TCGA-XF-AAMQ TCGA-XF-AAMR 
       13.74        92.98        10.82        54.90        71.57        91.73 
TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN1 
        8.32         6.77        98.99        44.32        56.48        30.94 
TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-XF-AAN8 
       61.45        86.30        27.06        75.39        18.81         3.88 
TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R1 TCGA-ZF-A9R2 
       18.84         9.63         0.66        11.97         7.36        21.11 
TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RG TCGA-ZF-A9RL 
       27.19        21.86        13.41         3.48        52.60        82.49 
TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4V 
       47.84        20.22         2.89        19.69         8.61        59.38 
TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N 
       60.16        63.02         8.52        47.15        19.17         5.52 
TCGA-ZF-AA5P 
       10.13 

  10P GAIN MUTATED 10P GAIN WILD-TYPE 
              0.43               0.10 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
            166.03             140.81 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
             18.36              15.32 
[1] "0.4 - 166.0 (18.4)" "0.1 - 140.8 (15.3)"
[1] "hr=" "1.2"
D19V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  10P GAIN MUTATED         0       33        33       41
  10P GAIN WILD-TYPE       4       91        94       88
D19V3, multiclass
           clus
vv          10P GAIN MUTATED 10P GAIN WILD-TYPE
  STAGE I                  0                  4
  STAGE II                33                 91
  STAGE III               33                 94
  STAGE IV                41                 88
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1+T2  T3  T4
  10P GAIN MUTATED         33  56  12
  10P GAIN WILD-TYPE       88 128  41
D19V4, multiclass
          clus
vv         10P GAIN MUTATED 10P GAIN WILD-TYPE
  T0+T1+T2               33                 88
  T3                     56                128
  T4                     12                 41
[1] 3 2
[1] TRUE
[1] "dimension of 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    49  15  23   4
  10P GAIN WILD-TYPE 175  27  52   4
D19V5, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  N0               49                175
  N1               15                 27
  N2               23                 52
  N3                4                  4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V6, binary
                    cls
clus                   0   1
  10P GAIN MUTATED    50   2
  10P GAIN WILD-TYPE 135   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED     50    2
  10P GAIN WILD-TYPE  135    8
   clus
vv  10P GAIN MUTATED 10P GAIN WILD-TYPE
  0               50                135
  1                2                  8
[1] 2 2
[1] FALSE
D19V7, binary
                    cls
clus                   0   1
  10P GAIN MUTATED    23  86
  10P GAIN WILD-TYPE  78 202
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED     23   86
  10P GAIN WILD-TYPE   78  202
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  FEMALE               23                 78
  MALE                 86                202
[1] 2 2
[1] FALSE
D19V8, continuous
D19V9, continuous
D19V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  10P GAIN MUTATED       9                         2    91
  10P GAIN WILD-TYPE    33                        19   220
D19V11, multiclass
                           clus
vv                          10P GAIN MUTATED 10P GAIN WILD-TYPE
  ASIAN                                    9                 33
  BLACK OR AFRICAN AMERICAN                2                 19
  WHITE                                   91                220
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V12, binary
                    cls
clus                   0   1
  10P GAIN MUTATED     3  93
  10P GAIN WILD-TYPE   6 259
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      3   93
  10P GAIN WILD-TYPE    6  259
                        clus
vv                       10P GAIN MUTATED 10P GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                  6
  NOT HISPANIC OR LATINO               93                259
[1] 2 2
[1] FALSE

Clustering(20) Variable = 10Q GAIN MUTATION ANALYSIS
D20V1, survival
                    sevent
clus2                  0   1
  10Q GAIN MUTATED    16  23
  10Q GAIN WILD-TYPE 214 130
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                39                344 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                23                130 
$`10Q GAIN MUTATED`
TCGA-2F-A9KO TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA84 TCGA-BT-A0S7 TCGA-BT-A20R 
       22.29         0.62        41.75        15.12         6.58         5.06 
TCGA-BT-A20V TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1AD TCGA-DK-A3IN TCGA-DK-A6B2 
        5.06        21.86        66.41       112.44         8.22        15.68 
TCGA-E5-A4U1 TCGA-E7-A7PW TCGA-E7-A97Q TCGA-FD-A3B6 TCGA-FD-A3SS TCGA-FD-A5BR 
       38.83        13.68         8.09        33.04        12.85        26.73 
TCGA-FD-A5BZ TCGA-FD-A6TI TCGA-G2-AA3B TCGA-GC-A3RB TCGA-GU-A767 TCGA-GU-AATO 
       27.45         9.67        66.02         4.50         4.73        10.65 
TCGA-GU-AATQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-SY-A9G5 TCGA-UY-A78M 
        7.00        38.60         3.06         9.01        31.56        22.68 
TCGA-UY-A78N TCGA-XF-A8HG TCGA-XF-A9SX TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAMT 
       86.83        15.35        23.64       110.60        11.31         2.96 
TCGA-ZF-A9R0 TCGA-ZF-A9R3 TCGA-ZF-A9R9 
       18.64        24.13        28.41 

$`10Q GAIN WILD-TYPE`
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW TCGA-4Z-AA7M 
       11.97        91.63       103.50       105.70         8.35        16.27 
TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W 
       44.94        16.83        16.77        17.16        34.98        27.62 
TCGA-4Z-AA7Y TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 
       49.12        51.16        66.54        10.22        47.80        33.83 
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0YX 
       40.08         7.33         2.66         6.74        12.39        13.15 
TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20T 
       19.04        32.84        12.16        17.88        19.50        14.89 
TCGA-BT-A20U TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD 
       14.96         8.35         8.25        17.16        16.18        20.48 
TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E 
        4.67        12.82         9.96        17.56        28.70        24.26 
TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS 
       28.41         8.98         1.94        23.01         0.46         0.43 
TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X 
        0.69        10.95        12.66        12.46        12.10        12.62 
TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A8HY 
       12.26        13.12        12.00        12.10        11.34        11.34 
TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ 
       11.87        13.08        12.92         4.90         7.20         5.46 
TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1A7 
        5.19        16.31         1.84        13.58         2.14        18.41 
TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG 
       19.00        16.70       130.88        16.14        17.62        15.62 
TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK 
        1.81        10.59         7.79       123.85        87.32         2.20 
TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU 
       13.58         7.82        17.72        50.27        21.30        23.21 
TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 
        9.67        20.81        10.55       140.81        48.00        17.98 
TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B5 TCGA-DK-A6B6 
       64.18        41.56        76.60        67.36        41.06        30.67 
TCGA-DK-AA6L TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U 
       38.24        15.02        13.58       166.03        12.36        10.49 
TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA76 TCGA-DK-AA77 
        8.65         7.53        13.64        43.50        12.03        10.62 
TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ 
       43.59        15.35        24.66         0.10         0.49         2.24 
TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 
       16.70        17.39         0.56         0.66        14.56        13.97 
TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7XN TCGA-E7-A85H 
       12.99        14.33         0.92         1.22        14.07        12.95 
TCGA-E7-A8O7 TCGA-E7-A97P TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B7 
       15.32        14.37        32.02        16.77         8.94         4.01 
TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL 
       12.62        22.52        27.98        60.66        24.30        23.41 
TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR 
       17.98        29.16         5.52        25.74        46.78        19.79 
TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A43Y 
       22.98        27.35        14.96        20.91         3.62        15.58 
TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY 
       53.88        11.01        19.33         5.36         5.69         8.25 
TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S 
       18.08        58.92         2.70         7.10         6.28        13.35 
TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF 
       62.86        18.81         6.15        12.69        12.36         2.27 
TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE 
        3.06         4.31        10.85        31.07         7.13        10.65 
TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ 
       17.23         8.94         3.25         6.48        61.94        30.61 
TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE 
       15.95        26.93        35.24        33.01         7.23        20.12 
TCGA-G2-A3VY TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 
       17.62         6.94        64.44        19.46        21.40         2.24 
TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A4ZW 
       15.81        15.91        14.07        17.75        24.92         0.49 
TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS 
        8.94        13.91         7.73         2.10         3.12        20.98 
TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 
        2.20         7.36        10.92        11.31        11.31         7.63 
TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-AATP TCGA-GV-A3JV TCGA-GV-A3JW 
       27.09        20.05         5.62        32.98        14.27        21.34 
TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK 
       19.10        19.82        20.28         8.48        10.59        27.35 
TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A5NE 
        8.58        19.07        22.72         1.51        19.40         8.22 
TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R 
       25.02         3.45        21.24         2.76         9.14        27.68 
TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P 
        9.07        11.70         1.74         1.81        15.42         6.38 
TCGA-K4-AAQO TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FI 
       11.80        15.32        15.58        21.07        13.48        12.23 
TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-UY-A78K 
       16.67        14.24         1.84         3.75        12.43        17.62 
TCGA-UY-A78L TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A8OD 
       37.05        76.01        67.79        65.75         3.58       112.83 
TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HB 
       35.24        29.56        17.82         4.54         1.64        45.04 
TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HH TCGA-XF-A8HI 
        6.58        97.45       125.49        97.12         1.87        17.88 
TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SV 
       48.62        64.80        79.66         3.22        66.41        12.76 
TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 
       11.90        21.04        28.24        26.27        18.90         2.24 
TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF 
       16.27        66.64         2.10        13.74        92.98        10.82 
TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMW TCGA-XF-AAMX 
       54.90         7.63        71.57        91.73         8.32         6.77 
TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 
       98.99        44.32        56.48        30.94        61.45        86.30 
TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 
       27.06        75.39        18.81         3.88        18.84         9.63 
TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R4 
        0.66        11.97        13.64         7.36        21.11        30.28 
TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF 
       27.19        21.86        74.56        13.41         3.48        52.73 
TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4R 
       52.60        82.49        47.84        20.22         2.89        34.06 
TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 
       19.69         8.61        59.38        60.16        63.02        38.73 
TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H 
       35.41        57.90        19.40         8.52        47.15        19.17 
TCGA-ZF-AA5N TCGA-ZF-AA5P 
        5.52        10.13 

  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
              0.62               0.10 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
            112.44             166.03 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
            15.680             15.715 
[1] "0.6 - 112.4 (15.7)" "0.1 - 166.0 (15.7)"
[1] "hr=" "1.5"
D20V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  10Q GAIN MUTATED         0        8        11       21
  10Q GAIN WILD-TYPE       4      116       116      108
D20V3, multiclass
           clus
vv          10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  STAGE I                  0                  4
  STAGE II                 8                116
  STAGE III               11                116
  STAGE IV                21                108
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1+T2  T3  T4
  10Q GAIN MUTATED         12  20   9
  10Q GAIN WILD-TYPE      109 164  44
D20V4, multiclass
          clus
vv         10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  T0+T1+T2               12                109
  T3                     20                164
  T4                      9                 44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  10Q GAIN MUTATED    16   9  11   2
  10Q GAIN WILD-TYPE 208  33  64   6
D20V5, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  N0               16                208
  N1                9                 33
  N2               11                 64
  N3                2                  6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V6, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED    21   1
  10Q GAIN WILD-TYPE 164   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED     21    1
  10Q GAIN WILD-TYPE  164    9
   clus
vv  10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  0               21                164
  1                1                  9
[1] 2 2
[1] FALSE
D20V7, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED    10  31
  10Q GAIN WILD-TYPE  91 257
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED     10   31
  10Q GAIN WILD-TYPE   91  257
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  FEMALE               10                 91
  MALE                 31                257
[1] 2 2
[1] FALSE
D20V8, continuous
D20V9, continuous
D20V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  10Q GAIN MUTATED       4                         1    32
  10Q GAIN WILD-TYPE    38                        20   279
D20V11, multiclass
                           clus
vv                          10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  ASIAN                                    4                 38
  BLACK OR AFRICAN AMERICAN                1                 20
  WHITE                                   32                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"
D20V12, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED     1  32
  10Q GAIN WILD-TYPE   8 320
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      1   32
  10Q GAIN WILD-TYPE    8  320
                        clus
vv                       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  8
  NOT HISPANIC OR LATINO               32                320
[1] 2 2
[1] FALSE

Clustering(21) Variable = 11P GAIN MUTATION ANALYSIS
D21V1, survival
                    sevent
clus2                  0   1
  11P GAIN MUTATED    13  14
  11P GAIN WILD-TYPE 217 139
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                27                356 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                14                139 
$`11P GAIN MUTATED`
TCGA-BT-A3PJ TCGA-CU-A0YN TCGA-CU-A0YO TCGA-DK-A3IV TCGA-DK-A3WX TCGA-E7-A5KF 
       12.82        12.92         4.90         9.67        10.55         0.66 
TCGA-E7-A7DV TCGA-FD-A3B6 TCGA-FD-A5BT TCGA-FD-A62P TCGA-FD-A6TI TCGA-GC-A3I6 
        1.22        33.04        11.01         6.28         9.67         2.24 
TCGA-GC-A3RC TCGA-GU-A762 TCGA-GU-A766 TCGA-GV-A3JZ TCGA-GV-A3QI TCGA-GV-A40E 
       15.91         7.63         5.62        19.82        10.59         8.58 
TCGA-K4-A4AC TCGA-LC-A66R TCGA-PQ-A6FI TCGA-UY-A9PB TCGA-UY-A9PF TCGA-XF-A8HF 
        9.14        15.32        12.23        29.56         1.64        97.12 
TCGA-XF-A9SY TCGA-XF-AAMH TCGA-YF-AA3M 
       21.04        11.31        13.64 

$`11P GAIN WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        91.63       103.50       105.70         8.35 
TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S 
       16.27        44.94        16.83        16.77        17.16        34.98 
TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 
       27.62        49.12         0.62        41.75        51.16        66.54 
TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I 
       15.12        10.22        47.80        33.83        40.08         7.33 
TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J 
        2.66         6.74        12.39         6.58        13.15        19.04 
TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T 
       32.84        12.16        17.88        19.50         5.06        14.89 
TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB 
       14.96         5.06         8.35         8.25        17.16        16.18 
TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E 
       20.48         4.67         9.96        17.56        28.70        24.26 
TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS 
       28.41         8.98         1.94        23.01         0.46         0.43 
TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X 
        0.69        10.95        12.66        12.46        12.10        12.62 
TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A8HY 
       12.26        13.12        12.00        12.10        11.34        11.34 
TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL 
       11.87        13.08         7.20         5.46         5.19        16.31 
TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 
        1.84        13.58        21.86         2.14        66.41        18.41 
TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF 
       19.00        16.70       130.88       112.44        16.14        17.62 
TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 
       15.62         1.81        10.59         7.79       123.85        87.32 
TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS 
        2.20        13.58         7.82         8.22        17.72        50.27 
TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3WW TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 
       21.30        23.21        20.81       140.81        48.00        17.98 
TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 
       64.18        41.56        76.60        67.36        15.68        41.06 
TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6T 
       30.67        38.24        15.02        13.58       166.03        12.36 
TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA76 
       10.49         8.65         7.53        13.64        43.50        12.03 
TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 
       10.62        43.59        15.35        38.83        24.66         0.10 
TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A677 
        0.49         2.24        16.70        17.39         0.56        14.56 
TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7PW TCGA-E7-A7XN 
       13.97        12.99        14.33         0.92        13.68        14.07 
TCGA-E7-A85H TCGA-E7-A8O7 TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 
       12.95        15.32        14.37         8.09        32.02        16.77 
TCGA-FD-A3B5 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA 
        8.94         4.01        12.62        22.52        27.98        60.66 
TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP 
       24.30        23.41        17.98        29.16         5.52        25.74 
TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S 
       46.78        19.79        12.85        22.98        27.35        14.96 
TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BU 
       20.91         3.62        15.58        26.73        53.88        19.33 
TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 
        5.36         5.69         8.25        27.45        18.08        58.92 
TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC 
        2.70         7.10        13.35        62.86        18.81         6.15 
TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TK 
       12.69        12.36         2.27         3.06         4.31        10.85 
TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A3EE 
       31.07         7.13        10.65        17.23         8.94         3.25 
TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO 
        6.48        61.94        30.61        15.95        26.93        35.24 
TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C 
       33.01         7.23        20.12        17.62        66.02         6.94 
TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RD 
       64.44        19.46        21.40        15.81         4.50        14.07 
TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 
       17.75        24.92         0.49         8.94        13.91         7.73 
TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P 
        2.10         3.12        20.98         2.20         7.36        10.92 
TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A767 TCGA-GU-AATO 
       11.31        11.31        27.09        20.05         4.73        10.65 
TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QF 
       32.98         7.00        14.27        21.34        19.10        20.28 
TCGA-GV-A3QH TCGA-GV-A3QK TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ 
        8.48        27.35        19.07        22.72         1.51        19.40 
TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU 
       38.60         3.06         9.01         8.22        25.02         3.45 
TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ 
       21.24         2.76        27.68         9.07        11.70         1.74 
TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-LT-A5Z6 TCGA-LT-A8JT 
        1.81        15.42         6.38        11.80        15.58        21.07 
TCGA-MV-A51V TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G0 
       13.48        16.67        14.24         1.84         3.75        12.43 
TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A78O 
       31.56        17.62        37.05        22.68        86.83        76.01 
TCGA-UY-A78P TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A8OD TCGA-UY-A9PA TCGA-UY-A9PD 
       67.79        65.75         3.58       112.83        35.24        17.82 
TCGA-UY-A9PE TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HG 
        4.54        45.04         6.58        97.45       125.49        15.35 
TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ 
        1.87        17.88        48.62        64.80        79.66         3.22 
TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T0 
       66.41        12.76        11.90        23.64        28.24        26.27 
TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 
       18.90         2.24        16.27        66.64         2.10        13.74 
TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ 
       92.98        10.82       110.60        54.90         7.63        71.57 
TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ 
       91.73         2.96         8.32         6.77        98.99        44.32 
TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 
       56.48        30.94        61.45        86.30        27.06        75.39 
TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L 
       18.81         3.88        18.84         9.63         0.66        11.97 
TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 
       18.64         7.36        21.11        24.13        30.28        27.19 
TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF 
       21.86        28.41        74.56        13.41         3.48        52.73 
TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4R 
       52.60        82.49        47.84        20.22         2.89        34.06 
TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 
       19.69         8.61        59.38        60.16        63.02        38.73 
TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H 
       35.41        57.90        19.40         8.52        47.15        19.17 
TCGA-ZF-AA5N TCGA-ZF-AA5P 
        5.52        10.13 

  11P GAIN MUTATED 11P GAIN WILD-TYPE 
              0.66               0.10 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
             97.12             166.03 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
             10.59              16.49 
[1] "0.7 - 97.1 (10.6)"  "0.1 - 166.0 (16.5)"
[1] "hr=" "2.1"
D21V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  11P GAIN MUTATED         0       10         8        9
  11P GAIN WILD-TYPE       4      114       119      120
D21V3, multiclass
           clus
vv          11P GAIN MUTATED 11P GAIN WILD-TYPE
  STAGE I                  0                  4
  STAGE II                10                114
  STAGE III                8                119
  STAGE IV                 9                120
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1+T2  T3  T4
  11P GAIN MUTATED          8  12   5
  11P GAIN WILD-TYPE      113 172  48
D21V4, multiclass
          clus
vv         11P GAIN MUTATED 11P GAIN WILD-TYPE
  T0+T1+T2                8                113
  T3                     12                172
  T4                      5                 48
[1] 3 2
[1] TRUE
[1] "dimension of 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    14   2   5   3
  11P GAIN WILD-TYPE 210  40  70   5
D21V5, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  N0               14                210
  N1                2                 40
  N2                5                 70
  N3                3                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V6, binary
                    cls
clus                   0   1
  11P GAIN MUTATED     8   0
  11P GAIN WILD-TYPE 177  10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      8    0
  11P GAIN WILD-TYPE  177   10
   clus
vv  11P GAIN MUTATED 11P GAIN WILD-TYPE
  0                8                177
  1                0                 10
[1] 2 2
[1] FALSE
D21V7, binary
                    cls
clus                   0   1
  11P GAIN MUTATED     2  25
  11P GAIN WILD-TYPE  99 263
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      2   25
  11P GAIN WILD-TYPE   99  263
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  FEMALE                2                 99
  MALE                 25                263
[1] 2 2
[1] FALSE
D21V8, continuous
D21V9, continuous
D21V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  11P GAIN MUTATED       1                         0    25
  11P GAIN WILD-TYPE    41                        21   286
D21V11, multiclass
                           clus
vv                          11P GAIN MUTATED 11P GAIN WILD-TYPE
  ASIAN                                    1                 41
  BLACK OR AFRICAN AMERICAN                0                 21
  WHITE                                   25                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"
D21V12, binary
                    cls
clus                   0   1
  11P GAIN MUTATED     1  26
  11P GAIN WILD-TYPE   8 326
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      1   26
  11P GAIN WILD-TYPE    8  326
                        clus
vv                       11P GAIN MUTATED 11P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  8
  NOT HISPANIC OR LATINO               26                326
[1] 2 2
[1] FALSE

Clustering(22) Variable = 11Q GAIN MUTATION ANALYSIS
D22V1, survival
                    sevent
clus2                  0   1
  11Q GAIN MUTATED    24  23
  11Q GAIN WILD-TYPE 206 130
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                47                336 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                23                130 
$`11Q GAIN MUTATED`
TCGA-4Z-AA80 TCGA-4Z-AA84 TCGA-BT-A3PJ TCGA-C4-A0F6 TCGA-CU-A0YN TCGA-CU-A0YO 
        0.62        15.12        12.82        23.01        12.92         4.90 
TCGA-DK-A1A3 TCGA-DK-A3IM TCGA-DK-A3WX TCGA-DK-A3X2 TCGA-DK-AA76 TCGA-E7-A5KF 
       21.86         7.82        10.55        17.98        12.03         0.66 
TCGA-E7-A7DV TCGA-FD-A3B6 TCGA-FD-A3NA TCGA-FD-A43P TCGA-FD-A5BR TCGA-FD-A5BT 
        1.22        33.04        60.66        27.35        26.73        11.01 
TCGA-FD-A62P TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-G2-AA3D TCGA-G2-AA3F 
        6.28         3.06         9.67        31.07        64.44        19.46 
TCGA-GC-A3I6 TCGA-GC-A3RC TCGA-GU-A762 TCGA-GU-A766 TCGA-GU-A767 TCGA-GV-A3JZ 
        2.24        15.91         7.63         5.62         4.73        19.82 
TCGA-GV-A3QF TCGA-GV-A40E TCGA-K4-A4AC TCGA-LC-A66R TCGA-PQ-A6FI TCGA-S5-A6DX 
       20.28         8.58         9.14        15.32        12.23         1.84 
TCGA-SY-A9G0 TCGA-UY-A78M TCGA-UY-A8OC TCGA-UY-A9PF TCGA-XF-A8HF TCGA-XF-A9SY 
       12.43        22.68         3.58         1.64        97.12        21.04 
TCGA-XF-AAMH TCGA-XF-AAML TCGA-XF-AAMX TCGA-YF-AA3M TCGA-ZF-AA51 
       11.31         7.63         6.77        13.64        38.73 

$`11Q GAIN WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        91.63       103.50       105.70         8.35 
TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S 
       16.27        44.94        16.83        16.77        17.16        34.98 
TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA86 
       27.62        49.12        41.75        51.16        66.54        10.22 
TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM 
       47.80        33.83        40.08         7.33         2.66         6.74 
TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O 
       12.39         6.58        13.15        19.04        32.84        12.16 
TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V 
       17.88        19.50         5.06        14.89        14.96         5.06 
TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH 
        8.35         8.25        17.16        16.18        20.48         4.67 
TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ 
        9.96        17.56        28.70        24.26        28.41         8.98 
TCGA-C4-A0F0 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T 
        1.94         0.46         0.43         0.69        10.95        12.66 
TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA 
       12.46        12.10        12.62        12.26        13.12        12.00 
TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YR 
       12.10        11.34        11.34        11.87        13.08         7.20 
TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A5 
        5.46         5.19        16.31         1.84        13.58         2.14 
TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD 
       66.41        18.41        19.00        16.70       130.88       112.44 
TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 
       16.14        17.62        15.62         1.81        10.59         7.79 
TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IN TCGA-DK-A3IQ 
      123.85        87.32         2.20        13.58         8.22        17.72 
TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WY 
       50.27        21.30        23.21         9.67        20.81       140.81 
TCGA-DK-A3X1 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 
       48.00        64.18        41.56        76.60        67.36        15.68 
TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6S 
       41.06        30.67        38.24        15.02        13.58       166.03 
TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 
       12.36        10.49         8.65         7.53        13.64        43.50 
TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 
       10.62        43.59        15.35        38.83        24.66         0.10 
TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A677 
        0.49         2.24        16.70        17.39         0.56        14.56 
TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7PW TCGA-E7-A7XN 
       13.97        12.99        14.33         0.92        13.68        14.07 
TCGA-E7-A85H TCGA-E7-A8O7 TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 
       12.95        15.32        14.37         8.09        32.02        16.77 
TCGA-FD-A3B5 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SJ 
        8.94         4.01        12.62        22.52        27.98        24.30 
TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ 
       23.41        17.98        29.16         5.52        25.74        46.78 
TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X 
       19.79        12.85        22.98        14.96        20.91         3.62 
TCGA-FD-A43Y TCGA-FD-A5BS TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY 
       15.58        53.88        19.33         5.36         5.69         8.25 
TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S 
       27.45        18.08        58.92         2.70         7.10        13.35 
TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF 
       62.86        18.81         6.15        12.69        12.36         2.27 
TCGA-FD-A6TH TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FJ-A871 
        4.31        10.85         7.13        10.65        17.23         8.94 
TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL 
        3.25         6.48        61.94        30.61        15.95        26.93 
TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B 
       35.24        33.01         7.23        20.12        17.62        66.02 
TCGA-G2-AA3C TCGA-GC-A3BM TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RD TCGA-GC-A3WC 
        6.94        21.40        15.81         4.50        14.07        17.75 
TCGA-GC-A3YS TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP 
       24.92         0.49         8.94        13.91         7.73         2.10 
TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q 
        3.12        20.98         2.20         7.36        10.92        11.31 
TCGA-GU-A42R TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-AATO TCGA-GU-AATP TCGA-GU-AATQ 
       11.31        27.09        20.05        10.65        32.98         7.00 
TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK 
       14.27        21.34        19.10         8.48        10.59        27.35 
TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF 
       19.07        22.72         1.51        19.40        38.60         3.06 
TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB 
        9.01         8.22        25.02         3.45        21.24         2.76 
TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB 
       27.68         9.07        11.70         1.74         1.81        15.42 
TCGA-K4-A83P TCGA-K4-AAQO TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FN 
        6.38        11.80        15.58        21.07        13.48        16.67 
TCGA-R3-A69X TCGA-S5-AA26 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78N 
       14.24         3.75        31.56        17.62        37.05        86.83 
TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OB TCGA-UY-A8OD TCGA-UY-A9PA TCGA-UY-A9PB 
       76.01        67.79        65.75       112.83        35.24        29.56 
TCGA-UY-A9PD TCGA-UY-A9PE TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HE 
       17.82         4.54        45.04         6.58        97.45       125.49 
TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI 
       15.35         1.87        17.88        48.62        64.80        79.66 
TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SZ 
        3.22        66.41        12.76        11.90        23.64        28.24 
TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 
       26.27        18.90         2.24        16.27        66.64         2.10 
TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAMJ TCGA-XF-AAMQ 
       13.74        92.98        10.82       110.60        54.90        71.57 
TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN0 
       91.73         2.96         8.32        98.99        44.32        56.48 
TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 
       30.94        61.45        86.30        27.06        75.39        18.81 
TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R0 
        3.88        18.84         9.63         0.66        11.97        18.64 
TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 
        7.36        21.11        24.13        30.28        27.19        21.86 
TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG 
       28.41        74.56        13.41         3.48        52.73        52.60 
TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4T 
       82.49        47.84        20.22         2.89        34.06        19.69 
TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA52 TCGA-ZF-AA53 
        8.61        59.38        60.16        63.02        35.41        57.90 
TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
       19.40         8.52        47.15        19.17         5.52        10.13 

  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
              0.62               0.10 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
             97.12             166.03 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
             12.23              16.29 
[1] "0.6 - 97.1 (12.2)"  "0.1 - 166.0 (16.3)"
[1] "hr=" "1.7"
D22V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  11Q GAIN MUTATED         0       16         9       22
  11Q GAIN WILD-TYPE       4      108       118      107
D22V3, multiclass
           clus
vv          11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  STAGE I                  0                  4
  STAGE II                16                108
  STAGE III                9                118
  STAGE IV                22                107
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1+T2  T3  T4
  11Q GAIN MUTATED         15  21   9
  11Q GAIN WILD-TYPE      106 163  44
D22V4, multiclass
          clus
vv         11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  T0+T1+T2               15                106
  T3                     21                163
  T4                      9                 44
[1] 3 2
[1] TRUE
[1] "dimension of 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    21   5  15   3
  11Q GAIN WILD-TYPE 203  37  60   5
D22V5, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  N0               21                203
  N1                5                 37
  N2               15                 60
  N3                3                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V6, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED    17   1
  11Q GAIN WILD-TYPE 168   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED     17    1
  11Q GAIN WILD-TYPE  168    9
   clus
vv  11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  0               17                168
  1                1                  9
[1] 2 2
[1] FALSE
D22V7, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED     7  40
  11Q GAIN WILD-TYPE  94 248
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      7   40
  11Q GAIN WILD-TYPE   94  248
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  FEMALE                7                 94
  MALE                 40                248
[1] 2 2
[1] FALSE
D22V8, continuous
D22V9, continuous
D22V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  11Q GAIN MUTATED       2                         2    41
  11Q GAIN WILD-TYPE    40                        19   270
D22V11, multiclass
                           clus
vv                          11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  ASIAN                                    2                 40
  BLACK OR AFRICAN AMERICAN                2                 19
  WHITE                                   41                270
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V12, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED     1  43
  11Q GAIN WILD-TYPE   8 309
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      1   43
  11Q GAIN WILD-TYPE    8  309
                        clus
vv                       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  8
  NOT HISPANIC OR LATINO               43                309
[1] 2 2
[1] FALSE

Clustering(23) Variable = 12P GAIN MUTATION ANALYSIS
D23V1, survival
                    sevent
clus2                  0   1
  12P GAIN MUTATED    65  44
  12P GAIN WILD-TYPE 165 109
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
               109                274 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                44                109 
$`12P GAIN MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA84 TCGA-4Z-AA86 
       22.29        11.97         0.62        41.75        15.12        10.22 
TCGA-BL-A3JM TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20P TCGA-BT-A20R TCGA-BT-A20V 
        6.74        19.04        32.84        17.88         5.06         5.06 
TCGA-BT-A20X TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42E 
        8.25        16.18        20.48        12.82         9.96        24.26 
TCGA-CF-A5UA TCGA-CF-A8HX TCGA-CF-A8HY TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR 
       12.00        11.34        11.34        12.92         4.90         7.20 
TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A3IM TCGA-DK-A3IS TCGA-DK-A3WX TCGA-DK-A3X1 
       21.86        66.41         7.82        50.27        10.55        48.00 
TCGA-DK-A6AV TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B6 TCGA-DK-AA6P TCGA-DK-AA6S 
       64.18        67.36        15.68        30.67        15.02       166.03 
TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA76 TCGA-E7-A4IJ TCGA-E7-A5KE 
       12.36        10.49         7.53        12.03         0.49         0.56 
TCGA-E7-A6ME TCGA-FD-A3B3 TCGA-FD-A3B6 TCGA-FD-A3NA TCGA-FD-A3SS TCGA-FD-A43P 
       12.99        32.02        33.04        60.66        12.85        27.35 
TCGA-FD-A5BS TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BZ TCGA-FD-A62P TCGA-FD-A62S 
       53.88         5.36         5.69        27.45         6.28        13.35 
TCGA-FD-A6TB TCGA-FJ-A3Z7 TCGA-FT-A61P TCGA-G2-A2EO TCGA-G2-A3VY TCGA-G2-AA3B 
       18.81        31.07         6.48        35.24        17.62        66.02 
TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RD TCGA-GC-A6I3 TCGA-GU-A762 
       21.40         2.24        15.81        14.07        13.91         7.63 
TCGA-GU-AATO TCGA-GU-AATQ TCGA-GV-A3JZ TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK 
       10.65         7.00        19.82         8.48        10.59        27.35 
TCGA-GV-A40E TCGA-GV-A40G TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE 
        8.58        19.07        38.60         3.06         9.01         8.22 
TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AC TCGA-K4-A5RI TCGA-K4-A6FZ TCGA-K4-A83P 
        3.45        21.24         9.14        11.70         1.81         6.38 
TCGA-MV-A51V TCGA-SY-A9G5 TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OB TCGA-UY-A9PA 
       13.48        31.56        76.01        67.79        65.75        35.24 
TCGA-UY-A9PE TCGA-XF-A9SI TCGA-XF-A9SV TCGA-XF-AAML TCGA-XF-AAMT TCGA-XF-AAMY 
        4.54        79.66        12.76         7.63         2.96        98.99 
TCGA-XF-AAMZ TCGA-XF-AAN3 TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-YF-AA3M TCGA-ZF-A9R1 
       44.32        86.30        75.39        18.81        13.64         7.36 
TCGA-ZF-A9R2 TCGA-ZF-A9R4 TCGA-ZF-A9RD TCGA-ZF-AA4N TCGA-ZF-AA4V TCGA-ZF-AA53 
       21.11        30.28        13.41         2.89        59.38        57.90 
TCGA-ZF-AA54 
       19.40 

$`12P GAIN WILD-TYPE`
TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW TCGA-4Z-AA7M TCGA-4Z-AA7N 
       91.63       103.50       105.70         8.35        16.27        44.94 
TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA7Y 
       16.83        16.77        17.16        34.98        27.62        49.12 
TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I 
       51.16        66.54        47.80        33.83        40.08         7.33 
TCGA-BL-A13J TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20O TCGA-BT-A20Q 
        2.66        12.39         6.58        13.15        12.16        19.50 
TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20W TCGA-BT-A2LA TCGA-BT-A3PH TCGA-BT-A42B 
       14.89        14.96         8.35        17.16         4.67        17.56 
TCGA-BT-A42C TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR 
       28.70        28.41         8.98         1.94        23.01         0.46 
TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W 
        0.43         0.69        10.95        12.66        12.46        12.10 
TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A7I0 TCGA-CF-A9FF TCGA-CF-A9FM 
       12.62        12.26        13.12        12.10        11.87        13.08 
TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A5 
        5.46         5.19        16.31         1.84        13.58         2.14 
TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE 
       18.41        19.00        16.70       130.88       112.44        16.14 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 
       17.62        15.62         1.81        10.59         7.79       123.85 
TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IT 
       87.32         2.20        13.58         8.22        17.72        21.30 
TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WY TCGA-DK-A3X2 TCGA-DK-A6AW 
       23.21         9.67        20.81       140.81        17.98        41.56 
TCGA-DK-A6B0 TCGA-DK-A6B5 TCGA-DK-AA6L TCGA-DK-AA6Q TCGA-DK-AA6W TCGA-DK-AA71 
       76.60        41.06        38.24        13.58         8.65        13.64 
TCGA-DK-AA74 TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 
       43.50        10.62        43.59        15.35        38.83        24.66 
TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KF TCGA-E7-A677 
        0.10         2.24        16.70        17.39         0.66        14.56 
TCGA-E7-A678 TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A7XN 
       13.97        14.33         0.92         1.22        13.68        14.07 
TCGA-E7-A85H TCGA-E7-A8O7 TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B4 TCGA-FD-A3B5 
       12.95        15.32        14.37         8.09        16.77         8.94 
TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SJ TCGA-FD-A3SL 
        4.01        12.62        22.52        27.98        24.30        23.41 
TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR 
       17.98        29.16         5.52        25.74        46.78        19.79 
TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR 
       22.98        14.96        20.91         3.62        15.58        26.73 
TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N 
       11.01        19.33         8.25        18.08        58.92         2.70 
TCGA-FD-A62O TCGA-FD-A6TA TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF 
        7.10        62.86         6.15        12.69        12.36         2.27 
TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE 
        3.06         4.31         9.67        10.85         7.13        10.65 
TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK 
       17.23         8.94         3.25        61.94        30.61        15.95 
TCGA-G2-A2EL TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3C TCGA-G2-AA3D 
       26.93        33.01         7.23        20.12         6.94        64.44 
TCGA-G2-AA3F TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A4ZW 
       19.46         4.50        15.91        17.75        24.92         0.49 
TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 
        8.94         7.73         2.10         3.12        20.98         2.20 
TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A763 TCGA-GU-A764 
        7.36        10.92        11.31        11.31        27.09        20.05 
TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATP TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX 
        5.62         4.73        32.98        14.27        21.34        19.10 
TCGA-GV-A3QF TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-K4-A3WS TCGA-K4-A4AB 
       20.28        22.72         1.51        19.40        25.02         2.76 
TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RJ TCGA-K4-A6MB TCGA-K4-AAQO TCGA-LC-A66R 
       27.68         9.07         1.74        15.42        11.80        15.32 
TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX 
       15.58        21.07        12.23        16.67        14.24         1.84 
TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78N 
        3.75        12.43        17.62        37.05        22.68        86.83 
TCGA-UY-A8OC TCGA-UY-A8OD TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PF TCGA-XF-A8HB 
        3.58       112.83        29.56        17.82         1.64        45.04 
TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A8HH 
        6.58        97.45       125.49        97.12        15.35         1.87 
TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SW 
       17.88        48.62        64.80         3.22        66.41        11.90 
TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 
       23.64        21.04        28.24        26.27        18.90         2.24 
TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF 
       16.27        66.64         2.10        13.74        92.98        10.82 
TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMW 
      110.60        11.31        54.90        71.57        91.73         8.32 
TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN4 TCGA-XF-AAN8 
        6.77        56.48        30.94        61.45        27.06         3.88 
TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R3 
       18.84         9.63         0.66        11.97        18.64        24.13 
TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-A9RF 
       27.19        21.86        28.41        74.56         3.48        52.73 
TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4R TCGA-ZF-AA4T 
       52.60        82.49        47.84        20.22        34.06        19.69 
TCGA-ZF-AA4U TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA56 
        8.61        60.16        63.02        38.73        35.41         8.52 
TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
       47.15        19.17         5.52        10.13 

  12P GAIN MUTATED 12P GAIN WILD-TYPE 
              0.49               0.10 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
            166.03             140.81 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
             13.91              16.27 
[1] "0.5 - 166.0 (13.9)" "0.1 - 140.8 (16.3)"
[1] "hr=" "1"  
D23V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  12P GAIN MUTATED         1       41        33       35
  12P GAIN WILD-TYPE       3       83        94       94
D23V3, multiclass
           clus
vv          12P GAIN MUTATED 12P GAIN WILD-TYPE
  STAGE I                  1                  3
  STAGE II                41                 83
  STAGE III               33                 94
  STAGE IV                35                 94
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1+T2  T3  T4
  12P GAIN MUTATED         37  52  12
  12P GAIN WILD-TYPE       84 132  41
D23V4, multiclass
          clus
vv         12P GAIN MUTATED 12P GAIN WILD-TYPE
  T0+T1+T2               37                 84
  T3                     52                132
  T4                     12                 41
[1] 3 2
[1] TRUE
[1] "dimension of 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    64  14  19   3
  12P GAIN WILD-TYPE 160  28  56   5
D23V5, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  N0               64                160
  N1               14                 28
  N2               19                 56
  N3                3                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V6, binary
                    cls
clus                   0   1
  12P GAIN MUTATED    55   2
  12P GAIN WILD-TYPE 130   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     55    2
  12P GAIN WILD-TYPE  130    8
   clus
vv  12P GAIN MUTATED 12P GAIN WILD-TYPE
  0               55                130
  1                2                  8
[1] 2 2
[1] FALSE
D23V7, binary
                    cls
clus                   0   1
  12P GAIN MUTATED    31  80
  12P GAIN WILD-TYPE  70 208
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     31   80
  12P GAIN WILD-TYPE   70  208
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  FEMALE               31                 70
  MALE                 80                208
[1] 2 2
[1] FALSE
D23V8, continuous
D23V9, continuous
D23V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  12P GAIN MUTATED      11                         5    89
  12P GAIN WILD-TYPE    31                        16   222
D23V11, multiclass
                           clus
vv                          12P GAIN MUTATED 12P GAIN WILD-TYPE
  ASIAN                                   11                 31
  BLACK OR AFRICAN AMERICAN                5                 16
  WHITE                                   89                222
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V12, binary
                    cls
clus                   0   1
  12P GAIN MUTATED     3  98
  12P GAIN WILD-TYPE   6 254
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      3   98
  12P GAIN WILD-TYPE    6  254
                        clus
vv                       12P GAIN MUTATED 12P GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                  6
  NOT HISPANIC OR LATINO               98                254
[1] 2 2
[1] FALSE

Clustering(24) Variable = 12Q GAIN MUTATION ANALYSIS
D24V1, survival
                    sevent
clus2                  0   1
  12Q GAIN MUTATED    53  33
  12Q GAIN WILD-TYPE 177 120
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                86                297 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                33                120 
$`12Q GAIN MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-4Z-AA80 TCGA-4Z-AA84 TCGA-BL-A3JM TCGA-BT-A20J 
       22.29        11.97         0.62        15.12         6.74        19.04 
TCGA-BT-A20P TCGA-BT-A20R TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LB TCGA-BT-A3PK 
       17.88         5.06         5.06         8.25        16.18         9.96 
TCGA-BT-A42E TCGA-CF-A5UA TCGA-CF-A8HX TCGA-CF-A8HY TCGA-CU-A0YO TCGA-CU-A0YR 
       24.26        12.00        11.34        11.34         4.90         7.20 
TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1AC TCGA-DK-A3IS 
        1.84        21.86         2.14        66.41       130.88        50.27 
TCGA-DK-A3WX TCGA-DK-A3X1 TCGA-DK-A6AV TCGA-DK-A6B1 TCGA-DK-AA6P TCGA-DK-AA6S 
       10.55        48.00        64.18        67.36        15.02       166.03 
TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA76 TCGA-E7-A5KE 
       12.36        10.49         7.53        13.64        12.03         0.56 
TCGA-E7-A6ME TCGA-FD-A3NA TCGA-FD-A43P TCGA-FD-A43Y TCGA-FD-A5BV TCGA-FD-A5BX 
       12.99        60.66        27.35        15.58         5.36         5.69 
TCGA-FD-A5BZ TCGA-FD-A62P TCGA-FD-A62S TCGA-FJ-A3Z7 TCGA-G2-A2EF TCGA-G2-A2EO 
       27.45         6.28        13.35        31.07        61.94        35.24 
TCGA-G2-A3VY TCGA-G2-AA3B TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A6I3 TCGA-GU-AATO 
       17.62        66.02        21.40         2.24        13.91        10.65 
TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-HQ-A2OE TCGA-HQ-A2OF 
        8.48        10.59        27.35         8.58        38.60         3.06 
TCGA-K4-A3WU TCGA-K4-A5RI TCGA-K4-A6FZ TCGA-K4-A83P TCGA-MV-A51V TCGA-SY-A9G5 
        3.45        11.70         1.81         6.38        13.48        31.56 
TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PE TCGA-XF-A9SI 
       76.01        67.79        65.75        35.24         4.54        79.66 
TCGA-XF-A9SV TCGA-XF-AAML TCGA-XF-AAMT TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN3 
       12.76         7.63         2.96        98.99        44.32        86.30 
TCGA-XF-AAN7 TCGA-YF-AA3M TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R4 TCGA-ZF-A9RN 
       18.81        13.64         7.36        21.11        30.28        20.22 
TCGA-ZF-AA4V TCGA-ZF-AA53 
       59.38        57.90 

$`12Q GAIN WILD-TYPE`
TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW TCGA-4Z-AA7M TCGA-4Z-AA7N 
       91.63       103.50       105.70         8.35        16.27        44.94 
TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA7Y 
       16.83        16.77        17.16        34.98        27.62        49.12 
TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 
       41.75        51.16        66.54        10.22        47.80        33.83 
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX 
       40.08         7.33         2.66        12.39         6.58        13.15 
TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20Q TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20W 
       32.84        12.16        19.50        14.89        14.96         8.35 
TCGA-BT-A2LA TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A42B TCGA-BT-A42C 
       17.16        20.48         4.67        12.82        17.56        28.70 
TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS 
       28.41         8.98         1.94        23.01         0.46         0.43 
TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X 
        0.69        10.95        12.66        12.46        12.10        12.62 
TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A7I0 TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YN 
       12.26        13.12        12.10        11.87        13.08        12.92 
TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A72E TCGA-DK-A1A7 TCGA-DK-A1AA 
        5.46         5.19        16.31        13.58        18.41        19.00 
TCGA-DK-A1AB TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX 
       16.70       112.44        16.14        17.62        15.62         1.81 
TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL 
       10.59         7.79       123.85        87.32         2.20        13.58 
TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV 
        7.82         8.22        17.72        21.30        23.21         9.67 
TCGA-DK-A3WW TCGA-DK-A3WY TCGA-DK-A3X2 TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B2 
       20.81       140.81        17.98        41.56        76.60        15.68 
TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6Q TCGA-DK-AA6W TCGA-DK-AA74 
       41.06        30.67        38.24        13.58         8.65        43.50 
TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 
       10.62        43.59        15.35        38.83        24.66         0.10 
TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KF TCGA-E7-A677 
        0.49         2.24        16.70        17.39         0.66        14.56 
TCGA-E7-A678 TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A7XN 
       13.97        14.33         0.92         1.22        13.68        14.07 
TCGA-E7-A85H TCGA-E7-A8O7 TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 
       12.95        15.32        14.37         8.09        32.02        16.77 
TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 
        8.94        33.04         4.01        12.62        22.52        27.98 
TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP 
       24.30        23.41        17.98        29.16         5.52        25.74 
TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43U 
       46.78        19.79        12.85        22.98        14.96        20.91 
TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BY 
        3.62        26.73        53.88        11.01        19.33         8.25 
TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A6TA TCGA-FD-A6TB 
       18.08        58.92         2.70         7.10        62.86        18.81 
TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH 
        6.15        12.69        12.36         2.27         3.06         4.31 
TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FJ-A871 
        9.67        10.85         7.13        10.65        17.23         8.94 
TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2ES 
        3.25         6.48        30.61        15.95        26.93        33.01 
TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3OO 
        7.23        20.12         6.94        64.44        19.46        15.81 
TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A4ZW 
        4.50        15.91        14.07        17.75        24.92         0.49 
TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 
        8.94         7.73         2.10         3.12        20.98         2.20 
TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 
        7.36        10.92        11.31        11.31         7.63        27.09 
TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JV 
       20.05         5.62         4.73        32.98         7.00        14.27 
TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A40G TCGA-GV-A6ZA 
       21.34        19.10        19.82        20.28        19.07        22.72 
TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WV 
        1.51        19.40         9.01         8.22        25.02        21.24 
TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RJ TCGA-K4-A6MB 
        2.76         9.14        27.68         9.07         1.74        15.42 
TCGA-K4-AAQO TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-PQ-A6FI TCGA-PQ-A6FN 
       11.80        15.32        15.58        21.07        12.23        16.67 
TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-UY-A78K TCGA-UY-A78L 
       14.24         1.84         3.75        12.43        17.62        37.05 
TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A8OC TCGA-UY-A8OD TCGA-UY-A9PB TCGA-UY-A9PD 
       22.68        86.83         3.58       112.83        29.56        17.82 
TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF 
        1.64        45.04         6.58        97.45       125.49        97.12 
TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SJ 
       15.35         1.87        17.88        48.62        64.80         3.22 
TCGA-XF-A9SL TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 
       66.41        11.90        23.64        21.04        28.24        26.27 
TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 
       18.90         2.24        16.27        66.64         2.10        13.74 
TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAMQ 
       92.98        10.82       110.60        11.31        54.90        71.57 
TCGA-XF-AAMR TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN2 
       91.73         8.32         6.77        56.48        30.94        61.45 
TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC 
       27.06        75.39         3.88        18.84         9.63         0.66 
TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 
       11.97        18.64        24.13        27.19        21.86        28.41 
TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL 
       74.56        13.41         3.48        52.73        52.60        82.49 
TCGA-ZF-A9RM TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4W 
       47.84         2.89        34.06        19.69         8.61        60.16 
TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 
       63.02        38.73        35.41        19.40         8.52        47.15 
TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
       19.17         5.52        10.13 

  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
              0.56               0.10 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
            166.03             140.81 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
            13.775             16.140 
[1] "0.6 - 166.0 (13.8)" "0.1 - 140.8 (16.1)"
[1] "hr=" "1.1"
D24V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  12Q GAIN MUTATED         1       35        26       26
  12Q GAIN WILD-TYPE       3       89       101      103
D24V3, multiclass
           clus
vv          12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  STAGE I                  1                  3
  STAGE II                35                 89
  STAGE III               26                101
  STAGE IV                26                103
[1] 4 2
[1] TRUE
[1] "dimension of contingency 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         32  37  11
  12Q GAIN WILD-TYPE       89 147  42
D24V4, multiclass
          clus
vv         12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  T0+T1+T2               32                 89
  T3                     37                147
  T4                     11                 42
[1] 3 2
[1] TRUE
[1] "dimension of 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    55  10  16   0
  12Q GAIN WILD-TYPE 169  32  59   8
D24V5, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  N0               55                169
  N1               10                 32
  N2               16                 59
  N3                0                  8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V6, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED    50   2
  12Q GAIN WILD-TYPE 135   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     50    2
  12Q GAIN WILD-TYPE  135    8
   clus
vv  12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  0               50                135
  1                2                  8
[1] 2 2
[1] FALSE
D24V7, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED    26  63
  12Q GAIN WILD-TYPE  75 225
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     26   63
  12Q GAIN WILD-TYPE   75  225
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  FEMALE               26                 75
  MALE                 63                225
[1] 2 2
[1] FALSE
D24V8, continuous
D24V9, continuous
D24V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  12Q GAIN MUTATED      11                         4    71
  12Q GAIN WILD-TYPE    31                        17   240
D24V11, multiclass
                           clus
vv                          12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  ASIAN                                   11                 31
  BLACK OR AFRICAN AMERICAN                4                 17
  WHITE                                   71                240
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V12, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED     2  81
  12Q GAIN WILD-TYPE   7 271
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      2   81
  12Q GAIN WILD-TYPE    7  271
                        clus
vv                       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  7
  NOT HISPANIC OR LATINO               81                271
[1] 2 2
[1] FALSE

Clustering(25) Variable = 13Q GAIN MUTATION ANALYSIS
D25V1, survival
                    sevent
clus2                  0   1
  13Q GAIN MUTATED    55  37
  13Q GAIN WILD-TYPE 175 116
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                92                291 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                37                116 
$`13Q GAIN MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KT TCGA-4Z-AA81 TCGA-4Z-AA87 TCGA-BL-A3JM TCGA-BT-A0S7 
       22.29       105.70        41.75        47.80         6.74         6.58 
TCGA-BT-A20J TCGA-BT-A20Q TCGA-BT-A20U TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-C4-A0EZ 
       19.04        19.50        14.96        20.48        12.82         8.98 
TCGA-CF-A1HS TCGA-CF-A8HX TCGA-CU-A0YN TCGA-CU-A0YR TCGA-CU-A3QU TCGA-CU-A3YL 
        0.43        11.34        12.92         7.20         5.19        16.31 
TCGA-DK-A2HX TCGA-DK-A3IL TCGA-DK-A3IS TCGA-DK-A3IU TCGA-DK-A3X1 TCGA-DK-A3X2 
        1.81        13.58        50.27        23.21        48.00        17.98 
TCGA-DK-A6B1 TCGA-DK-AA6L TCGA-DK-AA6P TCGA-DK-AA6S TCGA-DK-AA6U TCGA-E5-A2PC 
       67.36        38.24        15.02       166.03        10.49        43.59 
TCGA-E7-A541 TCGA-E7-A6ME TCGA-E7-A7DU TCGA-E7-A7PW TCGA-E7-A97Q TCGA-FD-A3B6 
       17.39        12.99         0.92        13.68         8.09        33.04 
TCGA-FD-A3SM TCGA-FD-A3SQ TCGA-FD-A43X TCGA-FD-A5BT TCGA-FD-A62O TCGA-FD-A6TE 
       17.98        46.78         3.62        11.01         7.10        12.36 
TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FJ-A3ZE TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EK 
        3.06         4.31        10.65         6.48        61.94        15.95 
TCGA-G2-AA3B TCGA-G2-AA3D TCGA-GC-A3OO TCGA-GC-A3WC TCGA-GC-A4ZW TCGA-GD-A3OP 
       66.02        64.44        15.81        17.75         0.49         2.10 
TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATQ TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF 
        4.73        10.65         7.00        19.10        19.82        20.28 
TCGA-GV-A3QH TCGA-GV-A3QK TCGA-H4-A2HQ TCGA-HQ-A5NE TCGA-K4-A54R TCGA-K4-A5RH 
        8.48        27.35        19.40         8.22        27.68         9.07 
TCGA-K4-AAQO TCGA-LC-A66R TCGA-MV-A51V TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G5 
       11.80        15.32        13.48        14.24         1.84        31.56 
TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OD 
       17.62        37.05        22.68        76.01        67.79       112.83 
TCGA-UY-A9PA TCGA-XF-A8HD TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A9SJ TCGA-XF-AAMQ 
       35.24        97.45        97.12        15.35         3.22        71.57 
TCGA-XF-AAMR TCGA-XF-AAMY TCGA-XF-AAN0 TCGA-XF-AAN2 TCGA-ZF-A9R0 TCGA-ZF-AA4T 
       91.73        98.99        56.48        61.45        18.64        19.69 
TCGA-ZF-AA4X TCGA-ZF-AA56 
       63.02         8.52 

$`13Q GAIN WILD-TYPE`
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7M TCGA-4Z-AA7N 
       11.97        91.63       103.50         8.35        16.27        44.94 
TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA7Y 
       16.83        16.77        17.16        34.98        27.62        49.12 
TCGA-4Z-AA80 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-4Z-AA89 
        0.62        51.16        66.54        15.12        10.22        33.83 
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A5ZZ TCGA-BT-A0YX TCGA-BT-A20N 
       40.08         7.33         2.66        12.39        13.15        32.84 
TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20V TCGA-BT-A20W 
       12.16        17.88         5.06        14.89         5.06         8.35 
TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A3PK TCGA-BT-A42B 
        8.25        17.16        16.18         4.67         9.96        17.56 
TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR 
       28.70        24.26        28.41         1.94        23.01         0.46 
TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X 
        0.69        10.95        12.66        12.46        12.10        12.62 
TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A8HY TCGA-CF-A9FF 
       12.26        13.12        12.00        12.10        11.34        11.87 
TCGA-CF-A9FM TCGA-CU-A0YO TCGA-CU-A3KJ TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 
       13.08         4.90         5.46         1.84        13.58        21.86 
TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC 
        2.14        66.41        18.41        19.00        16.70       130.88 
TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A2I2 
      112.44        16.14        17.62        15.62        10.59         7.79 
TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ 
      123.85        87.32         2.20         7.82         8.22        17.72 
TCGA-DK-A3IT TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A6AV 
       21.30         9.67        20.81        10.55       140.81        64.18 
TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6Q 
       41.56        76.60        15.68        41.06        30.67        13.58 
TCGA-DK-AA6T TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA76 
       12.36         8.65         7.53        13.64        43.50        12.03 
TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ 
       10.62        15.35        38.83        24.66         0.10         0.49 
TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 
        2.24        16.70         0.56         0.66        14.56        13.97 
TCGA-E7-A6MF TCGA-E7-A7DV TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A8O7 TCGA-E7-A97P 
       14.33         1.22        14.07        12.95        15.32        14.37 
TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 
       32.02        16.77         8.94         4.01        12.62        22.52 
TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SN TCGA-FD-A3SO 
       27.98        60.66        24.30        23.41        29.16         5.52 
TCGA-FD-A3SP TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S 
       25.74        19.79        12.85        22.98        27.35        14.96 
TCGA-FD-A43U TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BU TCGA-FD-A5BV 
       20.91        15.58        26.73        53.88        19.33         5.36 
TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N 
        5.69         8.25        27.45        18.08        58.92         2.70 
TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD 
        6.28        13.35        62.86        18.81         6.15        12.69 
TCGA-FD-A6TF TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZF 
        2.27         9.67        10.85        31.07         7.13        17.23 
TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EJ TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES 
        8.94         3.25        30.61        26.93        35.24        33.01 
TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3BM 
        7.23        20.12        17.62         6.94        19.46        21.40 
TCGA-GC-A3I6 TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3YS TCGA-GC-A6I1 
        2.24         4.50        15.91        14.07        24.92         8.94 
TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B 
       13.91         7.73         3.12        20.98         2.20         7.36 
TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 
       10.92        11.31        11.31         7.63        27.09        20.05 
TCGA-GU-A766 TCGA-GU-AATP TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3QI TCGA-GV-A40E 
        5.62        32.98        14.27        21.34        10.59         8.58 
TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND 
       19.07        22.72         1.51        38.60         3.06         9.01 
TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A5RI 
       25.02         3.45        21.24         2.76         9.14        11.70 
TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-LT-A5Z6 TCGA-LT-A8JT 
        1.74         1.81        15.42         6.38        15.58        21.07 
TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-UY-A78N TCGA-UY-A8OB 
       12.23        16.67         3.75        12.43        86.83        65.75 
TCGA-UY-A8OC TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HB 
        3.58        29.56        17.82         4.54         1.64        45.04 
TCGA-XF-A8HC TCGA-XF-A8HE TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH 
        6.58       125.49         1.87        17.88        48.62        64.80 
TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY 
       79.66        66.41        12.76        11.90        23.64        21.04 
TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 
       28.24        26.27        18.90         2.24        16.27        66.64 
TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAMH 
        2.10        13.74        92.98        10.82       110.60        11.31 
TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMZ 
       54.90         7.63         2.96         8.32         6.77        44.32 
TCGA-XF-AAN1 TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-XF-AAN8 
       30.94        86.30        27.06        75.39        18.81         3.88 
TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R1 
       18.84         9.63         0.66        11.97        13.64         7.36 
TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 
       21.11        24.13        30.28        27.19        21.86        28.41 
TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL 
       74.56        13.41         3.48        52.73        52.60        82.49 
TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4U TCGA-ZF-AA4V 
       47.84        20.22         2.89        34.06         8.61        59.38 
TCGA-ZF-AA4W TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA58 
       60.16        38.73        35.41        57.90        19.40        47.15 
TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
       19.17         5.52        10.13 

  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
              0.43               0.10 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
            166.03             140.81 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
            17.505             15.420 
[1] "0.4 - 166.0 (17.5)" "0.1 - 140.8 (15.4)"
[1] "hr=" "1.1"
D25V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  13Q GAIN MUTATED         1       26        30       36
  13Q GAIN WILD-TYPE       3       98        97       93
D25V3, multiclass
           clus
vv          13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  STAGE I                  1                  3
  STAGE II                26                 98
  STAGE III               30                 97
  STAGE IV                36                 93
[1] 4 2
[1] TRUE
[1] "dimension of contingency 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         26  46  14
  13Q GAIN WILD-TYPE       95 138  39
D25V4, multiclass
          clus
vv         13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  T0+T1+T2               26                 95
  T3                     46                138
  T4                     14                 39
[1] 3 2
[1] TRUE
[1] "dimension of 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    52   7  25   5
  13Q GAIN WILD-TYPE 172  35  50   3
D25V5, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  N0               52                172
  N1                7                 35
  N2               25                 50
  N3                5                  3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V6, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED    45   4
  13Q GAIN WILD-TYPE 140   6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED     45    4
  13Q GAIN WILD-TYPE  140    6
   clus
vv  13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  0               45                140
  1                4                  6
[1] 2 2
[1] FALSE
D25V7, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED    22  73
  13Q GAIN WILD-TYPE  79 215
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED     22   73
  13Q GAIN WILD-TYPE   79  215
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  FEMALE               22                 79
  MALE                 73                215
[1] 2 2
[1] FALSE
D25V8, continuous
D25V9, continuous
D25V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  13Q GAIN MUTATED       7                         3    83
  13Q GAIN WILD-TYPE    35                        18   228
D25V11, multiclass
                           clus
vv                          13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  ASIAN                                    7                 35
  BLACK OR AFRICAN AMERICAN                3                 18
  WHITE                                   83                228
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V12, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED     0  91
  13Q GAIN WILD-TYPE   9 261
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      0   91
  13Q GAIN WILD-TYPE    9  261
                        clus
vv                       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  9
  NOT HISPANIC OR LATINO               91                261
[1] 2 2
[1] FALSE

Clustering(26) Variable = 14Q GAIN MUTATION ANALYSIS
D26V1, survival
                    sevent
clus2                  0   1
  14Q GAIN MUTATED    26  29
  14Q GAIN WILD-TYPE 204 124
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                55                328 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                29                124 
$`14Q GAIN MUTATED`
TCGA-4Z-AA7R TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A20N TCGA-C4-A0EZ TCGA-C4-A0F0 
       17.16        12.39         6.58        32.84         8.98         1.94 
TCGA-C4-A0F6 TCGA-CU-A0YN TCGA-DK-A3IK TCGA-DK-A3IN TCGA-DK-A3IT TCGA-DK-A3WX 
       23.01        12.92         2.20         8.22        21.30        10.55 
TCGA-DK-A6B6 TCGA-DK-AA74 TCGA-E5-A2PC TCGA-FD-A3B3 TCGA-FD-A3B7 TCGA-FD-A3N5 
       30.67        43.50        43.59        32.02         4.01        22.52 
TCGA-FD-A5BT TCGA-FD-A5BZ TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TD TCGA-FD-A6TE 
       11.01        27.45         7.10        13.35        12.69        12.36 
TCGA-FJ-A3ZE TCGA-G2-A2EL TCGA-G2-A2EO TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3YS 
       10.65        26.93        35.24        21.40         2.24        24.92 
TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42P TCGA-GU-AATO TCGA-GU-AATQ TCGA-GV-A3QH 
       20.98         2.20        10.92        10.65         7.00         8.48 
TCGA-K4-A3WV TCGA-K4-A4AC TCGA-K4-A5RI TCGA-K4-A6FZ TCGA-LT-A5Z6 TCGA-PQ-A6FN 
       21.24         9.14        11.70         1.81        15.58        16.67 
TCGA-UY-A78O TCGA-UY-A8OD TCGA-XF-A8HB TCGA-XF-A8HG TCGA-XF-A9T3 TCGA-XF-AAMF 
       76.01       112.83        45.04        15.35         2.24        10.82 
TCGA-XF-AAMQ TCGA-XF-AAMT TCGA-ZF-A9R0 TCGA-ZF-A9RD TCGA-ZF-A9RG TCGA-ZF-AA4R 
       71.57         2.96        18.64        13.41        52.60        34.06 
TCGA-ZF-AA5H 
       19.17 

$`14Q GAIN WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        91.63       103.50       105.70         8.35 
TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7S TCGA-4Z-AA7W 
       16.27        44.94        16.83        16.77        34.98        27.62 
TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA84 
       49.12         0.62        41.75        51.16        66.54        15.12 
TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J 
       10.22        47.80        33.83        40.08         7.33         2.66 
TCGA-BL-A3JM TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q 
        6.74        13.15        19.04        12.16        17.88        19.50 
TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X 
        5.06        14.89        14.96         5.06         8.35         8.25 
TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK 
       17.16        16.18        20.48         4.67        12.82         9.96 
TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F TCGA-CF-A1HR TCGA-CF-A1HS 
       17.56        28.70        24.26        28.41         0.46         0.43 
TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X 
        0.69        10.95        12.66        12.46        12.10        12.62 
TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A8HY 
       12.26        13.12        12.00        12.10        11.34        11.34 
TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU 
       11.87        13.08         4.90         7.20         5.46         5.19 
TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 
       16.31         1.84        13.58        21.86         2.14        66.41 
TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE 
       18.41        19.00        16.70       130.88       112.44        16.14 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 
       17.62        15.62         1.81        10.59         7.79       123.85 
TCGA-DK-A2I6 TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IU 
       87.32        13.58         7.82        17.72        50.27        23.21 
TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV 
        9.67        20.81       140.81        48.00        17.98        64.18 
TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-AA6L 
       41.56        76.60        67.36        15.68        41.06        38.24 
TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W 
       15.02        13.58       166.03        12.36        10.49         8.65 
TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E5-A4U1 
        7.53        13.64        12.03        10.62        15.35        38.83 
TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 
       24.66         0.10         0.49         2.24        16.70        17.39 
TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF 
        0.56         0.66        14.56        13.97        12.99        14.33 
TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A8O7 
        0.92         1.22        13.68        14.07        12.95        15.32 
TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B8 
       14.37         8.09        16.77         8.94        33.04        12.62 
TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN 
       27.98        60.66        24.30        23.41        17.98        29.16 
TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N 
        5.52        25.74        46.78        19.79        12.85        22.98 
TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR 
       27.35        14.96        20.91         3.62        15.58        26.73 
TCGA-FD-A5BS TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C0 
       53.88        19.33         5.36         5.69         8.25        18.08 
TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC 
       58.92         2.70         6.28        62.86        18.81         6.15 
TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 
        2.27         3.06         4.31         9.67        10.85        31.07 
TCGA-FJ-A3Z9 TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EF 
        7.13        17.23         8.94         3.25         6.48        61.94 
TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY 
       30.61        15.95        33.01         7.23        20.12        17.62 
TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3OO TCGA-GC-A3RB 
       66.02         6.94        64.44        19.46        15.81         4.50 
TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GC-A6I3 
       15.91        14.07        17.75         0.49         8.94        13.91 
TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A76B TCGA-GU-A42Q TCGA-GU-A42R 
        7.73         2.10         3.12         7.36        11.31        11.31 
TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATP 
        7.63        27.09        20.05         5.62         4.73        32.98 
TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QI 
       14.27        21.34        19.10        19.82        20.28        10.59 
TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ 
       27.35         8.58        19.07        22.72         1.51        19.40 
TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU 
       38.60         3.06         9.01         8.22        25.02         3.45 
TCGA-K4-A4AB TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RJ TCGA-K4-A6MB TCGA-K4-A83P 
        2.76        27.68         9.07         1.74        15.42         6.38 
TCGA-K4-AAQO TCGA-LC-A66R TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FI TCGA-R3-A69X 
       11.80        15.32        21.07        13.48        12.23        14.24 
TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L 
        1.84         3.75        12.43        31.56        17.62        37.05 
TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A78P TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A9PA 
       22.68        86.83        67.79        65.75         3.58        35.24 
TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HC TCGA-XF-A8HD 
       29.56        17.82         4.54         1.64         6.58        97.45 
TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH 
      125.49        97.12         1.87        17.88        48.62        64.80 
TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX 
       79.66         3.22        66.41        12.76        11.90        23.64 
TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T4 TCGA-XF-A9T5 
       21.04        28.24        26.27        18.90        16.27        66.64 
TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAMJ 
        2.10        13.74        92.98       110.60        11.31        54.90 
TCGA-XF-AAML TCGA-XF-AAMR TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ 
        7.63        91.73         8.32         6.77        98.99        44.32 
TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 
       56.48        30.94        61.45        86.30        27.06        75.39 
TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L 
       18.81         3.88        18.84         9.63         0.66        11.97 
TCGA-YF-AA3M TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 
       13.64         7.36        21.11        24.13        30.28        27.19 
TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RL 
       21.86        28.41        74.56         3.48        52.73        82.49 
TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4V 
       47.84        20.22         2.89        19.69         8.61        59.38 
TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA54 
       60.16        63.02        38.73        35.41        57.90        19.40 
TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5N TCGA-ZF-AA5P 
        8.52        47.15         5.52        10.13 

  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
              1.81               0.10 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
            112.83             166.03 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
             13.41              15.93 
[1] "1.8 - 112.8 (13.4)" "0.1 - 166.0 (15.9)"
[1] "hr=" "1.5"
D26V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  14Q GAIN MUTATED         0       14        24       17
  14Q GAIN WILD-TYPE       4      110       103      112
D26V3, multiclass
           clus
vv          14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  STAGE I                  0                  4
  STAGE II                14                110
  STAGE III               24                103
  STAGE IV                17                112
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1+T2  T3  T4
  14Q GAIN MUTATED         10  33   6
  14Q GAIN WILD-TYPE      111 151  47
D26V4, multiclass
          clus
vv         14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  T0+T1+T2               10                111
  T3                     33                151
  T4                      6                 47
[1] 3 2
[1] TRUE
[1] "dimension of 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    34   6   9   1
  14Q GAIN WILD-TYPE 190  36  66   7
D26V5, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  N0               34                190
  N1                6                 36
  N2                9                 66
  N3                1                  7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V6, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED    16   2
  14Q GAIN WILD-TYPE 169   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED     16    2
  14Q GAIN WILD-TYPE  169    8
   clus
vv  14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  0               16                169
  1                2                  8
[1] 2 2
[1] FALSE
D26V7, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED    22  33
  14Q GAIN WILD-TYPE  79 255
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED     22   33
  14Q GAIN WILD-TYPE   79  255
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  FEMALE               22                 79
  MALE                 33                255
[1] 2 2
[1] FALSE
D26V8, continuous
D26V9, continuous
D26V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  14Q GAIN MUTATED       0                         5    45
  14Q GAIN WILD-TYPE    42                        16   266
D26V11, multiclass
                           clus
vv                          14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  ASIAN                                    0                 42
  BLACK OR AFRICAN AMERICAN                5                 16
  WHITE                                   45                266
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V12, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED     2  48
  14Q GAIN WILD-TYPE   7 304
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      2   48
  14Q GAIN WILD-TYPE    7  304
                        clus
vv                       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  7
  NOT HISPANIC OR LATINO               48                304
[1] 2 2
[1] FALSE

Clustering(27) Variable = 15Q GAIN MUTATION ANALYSIS
D27V1, survival
                    sevent
clus2                  0   1
  15Q GAIN MUTATED    15  15
  15Q GAIN WILD-TYPE 215 138
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                30                353 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                15                138 
$`15Q GAIN MUTATED`
TCGA-4Z-AA7R TCGA-4Z-AA89 TCGA-BT-A20Q TCGA-BT-A42F TCGA-C4-A0F6 TCGA-CF-A5UA 
       17.16        33.83        19.50        28.41        23.01        12.00 
TCGA-CF-A8HY TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A5 TCGA-DK-A2HX TCGA-DK-A3IS 
       11.34        16.31         1.84         2.14         1.81        50.27 
TCGA-DK-A3WX TCGA-DK-A6B1 TCGA-DK-AA6Q TCGA-E5-A4TZ TCGA-FD-A43U TCGA-FD-A43X 
       10.55        67.36        13.58        15.35        20.91         3.62 
TCGA-FD-A6TG TCGA-FJ-A3ZE TCGA-G2-A2EO TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GU-AATP 
        3.06        10.65        35.24        21.40         2.24        32.98 
TCGA-S5-A6DX TCGA-UY-A8OB TCGA-XF-AAMQ TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-ZF-A9RE 
        1.84        65.75        71.57        44.32        30.94         3.48 

$`15Q GAIN WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        91.63       103.50       105.70         8.35 
TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7S TCGA-4Z-AA7W 
       16.27        44.94        16.83        16.77        34.98        27.62 
TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA84 
       49.12         0.62        41.75        51.16        66.54        15.12 
TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM 
       10.22        47.80        40.08         7.33         2.66         6.74 
TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O 
       12.39         6.58        13.15        19.04        32.84        12.16 
TCGA-BT-A20P TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W 
       17.88         5.06        14.89        14.96         5.06         8.35 
TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ 
        8.25        17.16        16.18        20.48         4.67        12.82 
TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E TCGA-C4-A0EZ TCGA-C4-A0F0 
        9.96        17.56        28.70        24.26         8.98         1.94 
TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V 
        0.46         0.43         0.69        10.95        12.66        12.46 
TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A7I0 TCGA-CF-A8HX 
       12.10        12.62        12.26        13.12        12.10        11.34 
TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ 
       11.87        13.08        12.92         4.90         7.20         5.46 
TCGA-CU-A3QU TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA 
        5.19        13.58        21.86        66.41        18.41        19.00 
TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG 
       16.70       130.88       112.44        16.14        17.62        15.62 
TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL 
       10.59         7.79       123.85        87.32         2.20        13.58 
TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV 
        7.82         8.22        17.72        21.30        23.21         9.67 
TCGA-DK-A3WW TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW 
       20.81       140.81        48.00        17.98        64.18        41.56 
TCGA-DK-A6B0 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6P 
       76.60        15.68        41.06        30.67        38.24        15.02 
TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 
      166.03        12.36        10.49         8.65         7.53        13.64 
TCGA-DK-AA74 TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A3X6 
       43.50        12.03        10.62        43.59        38.83        24.66 
TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE 
        0.10         0.49         2.24        16.70        17.39         0.56 
TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU 
        0.66        14.56        13.97        12.99        14.33         0.92 
TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A8O7 TCGA-E7-A97P 
        1.22        13.68        14.07        12.95        15.32        14.37 
TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 
        8.09        32.02        16.77         8.94        33.04         4.01 
TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL 
       12.62        22.52        27.98        60.66        24.30        23.41 
TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR 
       17.98        29.16         5.52        25.74        46.78        19.79 
TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43Y TCGA-FD-A5BR 
       12.85        22.98        27.35        14.96        15.58        26.73 
TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY 
       53.88        11.01        19.33         5.36         5.69         8.25 
TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P 
       27.45        18.08        58.92         2.70         7.10         6.28 
TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE 
       13.35        62.86        18.81         6.15        12.69        12.36 
TCGA-FD-A6TF TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 
        2.27         4.31         9.67        10.85        31.07         7.13 
TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ 
       17.23         8.94         3.25         6.48        61.94        30.61 
TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY 
       15.95        26.93        33.01         7.23        20.12        17.62 
TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3OO TCGA-GC-A3RB 
       66.02         6.94        64.44        19.46        15.81         4.50 
TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A4ZW TCGA-GC-A6I1 
       15.91        14.07        17.75        24.92         0.49         8.94 
TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 
       13.91         7.73         2.10         3.12        20.98         2.20 
TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 
        7.36        10.92        11.31        11.31         7.63        27.09 
TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATQ TCGA-GV-A3JV 
       20.05         5.62         4.73        10.65         7.00        14.27 
TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI 
       21.34        19.10        19.82        20.28         8.48        10.59 
TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ 
       27.35         8.58        19.07        22.72         1.51        19.40 
TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU 
       38.60         3.06         9.01         8.22        25.02         3.45 
TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RI 
       21.24         2.76         9.14        27.68         9.07        11.70 
TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-LC-A66R 
        1.74         1.81        15.42         6.38        11.80        15.32 
TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X 
       15.58        21.07        13.48        12.23        16.67        14.24 
TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M 
        3.75        12.43        31.56        17.62        37.05        22.68 
TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OC TCGA-UY-A8OD TCGA-UY-A9PA 
       86.83        76.01        67.79         3.58       112.83        35.24 
TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HC 
       29.56        17.82         4.54         1.64        45.04         6.58 
TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A8HI 
       97.45       125.49        97.12        15.35         1.87        17.88 
TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SV 
       48.62        64.80        79.66         3.22        66.41        12.76 
TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 
       11.90        23.64        21.04        28.24        26.27        18.90 
TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME 
        2.24        16.27        66.64         2.10        13.74        92.98 
TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMR 
       10.82       110.60        11.31        54.90         7.63        91.73 
TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAN0 TCGA-XF-AAN2 
        2.96         8.32         6.77        98.99        56.48        61.45 
TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A89H 
       86.30        27.06        75.39        18.81         3.88        18.84 
TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R1 
        9.63         0.66        11.97        13.64        18.64         7.36 
TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 
       21.11        24.13        30.28        27.19        21.86        28.41 
TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM 
       74.56        13.41        52.73        52.60        82.49        47.84 
TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4V 
       20.22         2.89        34.06        19.69         8.61        59.38 
TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA54 
       60.16        63.02        38.73        35.41        57.90        19.40 
TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
        8.52        47.15        19.17         5.52        10.13 

  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
              1.81               0.10 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
             71.57             166.03 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
            16.735             15.620 
[1] "1.8 - 71.6 (16.7)"  "0.1 - 166.0 (15.6)"
[1] "hr=" "1.3"
D27V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  15Q GAIN MUTATED         0       11         7       15
  15Q GAIN WILD-TYPE       4      113       120      114
D27V3, multiclass
           clus
vv          15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  STAGE I                  0                  4
  STAGE II                11                113
  STAGE III                7                120
  STAGE IV                15                114
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1+T2  T3  T4
  15Q GAIN MUTATED         11  11   9
  15Q GAIN WILD-TYPE      110 173  44
D27V4, multiclass
          clus
vv         15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  T0+T1+T2               11                110
  T3                     11                173
  T4                      9                 44
[1] 3 2
[1] TRUE
[1] "dimension of 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    19   3   8   2
  15Q GAIN WILD-TYPE 205  39  67   6
D27V5, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  N0               19                205
  N1                3                 39
  N2                8                 67
  N3                2                  6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V6, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED    20   1
  15Q GAIN WILD-TYPE 165   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED     20    1
  15Q GAIN WILD-TYPE  165    9
   clus
vv  15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  0               20                165
  1                1                  9
[1] 2 2
[1] FALSE
D27V7, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED     8  25
  15Q GAIN WILD-TYPE  93 263
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      8   25
  15Q GAIN WILD-TYPE   93  263
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  FEMALE                8                 93
  MALE                 25                263
[1] 2 2
[1] FALSE
D27V8, continuous
D27V9, continuous
D27V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  15Q GAIN MUTATED       4                         1    26
  15Q GAIN WILD-TYPE    38                        20   285
D27V11, multiclass
                           clus
vv                          15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  ASIAN                                    4                 38
  BLACK OR AFRICAN AMERICAN                1                 20
  WHITE                                   26                285
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V12, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED     1  29
  15Q GAIN WILD-TYPE   8 323
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      1   29
  15Q GAIN WILD-TYPE    8  323
                        clus
vv                       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  8
  NOT HISPANIC OR LATINO               29                323
[1] 2 2
[1] FALSE

Clustering(28) Variable = 16P GAIN MUTATION ANALYSIS
D28V1, survival
                    sevent
clus2                  0   1
  16P GAIN MUTATED    39  29
  16P GAIN WILD-TYPE 191 124
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                68                315 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                29                124 
$`16P GAIN MUTATED`
TCGA-4Z-AA7W TCGA-4Z-AA80 TCGA-4Z-AA87 TCGA-BT-A0S7 TCGA-BT-A20V TCGA-BT-A20X 
       27.62         0.62        47.80         6.58         5.06         8.25 
TCGA-BT-A2LA TCGA-BT-A42C TCGA-C4-A0EZ TCGA-CF-A47X TCGA-DK-A2I2 TCGA-DK-A3IL 
       17.16        28.70         8.98        12.62         7.79        13.58 
TCGA-DK-A3IN TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-DK-A6B2 
        8.22        50.27        21.30         9.67        48.00        15.68 
TCGA-DK-AA6S TCGA-DK-AA6U TCGA-DK-AA6X TCGA-E5-A2PC TCGA-E7-A4IJ TCGA-E7-A6ME 
      166.03        10.49         7.53        43.59         0.49        12.99 
TCGA-E7-A97Q TCGA-FD-A3SJ TCGA-FD-A5BY TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TI 
        8.09        24.30         8.25         2.27         3.06         9.67 
TCGA-FJ-A3ZE TCGA-FT-A3EE TCGA-G2-A2EO TCGA-G2-AA3B TCGA-GC-A3BM TCGA-GC-A3I6 
       10.65         3.25        35.24        66.02        21.40         2.24 
TCGA-GD-A76B TCGA-GU-A762 TCGA-GU-AATP TCGA-GV-A3JV TCGA-H4-A2HQ TCGA-HQ-A2OF 
        7.36         7.63        32.98        14.27        19.40         3.06 
TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A83P TCGA-LC-A66R 
        9.01        25.02         3.45         2.76         6.38        15.32 
TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G5 TCGA-UY-A78M TCGA-XF-A9SJ TCGA-XF-A9SZ 
       14.24         1.84        31.56        22.68         3.22        28.24 
TCGA-XF-A9T3 TCGA-XF-A9T5 TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAML TCGA-XF-AAMR 
        2.24        66.64        10.82       110.60         7.63        91.73 
TCGA-XF-AAMX TCGA-XF-AAMZ TCGA-ZF-A9R0 TCGA-ZF-A9R2 TCGA-ZF-A9RD TCGA-ZF-AA4V 
        6.77        44.32        18.64        21.11        13.41        59.38 
TCGA-ZF-AA4W TCGA-ZF-AA5H 
       60.16        19.17 

$`16P GAIN WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        91.63       103.50       105.70         8.35 
TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S 
       16.27        44.94        16.83        16.77        17.16        34.98 
TCGA-4Z-AA7Y TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA84 TCGA-4Z-AA86 
       49.12        41.75        51.16        66.54        15.12        10.22 
TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ 
       33.83        40.08         7.33         2.66         6.74        12.39 
TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q 
       13.15        19.04        32.84        12.16        17.88        19.50 
TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20W TCGA-BT-A2LB TCGA-BT-A2LD 
        5.06        14.89        14.96         8.35        16.18        20.48 
TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F 
        4.67        12.82         9.96        17.56        24.26        28.41 
TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S 
        1.94        23.01         0.46         0.43         0.69        10.95 
TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA 
       12.66        12.46        12.10        12.26        13.12        12.00 
TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YN 
       12.10        11.34        11.34        11.87        13.08        12.92 
TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 
        4.90         7.20         5.46         5.19        16.31         1.84 
TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA 
       13.58        21.86         2.14        66.41        18.41        19.00 
TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG 
       16.70       130.88       112.44        16.14        17.62        15.62 
TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IM 
        1.81        10.59       123.85        87.32         2.20         7.82 
TCGA-DK-A3IQ TCGA-DK-A3IU TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X2 
       17.72        23.21        20.81        10.55       140.81        17.98 
TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B5 TCGA-DK-A6B6 
       64.18        41.56        76.60        67.36        41.06        30.67 
TCGA-DK-AA6L TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6W TCGA-DK-AA71 
       38.24        15.02        13.58        12.36         8.65        13.64 
TCGA-DK-AA74 TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 
       43.50        12.03        10.62        15.35        38.83        24.66 
TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF 
        0.10         2.24        16.70        17.39         0.56         0.66 
TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW 
       14.56        13.97        14.33         0.92         1.22        13.68 
TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A8O7 TCGA-E7-A97P TCGA-FD-A3B3 TCGA-FD-A3B4 
       14.07        12.95        15.32        14.37        32.02        16.77 
TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 
        8.94        33.04         4.01        12.62        22.52        27.98 
TCGA-FD-A3NA TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP 
       60.66        23.41        17.98        29.16         5.52        25.74 
TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S 
       46.78        19.79        12.85        22.98        27.35        14.96 
TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT 
       20.91         3.62        15.58        26.73        53.88        11.01 
TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 
       19.33         5.36         5.69        27.45        18.08        58.92 
TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB 
        2.70         7.10         6.28        13.35        62.86        18.81 
TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TH TCGA-FD-A6TK TCGA-FJ-A3Z7 
        6.15        12.69        12.36         4.31        10.85        31.07 
TCGA-FJ-A3Z9 TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ 
        7.13        17.23         8.94         6.48        61.94        30.61 
TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY 
       15.95        26.93        33.01         7.23        20.12        17.62 
TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC 
        6.94        64.44        19.46        15.81         4.50        15.91 
TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GC-A6I3 
       14.07        17.75        24.92         0.49         8.94        13.91 
TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42P 
        7.73         2.10         3.12        20.98         2.20        10.92 
TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 
       11.31        11.31        27.09        20.05         5.62         4.73 
TCGA-GU-AATO TCGA-GU-AATQ TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF 
       10.65         7.00        21.34        19.10        19.82        20.28 
TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA 
        8.48        10.59        27.35         8.58        19.07        22.72 
TCGA-H4-A2HO TCGA-HQ-A2OE TCGA-HQ-A5NE TCGA-K4-A3WV TCGA-K4-A4AC TCGA-K4-A54R 
        1.51        38.60         8.22        21.24         9.14        27.68 
TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-AAQO 
        9.07        11.70         1.74         1.81        15.42        11.80 
TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-S5-AA26 
       15.58        21.07        13.48        12.23        16.67         3.75 
TCGA-SY-A9G0 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A78P 
       12.43        17.62        37.05        86.83        76.01        67.79 
TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A8OD TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD 
       65.75         3.58       112.83        35.24        29.56        17.82 
TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HE 
        4.54         1.64        45.04         6.58        97.45       125.49 
TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH 
       97.12        15.35         1.87        17.88        48.62        64.80 
TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY 
       79.66        66.41        12.76        11.90        23.64        21.04 
TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T4 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME 
       26.27        18.90        16.27         2.10        13.74        92.98 
TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAMQ TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMY 
       11.31        54.90        71.57         2.96         8.32        98.99 
TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 
       56.48        30.94        61.45        86.30        27.06        75.39 
TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L 
       18.81         3.88        18.84         9.63         0.66        11.97 
TCGA-YF-AA3M TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 
       13.64         7.36        24.13        30.28        27.19        21.86 
TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL 
       28.41        74.56         3.48        52.73        52.60        82.49 
TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4U 
       47.84        20.22         2.89        34.06        19.69         8.61 
TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 
       63.02        38.73        35.41        57.90        19.40         8.52 
TCGA-ZF-AA58 TCGA-ZF-AA5N TCGA-ZF-AA5P 
       47.15         5.52        10.13 

  16P GAIN MUTATED 16P GAIN WILD-TYPE 
              0.49               0.10 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
            166.03             140.81 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
             13.20              16.27 
[1] "0.5 - 166.0 (13.2)" "0.1 - 140.8 (16.3)"
[1] "hr=" "1.2"
D28V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  16P GAIN MUTATED         1       14        23       30
  16P GAIN WILD-TYPE       3      110       104       99
D28V3, multiclass
           clus
vv          16P GAIN MUTATED 16P GAIN WILD-TYPE
  STAGE I                  1                  3
  STAGE II                14                110
  STAGE III               23                104
  STAGE IV                30                 99
[1] 4 2
[1] TRUE
[1] "dimension of contingency 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         15  30  17
  16P GAIN WILD-TYPE      106 154  36
D28V4, multiclass
          clus
vv         16P GAIN MUTATED 16P GAIN WILD-TYPE
  T0+T1+T2               15                106
  T3                     30                154
  T4                     17                 36
[1] 3 2
[1] TRUE
[1] "dimension of 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    34   8  18   3
  16P GAIN WILD-TYPE 190  34  57   5
D28V5, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  N0               34                190
  N1                8                 34
  N2               18                 57
  N3                3                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V6, binary
                    cls
clus                   0   1
  16P GAIN MUTATED    33   4
  16P GAIN WILD-TYPE 152   6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     33    4
  16P GAIN WILD-TYPE  152    6
   clus
vv  16P GAIN MUTATED 16P GAIN WILD-TYPE
  0               33                152
  1                4                  6
[1] 2 2
[1] FALSE
D28V7, binary
                    cls
clus                   0   1
  16P GAIN MUTATED    21  47
  16P GAIN WILD-TYPE  80 241
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     21   47
  16P GAIN WILD-TYPE   80  241
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  FEMALE               21                 80
  MALE                 47                241
[1] 2 2
[1] FALSE
D28V8, continuous
D28V9, continuous
D28V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16P GAIN MUTATED       4                         4    57
  16P GAIN WILD-TYPE    38                        17   254
D28V11, multiclass
                           clus
vv                          16P GAIN MUTATED 16P GAIN WILD-TYPE
  ASIAN                                    4                 38
  BLACK OR AFRICAN AMERICAN                4                 17
  WHITE                                   57                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"
D28V12, binary
                    cls
clus                   0   1
  16P GAIN MUTATED     1  61
  16P GAIN WILD-TYPE   8 291
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      1   61
  16P GAIN WILD-TYPE    8  291
                        clus
vv                       16P GAIN MUTATED 16P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  8
  NOT HISPANIC OR LATINO               61                291
[1] 2 2
[1] FALSE

Clustering(29) Variable = 16Q GAIN MUTATION ANALYSIS
D29V1, survival
                    sevent
clus2                  0   1
  16Q GAIN MUTATED    46  31
  16Q GAIN WILD-TYPE 184 122
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                77                306 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                31                122 
$`16Q GAIN MUTATED`
TCGA-4Z-AA7W TCGA-4Z-AA80 TCGA-4Z-AA87 TCGA-BT-A0S7 TCGA-BT-A20R TCGA-BT-A20V 
       27.62         0.62        47.80         6.58         5.06         5.06 
TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A3PJ TCGA-BT-A42C TCGA-C4-A0EZ TCGA-CF-A47X 
        8.25        17.16        12.82        28.70         8.98        12.62 
TCGA-DK-A2I2 TCGA-DK-A3IL TCGA-DK-A3IN TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3X1 
        7.79        13.58         8.22        50.27        21.30        48.00 
TCGA-DK-A6B2 TCGA-DK-AA6S TCGA-DK-AA6U TCGA-DK-AA6X TCGA-E5-A2PC TCGA-E7-A6ME 
       15.68       166.03        10.49         7.53        43.59        12.99 
TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A43P TCGA-FD-A43Y TCGA-FD-A5BV TCGA-FD-A5BY 
        8.09        32.02        27.35        15.58         5.36         8.25 
TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FD-A6TK 
        6.28        13.35         2.27         3.06         9.67        10.85 
TCGA-FJ-A3ZE TCGA-FT-A3EE TCGA-G2-A2EO TCGA-G2-A3VY TCGA-G2-AA3B TCGA-GC-A3BM 
       10.65         3.25        35.24        17.62        66.02        21.40 
TCGA-GC-A3I6 TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OS TCGA-GD-A76B 
        2.24        24.92         8.94         7.73        20.98         7.36 
TCGA-GU-A762 TCGA-GU-AATP TCGA-GV-A3JW TCGA-H4-A2HQ TCGA-HQ-A2OF TCGA-HQ-A5ND 
        7.63        32.98        21.34        19.40         3.06         9.01 
TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A6MB TCGA-LC-A66R TCGA-R3-A69X 
       25.02         3.45         2.76        15.42        15.32        14.24 
TCGA-S5-A6DX TCGA-SY-A9G5 TCGA-UY-A78M TCGA-UY-A9PE TCGA-XF-A9SG TCGA-XF-A9T3 
        1.84        31.56        22.68         4.54        48.62         2.24 
TCGA-XF-AAMF TCGA-XF-AAMR TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-ZF-A9R0 
       10.82        91.73         6.77        98.99        44.32        18.64 
TCGA-ZF-A9R2 TCGA-ZF-A9RD TCGA-ZF-AA4W TCGA-ZF-AA54 TCGA-ZF-AA5H 
       21.11        13.41        60.16        19.40        19.17 

$`16Q GAIN WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        91.63       103.50       105.70         8.35 
TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S 
       16.27        44.94        16.83        16.77        17.16        34.98 
TCGA-4Z-AA7Y TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA84 TCGA-4Z-AA86 
       49.12        41.75        51.16        66.54        15.12        10.22 
TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ 
       33.83        40.08         7.33         2.66         6.74        12.39 
TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q 
       13.15        19.04        32.84        12.16        17.88        19.50 
TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20W TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH 
       14.89        14.96         8.35        16.18        20.48         4.67 
TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F6 
        9.96        17.56        24.26        28.41         1.94        23.01 
TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V 
        0.46         0.43         0.69        10.95        12.66        12.46 
TCGA-CF-A47W TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A8HX 
       12.10        12.26        13.12        12.00        12.10        11.34 
TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR 
       11.34        11.87        13.08        12.92         4.90         7.20 
TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 
        5.46         5.19        16.31         1.84        13.58        21.86 
TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC 
        2.14        66.41        18.41        19.00        16.70       130.88 
TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 
      112.44        16.14        17.62        15.62         1.81        10.59 
TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IM TCGA-DK-A3IQ TCGA-DK-A3IU 
      123.85        87.32         2.20         7.82        17.72        23.21 
TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X2 TCGA-DK-A6AV 
        9.67        20.81        10.55       140.81        17.98        64.18 
TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L 
       41.56        76.60        67.36        41.06        30.67        38.24 
TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA74 
       15.02        13.58        12.36         8.65        13.64        43.50 
TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 
       12.03        10.62        15.35        38.83        24.66         0.10 
TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF 
        0.49         2.24        16.70        17.39         0.56         0.66 
TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW 
       14.56        13.97        14.33         0.92         1.22        13.68 
TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A8O7 TCGA-E7-A97P TCGA-FD-A3B4 TCGA-FD-A3B5 
       14.07        12.95        15.32        14.37        16.77         8.94 
TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA 
       33.04         4.01        12.62        22.52        27.98        60.66 
TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP 
       24.30        23.41        17.98        29.16         5.52        25.74 
TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43U 
       46.78        19.79        12.85        22.98        14.96        20.91 
TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BX 
        3.62        26.73        53.88        11.01        19.33         5.69 
TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A6TA 
       27.45        18.08        58.92         2.70         7.10        62.86 
TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TH TCGA-FJ-A3Z7 
       18.81         6.15        12.69        12.36         4.31        31.07 
TCGA-FJ-A3Z9 TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ 
        7.13        17.23         8.94         6.48        61.94        30.61 
TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3C 
       15.95        26.93        33.01         7.23        20.12         6.94 
TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD 
       64.44        19.46        15.81         4.50        15.91        14.07 
TCGA-GC-A3WC TCGA-GC-A4ZW TCGA-GC-A6I3 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A6C6 
       17.75         0.49        13.91         2.10         3.12         2.20 
TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 
       10.92        11.31        11.31        27.09        20.05         5.62 
TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JX TCGA-GV-A3JZ 
        4.73        10.65         7.00        14.27        19.10        19.82 
TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G 
       20.28         8.48        10.59        27.35         8.58        19.07 
TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-HQ-A2OE TCGA-HQ-A5NE TCGA-K4-A3WV TCGA-K4-A4AC 
       22.72         1.51        38.60         8.22        21.24         9.14 
TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A83P 
       27.68         9.07        11.70         1.74         1.81         6.38 
TCGA-K4-AAQO TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN 
       11.80        15.58        21.07        13.48        12.23        16.67 
TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78N TCGA-UY-A78O 
        3.75        12.43        17.62        37.05        86.83        76.01 
TCGA-UY-A78P TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A8OD TCGA-UY-A9PA TCGA-UY-A9PB 
       67.79        65.75         3.58       112.83        35.24        29.56 
TCGA-UY-A9PD TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HE 
       17.82         1.64        45.04         6.58        97.45       125.49 
TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SI 
       97.12        15.35         1.87        17.88        64.80        79.66 
TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY 
        3.22        66.41        12.76        11.90        23.64        21.04 
TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 
       28.24        26.27        18.90        16.27        66.64         2.10 
TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML 
       13.74        92.98       110.60        11.31        54.90         7.63 
TCGA-XF-AAMQ TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN2 
       71.57         2.96         8.32        56.48        30.94        61.45 
TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A89H 
       86.30        27.06        75.39        18.81         3.88        18.84 
TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R1 TCGA-ZF-A9R3 
        9.63         0.66        11.97        13.64         7.36        24.13 
TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RE 
       30.28        27.19        21.86        28.41        74.56         3.48 
TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N 
       52.73        52.60        82.49        47.84        20.22         2.89 
TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4X TCGA-ZF-AA51 
       34.06        19.69         8.61        59.38        63.02        38.73 
TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5N TCGA-ZF-AA5P 
       35.41        57.90         8.52        47.15         5.52        10.13 

  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
              0.62               0.10 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
            166.03             140.81 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
             13.41              16.27 
[1] "0.6 - 166.0 (13.4)" "0.1 - 140.8 (16.3)"
[1] "hr=" "1.2"
D29V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  16Q GAIN MUTATED         1       18        29       29
  16Q GAIN WILD-TYPE       3      106        98      100
D29V3, multiclass
           clus
vv          16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  STAGE I                  1                  3
  STAGE II                18                106
  STAGE III               29                 98
  STAGE IV                29                100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1+T2  T3  T4
  16Q GAIN MUTATED         18  36  16
  16Q GAIN WILD-TYPE      103 148  37
D29V4, multiclass
          clus
vv         16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  T0+T1+T2               18                103
  T3                     36                148
  T4                     16                 37
[1] 3 2
[1] TRUE
[1] "dimension of 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    41   8  17   4
  16Q GAIN WILD-TYPE 183  34  58   4
D29V5, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  N0               41                183
  N1                8                 34
  N2               17                 58
  N3                4                  4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V6, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED    32   4
  16Q GAIN WILD-TYPE 153   6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     32    4
  16Q GAIN WILD-TYPE  153    6
   clus
vv  16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  0               32                153
  1                4                  6
[1] 2 2
[1] FALSE
D29V7, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED    27  50
  16Q GAIN WILD-TYPE  74 238
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     27   50
  16Q GAIN WILD-TYPE   74  238
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  FEMALE               27                 74
  MALE                 50                238
[1] 2 2
[1] FALSE
D29V8, continuous
D29V9, continuous
D29V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16Q GAIN MUTATED       4                         6    63
  16Q GAIN WILD-TYPE    38                        15   248
D29V11, multiclass
                           clus
vv                          16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  ASIAN                                    4                 38
  BLACK OR AFRICAN AMERICAN                6                 15
  WHITE                                   63                248
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V12, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED     1  70
  16Q GAIN WILD-TYPE   8 282
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      1   70
  16Q GAIN WILD-TYPE    8  282
                        clus
vv                       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  8
  NOT HISPANIC OR LATINO               70                282
[1] 2 2
[1] FALSE

Clustering(30) Variable = 17P GAIN MUTATION ANALYSIS
D30V1, survival
                    sevent
clus2                  0   1
  17P GAIN MUTATED    30  26
  17P GAIN WILD-TYPE 200 127
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                56                327 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                26                127 
$`17P GAIN MUTATED`
TCGA-2F-A9KP TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-4Z-AA87 
       11.97         0.62        41.75        15.12        10.22        47.80 
TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20W TCGA-BT-A2LD 
        6.74         6.58         5.06        14.96         8.35        20.48 
TCGA-BT-A3PJ TCGA-BT-A42C TCGA-C4-A0EZ TCGA-CF-A8HY TCGA-CU-A0YR TCGA-DK-A3IM 
       12.82        28.70         8.98        11.34         7.20         7.82 
TCGA-DK-A6B1 TCGA-DK-A6B6 TCGA-DK-AA6P TCGA-FD-A3B7 TCGA-FD-A3SP TCGA-FD-A5BT 
       67.36        30.67        15.02         4.01        25.74        11.01 
TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TH TCGA-FJ-A3Z7 TCGA-FT-A3EE TCGA-G2-AA3F 
       12.36         2.27         4.31        31.07         3.25        19.46 
TCGA-GD-A2C5 TCGA-GD-A76B TCGA-GV-A3JV TCGA-GV-A3QH TCGA-GV-A40E TCGA-HQ-A2OE 
        7.73         7.36        14.27         8.48         8.58        38.60 
TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A6FZ TCGA-LC-A66R TCGA-MV-A51V TCGA-UY-A78N 
        3.45        21.24         1.81        15.32        13.48        86.83 
TCGA-UY-A8OB TCGA-UY-A9PB TCGA-XF-A8HI TCGA-XF-A9T0 TCGA-XF-A9T8 TCGA-XF-AAML 
       65.75        29.56        17.88        26.27        13.74         7.63 
TCGA-XF-AAMQ TCGA-ZF-A9R4 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-AA4V TCGA-ZF-AA4X 
       71.57        30.28        74.56        13.41        59.38        63.02 
TCGA-ZF-AA52 TCGA-ZF-AA5H 
       35.41        19.17 

$`17P GAIN WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW TCGA-4Z-AA7M 
       22.29        91.63       103.50       105.70         8.35        16.27 
TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W 
       44.94        16.83        16.77        17.16        34.98        27.62 
TCGA-4Z-AA7Y TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I 
       49.12        51.16        66.54        33.83        40.08         7.33 
TCGA-BL-A13J TCGA-BL-A5ZZ TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O 
        2.66        12.39        13.15        19.04        32.84        12.16 
TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20T TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA 
       17.88        19.50        14.89         5.06         8.25        17.16 
TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F 
       16.18         4.67         9.96        17.56        24.26        28.41 
TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S 
        1.94        23.01         0.46         0.43         0.69        10.95 
TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 
       12.66        12.46        12.10        12.62        12.26        13.12 
TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YN 
       12.00        12.10        11.34        11.87        13.08        12.92 
TCGA-CU-A0YO TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E 
        4.90         5.46         5.19        16.31         1.84        13.58 
TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB 
       21.86         2.14        66.41        18.41        19.00        16.70 
TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX 
      130.88       112.44        16.14        17.62        15.62         1.81 
TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL 
       10.59         7.79       123.85        87.32         2.20        13.58 
TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV 
        8.22        17.72        50.27        21.30        23.21         9.67 
TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV 
       20.81        10.55       140.81        48.00        17.98        64.18 
TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-AA6L TCGA-DK-AA6Q 
       41.56        76.60        15.68        41.06        38.24        13.58 
TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 
      166.03        12.36        10.49         8.65         7.53        13.64 
TCGA-DK-AA74 TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 
       43.50        12.03        10.62        43.59        15.35        38.83 
TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 
       24.66         0.10         0.49         2.24        16.70        17.39 
TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF 
        0.56         0.66        14.56        13.97        12.99        14.33 
TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A8O7 
        0.92         1.22        13.68        14.07        12.95        15.32 
TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 
       14.37         8.09        32.02        16.77         8.94        33.04 
TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL 
       12.62        22.52        27.98        60.66        24.30        23.41 
TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS 
       17.98        29.16         5.52        46.78        19.79        12.85 
TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A43Y 
       22.98        27.35        14.96        20.91         3.62        15.58 
TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY 
       26.73        53.88        19.33         5.36         5.69         8.25 
TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P 
       27.45        18.08        58.92         2.70         7.10         6.28 
TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TG 
       13.35        62.86        18.81         6.15        12.69         3.06 
TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FJ-A871 
        9.67        10.85         7.13        10.65        17.23         8.94 
TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO 
        6.48        61.94        30.61        15.95        26.93        35.24 
TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C 
       33.01         7.23        20.12        17.62        66.02         6.94 
TCGA-G2-AA3D TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC 
       64.44        21.40         2.24        15.81         4.50        15.91 
TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GC-A6I3 
       14.07        17.75        24.92         0.49         8.94        13.91 
TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42P TCGA-GU-A42Q 
        2.10         3.12        20.98         2.20        10.92        11.31 
TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 
       11.31         7.63        27.09        20.05         5.62         4.73 
TCGA-GU-AATO TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ 
       10.65        32.98         7.00        21.34        19.10        19.82 
TCGA-GV-A3QF TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO 
       20.28        10.59        27.35        19.07        22.72         1.51 
TCGA-H4-A2HQ TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A4AB 
       19.40         3.06         9.01         8.22        25.02         2.76 
TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6MB 
        9.14        27.68         9.07        11.70         1.74        15.42 
TCGA-K4-A83P TCGA-K4-AAQO TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-PQ-A6FI TCGA-PQ-A6FN 
        6.38        11.80        15.58        21.07        12.23        16.67 
TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78K 
       14.24         1.84         3.75        12.43        31.56        17.62 
TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OC TCGA-UY-A8OD 
       37.05        22.68        76.01        67.79         3.58       112.83 
TCGA-UY-A9PA TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HC 
       35.24        17.82         4.54         1.64        45.04         6.58 
TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A9SG 
       97.45       125.49        97.12        15.35         1.87        48.62 
TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SW 
       64.80        79.66         3.22        66.41        12.76        11.90 
TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 
       23.64        21.04        28.24        18.90         2.24        16.27 
TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAMH 
       66.64         2.10        92.98        10.82       110.60        11.31 
TCGA-XF-AAMJ TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMY 
       54.90        91.73         2.96         8.32         6.77        98.99 
TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN4 
       44.32        56.48        30.94        61.45        86.30        27.06 
TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC 
       75.39        18.81         3.88        18.84         9.63         0.66 
TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 
       11.97        13.64        18.64         7.36        21.11        24.13 
TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG 
       27.19        21.86        28.41         3.48        52.73        52.60 
TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4T 
       82.49        47.84        20.22         2.89        34.06        19.69 
TCGA-ZF-AA4U TCGA-ZF-AA4W TCGA-ZF-AA51 TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 
        8.61        60.16        38.73        57.90        19.40         8.52 
TCGA-ZF-AA58 TCGA-ZF-AA5N TCGA-ZF-AA5P 
       47.15         5.52        10.13 

  17P GAIN MUTATED 17P GAIN WILD-TYPE 
              0.62               0.10 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
             86.83             166.03 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
            14.005             16.180 
[1] "0.6 - 86.8 (14.0)"  "0.1 - 166.0 (16.2)"
[1] "hr=" "1.3"
D30V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  17P GAIN MUTATED         0       16        20       20
  17P GAIN WILD-TYPE       4      108       107      109
D30V3, multiclass
           clus
vv          17P GAIN MUTATED 17P GAIN WILD-TYPE
  STAGE I                  0                  4
  STAGE II                16                108
  STAGE III               20                107
  STAGE IV                20                109
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1+T2  T3  T4
  17P GAIN MUTATED         15  31   6
  17P GAIN WILD-TYPE      106 153  47
D30V4, multiclass
          clus
vv         17P GAIN MUTATED 17P GAIN WILD-TYPE
  T0+T1+T2               15                106
  T3                     31                153
  T4                      6                 47
[1] 3 2
[1] TRUE
[1] "dimension of 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    29   8  13   1
  17P GAIN WILD-TYPE 195  34  62   7
D30V5, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  N0               29                195
  N1                8                 34
  N2               13                 62
  N3                1                  7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V6, binary
                    cls
clus                   0   1
  17P GAIN MUTATED    23   3
  17P GAIN WILD-TYPE 162   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED     23    3
  17P GAIN WILD-TYPE  162    7
   clus
vv  17P GAIN MUTATED 17P GAIN WILD-TYPE
  0               23                162
  1                3                  7
[1] 2 2
[1] FALSE
D30V7, binary
                    cls
clus                   0   1
  17P GAIN MUTATED    15  42
  17P GAIN WILD-TYPE  86 246
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED     15   42
  17P GAIN WILD-TYPE   86  246
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  FEMALE               15                 86
  MALE                 42                246
[1] 2 2
[1] FALSE
D30V8, continuous
D30V9, continuous
D30V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  17P GAIN MUTATED       2                         3    50
  17P GAIN WILD-TYPE    40                        18   261
D30V11, multiclass
                           clus
vv                          17P GAIN MUTATED 17P GAIN WILD-TYPE
  ASIAN                                    2                 40
  BLACK OR AFRICAN AMERICAN                3                 18
  WHITE                                   50                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"
D30V12, binary
                    cls
clus                   0   1
  17P GAIN MUTATED     2  48
  17P GAIN WILD-TYPE   7 304
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      2   48
  17P GAIN WILD-TYPE    7  304
                        clus
vv                       17P GAIN MUTATED 17P GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  7
  NOT HISPANIC OR LATINO               48                304
[1] 2 2
[1] FALSE

Clustering(31) Variable = 17Q GAIN MUTATION ANALYSIS
D31V1, survival
                    sevent
clus2                  0   1
  17Q GAIN MUTATED    72  56
  17Q GAIN WILD-TYPE 158  97
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
               128                255 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                56                 97 
$`17Q GAIN MUTATED`
TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-BL-A3JM 
        0.62        41.75        15.12        10.22        47.80         6.74 
TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A20O TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T 
       12.39         6.58        12.16        19.50         5.06        14.89 
TCGA-BT-A20U TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LD TCGA-BT-A42C TCGA-C4-A0EZ 
       14.96         8.35         8.25        20.48        28.70         8.98 
TCGA-CF-A47X TCGA-CF-A8HY TCGA-CU-A0YR TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A6 
       12.62        11.34         7.20        16.31         1.84        66.41 
TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A2I2 TCGA-DK-A3IM TCGA-DK-A3IS TCGA-DK-A3WX 
       18.41       112.44         7.79         7.82        50.27        10.55 
TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6B1 TCGA-DK-A6B6 TCGA-DK-AA6P TCGA-DK-AA6U 
       48.00        17.98        67.36        30.67        15.02        10.49 
TCGA-DK-AA6X TCGA-DK-AA71 TCGA-E5-A2PC TCGA-E7-A4IJ TCGA-E7-A541 TCGA-E7-A5KE 
        7.53        13.64        43.59         0.49        17.39         0.56 
TCGA-E7-A677 TCGA-E7-A6ME TCGA-E7-A7PW TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 
       14.56        12.99        13.68         8.94        33.04         4.01 
TCGA-FD-A3SJ TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A5BR TCGA-FD-A5BV TCGA-FD-A5C1 
       24.30        25.74        46.78        26.73         5.36        58.92 
TCGA-FD-A62O TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TH 
        7.10        62.86        18.81        12.36         2.27         4.31 
TCGA-FJ-A3Z7 TCGA-FT-A3EE TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GD-A2C5 
       31.07         3.25        64.44        19.46        21.40         7.73 
TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42R TCGA-GU-AATO TCGA-GU-AATP TCGA-GV-A3JV 
        7.36        10.92        11.31        10.65        32.98        14.27 
TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G 
       19.82        20.28         8.48        27.35         8.58        19.07 
TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WU TCGA-K4-A3WV 
       19.40        38.60         9.01         8.22         3.45        21.24 
TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A6FZ TCGA-K4-AAQO TCGA-LC-A66R TCGA-MV-A51V 
        9.07        11.70         1.81        11.80        15.32        13.48 
TCGA-R3-A69X TCGA-S5-A6DX TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A78O 
       14.24         1.84        37.05        22.68        86.83        76.01 
TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A9PB TCGA-XF-A8HD TCGA-XF-A8HF TCGA-XF-A8HG 
       65.75         3.58        29.56        97.45        97.12        15.35 
TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SJ TCGA-XF-A9T0 TCGA-XF-A9T8 
        1.87        17.88        48.62         3.22        26.27        13.74 
TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMT 
      110.60        11.31         7.63        71.57        91.73         2.96 
TCGA-XF-AAMW TCGA-XF-AAN0 TCGA-XF-AAN3 TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R4 
        8.32        56.48        86.30        11.97        13.64        30.28 
TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-AA4V TCGA-ZF-AA4X TCGA-ZF-AA52 
       28.41        74.56        13.41        59.38        63.02        35.41 
TCGA-ZF-AA56 TCGA-ZF-AA5H 
        8.52        19.17 

$`17Q GAIN WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        91.63       103.50       105.70         8.35 
TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S 
       16.27        44.94        16.83        16.77        17.16        34.98 
TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA89 TCGA-BL-A0C8 
       27.62        49.12        51.16        66.54        33.83        40.08 
TCGA-BL-A13I TCGA-BL-A13J TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20P 
        7.33         2.66        13.15        19.04        32.84        17.88 
TCGA-BT-A20V TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK 
        5.06        17.16        16.18         4.67        12.82         9.96 
TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR 
       17.56        24.26        28.41         1.94        23.01         0.46 
TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W 
        0.43         0.69        10.95        12.66        12.46        12.10 
TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A9FF 
       12.26        13.12        12.00        12.10        11.34        11.87 
TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A72E 
       13.08        12.92         4.90         5.46         5.19        13.58 
TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AE 
       21.86         2.14        19.00        16.70       130.88        16.14 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I4 TCGA-DK-A2I6 
       17.62        15.62         1.81        10.59       123.85        87.32 
TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3IU 
        2.20        13.58         8.22        17.72        21.30        23.21 
TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WY TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 
        9.67        20.81       140.81        64.18        41.56        76.60 
TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-AA6L TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6T 
       15.68        41.06        38.24        13.58       166.03        12.36 
TCGA-DK-AA6W TCGA-DK-AA74 TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E5-A4U1 
        8.65        43.50        12.03        10.62        15.35        38.83 
TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KF TCGA-E7-A678 
       24.66         0.10         2.24        16.70         0.66        13.97 
TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A8O7 
       14.33         0.92         1.22        14.07        12.95        15.32 
TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B8 TCGA-FD-A3N5 
       14.37         8.09        32.02        16.77        12.62        22.52 
TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO 
       27.98        60.66        23.41        17.98        29.16         5.52 
TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U 
       19.79        12.85        22.98        27.35        14.96        20.91 
TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BX 
        3.62        15.58        53.88        11.01        19.33         5.69 
TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A62N TCGA-FD-A62P TCGA-FD-A62S 
        8.25        27.45        18.08         2.70         6.28        13.35 
TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z9 
        6.15        12.69         3.06         9.67        10.85         7.13 
TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ 
       10.65        17.23         8.94         6.48        61.94        30.61 
TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE 
       15.95        26.93        35.24        33.01         7.23        20.12 
TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB 
       17.62        66.02         6.94         2.24        15.81         4.50 
TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A4ZW TCGA-GC-A6I1 
       15.91        14.07        17.75        24.92         0.49         8.94 
TCGA-GC-A6I3 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42Q 
       13.91         2.10         3.12        20.98         2.20        11.31 
TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATQ 
        7.63        27.09        20.05         5.62         4.73         7.00 
TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QI TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-HQ-A2OF 
       21.34        19.10        10.59        22.72         1.51         3.06 
TCGA-K4-A3WS TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6MB 
       25.02         2.76         9.14        27.68         1.74        15.42 
TCGA-K4-A83P TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-S5-AA26 
        6.38        15.58        21.07        12.23        16.67         3.75 
TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78P TCGA-UY-A8OD TCGA-UY-A9PA 
       12.43        31.56        17.62        67.79       112.83        35.24 
TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HE 
       17.82         4.54         1.64        45.04         6.58       125.49 
TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX 
       64.80        79.66        66.41        12.76        11.90        23.64 
TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 
       21.04        28.24        18.90         2.24        16.27        66.64 
TCGA-XF-A9T6 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMJ TCGA-XF-AAMX TCGA-XF-AAMY 
        2.10        92.98        10.82        54.90         6.77        98.99 
TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 
       44.32        30.94        61.45        27.06        75.39        18.81 
TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-ZF-A9R0 TCGA-ZF-A9R1 
        3.88        18.84         9.63         0.66        18.64         7.36 
TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9RE TCGA-ZF-A9RF 
       21.11        24.13        27.19        21.86         3.48        52.73 
TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4R 
       52.60        82.49        47.84        20.22         2.89        34.06 
TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4W TCGA-ZF-AA51 TCGA-ZF-AA53 TCGA-ZF-AA54 
       19.69         8.61        60.16        38.73        57.90        19.40 
TCGA-ZF-AA58 TCGA-ZF-AA5N TCGA-ZF-AA5P 
       47.15         5.52        10.13 

  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
              0.49               0.10 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
            112.44             166.03 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
            14.925             16.180 
[1] "0.5 - 112.4 (14.9)" "0.1 - 166.0 (16.2)"
[1] "hr=" "1.1"
D31V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  17Q GAIN MUTATED         1       35        39       55
  17Q GAIN WILD-TYPE       3       89        88       74
D31V3, multiclass
           clus
vv          17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  STAGE I                  1                  3
  STAGE II                35                 89
  STAGE III               39                 88
  STAGE IV                55                 74
[1] 4 2
[1] TRUE
[1] "dimension of contingency 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         40  63  19
  17Q GAIN WILD-TYPE       81 121  34
D31V4, multiclass
          clus
vv         17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  T0+T1+T2               40                 81
  T3                     63                121
  T4                     19                 34
[1] 3 2
[1] TRUE
[1] "dimension of 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    66  17  35   2
  17Q GAIN WILD-TYPE 158  25  40   6
D31V5, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  N0               66                158
  N1               17                 25
  N2               35                 40
  N3                2                  6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V6, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED    56   4
  17Q GAIN WILD-TYPE 129   6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     56    4
  17Q GAIN WILD-TYPE  129    6
   clus
vv  17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  0               56                129
  1                4                  6
[1] 2 2
[1] FALSE
D31V7, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED    34  97
  17Q GAIN WILD-TYPE  67 191
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     34   97
  17Q GAIN WILD-TYPE   67  191
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  FEMALE               34                 67
  MALE                 97                191
[1] 2 2
[1] FALSE
D31V8, continuous
D31V9, continuous
D31V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  17Q GAIN MUTATED      11                         5   108
  17Q GAIN WILD-TYPE    31                        16   203
D31V11, multiclass
                           clus
vv                          17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  ASIAN                                   11                 31
  BLACK OR AFRICAN AMERICAN                5                 16
  WHITE                                  108                203
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V12, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED     6 114
  17Q GAIN WILD-TYPE   3 238
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      6  114
  17Q GAIN WILD-TYPE    3  238
                        clus
vv                       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    6                  3
  NOT HISPANIC OR LATINO              114                238
[1] 2 2
[1] FALSE

Clustering(32) Variable = 18P GAIN MUTATION ANALYSIS
D32V1, survival
                    sevent
clus2                  0   1
  18P GAIN MUTATED    65  43
  18P GAIN WILD-TYPE 165 110
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
               108                275 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                43                110 
$`18P GAIN MUTATED`
TCGA-4Z-AA7R TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA84 TCGA-BL-A3JM TCGA-BT-A20V 
       17.16         0.62        41.75        15.12         6.74         5.06 
TCGA-BT-A20W TCGA-BT-A2LB TCGA-BT-A42C TCGA-BT-A42E TCGA-C4-A0EZ TCGA-C4-A0F0 
        8.35        16.18        28.70        24.26         8.98         1.94 
TCGA-CF-A1HS TCGA-CU-A0YN TCGA-CU-A3KJ TCGA-DK-A2I2 TCGA-DK-A2I6 TCGA-DK-A3IM 
        0.43        12.92         5.46         7.79        87.32         7.82 
TCGA-DK-A3IN TCGA-DK-A3X1 TCGA-DK-A6B6 TCGA-DK-AA6W TCGA-E5-A4TZ TCGA-E7-A6ME 
        8.22        48.00        30.67         8.65        15.35        12.99 
TCGA-E7-A7PW TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3N5 TCGA-FD-A3NA TCGA-FD-A3SR 
       13.68         8.94        33.04        22.52        60.66        19.79 
TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BT TCGA-FD-A5BV 
       12.85        27.35        15.58        26.73        11.01         5.36 
TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A6TE TCGA-FD-A6TF 
        8.25        27.45        58.92         6.28        12.36         2.27 
TCGA-FD-A6TH TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EL 
        4.31        31.07        17.23         6.48        61.94        26.93 
TCGA-G2-A2EO TCGA-G2-A3VY TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3RC TCGA-GC-A4ZW 
       35.24        17.62        64.44        19.46        15.91         0.49 
TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P 
        8.94         7.73         2.10         2.20         7.36        10.92 
TCGA-GU-A42Q TCGA-GU-A762 TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JX TCGA-GV-A3JZ 
       11.31         7.63        32.98         7.00        19.10        19.82 
TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40G TCGA-H4-A2HQ TCGA-HQ-A5NE 
        8.48        10.59        27.35        19.07        19.40         8.22 
TCGA-K4-A3WV TCGA-K4-A5RH TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-AAQO TCGA-LC-A66R 
       21.24         9.07         1.74         1.81        11.80        15.32 
TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-R3-A69X TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78N 
       15.58        13.48        14.24        17.62        37.05        86.83 
TCGA-UY-A78O TCGA-UY-A9PB TCGA-XF-A8HB TCGA-XF-A8HD TCGA-XF-A8HG TCGA-XF-A9SJ 
       76.01        29.56        45.04        97.45        15.35         3.22 
TCGA-XF-A9SX TCGA-XF-A9T3 TCGA-XF-AAMG TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ 
       23.64         2.24       110.60        54.90         7.63        71.57 
TCGA-XF-AAMT TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAN0 TCGA-ZF-A9R7 TCGA-ZF-A9RF 
        2.96         6.77        98.99        56.48        21.86        52.73 
TCGA-ZF-A9RN TCGA-ZF-AA4X TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA58 TCGA-ZF-AA5H 
       20.22        63.02        35.41        57.90        47.15        19.17 

$`18P GAIN WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        91.63       103.50       105.70         8.35 
TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7S TCGA-4Z-AA7W 
       16.27        44.94        16.83        16.77        34.98        27.62 
TCGA-4Z-AA7Y TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 
       49.12        51.16        66.54        10.22        47.80        33.83 
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX 
       40.08         7.33         2.66        12.39         6.58        13.15 
TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R 
       19.04        32.84        12.16        17.88        19.50         5.06 
TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LD TCGA-BT-A3PH 
       14.89        14.96         8.25        17.16        20.48         4.67 
TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42F TCGA-C4-A0F6 TCGA-CF-A1HR 
       12.82         9.96        17.56        28.41        23.01         0.46 
TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X 
        0.69        10.95        12.66        12.46        12.10        12.62 
TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A8HY 
       12.26        13.12        12.00        12.10        11.34        11.34 
TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3QU TCGA-CU-A3YL 
       11.87        13.08         4.90         7.20         5.19        16.31 
TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 
        1.84        13.58        21.86         2.14        66.41        18.41 
TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF 
       19.00        16.70       130.88       112.44        16.14        17.62 
TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IL 
       15.62         1.81        10.59       123.85         2.20        13.58 
TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW 
       17.72        50.27        21.30        23.21         9.67        20.81 
TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 
       10.55       140.81        17.98        64.18        41.56        76.60 
TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-AA6L TCGA-DK-AA6P TCGA-DK-AA6Q 
       67.36        15.68        41.06        38.24        15.02        13.58 
TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 
      166.03        12.36        10.49         7.53        13.64        43.50 
TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 
       12.03        10.62        43.59        38.83        24.66         0.10 
TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF 
        0.49         2.24        16.70        17.39         0.56         0.66 
TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7XN 
       14.56        13.97        14.33         0.92         1.22        14.07 
TCGA-E7-A85H TCGA-E7-A8O7 TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 
       12.95        15.32        14.37         8.09        32.02        16.77 
TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N6 TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM 
        4.01        12.62        27.98        24.30        23.41        17.98 
TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A43N TCGA-FD-A43S 
       29.16         5.52        25.74        46.78        22.98        14.96 
TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BS TCGA-FD-A5BU TCGA-FD-A5BX TCGA-FD-A5C0 
       20.91         3.62        53.88        19.33         5.69        18.08 
TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC 
        2.70         7.10        13.35        62.86        18.81         6.15 
TCGA-FD-A6TD TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE 
       12.69         3.06         9.67        10.85         7.13        10.65 
TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2ES TCGA-G2-A3IB 
        8.94         3.25        30.61        15.95        33.01         7.23 
TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3C TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO 
       20.12        66.02         6.94        21.40         2.24        15.81 
TCGA-GC-A3RB TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I3 TCGA-GD-A3OQ 
        4.50        14.07        17.75        24.92        13.91         3.12 
TCGA-GD-A3OS TCGA-GU-A42R TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 
       20.98        11.31        27.09        20.05         5.62         4.73 
TCGA-GU-AATO TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3QF TCGA-GV-A40E TCGA-GV-A6ZA 
       10.65        14.27        21.34        20.28         8.58        22.72 
TCGA-H4-A2HO TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A3WU 
        1.51        38.60         3.06         9.01        25.02         3.45 
TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RI TCGA-K4-A6MB TCGA-K4-A83P 
        2.76         9.14        27.68        11.70        15.42         6.38 
TCGA-LT-A8JT TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G0 
       21.07        12.23        16.67         1.84         3.75        12.43 
TCGA-SY-A9G5 TCGA-UY-A78M TCGA-UY-A78P TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A8OD 
       31.56        22.68        67.79        65.75         3.58       112.83 
TCGA-UY-A9PA TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HC TCGA-XF-A8HE 
       35.24        17.82         4.54         1.64         6.58       125.49 
TCGA-XF-A8HF TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI 
       97.12         1.87        17.88        48.62        64.80        79.66 
TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 
       66.41        12.76        11.90        21.04        28.24        26.27 
TCGA-XF-A9T2 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME 
       18.90        16.27        66.64         2.10        13.74        92.98 
TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMR TCGA-XF-AAMW TCGA-XF-AAMZ TCGA-XF-AAN1 
       10.82        11.31        91.73         8.32        44.32        30.94 
TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-XF-AAN8 
       61.45        86.30        27.06        75.39        18.81         3.88 
TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R0 
       18.84         9.63         0.66        11.97        13.64        18.64 
TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R9 
        7.36        21.11        24.13        30.28        27.19        28.41 
TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM 
       74.56        13.41         3.48        52.60        82.49        47.84 
TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W 
        2.89        34.06        19.69         8.61        59.38        60.16 
TCGA-ZF-AA51 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA5N TCGA-ZF-AA5P 
       38.73        19.40         8.52         5.52        10.13 

  18P GAIN MUTATED 18P GAIN WILD-TYPE 
              0.43               0.10 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
            110.60             166.03 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
             15.58              15.81 
[1] "0.4 - 110.6 (15.6)" "0.1 - 166.0 (15.8)"
[1] "hr=" "1"  
D32V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  18P GAIN MUTATED         0       33        37       37
  18P GAIN WILD-TYPE       4       91        90       92
D32V3, multiclass
           clus
vv          18P GAIN MUTATED 18P GAIN WILD-TYPE
  STAGE I                  0                  4
  STAGE II                33                 91
  STAGE III               37                 90
  STAGE IV                37                 92
[1] 4 2
[1] TRUE
[1] "dimension of contingency 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         29  52  15
  18P GAIN WILD-TYPE       92 132  38
D32V4, multiclass
          clus
vv         18P GAIN MUTATED 18P GAIN WILD-TYPE
  T0+T1+T2               29                 92
  T3                     52                132
  T4                     15                 38
[1] 3 2
[1] TRUE
[1] "dimension of 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    60   8  24   3
  18P GAIN WILD-TYPE 164  34  51   5
D32V5, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  N0               60                164
  N1                8                 34
  N2               24                 51
  N3                3                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V6, binary
                    cls
clus                   0   1
  18P GAIN MUTATED    43   4
  18P GAIN WILD-TYPE 142   6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED     43    4
  18P GAIN WILD-TYPE  142    6
   clus
vv  18P GAIN MUTATED 18P GAIN WILD-TYPE
  0               43                142
  1                4                  6
[1] 2 2
[1] FALSE
D32V7, binary
                    cls
clus                   0   1
  18P GAIN MUTATED    30  78
  18P GAIN WILD-TYPE  71 210
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED     30   78
  18P GAIN WILD-TYPE   71  210
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  FEMALE               30                 71
  MALE                 78                210
[1] 2 2
[1] FALSE
D32V8, continuous
D32V9, continuous
D32V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18P GAIN MUTATED       5                         7    92
  18P GAIN WILD-TYPE    37                        14   219
D32V11, multiclass
                           clus
vv                          18P GAIN MUTATED 18P GAIN WILD-TYPE
  ASIAN                                    5                 37
  BLACK OR AFRICAN AMERICAN                7                 14
  WHITE                                   92                219
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V12, binary
                    cls
clus                   0   1
  18P GAIN MUTATED     3  98
  18P GAIN WILD-TYPE   6 254
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      3   98
  18P GAIN WILD-TYPE    6  254
                        clus
vv                       18P GAIN MUTATED 18P GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                  6
  NOT HISPANIC OR LATINO               98                254
[1] 2 2
[1] FALSE

Clustering(33) Variable = 18Q GAIN MUTATION ANALYSIS
D33V1, survival
                    sevent
clus2                  0   1
  18Q GAIN MUTATED    32  27
  18Q GAIN WILD-TYPE 198 126
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                59                324 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                27                126 
$`18Q GAIN MUTATED`
TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-BL-A3JM TCGA-BT-A20V TCGA-BT-A2LB TCGA-BT-A42E 
        0.62        41.75         6.74         5.06        16.18        24.26 
TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-DK-A1AE TCGA-DK-A2I2 TCGA-DK-A3IN TCGA-DK-A6B6 
        8.98         1.94        16.14         7.79         8.22        30.67 
TCGA-DK-AA6W TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-FD-A3B6 TCGA-FD-A3SR TCGA-FD-A43P 
        8.65        10.62        15.35        33.04        19.79        27.35 
TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A6TC TCGA-FD-A6TE 
       15.58        26.73         5.36        27.45         6.15        12.36 
TCGA-FD-A6TH TCGA-FJ-A3Z7 TCGA-FT-A61P TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-AA3D 
        4.31        31.07         6.48        26.93        35.24        64.44 
TCGA-GC-A6I1 TCGA-GD-A3OP TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-AATP 
        8.94         2.10         7.36        10.92        11.31        32.98 
TCGA-GU-AATQ TCGA-GV-A3QH TCGA-GV-A3QI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-LT-A5Z6 
        7.00         8.48        10.59         1.74         1.81        15.58 
TCGA-R3-A69X TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A9PB TCGA-XF-A8HB 
       14.24        22.68        86.83        76.01        29.56        45.04 
TCGA-XF-A8HG TCGA-XF-A9SG TCGA-XF-AAML TCGA-XF-AAMY TCGA-XF-AAN0 TCGA-ZF-A9R7 
       15.35        48.62         7.63        98.99        56.48        21.86 
TCGA-ZF-A9RF TCGA-ZF-A9RN TCGA-ZF-AA4X TCGA-ZF-AA53 TCGA-ZF-AA58 
       52.73        20.22        63.02        57.90        47.15 

$`18Q GAIN WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        91.63       103.50       105.70         8.35 
TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S 
       16.27        44.94        16.83        16.77        17.16        34.98 
TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA84 TCGA-4Z-AA86 
       27.62        49.12        51.16        66.54        15.12        10.22 
TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A5ZZ 
       47.80        33.83        40.08         7.33         2.66        12.39 
TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P 
        6.58        13.15        19.04        32.84        12.16        17.88 
TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20W TCGA-BT-A20X 
       19.50         5.06        14.89        14.96         8.35         8.25 
TCGA-BT-A2LA TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B 
       17.16        20.48         4.67        12.82         9.96        17.56 
TCGA-BT-A42C TCGA-BT-A42F TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C 
       28.70        28.41        23.01         0.46         0.43         0.69 
TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y 
       10.95        12.66        12.46        12.10        12.62        12.26 
TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A8HY TCGA-CF-A9FF 
       13.12        12.00        12.10        11.34        11.34        11.87 
TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU 
       13.08        12.92         4.90         7.20         5.46         5.19 
TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 
       16.31         1.84        13.58        21.86         2.14        66.41 
TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AF 
       18.41        19.00        16.70       130.88       112.44        17.62 
TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK 
       15.62         1.81        10.59       123.85        87.32         2.20 
TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU 
       13.58         7.82        17.72        50.27        21.30        23.21 
TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 
        9.67        20.81        10.55       140.81        48.00        17.98 
TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 
       64.18        41.56        76.60        67.36        15.68        41.06 
TCGA-DK-AA6L TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U 
       38.24        15.02        13.58       166.03        12.36        10.49 
TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E5-A4U1 
        7.53        13.64        43.50        12.03        43.59        38.83 
TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 
       24.66         0.10         0.49         2.24        16.70        17.39 
TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF 
        0.56         0.66        14.56        13.97        12.99        14.33 
TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A8O7 
        0.92         1.22        13.68        14.07        12.95        15.32 
TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B7 
       14.37         8.09        32.02        16.77         8.94         4.01 
TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL 
       12.62        22.52        27.98        60.66        24.30        23.41 
TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SS 
       17.98        29.16         5.52        25.74        46.78        12.85 
TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BS TCGA-FD-A5BT 
       22.98        14.96        20.91         3.62        53.88        11.01 
TCGA-FD-A5BU TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N 
       19.33         5.69         8.25        18.08        58.92         2.70 
TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TD 
        7.10         6.28        13.35        62.86        18.81        12.69 
TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE 
        2.27         3.06         9.67        10.85         7.13        10.65 
TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK 
       17.23         8.94         3.25        61.94        30.61        15.95 
TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C 
       33.01         7.23        20.12        17.62        66.02         6.94 
TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC 
       19.46        21.40         2.24        15.81         4.50        15.91 
TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A4ZW TCGA-GC-A6I3 TCGA-GD-A2C5 
       14.07        17.75        24.92         0.49        13.91         7.73 
TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 
        3.12        20.98         2.20        11.31         7.63        27.09 
TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO TCGA-GV-A3JV TCGA-GV-A3JW 
       20.05         5.62         4.73        10.65        14.27        21.34 
TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G 
       19.10        19.82        20.28        27.35         8.58        19.07 
TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND 
       22.72         1.51        19.40        38.60         3.06         9.01 
TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC 
        8.22        25.02         3.45        21.24         2.76         9.14 
TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO 
       27.68         9.07        11.70        15.42         6.38        11.80 
TCGA-LC-A66R TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-S5-A6DX 
       15.32        21.07        13.48        12.23        16.67         1.84 
TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78P 
        3.75        12.43        31.56        17.62        37.05        67.79 
TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A8OD TCGA-UY-A9PA TCGA-UY-A9PD TCGA-UY-A9PE 
       65.75         3.58       112.83        35.24        17.82         4.54 
TCGA-UY-A9PF TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HH 
        1.64         6.58        97.45       125.49        97.12         1.87 
TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SV 
       17.88        64.80        79.66         3.22        66.41        12.76 
TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 
       11.90        23.64        21.04        28.24        26.27        18.90 
TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME 
        2.24        16.27        66.64         2.10        13.74        92.98 
TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAMQ TCGA-XF-AAMR 
       10.82       110.60        11.31        54.90        71.57        91.73 
TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN2 
        2.96         8.32         6.77        44.32        30.94        61.45 
TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A89H 
       86.30        27.06        75.39        18.81         3.88        18.84 
TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R1 
        9.63         0.66        11.97        13.64        18.64         7.36 
TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R9 TCGA-ZF-A9RC 
       21.11        24.13        30.28        27.19        28.41        74.56 
TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-AA4N 
       13.41         3.48        52.60        82.49        47.84         2.89 
TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA51 
       34.06        19.69         8.61        59.38        60.16        38.73 
TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
       35.41        19.40         8.52        19.17         5.52        10.13 

  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
              0.62               0.10 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             98.99             166.03 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
            15.580             15.745 
[1] "0.6 - 99.0 (15.6)"  "0.1 - 166.0 (15.7)"
[1] "hr=" "1.2"
D33V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  18Q GAIN MUTATED         0       23        18       18
  18Q GAIN WILD-TYPE       4      101       109      111
D33V3, multiclass
           clus
vv          18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  STAGE I                  0                  4
  STAGE II                23                101
  STAGE III               18                109
  STAGE IV                18                111
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1+T2  T3  T4
  18Q GAIN MUTATED         21  24   9
  18Q GAIN WILD-TYPE      100 160  44
D33V4, multiclass
          clus
vv         18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  T0+T1+T2               21                100
  T3                     24                160
  T4                      9                 44
[1] 3 2
[1] TRUE
[1] "dimension of 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    33   4  13   1
  18Q GAIN WILD-TYPE 191  38  62   7
D33V5, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  N0               33                191
  N1                4                 38
  N2               13                 62
  N3                1                  7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V6, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED    24   1
  18Q GAIN WILD-TYPE 161   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED     24    1
  18Q GAIN WILD-TYPE  161    9
   clus
vv  18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  0               24                161
  1                1                  9
[1] 2 2
[1] FALSE
D33V7, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED    17  42
  18Q GAIN WILD-TYPE  84 246
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED     17   42
  18Q GAIN WILD-TYPE   84  246
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  FEMALE               17                 84
  MALE                 42                246
[1] 2 2
[1] FALSE
D33V8, continuous
D33V9, continuous
D33V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18Q GAIN MUTATED       1                         2    52
  18Q GAIN WILD-TYPE    41                        19   259
D33V11, multiclass
                           clus
vv                          18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  ASIAN                                    1                 41
  BLACK OR AFRICAN AMERICAN                2                 19
  WHITE                                   52                259
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V12, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED     2  53
  18Q GAIN WILD-TYPE   7 299
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      2   53
  18Q GAIN WILD-TYPE    7  299
                        clus
vv                       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  7
  NOT HISPANIC OR LATINO               53                299
[1] 2 2
[1] FALSE

Clustering(34) Variable = 19P GAIN MUTATION ANALYSIS
D34V1, survival
                    sevent
clus2                  0   1
  19P GAIN MUTATED    51  28
  19P GAIN WILD-TYPE 179 125
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                79                304 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                28                125 
$`19P GAIN MUTATED`
TCGA-4Z-AA7M TCGA-4Z-AA80 TCGA-4Z-AA82 TCGA-4Z-AA84 TCGA-BL-A3JM TCGA-BT-A20N 
       16.27         0.62        51.16        15.12         6.74        32.84 
TCGA-BT-A20X TCGA-BT-A2LA TCGA-C4-A0F0 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A47V 
        8.25        17.16         1.94         0.46         0.43        12.46 
TCGA-CF-A47X TCGA-CF-A8HY TCGA-CU-A3KJ TCGA-CU-A3YL TCGA-DK-A1A3 TCGA-DK-A1A7 
       12.62        11.34         5.46        16.31        21.86        18.41 
TCGA-DK-A2HX TCGA-DK-A2I4 TCGA-DK-A6AV TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B6 
        1.81       123.85        64.18        67.36        15.68        30.67 
TCGA-DK-AA6S TCGA-DK-AA6U TCGA-DK-AA71 TCGA-DK-AA76 TCGA-E5-A4U1 TCGA-E7-A5KE 
      166.03        10.49        13.64        12.03        38.83         0.56 
TCGA-E7-A6ME TCGA-E7-A7DU TCGA-E7-A7DV TCGA-FD-A3SR TCGA-FD-A43U TCGA-FD-A43X 
       12.99         0.92         1.22        19.79        20.91         3.62 
TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FJ-A3Z7 TCGA-FT-A3EE TCGA-G2-A3VY 
        2.27         3.06         4.31        31.07         3.25        17.62 
TCGA-G2-AA3B TCGA-G2-AA3D TCGA-GC-A3YS TCGA-GD-A2C5 TCGA-GD-A76B TCGA-GU-A767 
       66.02        64.44        24.92         7.73         7.36         4.73 
TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A40G TCGA-HQ-A2OE TCGA-K4-A5RH 
        7.00        14.27        21.34        19.07        38.60         9.07 
TCGA-S5-A6DX TCGA-S5-AA26 TCGA-UY-A78L TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A9PA 
        1.84         3.75        37.05        65.75         3.58        35.24 
TCGA-UY-A9PB TCGA-XF-A8HC TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A9SI TCGA-XF-A9SV 
       29.56         6.58        97.12        15.35        79.66        12.76 
TCGA-XF-A9T8 TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-YC-A8S6 
       13.74        44.32        56.48        75.39        18.81         9.63 
TCGA-ZF-A9R2 TCGA-ZF-A9RF TCGA-ZF-A9RN TCGA-ZF-AA4T TCGA-ZF-AA51 TCGA-ZF-AA54 
       21.11        52.73        20.22        19.69        38.73        19.40 
TCGA-ZF-AA56 
        8.52 

$`19P GAIN WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        91.63       103.50       105.70         8.35 
TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W 
       44.94        16.83        16.77        17.16        34.98        27.62 
TCGA-4Z-AA7Y TCGA-4Z-AA81 TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 
       49.12        41.75        66.54        10.22        47.80        33.83 
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX 
       40.08         7.33         2.66        12.39         6.58        13.15 
TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T 
       19.04        12.16        17.88        19.50         5.06        14.89 
TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH 
       14.96         5.06         8.35        16.18        20.48         4.67 
TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F 
       12.82         9.96        17.56        28.70        24.26        28.41 
TCGA-C4-A0EZ TCGA-C4-A0F6 TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47W 
        8.98        23.01         0.69        10.95        12.66        12.10 
TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A9FF 
       12.26        13.12        12.00        12.10        11.34        11.87 
TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3QU TCGA-CU-A5W6 
       13.08        12.92         4.90         7.20         5.19         1.84 
TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC 
       13.58         2.14        66.41        19.00        16.70       130.88 
TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A2I2 
      112.44        16.14        17.62        15.62        10.59         7.79 
TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ 
       87.32         2.20        13.58         7.82         8.22        17.72 
TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX 
       50.27        21.30        23.21         9.67        20.81        10.55 
TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B5 
      140.81        48.00        17.98        41.56        76.60        41.06 
TCGA-DK-AA6L TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6W TCGA-DK-AA6X 
       38.24        15.02        13.58        12.36         8.65         7.53 
TCGA-DK-AA74 TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E7-A3X6 TCGA-E7-A3Y1 
       43.50        10.62        43.59        15.35        24.66         0.10 
TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KF TCGA-E7-A677 
        0.49         2.24        16.70        17.39         0.66        14.56 
TCGA-E7-A678 TCGA-E7-A6MF TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A8O7 
       13.97        14.33        13.68        14.07        12.95        15.32 
TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 
       14.37         8.09        32.02        16.77         8.94        33.04 
TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ 
        4.01        12.62        22.52        27.98        60.66        24.30 
TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ 
       23.41        17.98        29.16         5.52        25.74        46.78 
TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43Y TCGA-FD-A5BR 
       12.85        22.98        27.35        14.96        15.58        26.73 
TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY 
       53.88        11.01        19.33         5.36         5.69         8.25 
TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P 
       27.45        18.08        58.92         2.70         7.10         6.28 
TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE 
       13.35        62.86        18.81         6.15        12.69        12.36 
TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FJ-A871 
        9.67        10.85         7.13        10.65        17.23         8.94 
TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO 
        6.48        61.94        30.61        15.95        26.93        35.24 
TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3BM 
       33.01         7.23        20.12         6.94        19.46        21.40 
TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC 
        2.24        15.81         4.50        15.91        14.07        17.75 
TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS 
        0.49         8.94        13.91         2.10         3.12        20.98 
TCGA-GD-A6C6 TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 
        2.20        10.92        11.31        11.31         7.63        27.09 
TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-AATO TCGA-GU-AATP TCGA-GV-A3JX TCGA-GV-A3JZ 
       20.05         5.62        10.65        32.98        19.10        19.82 
TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A6ZA 
       20.28         8.48        10.59        27.35         8.58        22.72 
TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS 
        1.51        19.40         3.06         9.01         8.22        25.02 
TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RI 
        3.45        21.24         2.76         9.14        27.68        11.70 
TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-LC-A66R 
        1.74         1.81        15.42         6.38        11.80        15.32 
TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X 
       15.58        21.07        13.48        12.23        16.67        14.24 
TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A78O 
       12.43        31.56        17.62        22.68        86.83        76.01 
TCGA-UY-A78P TCGA-UY-A8OD TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HB 
       67.79       112.83        17.82         4.54         1.64        45.04 
TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH 
       97.45       125.49         1.87        17.88        48.62        64.80 
TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ 
        3.22        66.41        11.90        23.64        21.04        28.24 
TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 
       26.27        18.90         2.24        16.27        66.64         2.10 
TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML 
       92.98        10.82       110.60        11.31        54.90         7.63 
TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMY 
       71.57        91.73         2.96         8.32         6.77        98.99 
TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN8 TCGA-YC-A89H 
       30.94        61.45        86.30        27.06         3.88        18.84 
TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R3 
        0.66        11.97        13.64        18.64         7.36        24.13 
TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RD 
       30.28        27.19        21.86        28.41        74.56        13.41 
TCGA-ZF-A9RE TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-AA4N TCGA-ZF-AA4R 
        3.48        52.60        82.49        47.84         2.89        34.06 
TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA52 TCGA-ZF-AA53 
        8.61        59.38        60.16        63.02        35.41        57.90 
TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
       47.15        19.17         5.52        10.13 

  19P GAIN MUTATED 19P GAIN WILD-TYPE 
              0.43               0.10 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
            166.03             140.81 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
            15.680             15.715 
[1] "0.4 - 166.0 (15.7)" "0.1 - 140.8 (15.7)"
[1] "hr=" "1.1"
D34V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  19P GAIN MUTATED         1       25        23       29
  19P GAIN WILD-TYPE       3       99       104      100
D34V3, multiclass
           clus
vv          19P GAIN MUTATED 19P GAIN WILD-TYPE
  STAGE I                  1                  3
  STAGE II                25                 99
  STAGE III               23                104
  STAGE IV                29                100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1+T2  T3  T4
  19P GAIN MUTATED         24  39  13
  19P GAIN WILD-TYPE       97 145  40
D34V4, multiclass
          clus
vv         19P GAIN MUTATED 19P GAIN WILD-TYPE
  T0+T1+T2               24                 97
  T3                     39                145
  T4                     13                 40
[1] 3 2
[1] TRUE
[1] "dimension of 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    43   8  21   1
  19P GAIN WILD-TYPE 181  34  54   7
D34V5, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  N0               43                181
  N1                8                 34
  N2               21                 54
  N3                1                  7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V6, binary
                    cls
clus                   0   1
  19P GAIN MUTATED    39   3
  19P GAIN WILD-TYPE 146   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     39    3
  19P GAIN WILD-TYPE  146    7
   clus
vv  19P GAIN MUTATED 19P GAIN WILD-TYPE
  0               39                146
  1                3                  7
[1] 2 2
[1] FALSE
D34V7, binary
                    cls
clus                   0   1
  19P GAIN MUTATED    17  64
  19P GAIN WILD-TYPE  84 224
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     17   64
  19P GAIN WILD-TYPE   84  224
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  FEMALE               17                 84
  MALE                 64                224
[1] 2 2
[1] FALSE
D34V8, continuous
D34V9, continuous
D34V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  19P GAIN MUTATED      13                         2    62
  19P GAIN WILD-TYPE    29                        19   249
D34V11, multiclass
                           clus
vv                          19P GAIN MUTATED 19P GAIN WILD-TYPE
  ASIAN                                   13                 29
  BLACK OR AFRICAN AMERICAN                2                 19
  WHITE                                   62                249
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V12, binary
                    cls
clus                   0   1
  19P GAIN MUTATED     1  73
  19P GAIN WILD-TYPE   8 279
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      1   73
  19P GAIN WILD-TYPE    8  279
                        clus
vv                       19P GAIN MUTATED 19P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  8
  NOT HISPANIC OR LATINO               73                279
[1] 2 2
[1] FALSE

Clustering(35) Variable = 19Q GAIN MUTATION ANALYSIS
D35V1, survival
                    sevent
clus2                  0   1
  19Q GAIN MUTATED    79  43
  19Q GAIN WILD-TYPE 151 110
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
               122                261 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                43                110 
$`19Q GAIN MUTATED`
TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA84 
       16.27        16.77         0.62        41.75        51.16        15.12 
TCGA-BL-A3JM TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA 
        6.74        19.04        32.84         5.06         8.25        17.16 
TCGA-BT-A2LB TCGA-BT-A42C TCGA-BT-A42E TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR 
       16.18        28.70        24.26         1.94        23.01         0.46 
TCGA-CF-A1HS TCGA-CF-A47X TCGA-CF-A5UA TCGA-CF-A8HY TCGA-CU-A3KJ TCGA-CU-A3YL 
        0.43        12.62        12.00        11.34         5.46        16.31 
TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AB TCGA-DK-A2HX TCGA-DK-A2I4 
       21.86        66.41        18.41        16.70         1.81       123.85 
TCGA-DK-A2I6 TCGA-DK-A3IL TCGA-DK-A3X1 TCGA-DK-A6AV TCGA-DK-A6B1 TCGA-DK-A6B2 
       87.32        13.58        48.00        64.18        67.36        15.68 
TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6P TCGA-DK-AA6S TCGA-DK-AA6U TCGA-DK-AA71 
       30.67        38.24        15.02       166.03        10.49        13.64 
TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A541 TCGA-E7-A5KE 
       12.03        43.59        15.35        38.83        17.39         0.56 
TCGA-E7-A6ME TCGA-E7-A7DU TCGA-E7-A7DV TCGA-FD-A3SJ TCGA-FD-A3SR TCGA-FD-A3SS 
       12.99         0.92         1.22        24.30        19.79        12.85 
TCGA-FD-A43N TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BZ TCGA-FD-A6TB TCGA-FD-A6TF 
       22.98        20.91         3.62        27.45        18.81         2.27 
TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-FT-A3EE 
        3.06         4.31        10.85        31.07        17.23         3.25 
TCGA-G2-A2EF TCGA-G2-A2EO TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3D TCGA-GC-A3RC 
       61.94        35.24        17.62        66.02        64.44        15.91 
TCGA-GC-A3RD TCGA-GC-A3YS TCGA-GD-A2C5 TCGA-GD-A76B TCGA-GU-A42R TCGA-GU-A767 
       14.07        24.92         7.73         7.36        11.31         4.73 
TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JZ TCGA-GV-A3QF 
       32.98         7.00        14.27        21.34        19.82        20.28 
TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A4AB TCGA-K4-A5RH 
       19.40        38.60         9.01        25.02         2.76         9.07 
TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A8OB 
       14.24         1.84         3.75        17.62        37.05        65.75 
TCGA-UY-A8OC TCGA-UY-A9PA TCGA-UY-A9PB TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HF 
        3.58        35.24        29.56        45.04         6.58        97.12 
TCGA-XF-A8HG TCGA-XF-A9SI TCGA-XF-A9SV TCGA-XF-A9T3 TCGA-XF-AAMQ TCGA-XF-AAMX 
       15.35        79.66        12.76         2.24        71.57         6.77 
TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN3 TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-YC-A8S6 
       44.32        56.48        86.30        75.39        18.81         9.63 
TCGA-YF-AA3M TCGA-ZF-A9R2 TCGA-ZF-A9RL TCGA-ZF-A9RN TCGA-ZF-AA4T TCGA-ZF-AA51 
       13.64        21.11        82.49        20.22        19.69        38.73 
TCGA-ZF-AA54 TCGA-ZF-AA56 
       19.40         8.52 

$`19Q GAIN WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        91.63       103.50       105.70         8.35 
TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA7Y 
       44.94        16.83        17.16        34.98        27.62        49.12 
TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I 
       66.54        10.22        47.80        33.83        40.08         7.33 
TCGA-BL-A13J TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20O TCGA-BT-A20P 
        2.66        12.39         6.58        13.15        12.16        17.88 
TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20W TCGA-BT-A2LD 
       19.50         5.06        14.89        14.96         8.35        20.48 
TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42F TCGA-C4-A0EZ 
        4.67        12.82         9.96        17.56        28.41         8.98 
TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47Y 
        0.69        10.95        12.66        12.46        12.10        12.26 
TCGA-CF-A5U8 TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YN 
       13.12        12.10        11.34        11.87        13.08        12.92 
TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3QU TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A5 
        4.90         7.20         5.19         1.84        13.58         2.14 
TCGA-DK-A1AA TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG 
       19.00       130.88       112.44        16.14        17.62        15.62 
TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A3IK TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ 
       10.59         7.79         2.20         7.82         8.22        17.72 
TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX 
       50.27        21.30        23.21         9.67        20.81        10.55 
TCGA-DK-A3WY TCGA-DK-A3X2 TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B5 TCGA-DK-AA6Q 
      140.81        17.98        41.56        76.60        41.06        13.58 
TCGA-DK-AA6T TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA74 TCGA-DK-AA77 TCGA-E7-A3X6 
       12.36         8.65         7.53        43.50        10.62        24.66 
TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KF TCGA-E7-A677 
        0.10         0.49         2.24        16.70         0.66        14.56 
TCGA-E7-A678 TCGA-E7-A6MF TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A8O7 
       13.97        14.33        13.68        14.07        12.95        15.32 
TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 
       14.37         8.09        32.02        16.77         8.94        33.04 
TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SL 
        4.01        12.62        22.52        27.98        60.66        23.41 
TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A43P 
       17.98        29.16         5.52        25.74        46.78        27.35 
TCGA-FD-A43S TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU 
       14.96        15.58        26.73        53.88        11.01        19.33 
TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N 
        5.36         5.69         8.25        18.08        58.92         2.70 
TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TC TCGA-FD-A6TD 
        7.10         6.28        13.35        62.86         6.15        12.69 
TCGA-FD-A6TE TCGA-FD-A6TI TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-FT-A61P 
       12.36         9.67         7.13        10.65         8.94         6.48 
TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE 
       30.61        15.95        26.93        33.01         7.23        20.12 
TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB 
        6.94        19.46        21.40         2.24        15.81         4.50 
TCGA-GC-A3WC TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A3OP TCGA-GD-A3OQ 
       17.75         0.49         8.94        13.91         2.10         3.12 
TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A762 TCGA-GU-A763 
       20.98         2.20        10.92        11.31         7.63        27.09 
TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-AATO TCGA-GV-A3JX TCGA-GV-A3QH TCGA-GV-A3QI 
       20.05         5.62        10.65        19.10         8.48        10.59 
TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-HQ-A2OF 
       27.35         8.58        19.07        22.72         1.51         3.06 
TCGA-HQ-A5NE TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RI 
        8.22         3.45        21.24         9.14        27.68        11.70 
TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-LC-A66R 
        1.74         1.81        15.42         6.38        11.80        15.32 
TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-SY-A9G0 
       15.58        21.07        13.48        12.23        16.67        12.43 
TCGA-SY-A9G5 TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OD 
       31.56        22.68        86.83        76.01        67.79       112.83 
TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HH 
       17.82         4.54         1.64        97.45       125.49         1.87 
TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SW 
       17.88        48.62        64.80         3.22        66.41        11.90 
TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T4 
       23.64        21.04        28.24        26.27        18.90        16.27 
TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMG 
       66.64         2.10        13.74        92.98        10.82       110.60 
TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW 
       11.31        54.90         7.63        91.73         2.96         8.32 
TCGA-XF-AAMY TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN4 TCGA-XF-AAN8 TCGA-YC-A89H 
       98.99        30.94        61.45        27.06         3.88        18.84 
TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R4 
        0.66        11.97        18.64         7.36        24.13        30.28 
TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE 
       27.19        21.86        28.41        74.56        13.41         3.48 
TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4U 
       52.73        52.60        47.84         2.89        34.06         8.61 
TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA58 
       59.38        60.16        63.02        35.41        57.90        47.15 
TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
       19.17         5.52        10.13 

  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
              0.43               0.10 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
            166.03             140.81 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
             17.31              14.89 
[1] "0.4 - 166.0 (17.3)" "0.1 - 140.8 (14.9)"
[1] "hr=" "1.3"
D35V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  19Q GAIN MUTATED         1       34        37       48
  19Q GAIN WILD-TYPE       3       90        90       81
D35V3, multiclass
           clus
vv          19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  STAGE I                  1                  3
  STAGE II                34                 90
  STAGE III               37                 90
  STAGE IV                48                 81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1+T2  T3  T4
  19Q GAIN MUTATED         34  58  20
  19Q GAIN WILD-TYPE       87 126  33
D35V4, multiclass
          clus
vv         19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  T0+T1+T2               34                 87
  T3                     58                126
  T4                     20                 33
[1] 3 2
[1] TRUE
[1] "dimension of 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    64  14  32   3
  19Q GAIN WILD-TYPE 160  28  43   5
D35V5, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  N0               64                160
  N1               14                 28
  N2               32                 43
  N3                3                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V6, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED    58   4
  19Q GAIN WILD-TYPE 127   6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     58    4
  19Q GAIN WILD-TYPE  127    6
   clus
vv  19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  0               58                127
  1                4                  6
[1] 2 2
[1] FALSE
D35V7, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED    32  92
  19Q GAIN WILD-TYPE  69 196
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     32   92
  19Q GAIN WILD-TYPE   69  196
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  FEMALE               32                 69
  MALE                 92                196
[1] 2 2
[1] FALSE
D35V8, continuous
D35V9, continuous
D35V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  19Q GAIN MUTATED      13                         5    98
  19Q GAIN WILD-TYPE    29                        16   213
D35V11, multiclass
                           clus
vv                          19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  ASIAN                                   13                 29
  BLACK OR AFRICAN AMERICAN                5                 16
  WHITE                                   98                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"
D35V12, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED     3 109
  19Q GAIN WILD-TYPE   6 243
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      3  109
  19Q GAIN WILD-TYPE    6  243
                        clus
vv                       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                  6
  NOT HISPANIC OR LATINO              109                243
[1] 2 2
[1] FALSE

Clustering(36) Variable = 20P GAIN MUTATION ANALYSIS
D36V1, survival
                    sevent
clus2                  0   1
  20P GAIN MUTATED   110  76
  20P GAIN WILD-TYPE 120  77
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               186                197 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                76                 77 
$`20P GAIN MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7S 
       22.29        11.97       105.70        16.27        44.94        34.98 
TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-BL-A3JM 
        0.62        41.75        66.54        10.22        47.80         6.74 
TCGA-BT-A0S7 TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X 
        6.58         5.06        14.89         5.06         8.35         8.25 
TCGA-BT-A2LD TCGA-BT-A3PK TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ 
       20.48         9.96        28.70        24.26        28.41         8.98 
TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A47T TCGA-CF-A47X 
        1.94        23.01         0.46         0.43        12.66        12.62 
TCGA-CF-A8HX TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A5W6 
       11.34        12.92         4.90         7.20         5.46         1.84 
TCGA-DK-A1A5 TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 
        2.14       130.88       112.44         1.81        10.59         7.79 
TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IN TCGA-DK-A3IU TCGA-DK-A3WX 
      123.85         2.20        13.58         8.22        23.21        10.55 
TCGA-DK-A3X2 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6P 
       17.98        67.36        15.68        30.67        38.24        15.02 
TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 TCGA-E5-A2PC TCGA-E5-A4TZ 
       10.49         7.53        13.64        43.50        43.59        15.35 
TCGA-E5-A4U1 TCGA-E7-A541 TCGA-E7-A6ME TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A97Q 
       38.83        17.39        12.99         1.22        13.68         8.09 
TCGA-FD-A3B3 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3N5 TCGA-FD-A3NA TCGA-FD-A3SJ 
       32.02        33.04         4.01        22.52        60.66        24.30 
TCGA-FD-A3SL TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N 
       23.41        25.74        46.78        19.79        12.85        22.98 
TCGA-FD-A43P TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BT TCGA-FD-A5BZ TCGA-FD-A62O 
       27.35         3.62        26.73        11.01        27.45         7.10 
TCGA-FD-A62S TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TH 
       13.35         6.15        12.69        12.36         2.27         4.31 
TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3ZE TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EF 
        9.67        10.85        10.65         3.25         6.48        61.94 
TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EO TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 
       30.61        15.95        35.24        19.46        21.40         2.24 
TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A4ZW TCGA-GC-A6I1 
       15.81         4.50        15.91        14.07         0.49         8.94 
TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A764 
       13.91         7.73         2.10         2.20         7.36        20.05 
TCGA-GU-A766 TCGA-GU-AATO TCGA-GU-AATP TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX 
        5.62        10.65        32.98        14.27        21.34        19.10 
TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A40G TCGA-H4-A2HQ 
       19.82        20.28         8.48        10.59        19.07        19.40 
TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A6FZ 
        8.22        25.02         3.45         9.07        11.70         1.81 
TCGA-K4-AAQO TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-S5-A6DX TCGA-SY-A9G0 
       11.80        13.48        12.23        16.67         1.84        12.43 
TCGA-SY-A9G5 TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A8OC 
       31.56        37.05        22.68        76.01        65.75         3.58 
TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HD TCGA-XF-A8HF 
       35.24        29.56         4.54         1.64        97.45        97.12 
TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SV TCGA-XF-A9SY 
       15.35         1.87        79.66         3.22        12.76        21.04 
TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-AAMF TCGA-XF-AAMQ TCGA-XF-AAMR 
        2.24        16.27        66.64        10.82        71.57        91.73 
TCGA-XF-AAMT TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-YC-A89H TCGA-YF-AA3M TCGA-ZF-A9R0 
        2.96        98.99        44.32        18.84        13.64        18.64 
TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9RC TCGA-ZF-A9RL 
        7.36        21.11        24.13        30.28        74.56        82.49 
TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4V 
       47.84        20.22         2.89        19.69         8.61        59.38 
TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N 
       38.73        35.41        19.40        47.15        19.17         5.52 

$`20P GAIN WILD-TYPE`
TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R 
       91.63       103.50         8.35        16.83        16.77        17.16 
TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA82 TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A0C8 
       27.62        49.12        51.16        15.12        33.83        40.08 
TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A5ZZ TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N 
        7.33         2.66        12.39        13.15        19.04        32.84 
TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20U TCGA-BT-A2LA TCGA-BT-A2LB 
       12.16        17.88        19.50        14.96        17.16        16.18 
TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A42B TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47V 
        4.67        12.82        17.56         0.69        10.95        12.46 
TCGA-CF-A47W TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A8HY 
       12.10        12.26        13.12        12.00        12.10        11.34 
TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A72E TCGA-DK-A1A3 
       11.87        13.08         5.19        16.31        13.58        21.86 
TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AE TCGA-DK-A1AF 
       66.41        18.41        19.00        16.70        16.14        17.62 
TCGA-DK-A1AG TCGA-DK-A2I6 TCGA-DK-A3IM TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT 
       15.62        87.32         7.82        17.72        50.27        21.30 
TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A6AV TCGA-DK-A6AW 
        9.67        20.81       140.81        48.00        64.18        41.56 
TCGA-DK-A6B0 TCGA-DK-A6B5 TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6W 
       76.60        41.06        13.58       166.03        12.36         8.65 
TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ 
       12.03        10.62        24.66         0.10         0.49         2.24 
TCGA-E7-A519 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MF 
       16.70         0.56         0.66        14.56        13.97        14.33 
TCGA-E7-A7DU TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A8O7 TCGA-E7-A97P TCGA-FD-A3B4 
        0.92        14.07        12.95        15.32        14.37        16.77 
TCGA-FD-A3B5 TCGA-FD-A3B8 TCGA-FD-A3N6 TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO 
        8.94        12.62        27.98        17.98        29.16         5.52 
TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43Y TCGA-FD-A5BS TCGA-FD-A5BU TCGA-FD-A5BV 
       14.96        20.91        15.58        53.88        19.33         5.36 
TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62P 
        5.69         8.25        18.08        58.92         2.70         6.28 
TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TG TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZF 
       62.86        18.81         3.06        31.07         7.13        17.23 
TCGA-FJ-A871 TCGA-G2-A2EL TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY 
        8.94        26.93        33.01         7.23        20.12        17.62 
TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3D TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GD-A3OQ 
       66.02         6.94        64.44        17.75        24.92         3.12 
TCGA-GD-A3OS TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 
       20.98        10.92        11.31        11.31         7.63        27.09 
TCGA-GU-A767 TCGA-GU-AATQ TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A6ZA TCGA-H4-A2HO 
        4.73         7.00        27.35         8.58        22.72         1.51 
TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC 
       38.60         3.06         9.01        21.24         2.76         9.14 
TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6MB TCGA-K4-A83P TCGA-LC-A66R TCGA-LT-A5Z6 
       27.68         1.74        15.42         6.38        15.32        15.58 
TCGA-LT-A8JT TCGA-R3-A69X TCGA-S5-AA26 TCGA-UY-A78K TCGA-UY-A78N TCGA-UY-A78P 
       21.07        14.24         3.75        17.62        86.83        67.79 
TCGA-UY-A8OD TCGA-UY-A9PD TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HE TCGA-XF-A8HI 
      112.83        17.82        45.04         6.58       125.49        17.88 
TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SL TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SZ 
       48.62        64.80        66.41        11.90        23.64        28.24 
TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMG 
       26.27        18.90         2.10        13.74        92.98       110.60 
TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 
       11.31        54.90         7.63         8.32         6.77        56.48 
TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 
       30.94        61.45        86.30        27.06        75.39        18.81 
TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R5 TCGA-ZF-A9R7 
        3.88         9.63         0.66        11.97        27.19        21.86 
TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-AA4R 
       28.41        13.41         3.48        52.73        52.60        34.06 
TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA53 TCGA-ZF-AA56 TCGA-ZF-AA5P 
       60.16        63.02        57.90         8.52        10.13 

  20P GAIN MUTATED 20P GAIN WILD-TYPE 
              0.43               0.10 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
            130.88             166.03 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
            14.955             16.700 
[1] "0.4 - 130.9 (15.0)" "0.1 - 166.0 (16.7)"
[1] "hr=" "1.1"
D36V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  20P GAIN MUTATED         1       56        60       70
  20P GAIN WILD-TYPE       3       68        67       59
D36V3, multiclass
           clus
vv          20P GAIN MUTATED 20P GAIN WILD-TYPE
  STAGE I                  1                  3
  STAGE II                56                 68
  STAGE III               60                 67
  STAGE IV                70                 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                 T0+T1+T2 T3 T4
  20P GAIN MUTATED         53 93 29
  20P GAIN WILD-TYPE       68 91 24
D36V4, multiclass
          clus
vv         20P GAIN MUTATED 20P GAIN WILD-TYPE
  T0+T1+T2               53                 68
  T3                     93                 91
  T4                     29                 24
[1] 3 2
[1] TRUE
[1] "dimension of 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   102  22  40   7
  20P GAIN WILD-TYPE 122  20  35   1
D36V5, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  N0              102                122
  N1               22                 20
  N2               40                 35
  N3                7                  1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V6, binary
                    cls
clus                   0   1
  20P GAIN MUTATED    83   7
  20P GAIN WILD-TYPE 102   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     83    7
  20P GAIN WILD-TYPE  102    3
   clus
vv  20P GAIN MUTATED 20P GAIN WILD-TYPE
  0               83                102
  1                7                  3
[1] 2 2
[1] FALSE
D36V7, binary
                    cls
clus                   0   1
  20P GAIN MUTATED    50 140
  20P GAIN WILD-TYPE  51 148
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     50  140
  20P GAIN WILD-TYPE   51  148
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  FEMALE               50                 51
  MALE                140                148
[1] 2 2
[1] FALSE
D36V8, continuous
D36V9, continuous
D36V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  20P GAIN MUTATED      12                        10   162
  20P GAIN WILD-TYPE    30                        11   149
D36V11, multiclass
                           clus
vv                          20P GAIN MUTATED 20P GAIN WILD-TYPE
  ASIAN                                   12                 30
  BLACK OR AFRICAN AMERICAN               10                 11
  WHITE                                  162                149
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V12, binary
                    cls
clus                   0   1
  20P GAIN MUTATED     2 174
  20P GAIN WILD-TYPE   7 178
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      2  174
  20P GAIN WILD-TYPE    7  178
                        clus
vv                       20P GAIN MUTATED 20P GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  7
  NOT HISPANIC OR LATINO              174                178
[1] 2 2
[1] FALSE

Clustering(37) Variable = 20Q GAIN MUTATION ANALYSIS
D37V1, survival
                    sevent
clus2                  0   1
  20Q GAIN MUTATED   129  84
  20Q GAIN WILD-TYPE 101  69
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               213                170 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                84                 69 
$`20Q GAIN MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KR TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7N 
       22.29        11.97       103.50       105.70        16.27        44.94 
TCGA-4Z-AA7S TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA83 TCGA-4Z-AA87 TCGA-BL-A3JM 
       34.98         0.62        41.75        66.54        47.80         6.74 
TCGA-BT-A0S7 TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20Q TCGA-BT-A20T TCGA-BT-A20W 
        6.58        19.04        32.84        19.50        14.89         8.35 
TCGA-BT-A20X TCGA-BT-A2LD TCGA-BT-A3PK TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F 
        8.25        20.48         9.96        28.70        24.26        28.41 
TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A47S 
        8.98         1.94        23.01         0.46         0.43        10.95 
TCGA-CF-A47T TCGA-CF-A47X TCGA-CF-A8HX TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR 
       12.66        12.62        11.34        12.92         4.90         7.20 
TCGA-CU-A3KJ TCGA-CU-A5W6 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AC 
        5.46         1.84         2.14        66.41        18.41       130.88 
TCGA-DK-A1AD TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IL 
      112.44         1.81        10.59         7.79       123.85        13.58 
TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IS TCGA-DK-A3IU TCGA-DK-A3WX TCGA-DK-A3X2 
        7.82         8.22        50.27        23.21        10.55        17.98 
TCGA-DK-A6AV TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6P 
       64.18        67.36        15.68        30.67        38.24        15.02 
TCGA-DK-AA6S TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 
      166.03        10.49         8.65         7.53        13.64        43.50 
TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A4IJ TCGA-E7-A541 TCGA-E7-A6ME 
       43.59        15.35        38.83         0.49        17.39        12.99 
TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A85H TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B6 
        1.22        13.68        12.95         8.09        32.02        33.04 
TCGA-FD-A3B7 TCGA-FD-A3N5 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SP TCGA-FD-A3SQ 
        4.01        22.52        60.66        24.30        25.74        46.78 
TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43X TCGA-FD-A5BR 
       19.79        12.85        22.98        27.35         3.62        26.73 
TCGA-FD-A5BT TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62O TCGA-FD-A62S 
       11.01        27.45        18.08        58.92         7.10        13.35 
TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TH TCGA-FD-A6TI 
        6.15        12.69        12.36         2.27         4.31         9.67 
TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3ZE TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EF 
       10.85        31.07        10.65         3.25         6.48        61.94 
TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EO TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3D 
       30.61        15.95        35.24        17.62        66.02        64.44 
TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC 
       19.46        21.40         2.24        15.81         4.50        15.91 
TCGA-GC-A3RD TCGA-GC-A3YS TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 
       14.07        24.92         0.49         8.94        13.91         7.73 
TCGA-GD-A3OP TCGA-GD-A76B TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A766 TCGA-GU-AATO 
        2.10         7.36        11.31        11.31         5.62        10.65 
TCGA-GU-AATP TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF 
       32.98        14.27        21.34        19.10        19.82        20.28 
TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A40E TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF 
        8.48        10.59         8.58        19.40        38.60         3.06 
TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AC TCGA-K4-A5RH TCGA-K4-A5RI 
        8.22        25.02         3.45         9.14         9.07        11.70 
TCGA-K4-A6FZ TCGA-K4-AAQO TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN 
        1.81        11.80        15.58        13.48        12.23        16.67 
TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M 
        1.84        12.43        31.56        17.62        37.05        22.68 
TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PE 
       76.01        65.75         3.58        35.24        29.56         4.54 
TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HD TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A8HH 
        1.64        45.04        97.45        97.12        15.35         1.87 
TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SV TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9T3 
       79.66         3.22        12.76        23.64        21.04         2.24 
TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-AAMF TCGA-XF-AAMQ TCGA-XF-AAMR 
       16.27        66.64         2.10        10.82        71.57        91.73 
TCGA-XF-AAMT TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-YF-AA3M 
        2.96         6.77        98.99        44.32        30.94        13.64 
TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R7 
       18.64         7.36        21.11        24.13        30.28        21.86 
TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN 
       74.56        13.41        52.60        82.49        47.84        20.22 
TCGA-ZF-AA4N TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA54 
        2.89        19.69         8.61        38.73        35.41        19.40 
TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N 
       47.15        19.17         5.52 

$`20Q GAIN WILD-TYPE`
TCGA-2F-A9KQ TCGA-2F-A9KW TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7W 
       91.63         8.35        16.83        16.77        17.16        27.62 
TCGA-4Z-AA7Y TCGA-4Z-AA82 TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-4Z-AA89 TCGA-BL-A0C8 
       49.12        51.16        15.12        10.22        33.83        40.08 
TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A5ZZ TCGA-BT-A0YX TCGA-BT-A20O TCGA-BT-A20P 
        7.33         2.66        12.39        13.15        12.16        17.88 
TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A3PH 
        5.06        14.96         5.06        17.16        16.18         4.67 
TCGA-BT-A3PJ TCGA-BT-A42B TCGA-CF-A27C TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47Y 
       12.82        17.56         0.69        12.46        12.10        12.26 
TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CF-A9FM 
       13.12        12.00        12.10        11.34        11.87        13.08 
TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1AA TCGA-DK-A1AB 
        5.19        16.31        13.58        21.86        19.00        16.70 
TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IQ 
       16.14        17.62        15.62        87.32         2.20        17.72 
TCGA-DK-A3IT TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A6AW 
       21.30         9.67        20.81       140.81        48.00        41.56 
TCGA-DK-A6B0 TCGA-DK-A6B5 TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA76 TCGA-DK-AA77 
       76.60        41.06        13.58        12.36        12.03        10.62 
TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KE TCGA-E7-A5KF 
       24.66         0.10         2.24        16.70         0.56         0.66 
TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7XN TCGA-E7-A8O7 
       14.56        13.97        14.33         0.92        14.07        15.32 
TCGA-E7-A97P TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B8 TCGA-FD-A3N6 TCGA-FD-A3SL 
       14.37        16.77         8.94        12.62        27.98        23.41 
TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43Y 
       17.98        29.16         5.52        14.96        20.91        15.58 
TCGA-FD-A5BS TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A62N 
       53.88        19.33         5.36         5.69         8.25         2.70 
TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TG TCGA-FJ-A3Z9 TCGA-FJ-A3ZF 
        6.28        62.86        18.81         3.06         7.13        17.23 
TCGA-FJ-A871 TCGA-G2-A2EL TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3C 
        8.94        26.93        33.01         7.23        20.12         6.94 
TCGA-GC-A3WC TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42P TCGA-GU-A762 
       17.75         3.12        20.98         2.20        10.92         7.63 
TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A767 TCGA-GU-AATQ TCGA-GV-A3QK TCGA-GV-A40G 
       27.09        20.05         4.73         7.00        27.35        19.07 
TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-HQ-A5ND TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A54R 
       22.72         1.51         9.01        21.24         2.76        27.68 
TCGA-K4-A5RJ TCGA-K4-A6MB TCGA-K4-A83P TCGA-LC-A66R TCGA-LT-A8JT TCGA-R3-A69X 
        1.74        15.42         6.38        15.32        21.07        14.24 
TCGA-S5-AA26 TCGA-UY-A78N TCGA-UY-A78P TCGA-UY-A8OD TCGA-UY-A9PD TCGA-XF-A8HC 
        3.75        86.83        67.79       112.83        17.82         6.58 
TCGA-XF-A8HE TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SL TCGA-XF-A9SW 
      125.49        17.88        48.62        64.80        66.41        11.90 
TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMG 
       28.24        26.27        18.90        13.74        92.98       110.60 
TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMW TCGA-XF-AAN0 TCGA-XF-AAN2 
       11.31        54.90         7.63         8.32        56.48        61.45 
TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A89H 
       86.30        27.06        75.39        18.81         3.88        18.84 
TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R5 TCGA-ZF-A9R9 TCGA-ZF-A9RE 
        9.63         0.66        11.97        27.19        28.41         3.48 
TCGA-ZF-A9RF TCGA-ZF-AA4R TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA53 
       52.73        34.06        59.38        60.16        63.02        57.90 
TCGA-ZF-AA56 TCGA-ZF-AA5P 
        8.52        10.13 

  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
              0.43               0.10 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
            166.03             140.81 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
             15.81              15.60 
[1] "0.4 - 166.0 (15.8)" "0.1 - 140.8 (15.6)"
[1] "hr=" "1.1"
D37V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  20Q GAIN MUTATED         1       66        70       76
  20Q GAIN WILD-TYPE       3       58        57       53
D37V3, multiclass
           clus
vv          20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  STAGE I                  1                  3
  STAGE II                66                 58
  STAGE III               70                 57
  STAGE IV                76                 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                 T0+T1+T2  T3  T4
  20Q GAIN MUTATED         62 106  30
  20Q GAIN WILD-TYPE       59  78  23
D37V4, multiclass
          clus
vv         20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  T0+T1+T2               62                 59
  T3                    106                 78
  T4                     30                 23
[1] 3 2
[1] TRUE
[1] "dimension of 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   118  22  47   7
  20Q GAIN WILD-TYPE 106  20  28   1
D37V5, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  N0              118                106
  N1               22                 20
  N2               47                 28
  N3                7                  1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V6, binary
                    cls
clus                  0  1
  20Q GAIN MUTATED   96  6
  20Q GAIN WILD-TYPE 89  4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     96    6
  20Q GAIN WILD-TYPE   89    4
   clus
vv  20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  0               96                 89
  1                6                  4
[1] 2 2
[1] FALSE
D37V7, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED    61 156
  20Q GAIN WILD-TYPE  40 132
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     61  156
  20Q GAIN WILD-TYPE   40  132
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  FEMALE               61                 40
  MALE                156                132
[1] 2 2
[1] FALSE
D37V8, continuous
D37V9, continuous
D37V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  20Q GAIN MUTATED      17                         9   179
  20Q GAIN WILD-TYPE    25                        12   132
D37V11, multiclass
                           clus
vv                          20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  ASIAN                                   17                 25
  BLACK OR AFRICAN AMERICAN                9                 12
  WHITE                                  179                132
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V12, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED     3 196
  20Q GAIN WILD-TYPE   6 156
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      3  196
  20Q GAIN WILD-TYPE    6  156
                        clus
vv                       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                  6
  NOT HISPANIC OR LATINO              196                156
[1] 2 2
[1] FALSE

Clustering(38) Variable = 21Q GAIN MUTATION ANALYSIS
D38V1, survival
                    sevent
clus2                  0   1
  21Q GAIN MUTATED    66  38
  21Q GAIN WILD-TYPE 164 115
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
               104                279 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                38                115 
$`21Q GAIN MUTATED`
TCGA-2F-A9KQ TCGA-4Z-AA7M TCGA-4Z-AA81 TCGA-BL-A5ZZ TCGA-BT-A20N TCGA-BT-A20W 
       91.63        16.27        41.75        12.39        32.84         8.35 
TCGA-BT-A2LA TCGA-BT-A2LD TCGA-BT-A3PK TCGA-BT-A42C TCGA-C4-A0EZ TCGA-C4-A0F0 
       17.16        20.48         9.96        28.70         8.98         1.94 
TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47V TCGA-CF-A8HY TCGA-CU-A3KJ TCGA-DK-A1A3 
        0.43         0.69        12.46        11.34         5.46        21.86 
TCGA-DK-A1A7 TCGA-DK-A2I1 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL 
       18.41        10.59       123.85        87.32         2.20        13.58 
TCGA-DK-A3IM TCGA-DK-A3IS TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6B1 
        7.82        50.27         9.67        48.00        17.98        67.36 
TCGA-DK-A6B2 TCGA-DK-AA6P TCGA-DK-AA6S TCGA-DK-AA6U TCGA-E5-A4TZ TCGA-E7-A4IJ 
       15.68        15.02       166.03        10.49        15.35         0.49 
TCGA-E7-A6ME TCGA-E7-A7PW TCGA-E7-A97Q TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3NA 
       12.99        13.68         8.09        33.04         4.01        60.66 
TCGA-FD-A3SJ TCGA-FD-A3SN TCGA-FD-A3SP TCGA-FD-A3SR TCGA-FD-A43N TCGA-FD-A5BZ 
       24.30        29.16        25.74        19.79        22.98        27.45 
TCGA-FD-A5C0 TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A6TC TCGA-FD-A6TE TCGA-FD-A6TG 
       18.08         7.10         6.28         6.15        12.36         3.06 
TCGA-FD-A6TH TCGA-FJ-A3ZF TCGA-G2-A2EF TCGA-G2-A2EK TCGA-G2-A3VY TCGA-G2-AA3B 
        4.31        17.23        61.94        15.95        17.62        66.02 
TCGA-GC-A3BM TCGA-GC-A4ZW TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GU-A42P 
       21.40         0.49        13.91         7.73         2.10        10.92 
TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QF TCGA-GV-A40E TCGA-GV-A40G TCGA-H4-A2HQ 
       21.34        19.10        20.28         8.58        19.07        19.40 
TCGA-K4-A3WU TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-LC-A66R TCGA-MV-A51V TCGA-SY-A9G5 
        3.45         1.81        15.42        15.32        13.48        31.56 
TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A8OC TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HD 
       22.68        86.83         3.58         4.54         1.64        97.45 
TCGA-XF-A8HF TCGA-XF-A8HH TCGA-XF-A9SJ TCGA-XF-A9SZ TCGA-XF-AAMR TCGA-XF-AAMX 
       97.12         1.87         3.22        28.24        91.73         6.77 
TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-YF-AA3M TCGA-ZF-A9R1 TCGA-ZF-A9R4 TCGA-ZF-A9RC 
       98.99        44.32        13.64         7.36        30.28        74.56 
TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA51 
       82.49        47.84        19.69         8.61        59.38        38.73 
TCGA-ZF-AA52 TCGA-ZF-AA5P 
       35.41        10.13 

$`21Q GAIN WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW TCGA-4Z-AA7N 
       22.29        11.97       103.50       105.70         8.35        44.94 
TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA7Y 
       16.83        16.77        17.16        34.98        27.62        49.12 
TCGA-4Z-AA80 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-4Z-AA87 
        0.62        51.16        66.54        15.12        10.22        47.80 
TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0S7 
       33.83        40.08         7.33         2.66         6.74         6.58 
TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R 
       13.15        19.04        12.16        17.88        19.50         5.06 
TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LB TCGA-BT-A3PH 
       14.89        14.96         5.06         8.25        16.18         4.67 
TCGA-BT-A3PJ TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F6 TCGA-CF-A1HR 
       12.82        17.56        24.26        28.41        23.01         0.46 
TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 
       10.95        12.66        12.10        12.62        12.26        13.12 
TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YN 
       12.00        12.10        11.34        11.87        13.08        12.92 
TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E 
        4.90         7.20         5.19        16.31         1.84        13.58 
TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD 
        2.14        66.41        19.00        16.70       130.88       112.44 
TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I2 TCGA-DK-A3IN 
       16.14        17.62        15.62         1.81         7.79         8.22 
TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY 
       17.72        21.30        23.21        20.81        10.55       140.81 
TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L 
       64.18        41.56        76.60        41.06        30.67        38.24 
TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 
       13.58        12.36         8.65         7.53        13.64        43.50 
TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 
       12.03        10.62        43.59        38.83        24.66         0.10 
TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 
        2.24        16.70        17.39         0.56         0.66        14.56 
TCGA-E7-A678 TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7XN TCGA-E7-A85H 
       13.97        14.33         0.92         1.22        14.07        12.95 
TCGA-E7-A8O7 TCGA-E7-A97P TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B8 
       15.32        14.37        32.02        16.77         8.94        12.62 
TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SO TCGA-FD-A3SQ 
       22.52        27.98        23.41        17.98         5.52        46.78 
TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A43Y 
       12.85        27.35        14.96        20.91         3.62        15.58 
TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX 
       26.73        53.88        11.01        19.33         5.36         5.69 
TCGA-FD-A5BY TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB 
        8.25        58.92         2.70        13.35        62.86        18.81 
TCGA-FD-A6TD TCGA-FD-A6TF TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 
       12.69         2.27         9.67        10.85        31.07         7.13 
TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EJ TCGA-G2-A2EL 
       10.65         8.94         3.25         6.48        30.61        26.93 
TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3C TCGA-G2-AA3D 
       35.24        33.01         7.23        20.12         6.94        64.44 
TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD 
       19.46         2.24        15.81         4.50        15.91        14.07 
TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 
       17.75        24.92         8.94         3.12        20.98         2.20 
TCGA-GD-A76B TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 
        7.36        11.31        11.31         7.63        27.09        20.05 
TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JV 
        5.62         4.73        10.65        32.98         7.00        14.27 
TCGA-GV-A3JZ TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A6ZA TCGA-H4-A2HO 
       19.82         8.48        10.59        27.35        22.72         1.51 
TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WV 
       38.60         3.06         9.01         8.22        25.02        21.24 
TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ 
        2.76         9.14        27.68         9.07        11.70         1.74 
TCGA-K4-A83P TCGA-K4-AAQO TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-PQ-A6FI TCGA-PQ-A6FN 
        6.38        11.80        15.58        21.07        12.23        16.67 
TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-UY-A78K TCGA-UY-A78L 
       14.24         1.84         3.75        12.43        17.62        37.05 
TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OB TCGA-UY-A8OD TCGA-UY-A9PA TCGA-UY-A9PB 
       76.01        67.79        65.75       112.83        35.24        29.56 
TCGA-UY-A9PD TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HE TCGA-XF-A8HG TCGA-XF-A8HI 
       17.82        45.04         6.58       125.49        15.35        17.88 
TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SW 
       48.62        64.80        79.66        66.41        12.76        11.90 
TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 
       23.64        21.04        26.27        18.90         2.24        16.27 
TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMG 
       66.64         2.10        13.74        92.98        10.82       110.60 
TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMT TCGA-XF-AAMW 
       11.31        54.90         7.63        71.57         2.96         8.32 
TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 
       56.48        30.94        61.45        86.30        27.06        75.39 
TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L 
       18.81         3.88        18.84         9.63         0.66        11.97 
TCGA-ZF-A9R0 TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 
       18.64        21.11        24.13        27.19        21.86        28.41 
TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RN TCGA-ZF-AA4N 
       13.41         3.48        52.73        52.60        20.22         2.89 
TCGA-ZF-AA4R TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 
       34.06        60.16        63.02        57.90        19.40         8.52 
TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N 
       47.15        19.17         5.52 

  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
              0.43               0.10 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
            166.03             140.81 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
             16.11              15.58 
[1] "0.4 - 166.0 (16.1)" "0.1 - 140.8 (15.6)"
[1] "hr=" "1.2"
D38V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  21Q GAIN MUTATED         1       31        32       39
  21Q GAIN WILD-TYPE       3       93        95       90
D38V3, multiclass
           clus
vv          21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  STAGE I                  1                  3
  STAGE II                31                 93
  STAGE III               32                 95
  STAGE IV                39                 90
[1] 4 2
[1] TRUE
[1] "dimension of contingency 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         29  53  12
  21Q GAIN WILD-TYPE       92 131  41
D38V4, multiclass
          clus
vv         21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  T0+T1+T2               29                 92
  T3                     53                131
  T4                     12                 41
[1] 3 2
[1] TRUE
[1] "dimension of 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    53  11  26   1
  21Q GAIN WILD-TYPE 171  31  49   7
D38V5, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  N0               53                171
  N1               11                 31
  N2               26                 49
  N3                1                  7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V6, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED    50   2
  21Q GAIN WILD-TYPE 135   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED     50    2
  21Q GAIN WILD-TYPE  135    8
   clus
vv  21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  0               50                135
  1                2                  8
[1] 2 2
[1] FALSE
D38V7, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED    23  82
  21Q GAIN WILD-TYPE  78 206
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED     23   82
  21Q GAIN WILD-TYPE   78  206
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  FEMALE               23                 78
  MALE                 82                206
[1] 2 2
[1] FALSE
D38V8, continuous
D38V9, continuous
D38V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  21Q GAIN MUTATED      10                         4    87
  21Q GAIN WILD-TYPE    32                        17   224
D38V11, multiclass
                           clus
vv                          21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  ASIAN                                   10                 32
  BLACK OR AFRICAN AMERICAN                4                 17
  WHITE                                   87                224
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V12, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED     2  98
  21Q GAIN WILD-TYPE   7 254
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      2   98
  21Q GAIN WILD-TYPE    7  254
                        clus
vv                       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  7
  NOT HISPANIC OR LATINO               98                254
[1] 2 2
[1] FALSE

Clustering(39) Variable = 22Q GAIN MUTATION ANALYSIS
D39V1, survival
                    sevent
clus2                  0   1
  22Q GAIN MUTATED    27  19
  22Q GAIN WILD-TYPE 203 134
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                46                337 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                19                134 
$`22Q GAIN MUTATED`
TCGA-2F-A9KR TCGA-4Z-AA7N TCGA-4Z-AA7S TCGA-BT-A0S7 TCGA-BT-A20W TCGA-BT-A2LB 
      103.50        44.94        34.98         6.58         8.35        16.18 
TCGA-BT-A3PJ TCGA-CF-A8HY TCGA-DK-A1A6 TCGA-DK-A1AD TCGA-DK-A2I6 TCGA-DK-A3IS 
       12.82        11.34        66.41       112.44        87.32        50.27 
TCGA-DK-A3IU TCGA-DK-A3WX TCGA-DK-AA77 TCGA-E7-A4IJ TCGA-E7-A541 TCGA-FD-A3B7 
       23.21        10.55        10.62         0.49        17.39         4.01 
TCGA-FD-A62O TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-AA3D TCGA-GC-A3BM TCGA-GC-A3I6 
        7.10        35.24        33.01        64.44        21.40         2.24 
TCGA-GC-A3RD TCGA-GC-A4ZW TCGA-GU-A767 TCGA-GV-A3JV TCGA-GV-A3JZ TCGA-GV-A3QH 
       14.07         0.49         4.73        14.27        19.82         8.48 
TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-HQ-A2OE TCGA-LT-A5Z6 TCGA-S5-A6DX 
       10.59        27.35         8.58        38.60        15.58         1.84 
TCGA-SY-A9G0 TCGA-UY-A78O TCGA-XF-A9SI TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR 
       12.43        76.01        79.66         7.63        71.57        91.73 
TCGA-XF-AAMW TCGA-XF-AAMX TCGA-ZF-A9R0 TCGA-ZF-A9R4 
        8.32         6.77        18.64        30.28 

$`22Q GAIN WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KT TCGA-2F-A9KW TCGA-4Z-AA7M 
       22.29        11.97        91.63       105.70         8.35        16.27 
TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 
       16.83        16.77        17.16        27.62        49.12         0.62 
TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-4Z-AA87 
       41.75        51.16        66.54        15.12        10.22        47.80 
TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ 
       33.83        40.08         7.33         2.66         6.74        12.39 
TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q 
       13.15        19.04        32.84        12.16        17.88        19.50 
TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA 
        5.06        14.89        14.96         5.06         8.25        17.16 
TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E 
       20.48         4.67         9.96        17.56        28.70        24.26 
TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS 
       28.41         8.98         1.94        23.01         0.46         0.43 
TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X 
        0.69        10.95        12.66        12.46        12.10        12.62 
TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A9FF 
       12.26        13.12        12.00        12.10        11.34        11.87 
TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU 
       13.08        12.92         4.90         7.20         5.46         5.19 
TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A7 
       16.31         1.84        13.58        21.86         2.14        18.41 
TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG 
       19.00        16.70       130.88        16.14        17.62        15.62 
TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IL 
        1.81        10.59         7.79       123.85         2.20        13.58 
TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3IV TCGA-DK-A3WW 
        7.82         8.22        17.72        21.30         9.67        20.81 
TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 
      140.81        48.00        17.98        64.18        41.56        76.60 
TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6P 
       67.36        15.68        41.06        30.67        38.24        15.02 
TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X 
       13.58       166.03        12.36        10.49         8.65         7.53 
TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 
       13.64        43.50        12.03        43.59        15.35        38.83 
TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KE TCGA-E7-A5KF 
       24.66         0.10         2.24        16.70         0.56         0.66 
TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV 
       14.56        13.97        12.99        14.33         0.92         1.22 
TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A8O7 TCGA-E7-A97P TCGA-E7-A97Q 
       13.68        14.07        12.95        15.32        14.37         8.09 
TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B8 TCGA-FD-A3N5 
       32.02        16.77         8.94        33.04        12.62        22.52 
TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN 
       27.98        60.66        24.30        23.41        17.98        29.16 
TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N 
        5.52        25.74        46.78        19.79        12.85        22.98 
TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR 
       27.35        14.96        20.91         3.62        15.58        26.73 
TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY 
       53.88        11.01        19.33         5.36         5.69         8.25 
TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62P TCGA-FD-A62S 
       27.45        18.08        58.92         2.70         6.28        13.35 
TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF 
       62.86        18.81         6.15        12.69        12.36         2.27 
TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 
        3.06         4.31         9.67        10.85        31.07         7.13 
TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EF 
       10.65        17.23         8.94         3.25         6.48        61.94 
TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY 
       30.61        15.95        26.93         7.23        20.12        17.62 
TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC 
       66.02         6.94        19.46        15.81         4.50        15.91 
TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP 
       17.75        24.92         8.94        13.91         7.73         2.10 
TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q 
        3.12        20.98         2.20         7.36        10.92        11.31 
TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-AATO 
       11.31         7.63        27.09        20.05         5.62        10.65 
TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QF TCGA-GV-A40G 
       32.98         7.00        21.34        19.10        20.28        19.07 
TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE 
       22.72         1.51        19.40         3.06         9.01         8.22 
TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R 
       25.02         3.45        21.24         2.76         9.14        27.68 
TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P 
        9.07        11.70         1.74         1.81        15.42         6.38 
TCGA-K4-AAQO TCGA-LC-A66R TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN 
       11.80        15.32        21.07        13.48        12.23        16.67 
TCGA-R3-A69X TCGA-S5-AA26 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M 
       14.24         3.75        31.56        17.62        37.05        22.68 
TCGA-UY-A78N TCGA-UY-A78P TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A8OD TCGA-UY-A9PA 
       86.83        67.79        65.75         3.58       112.83        35.24 
TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HC 
       29.56        17.82         4.54         1.64        45.04         6.58 
TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A8HI 
       97.45       125.49        97.12        15.35         1.87        17.88 
TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SW 
       48.62        64.80         3.22        66.41        12.76        11.90 
TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 
       23.64        21.04        28.24        26.27        18.90         2.24 
TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF 
       16.27        66.64         2.10        13.74        92.98        10.82 
TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAMT TCGA-XF-AAMY TCGA-XF-AAMZ 
      110.60        11.31        54.90         2.96        98.99        44.32 
TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 
       56.48        30.94        61.45        86.30        27.06        75.39 
TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L 
       18.81         3.88        18.84         9.63         0.66        11.97 
TCGA-YF-AA3M TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 
       13.64         7.36        21.11        24.13        27.19        21.86 
TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG 
       28.41        74.56        13.41         3.48        52.73        52.60 
TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4T 
       82.49        47.84        20.22         2.89        34.06        19.69 
TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 
        8.61        59.38        60.16        63.02        38.73        35.41 
TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N 
       57.90        19.40         8.52        47.15        19.17         5.52 
TCGA-ZF-AA5P 
       10.13 

  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
              0.49               0.10 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
            112.44             166.03 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
             15.88              15.68 
[1] "0.5 - 112.4 (15.9)" "0.1 - 166.0 (15.7)"
[1] "hr=" "1.1"
D39V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  22Q GAIN MUTATED         0       17        16       12
  22Q GAIN WILD-TYPE       4      107       111      117
D39V3, multiclass
           clus
vv          22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  STAGE I                  0                  4
  STAGE II                17                107
  STAGE III               16                111
  STAGE IV                12                117
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1+T2  T3  T4
  22Q GAIN MUTATED         17  20   6
  22Q GAIN WILD-TYPE      104 164  47
D39V4, multiclass
          clus
vv         22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  T0+T1+T2               17                104
  T3                     20                164
  T4                      6                 47
[1] 3 2
[1] TRUE
[1] "dimension of 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    27   4   7   2
  22Q GAIN WILD-TYPE 197  38  68   6
D39V5, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  N0               27                197
  N1                4                 38
  N2                7                 68
  N3                2                  6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V6, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED    26   0
  22Q GAIN WILD-TYPE 159  10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED     26    0
  22Q GAIN WILD-TYPE  159   10
   clus
vv  22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  0               26                159
  1                0                 10
[1] 2 2
[1] FALSE
D39V7, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED    10  36
  22Q GAIN WILD-TYPE  91 252
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED     10   36
  22Q GAIN WILD-TYPE   91  252
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  FEMALE               10                 91
  MALE                 36                252
[1] 2 2
[1] FALSE
D39V8, continuous
D39V9, continuous
D39V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  22Q GAIN MUTATED       3                         3    38
  22Q GAIN WILD-TYPE    39                        18   273
D39V11, multiclass
                           clus
vv                          22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  ASIAN                                    3                 39
  BLACK OR AFRICAN AMERICAN                3                 18
  WHITE                                   38                273
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V12, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED     0  40
  22Q GAIN WILD-TYPE   9 312
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      0   40
  22Q GAIN WILD-TYPE    9  312
                        clus
vv                       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  9
  NOT HISPANIC OR LATINO               40                312
[1] 2 2
[1] FALSE

Clustering(40) Variable = XP GAIN MUTATION ANALYSIS
D40V1, survival
                   sevent
clus2                 0   1
  XP GAIN MUTATED    38  28
  XP GAIN WILD-TYPE 192 125
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               66               317 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               28               125 
$`XP GAIN MUTATED`
TCGA-4Z-AA7M TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA87 TCGA-BL-A3JM TCGA-BT-A0S7 
       16.27         0.62        41.75        47.80         6.74         6.58 
TCGA-BT-A20N TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A2LB TCGA-BT-A42C TCGA-CF-A1HS 
       32.84        17.88        19.50        16.18        28.70         0.43 
TCGA-CF-A5UA TCGA-CF-A8HX TCGA-DK-A1A6 TCGA-DK-A1AC TCGA-DK-A1AE TCGA-DK-AA71 
       12.00        11.34        66.41       130.88        16.14        13.64 
TCGA-E7-A4IJ TCGA-E7-A7PW TCGA-E7-A85H TCGA-E7-A97Q TCGA-FD-A43P TCGA-FD-A62S 
        0.49        13.68        12.95         8.09        27.35        13.35 
TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-G2-AA3B TCGA-GC-A3I6 
        9.67        31.07        17.23         3.25        66.02         2.24 
TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OS TCGA-GU-A42P TCGA-GU-A767 
        8.94        13.91         7.73        20.98        10.92         4.73 
TCGA-GU-AATP TCGA-GV-A3JZ TCGA-GV-A3QH TCGA-GV-A3QI TCGA-HQ-A2OE TCGA-HQ-A5ND 
       32.98        19.82         8.48        10.59        38.60         9.01 
TCGA-K4-A54R TCGA-MV-A51V TCGA-UY-A78K TCGA-UY-A78M TCGA-UY-A78O TCGA-UY-A8OB 
       27.68        13.48        17.62        22.68        76.01        65.75 
TCGA-UY-A8OC TCGA-UY-A9PD TCGA-UY-A9PF TCGA-XF-A8HC TCGA-XF-A8HI TCGA-XF-A9T5 
        3.58        17.82         1.64         6.58        17.88        66.64 
TCGA-XF-A9T8 TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAMQ TCGA-XF-AAMX TCGA-XF-AAMY 
       13.74       110.60        11.31        71.57         6.77        98.99 
TCGA-XF-AAMZ TCGA-XF-AAN7 TCGA-YF-AA3L TCGA-ZF-A9R2 TCGA-ZF-A9RF TCGA-ZF-AA4V 
       44.32        18.81        11.97        21.11        52.73        59.38 

$`XP GAIN WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        91.63       103.50       105.70         8.35 
TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W 
       44.94        16.83        16.77        17.16        34.98        27.62 
TCGA-4Z-AA7Y TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-4Z-AA89 
       49.12        51.16        66.54        15.12        10.22        33.83 
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A5ZZ TCGA-BT-A0YX TCGA-BT-A20J 
       40.08         7.33         2.66        12.39        13.15        19.04 
TCGA-BT-A20O TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W 
       12.16         5.06        14.89        14.96         5.06         8.35 
TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK 
        8.25        17.16        20.48         4.67        12.82         9.96 
TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F6 
       17.56        24.26        28.41         8.98         1.94        23.01 
TCGA-CF-A1HR TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W 
        0.46         0.69        10.95        12.66        12.46        12.10 
TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A7I0 TCGA-CF-A8HY TCGA-CF-A9FF 
       12.62        12.26        13.12        12.10        11.34        11.87 
TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU 
       13.08        12.92         4.90         7.20         5.46         5.19 
TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A7 
       16.31         1.84        13.58        21.86         2.14        18.41 
TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AD TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX 
       19.00        16.70       112.44        17.62        15.62         1.81 
TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL 
       10.59         7.79       123.85        87.32         2.20        13.58 
TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU 
        7.82         8.22        17.72        50.27        21.30        23.21 
TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 
        9.67        20.81        10.55       140.81        48.00        17.98 
TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 
       64.18        41.56        76.60        67.36        15.68        41.06 
TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6T 
       30.67        38.24        15.02        13.58       166.03        12.36 
TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA74 TCGA-DK-AA76 TCGA-DK-AA77 
       10.49         8.65         7.53        43.50        12.03        10.62 
TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ 
       43.59        15.35        38.83        24.66         0.10         2.24 
TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 
       16.70        17.39         0.56         0.66        14.56        13.97 
TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7XN TCGA-E7-A8O7 
       12.99        14.33         0.92         1.22        14.07        15.32 
TCGA-E7-A97P TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 
       14.37        32.02        16.77         8.94        33.04         4.01 
TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL 
       12.62        22.52        27.98        60.66        24.30        23.41 
TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR 
       17.98        29.16         5.52        25.74        46.78        19.79 
TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A43Y 
       12.85        22.98        14.96        20.91         3.62        15.58 
TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX 
       26.73        53.88        11.01        19.33         5.36         5.69 
TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O 
        8.25        27.45        18.08        58.92         2.70         7.10 
TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE 
        6.28        62.86        18.81         6.15        12.69        12.36 
TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE 
        2.27         3.06         4.31        10.85         7.13        10.65 
TCGA-FJ-A871 TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL 
        8.94         6.48        61.94        30.61        15.95        26.93 
TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3C 
       35.24        33.01         7.23        20.12        17.62         6.94 
TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC 
       64.44        19.46        21.40        15.81         4.50        15.91 
TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A4ZW TCGA-GD-A3OP TCGA-GD-A3OQ 
       14.07        17.75        24.92         0.49         2.10         3.12 
TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 
        2.20         7.36        11.31        11.31         7.63        27.09 
TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-AATO TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW 
       20.05         5.62        10.65         7.00        14.27        21.34 
TCGA-GV-A3JX TCGA-GV-A3QF TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA 
       19.10        20.28        27.35         8.58        19.07        22.72 
TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OF TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU 
        1.51        19.40         3.06         8.22        25.02         3.45 
TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ 
       21.24         2.76         9.14         9.07        11.70         1.74 
TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-LC-A66R TCGA-LT-A5Z6 
        1.81        15.42         6.38        11.80        15.32        15.58 
TCGA-LT-A8JT TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 
       21.07        12.23        16.67        14.24         1.84         3.75 
TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78L TCGA-UY-A78N TCGA-UY-A78P TCGA-UY-A8OD 
       12.43        31.56        37.05        86.83        67.79       112.83 
TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PE TCGA-XF-A8HB TCGA-XF-A8HD TCGA-XF-A8HE 
       35.24        29.56         4.54        45.04        97.45       125.49 
TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI 
       97.12        15.35         1.87        48.62        64.80        79.66 
TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY 
        3.22        66.41        12.76        11.90        23.64        21.04 
TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T6 
       28.24        26.27        18.90         2.24        16.27         2.10 
TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMR TCGA-XF-AAMT 
       92.98        10.82        54.90         7.63        91.73         2.96 
TCGA-XF-AAMW TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN4 
        8.32        56.48        30.94        61.45        86.30        27.06 
TCGA-XF-AAN5 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3M 
       75.39         3.88        18.84         9.63         0.66        13.64 
TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 
       18.64         7.36        24.13        30.28        27.19        21.86 
TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RG TCGA-ZF-A9RL 
       28.41        74.56        13.41         3.48        52.60        82.49 
TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4U 
       47.84        20.22         2.89        34.06        19.69         8.61 
TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA54 
       60.16        63.02        38.73        35.41        57.90        19.40 
TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
        8.52        47.15        19.17         5.52        10.13 

  XP GAIN MUTATED XP GAIN WILD-TYPE 
             0.43              0.10 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
           130.88            166.03 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
           16.225            15.580 
[1] "0.4 - 130.9 (16.2)" "0.1 - 166.0 (15.6)"
[1] "hr=" "1"  
D40V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  XP GAIN MUTATED         0       18        23       23
  XP GAIN WILD-TYPE       4      106       104      106
D40V3, multiclass
           clus
vv          XP GAIN MUTATED XP GAIN WILD-TYPE
  STAGE I                 0                 4
  STAGE II               18               106
  STAGE III              23               104
  STAGE IV               23               106
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1+T2  T3  T4
  XP GAIN MUTATED         20  32   9
  XP GAIN WILD-TYPE      101 152  44
D40V4, multiclass
          clus
vv         XP GAIN MUTATED XP GAIN WILD-TYPE
  T0+T1+T2              20               101
  T3                    32               152
  T4                     9                44
[1] 3 2
[1] TRUE
[1] "dimension of 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    37  10  12   2
  XP GAIN WILD-TYPE 187  32  63   6
D40V5, multiclass
    clus
vv   XP GAIN MUTATED XP GAIN WILD-TYPE
  N0              37               187
  N1              10                32
  N2              12                63
  N3               2                 6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V6, binary
                   cls
clus                  0   1
  XP GAIN MUTATED    28   0
  XP GAIN WILD-TYPE 157  10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED     28    0
  XP GAIN WILD-TYPE  157   10
   clus
vv  XP GAIN MUTATED XP GAIN WILD-TYPE
  0              28               157
  1               0                10
[1] 2 2
[1] FALSE
D40V7, binary
                   cls
clus                  0   1
  XP GAIN MUTATED    20  46
  XP GAIN WILD-TYPE  81 242
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED     20   46
  XP GAIN WILD-TYPE   81  242
        clus
vv       XP GAIN MUTATED XP GAIN WILD-TYPE
  FEMALE              20                81
  MALE                46               242
[1] 2 2
[1] FALSE
D40V8, continuous
D40V9, continuous
D40V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  XP GAIN MUTATED       8                         5    49
  XP GAIN WILD-TYPE    34                        16   262
D40V11, multiclass
                           clus
vv                          XP GAIN MUTATED XP GAIN WILD-TYPE
  ASIAN                                   8                34
  BLACK OR AFRICAN AMERICAN               5                16
  WHITE                                  49               262
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V12, binary
                   cls
clus                  0   1
  XP GAIN MUTATED     3  54
  XP GAIN WILD-TYPE   6 298
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED      3   54
  XP GAIN WILD-TYPE    6  298
                        clus
vv                       XP GAIN MUTATED XP GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                 6
  NOT HISPANIC OR LATINO              54               298
[1] 2 2
[1] FALSE

Clustering(41) Variable = XQ GAIN MUTATION ANALYSIS
D41V1, survival
                   sevent
clus2                 0   1
  XQ GAIN MUTATED    24  22
  XQ GAIN WILD-TYPE 206 131
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               46               337 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               22               131 
$`XQ GAIN MUTATED`
TCGA-4Z-AA7M TCGA-4Z-AA81 TCGA-4Z-AA87 TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A20N 
       16.27        41.75        47.80         6.74         6.58        32.84 
TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A42C TCGA-CF-A1HS TCGA-CF-A5UA TCGA-CF-A8HX 
       17.88        19.50        28.70         0.43        12.00        11.34 
TCGA-CU-A0YN TCGA-DK-A1A6 TCGA-DK-A1AE TCGA-DK-AA6L TCGA-E7-A7PW TCGA-FD-A3B6 
       12.92        66.41        16.14        38.24        13.68        33.04 
TCGA-FD-A43P TCGA-FD-A6TC TCGA-FD-A6TF TCGA-FD-A6TI TCGA-GC-A3I6 TCGA-GC-A6I1 
       27.35         6.15         2.27         9.67         2.24         8.94 
TCGA-GD-A2C5 TCGA-GD-A3OS TCGA-GU-AATP TCGA-GV-A3JZ TCGA-GV-A3QH TCGA-HQ-A5ND 
        7.73        20.98        32.98        19.82         8.48         9.01 
TCGA-MV-A51V TCGA-UY-A78M TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A8OC TCGA-XF-A8HC 
       13.48        22.68        76.01        65.75         3.58         6.58 
TCGA-XF-A9T5 TCGA-XF-A9T8 TCGA-XF-AAMH TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMX 
       66.64        13.74        11.31         7.63        71.57         6.77 
TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-ZF-A9R2 TCGA-ZF-AA4V 
       98.99        44.32        21.11        59.38 

$`XQ GAIN WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        91.63       103.50       105.70         8.35 
TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W 
       44.94        16.83        16.77        17.16        34.98        27.62 
TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA84 TCGA-4Z-AA86 
       49.12         0.62        51.16        66.54        15.12        10.22 
TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A5ZZ TCGA-BT-A0YX 
       33.83        40.08         7.33         2.66        12.39        13.15 
TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V 
       19.04        12.16         5.06        14.89        14.96         5.06 
TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH 
        8.35         8.25        17.16        16.18        20.48         4.67 
TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ 
       12.82         9.96        17.56        24.26        28.41         8.98 
TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T 
        1.94        23.01         0.46         0.69        10.95        12.66 
TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A7I0 
       12.46        12.10        12.62        12.26        13.12        12.10 
TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ 
       11.34        11.87        13.08         4.90         7.20         5.46 
TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 
        5.19        16.31         1.84        13.58        21.86         2.14 
TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AF 
       18.41        19.00        16.70       130.88       112.44        17.62 
TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 
       15.62         1.81        10.59         7.79       123.85        87.32 
TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS 
        2.20        13.58         7.82         8.22        17.72        50.27 
TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY 
       21.30        23.21         9.67        20.81        10.55       140.81 
TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 
       48.00        17.98        64.18        41.56        76.60        67.36 
TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6S 
       15.68        41.06        30.67        15.02        13.58       166.03 
TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 
       12.36        10.49         8.65         7.53        13.64        43.50 
TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 
       12.03        10.62        43.59        15.35        38.83        24.66 
TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE 
        0.10         0.49         2.24        16.70        17.39         0.56 
TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU 
        0.66        14.56        13.97        12.99        14.33         0.92 
TCGA-E7-A7DV TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A8O7 TCGA-E7-A97P TCGA-E7-A97Q 
        1.22        14.07        12.95        15.32        14.37         8.09 
TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 
       32.02        16.77         8.94         4.01        12.62        22.52 
TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN 
       27.98        60.66        24.30        23.41        17.98        29.16 
TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N 
        5.52        25.74        46.78        19.79        12.85        22.98 
TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS 
       14.96        20.91         3.62        15.58        26.73        53.88 
TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ 
       11.01        19.33         5.36         5.69         8.25        27.45 
TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S 
       18.08        58.92         2.70         7.10         6.28        13.35 
TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TH 
       62.86        18.81        12.69        12.36         3.06         4.31 
TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FJ-A871 
       10.85        31.07         7.13        10.65        17.23         8.94 
TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL 
        3.25         6.48        61.94        30.61        15.95        26.93 
TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B 
       35.24        33.01         7.23        20.12        17.62        66.02 
TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3OO TCGA-GC-A3RB 
        6.94        64.44        19.46        21.40        15.81         4.50 
TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A4ZW TCGA-GC-A6I3 
       15.91        14.07        17.75        24.92         0.49        13.91 
TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q 
        2.10         3.12         2.20         7.36        10.92        11.31 
TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 
       11.31         7.63        27.09        20.05         5.62         4.73 
TCGA-GU-AATO TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QF 
       10.65         7.00        14.27        21.34        19.10        20.28 
TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO 
       10.59        27.35         8.58        19.07        22.72         1.51 
TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU 
       19.40        38.60         3.06         8.22        25.02         3.45 
TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RI 
       21.24         2.76         9.14        27.68         9.07        11.70 
TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-LC-A66R 
        1.74         1.81        15.42         6.38        11.80        15.32 
TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX 
       15.58        21.07        12.23        16.67        14.24         1.84 
TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78N 
        3.75        12.43        31.56        17.62        37.05        86.83 
TCGA-UY-A78P TCGA-UY-A8OD TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE 
       67.79       112.83        35.24        29.56        17.82         4.54 
TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG 
        1.64        45.04        97.45       125.49        97.12        15.35 
TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ 
        1.87        17.88        48.62        64.80        79.66         3.22 
TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ 
       66.41        12.76        11.90        23.64        21.04        28.24 
TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T6 TCGA-XF-AAME 
       26.27        18.90         2.24        16.27         2.10        92.98 
TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAMJ TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW 
       10.82       110.60        54.90        91.73         2.96         8.32 
TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 
       56.48        30.94        61.45        86.30        27.06        75.39 
TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L 
       18.81         3.88        18.84         9.63         0.66        11.97 
TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 
       13.64        18.64         7.36        24.13        30.28        27.19 
TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF 
       21.86        28.41        74.56        13.41         3.48        52.73 
TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4R 
       52.60        82.49        47.84        20.22         2.89        34.06 
TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 
       19.69         8.61        60.16        63.02        38.73        35.41 
TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N 
       57.90        19.40         8.52        47.15        19.17         5.52 
TCGA-ZF-AA5P 
       10.13 

  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
             0.43              0.10 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
            98.99            166.03 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
           16.205            15.620 
[1] "0.4 - 99.0 (16.2)"  "0.1 - 166.0 (15.6)"
[1] "hr=" "1.2"
D41V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  XQ GAIN MUTATED         0       13        16       15
  XQ GAIN WILD-TYPE       4      111       111      114
D41V3, multiclass
           clus
vv          XQ GAIN MUTATED XQ GAIN WILD-TYPE
  STAGE I                 0                 4
  STAGE II               13               111
  STAGE III              16               111
  STAGE IV               15               114
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1+T2  T3  T4
  XQ GAIN MUTATED         13  24   6
  XQ GAIN WILD-TYPE      108 160  47
D41V4, multiclass
          clus
vv         XQ GAIN MUTATED XQ GAIN WILD-TYPE
  T0+T1+T2              13               108
  T3                    24               160
  T4                     6                47
[1] 3 2
[1] TRUE
[1] "dimension of 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    27   8   7   1
  XQ GAIN WILD-TYPE 197  34  68   7
D41V5, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  N0              27               197
  N1               8                34
  N2               7                68
  N3               1                 7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V6, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED    19   1
  XQ GAIN WILD-TYPE 166   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     19    1
  XQ GAIN WILD-TYPE  166    9
   clus
vv  XQ GAIN MUTATED XQ GAIN WILD-TYPE
  0              19               166
  1               1                 9
[1] 2 2
[1] FALSE
D41V7, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED    14  32
  XQ GAIN WILD-TYPE  87 256
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     14   32
  XQ GAIN WILD-TYPE   87  256
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  FEMALE              14                87
  MALE                32               256
[1] 2 2
[1] FALSE
D41V8, continuous
D41V9, continuous
D41V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  XQ GAIN MUTATED       6                         3    35
  XQ GAIN WILD-TYPE    36                        18   276
D41V11, multiclass
                           clus
vv                          XQ GAIN MUTATED XQ GAIN WILD-TYPE
  ASIAN                                   6                36
  BLACK OR AFRICAN AMERICAN               3                18
  WHITE                                  35               276
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V12, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED     1  39
  XQ GAIN WILD-TYPE   8 313
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      1   39
  XQ GAIN WILD-TYPE    8  313
                        clus
vv                       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 8
  NOT HISPANIC OR LATINO              39               313
[1] 2 2
[1] FALSE

Clustering(42) Variable = 1P LOSS MUTATION ANALYSIS
D42V1, survival
                   sevent
clus2                 0   1
  1P LOSS MUTATED    18  14
  1P LOSS WILD-TYPE 212 139
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               32               351 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               14               139 
$`1P LOSS MUTATED`
TCGA-2F-A9KO TCGA-4Z-AA80 TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BT-A3PK TCGA-CF-A47X 
       22.29         0.62        40.08         2.66         9.96        12.62 
TCGA-CU-A0YO TCGA-CU-A0YR TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A6B6 TCGA-DK-AA6Q 
        4.90         7.20        17.72        21.30        30.67        13.58 
TCGA-DK-AA76 TCGA-E5-A2PC TCGA-FD-A62P TCGA-FD-A6TE TCGA-FJ-A3ZE TCGA-GU-A766 
       12.03        43.59         6.28        12.36        10.65         5.62 
TCGA-GU-AATP TCGA-HQ-A2OF TCGA-K4-A3WS TCGA-PQ-A6FI TCGA-S5-A6DX TCGA-UY-A78K 
       32.98         3.06        25.02        12.23         1.84        17.62 
TCGA-UY-A78O TCGA-UY-A8OD TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A9SJ TCGA-XF-AAN2 
       76.01       112.83        97.12        15.35         3.22        61.45 
TCGA-ZF-A9R3 TCGA-ZF-A9RL 
       24.13        82.49 

$`1P LOSS WILD-TYPE`
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW TCGA-4Z-AA7M 
       11.97        91.63       103.50       105.70         8.35        16.27 
TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W 
       44.94        16.83        16.77        17.16        34.98        27.62 
TCGA-4Z-AA7Y TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA84 TCGA-4Z-AA86 
       49.12        41.75        51.16        66.54        15.12        10.22 
TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A13I TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 
       47.80        33.83         7.33         6.74        12.39         6.58 
TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q 
       13.15        19.04        32.84        12.16        17.88        19.50 
TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X 
        5.06        14.89        14.96         5.06         8.35         8.25 
TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A42B 
       17.16        16.18        20.48         4.67        12.82        17.56 
TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F6 
       28.70        24.26        28.41         8.98         1.94        23.01 
TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V 
        0.46         0.43         0.69        10.95        12.66        12.46 
TCGA-CF-A47W TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A8HX 
       12.10        12.26        13.12        12.00        12.10        11.34 
TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A3KJ TCGA-CU-A3QU 
       11.34        11.87        13.08        12.92         5.46         5.19 
TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 
       16.31         1.84        13.58        21.86         2.14        66.41 
TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE 
       18.41        19.00        16.70       130.88       112.44        16.14 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 
       17.62        15.62         1.81        10.59         7.79       123.85 
TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IS 
       87.32         2.20        13.58         7.82         8.22        50.27 
TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 
       23.21         9.67        20.81        10.55       140.81        48.00 
TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 
       17.98        64.18        41.56        76.60        67.36        15.68 
TCGA-DK-A6B5 TCGA-DK-AA6L TCGA-DK-AA6P TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U 
       41.06        38.24        15.02       166.03        12.36        10.49 
TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA77 TCGA-E5-A4TZ 
        8.65         7.53        13.64        43.50        10.62        15.35 
TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 
       38.83        24.66         0.10         0.49         2.24        16.70 
TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME 
       17.39         0.56         0.66        14.56        13.97        12.99 
TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H 
       14.33         0.92         1.22        13.68        14.07        12.95 
TCGA-E7-A8O7 TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 
       15.32        14.37         8.09        32.02        16.77         8.94 
TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA 
       33.04         4.01        12.62        22.52        27.98        60.66 
TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP 
       24.30        23.41        17.98        29.16         5.52        25.74 
TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S 
       46.78        19.79        12.85        22.98        27.35        14.96 
TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT 
       20.91         3.62        15.58        26.73        53.88        11.01 
TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 
       19.33         5.36         5.69         8.25        27.45        18.08 
TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB 
       58.92         2.70         7.10        13.35        62.86        18.81 
TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI 
        6.15        12.69         2.27         3.06         4.31         9.67 
TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A3EE 
       10.85        31.07         7.13        17.23         8.94         3.25 
TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO 
        6.48        61.94        30.61        15.95        26.93        35.24 
TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C 
       33.01         7.23        20.12        17.62        66.02         6.94 
TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB 
       64.44        19.46        21.40         2.24        15.81         4.50 
TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A4ZW TCGA-GC-A6I1 
       15.91        14.07        17.75        24.92         0.49         8.94 
TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 
       13.91         7.73         2.10         3.12        20.98         2.20 
TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 
        7.36        10.92        11.31        11.31         7.63        27.09 
TCGA-GU-A764 TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW 
       20.05         4.73        10.65         7.00        14.27        21.34 
TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK 
       19.10        19.82        20.28         8.48        10.59        27.35 
TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE 
        8.58        19.07        22.72         1.51        19.40        38.60 
TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC 
        9.01         8.22         3.45        21.24         2.76         9.14 
TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB 
       27.68         9.07        11.70         1.74         1.81        15.42 
TCGA-K4-A83P TCGA-K4-AAQO TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-MV-A51V 
        6.38        11.80        15.32        15.58        21.07        13.48 
TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78L 
       16.67        14.24         3.75        12.43        31.56        37.05 
TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A78P TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A9PA 
       22.68        86.83        67.79        65.75         3.58        35.24 
TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HC 
       29.56        17.82         4.54         1.64        45.04         6.58 
TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH 
       97.45       125.49         1.87        17.88        48.62        64.80 
TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY 
       79.66        66.41        12.76        11.90        23.64        21.04 
TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 
       28.24        26.27        18.90         2.24        16.27        66.64 
TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAMH 
        2.10        13.74        92.98        10.82       110.60        11.31 
TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW 
       54.90         7.63        71.57        91.73         2.96         8.32 
TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN3 
        6.77        98.99        44.32        56.48        30.94        86.30 
TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 
       27.06        75.39        18.81         3.88        18.84         9.63 
TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R2 
        0.66        11.97        13.64        18.64         7.36        21.11 
TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RD 
       30.28        27.19        21.86        28.41        74.56        13.41 
TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N 
        3.48        52.73        52.60        47.84        20.22         2.89 
TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X 
       34.06        19.69         8.61        59.38        60.16        63.02 
TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 
       38.73        35.41        57.90        19.40         8.52        47.15 
TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
       19.17         5.52        10.13 

  1P LOSS MUTATED 1P LOSS WILD-TYPE 
             0.62              0.10 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
           112.83            166.03 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
           14.465            15.810 
[1] "0.6 - 112.8 (14.5)" "0.1 - 166.0 (15.8)"
[1] "hr=" "1.1"
D42V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  1P LOSS MUTATED         1       13         6       12
  1P LOSS WILD-TYPE       3      111       121      117
D42V3, multiclass
           clus
vv          1P LOSS MUTATED 1P LOSS WILD-TYPE
  STAGE I                 1                 3
  STAGE II               13               111
  STAGE III               6               121
  STAGE IV               12               117
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1+T2  T3  T4
  1P LOSS MUTATED         14  11   2
  1P LOSS WILD-TYPE      107 173  51
D42V4, multiclass
          clus
vv         1P LOSS MUTATED 1P LOSS WILD-TYPE
  T0+T1+T2              14               107
  T3                    11               173
  T4                     2                51
[1] 3 2
[1] TRUE
[1] "dimension of 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    16   3   8   1
  1P LOSS WILD-TYPE 208  39  67   7
D42V5, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  N0              16               208
  N1               3                39
  N2               8                67
  N3               1                 7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V6, binary
                   cls
clus                  0   1
  1P LOSS MUTATED    13   1
  1P LOSS WILD-TYPE 172   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     13    1
  1P LOSS WILD-TYPE  172    9
   clus
vv  1P LOSS MUTATED 1P LOSS WILD-TYPE
  0              13               172
  1               1                 9
[1] 2 2
[1] FALSE
D42V7, binary
                   cls
clus                  0   1
  1P LOSS MUTATED     7  25
  1P LOSS WILD-TYPE  94 263
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      7   25
  1P LOSS WILD-TYPE   94  263
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  FEMALE               7                94
  MALE                25               263
[1] 2 2
[1] FALSE
D42V8, continuous
D42V9, continuous
D42V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  1P LOSS MUTATED       1                         1    29
  1P LOSS WILD-TYPE    41                        20   282
D42V11, multiclass
                           clus
vv                          1P LOSS MUTATED 1P LOSS WILD-TYPE
  ASIAN                                   1                41
  BLACK OR AFRICAN AMERICAN               1                20
  WHITE                                  29               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"
D42V12, binary
                   cls
clus                  0   1
  1P LOSS MUTATED     0  30
  1P LOSS WILD-TYPE   9 322
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      0   30
  1P LOSS WILD-TYPE    9  322
                        clus
vv                       1P LOSS MUTATED 1P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 9
  NOT HISPANIC OR LATINO              30               322
[1] 2 2
[1] FALSE

Clustering(43) Variable = 1Q LOSS MUTATION ANALYSIS
D43V1, survival
                   sevent
clus2                 0   1
  1Q LOSS MUTATED    18  15
  1Q LOSS WILD-TYPE 212 138
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               33               350 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               15               138 
$`1Q LOSS MUTATED`
TCGA-2F-A9KO TCGA-4Z-AA80 TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BT-A3PK TCGA-CU-A0YO 
       22.29         0.62        40.08         2.66         9.96         4.90 
TCGA-DK-A2HX TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3X1 TCGA-DK-A6B6 TCGA-DK-AA6Q 
        1.81        17.72        21.30        48.00        30.67        13.58 
TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E7-A4IJ TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TE 
       12.03        43.59         0.49         6.28        13.35        12.36 
TCGA-G2-A3IE TCGA-GC-A3RC TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-AATP TCGA-GV-A3QH 
       20.12        15.91        20.05         5.62        32.98         8.48 
TCGA-S5-A6DX TCGA-UY-A78K TCGA-UY-A78O TCGA-UY-A8OD TCGA-XF-A8HC TCGA-XF-A8HF 
        1.84        17.62        76.01       112.83         6.58        97.12 
TCGA-XF-AAN2 TCGA-ZF-A9R3 TCGA-ZF-A9RL 
       61.45        24.13        82.49 

$`1Q LOSS WILD-TYPE`
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW TCGA-4Z-AA7M 
       11.97        91.63       103.50       105.70         8.35        16.27 
TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W 
       44.94        16.83        16.77        17.16        34.98        27.62 
TCGA-4Z-AA7Y TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA84 TCGA-4Z-AA86 
       49.12        41.75        51.16        66.54        15.12        10.22 
TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A13I TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 
       47.80        33.83         7.33         6.74        12.39         6.58 
TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q 
       13.15        19.04        32.84        12.16        17.88        19.50 
TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X 
        5.06        14.89        14.96         5.06         8.35         8.25 
TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A42B 
       17.16        16.18        20.48         4.67        12.82        17.56 
TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F6 
       28.70        24.26        28.41         8.98         1.94        23.01 
TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V 
        0.46         0.43         0.69        10.95        12.66        12.46 
TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 
       12.10        12.62        12.26        13.12        12.00        12.10 
TCGA-CF-A8HX TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YR 
       11.34        11.34        11.87        13.08        12.92         7.20 
TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 
        5.46         5.19        16.31         1.84        13.58        21.86 
TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC 
        2.14        66.41        18.41        19.00        16.70       130.88 
TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A2I2 
      112.44        16.14        17.62        15.62        10.59         7.79 
TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN 
      123.85        87.32         2.20        13.58         7.82         8.22 
TCGA-DK-A3IS TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY 
       50.27        23.21         9.67        20.81        10.55       140.81 
TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 
       17.98        64.18        41.56        76.60        67.36        15.68 
TCGA-DK-A6B5 TCGA-DK-AA6L TCGA-DK-AA6P TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U 
       41.06        38.24        15.02       166.03        12.36        10.49 
TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA77 TCGA-E5-A4TZ 
        8.65         7.53        13.64        43.50        10.62        15.35 
TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 
       38.83        24.66         0.10         2.24        16.70        17.39 
TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF 
        0.56         0.66        14.56        13.97        12.99        14.33 
TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A8O7 
        0.92         1.22        13.68        14.07        12.95        15.32 
TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 
       14.37         8.09        32.02        16.77         8.94        33.04 
TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ 
        4.01        12.62        22.52        27.98        60.66        24.30 
TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ 
       23.41        17.98        29.16         5.52        25.74        46.78 
TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U 
       19.79        12.85        22.98        27.35        14.96        20.91 
TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU 
        3.62        15.58        26.73        53.88        11.01        19.33 
TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 
        5.36         5.69         8.25        27.45        18.08        58.92 
TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD 
        2.70         7.10        62.86        18.81         6.15        12.69 
TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 
        2.27         3.06         4.31         9.67        10.85        31.07 
TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A3EE TCGA-FT-A61P 
        7.13        10.65        17.23         8.94         3.25         6.48 
TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES 
       61.94        30.61        15.95        26.93        35.24        33.01 
TCGA-G2-A3IB TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F 
        7.23        17.62        66.02         6.94        64.44        19.46 
TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RD TCGA-GC-A3WC 
       21.40         2.24        15.81         4.50        14.07        17.75 
TCGA-GC-A3YS TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP 
       24.92         0.49         8.94        13.91         7.73         2.10 
TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q 
        3.12        20.98         2.20         7.36        10.92        11.31 
TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATQ 
       11.31         7.63        27.09         4.73        10.65         7.00 
TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QI 
       14.27        21.34        19.10        19.82        20.28        10.59 
TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ 
       27.35         8.58        19.07        22.72         1.51        19.40 
TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU 
       38.60         3.06         9.01         8.22        25.02         3.45 
TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RI 
       21.24         2.76         9.14        27.68         9.07        11.70 
TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-LC-A66R 
        1.74         1.81        15.42         6.38        11.80        15.32 
TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X 
       15.58        21.07        13.48        12.23        16.67        14.24 
TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78N 
        3.75        12.43        31.56        37.05        22.68        86.83 
TCGA-UY-A78P TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD 
       67.79        65.75         3.58        35.24        29.56        17.82 
TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HG 
        4.54         1.64        45.04        97.45       125.49        15.35 
TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ 
        1.87        17.88        48.62        64.80        79.66         3.22 
TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ 
       66.41        12.76        11.90        23.64        21.04        28.24 
TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 
       26.27        18.90         2.24        16.27        66.64         2.10 
TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAMJ 
       13.74        92.98        10.82       110.60        11.31        54.90 
TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX 
        7.63        71.57        91.73         2.96         8.32         6.77 
TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN3 TCGA-XF-AAN4 
       98.99        44.32        56.48        30.94        86.30        27.06 
TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC 
       75.39        18.81         3.88        18.84         9.63         0.66 
TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R4 
       11.97        13.64        18.64         7.36        21.11        30.28 
TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE 
       27.19        21.86        28.41        74.56        13.41         3.48 
TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4R 
       52.73        52.60        47.84        20.22         2.89        34.06 
TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 
       19.69         8.61        59.38        60.16        63.02        38.73 
TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H 
       35.41        57.90        19.40         8.52        47.15        19.17 
TCGA-ZF-AA5N TCGA-ZF-AA5P 
        5.52        10.13 

  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
             0.49              0.10 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
           112.83            166.03 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
            17.62             15.60 
[1] "0.5 - 112.8 (17.6)" "0.1 - 166.0 (15.6)"
[1] "hr=" "1.1"
D43V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  1Q LOSS MUTATED         1       16         5       11
  1Q LOSS WILD-TYPE       3      108       122      118
D43V3, multiclass
           clus
vv          1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  STAGE I                 1                 3
  STAGE II               16               108
  STAGE III               5               122
  STAGE IV               11               118
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1+T2  T3  T4
  1Q LOSS MUTATED         14  11   2
  1Q LOSS WILD-TYPE      107 173  51
D43V4, multiclass
          clus
vv         1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  T0+T1+T2              14               107
  T3                    11               173
  T4                     2                51
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  1Q LOSS MUTATED    15   3   8   0
  1Q LOSS WILD-TYPE 209  39  67   8
D43V5, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  N0              15               209
  N1               3                39
  N2               8                67
  N3               0                 8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V6, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED    14   0
  1Q LOSS WILD-TYPE 171  10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED     14    0
  1Q LOSS WILD-TYPE  171   10
   clus
vv  1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  0              14               171
  1               0                10
[1] 2 2
[1] FALSE
D43V7, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED     9  24
  1Q LOSS WILD-TYPE  92 264
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      9   24
  1Q LOSS WILD-TYPE   92  264
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  FEMALE               9                92
  MALE                24               264
[1] 2 2
[1] FALSE
D43V8, continuous
D43V9, continuous
D43V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  1Q LOSS MUTATED       2                         2    29
  1Q LOSS WILD-TYPE    40                        19   282
D43V11, multiclass
                           clus
vv                          1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  ASIAN                                   2                40
  BLACK OR AFRICAN AMERICAN               2                19
  WHITE                                  29               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"
D43V12, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED     0  32
  1Q LOSS WILD-TYPE   9 320
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      0   32
  1Q LOSS WILD-TYPE    9  320
                        clus
vv                       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 9
  NOT HISPANIC OR LATINO              32               320
[1] 2 2
[1] FALSE

Clustering(44) Variable = 2P LOSS MUTATION ANALYSIS
D44V1, survival
                   sevent
clus2                 0   1
  2P LOSS MUTATED    25  16
  2P LOSS WILD-TYPE 205 137
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               41               342 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               16               137 
$`2P LOSS MUTATED`
TCGA-2F-A9KW TCGA-4Z-AA7S TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BT-A20N TCGA-CU-A3KJ 
        8.35        34.98        40.08         2.66        32.84         5.46 
TCGA-CU-A3QU TCGA-DK-A2HX TCGA-DK-A3IS TCGA-DK-A3IV TCGA-E5-A4U1 TCGA-E7-A7DU 
        5.19         1.81        50.27         9.67        38.83         0.92 
TCGA-E7-A7PW TCGA-FD-A3B5 TCGA-FD-A3SJ TCGA-FD-A5BR TCGA-FJ-A3ZE TCGA-G2-A2EL 
       13.68         8.94        24.30        26.73        10.65        26.93 
TCGA-G2-AA3B TCGA-GC-A3OO TCGA-GC-A3YS TCGA-GC-A4ZW TCGA-GU-AATO TCGA-GV-A3JV 
       66.02        15.81        24.92         0.49        10.65        14.27 
TCGA-GV-A3JW TCGA-HQ-A5NE TCGA-K4-A3WU TCGA-K4-A5RJ TCGA-K4-AAQO TCGA-MV-A51V 
       21.34         8.22         3.45         1.74        11.80        13.48 
TCGA-S5-AA26 TCGA-UY-A9PF TCGA-XF-A8HH TCGA-XF-A9SV TCGA-XF-AAMF TCGA-XF-AAMT 
        3.75         1.64         1.87        12.76        10.82         2.96 
TCGA-YF-AA3M TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-AA4X TCGA-ZF-AA5H 
       13.64        52.60        47.84        63.02        19.17 

$`2P LOSS WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-4Z-AA7M 
       22.29        11.97        91.63       103.50       105.70        16.27 
TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7W TCGA-4Z-AA7Y 
       44.94        16.83        16.77        17.16        27.62        49.12 
TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA84 TCGA-4Z-AA86 
        0.62        41.75        51.16        66.54        15.12        10.22 
TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A13I TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 
       47.80        33.83         7.33         6.74        12.39         6.58 
TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R 
       13.15        19.04        12.16        17.88        19.50         5.06 
TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA 
       14.89        14.96         5.06         8.35         8.25        17.16 
TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B 
       16.18        20.48         4.67        12.82         9.96        17.56 
TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F6 
       28.70        24.26        28.41         8.98         1.94        23.01 
TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V 
        0.46         0.43         0.69        10.95        12.66        12.46 
TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 
       12.10        12.62        12.26        13.12        12.00        12.10 
TCGA-CF-A8HX TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO 
       11.34        11.34        11.87        13.08        12.92         4.90 
TCGA-CU-A0YR TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 
        7.20        16.31         1.84        13.58        21.86         2.14 
TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD 
       66.41        18.41        19.00        16.70       130.88       112.44 
TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 
       16.14        17.62        15.62        10.59         7.79       123.85 
TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ 
       87.32         2.20        13.58         7.82         8.22        17.72 
TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 
       21.30        23.21        20.81        10.55       140.81        48.00 
TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 
       17.98        64.18        41.56        76.60        67.36        15.68 
TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6S 
       41.06        30.67        38.24        15.02        13.58       166.03 
TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 
       12.36        10.49         8.65         7.53        13.64        43.50 
TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E7-A3X6 TCGA-E7-A3Y1 
       12.03        10.62        43.59        15.35        24.66         0.10 
TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF 
        0.49         2.24        16.70        17.39         0.56         0.66 
TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DV TCGA-E7-A7XN 
       14.56        13.97        12.99        14.33         1.22        14.07 
TCGA-E7-A85H TCGA-E7-A8O7 TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 
       12.95        15.32        14.37         8.09        32.02        16.77 
TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA 
       33.04         4.01        12.62        22.52        27.98        60.66 
TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ 
       23.41        17.98        29.16         5.52        25.74        46.78 
TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U 
       19.79        12.85        22.98        27.35        14.96        20.91 
TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV 
        3.62        15.58        53.88        11.01        19.33         5.36 
TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N 
        5.69         8.25        27.45        18.08        58.92         2.70 
TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC 
        7.10         6.28        13.35        62.86        18.81         6.15 
TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI 
       12.69        12.36         2.27         3.06         4.31         9.67 
TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A3EE 
       10.85        31.07         7.13        17.23         8.94         3.25 
TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EO TCGA-G2-A2ES 
        6.48        61.94        30.61        15.95        35.24        33.01 
TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F 
        7.23        20.12        17.62         6.94        64.44        19.46 
TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC 
       21.40         2.24         4.50        15.91        14.07        17.75 
TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS 
        8.94        13.91         7.73         2.10         3.12        20.98 
TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 
        2.20         7.36        10.92        11.31        11.31         7.63 
TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATP TCGA-GU-AATQ 
       27.09        20.05         5.62         4.73        32.98         7.00 
TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK 
       19.10        19.82        20.28         8.48        10.59        27.35 
TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE 
        8.58        19.07        22.72         1.51        19.40        38.60 
TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC 
        3.06         9.01        25.02        21.24         2.76         9.14 
TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P 
       27.68         9.07        11.70         1.81        15.42         6.38 
TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X 
       15.32        15.58        21.07        12.23        16.67        14.24 
TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M 
        1.84        12.43        31.56        17.62        37.05        22.68 
TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A8OD 
       86.83        76.01        67.79        65.75         3.58       112.83 
TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-XF-A8HB TCGA-XF-A8HC 
       35.24        29.56        17.82         4.54        45.04         6.58 
TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A8HI TCGA-XF-A9SG 
       97.45       125.49        97.12        15.35        17.88        48.62 
TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SW TCGA-XF-A9SX 
       64.80        79.66         3.22        66.41        11.90        23.64 
TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 
       21.04        28.24        26.27        18.90         2.24        16.27 
TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMG TCGA-XF-AAMH 
       66.64         2.10        13.74        92.98       110.60        11.31 
TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMW TCGA-XF-AAMX 
       54.90         7.63        71.57        91.73         8.32         6.77 
TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 
       98.99        44.32        56.48        30.94        61.45        86.30 
TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 
       27.06        75.39        18.81         3.88        18.84         9.63 
TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 
        0.66        11.97        18.64         7.36        21.11        24.13 
TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RD 
       30.28        27.19        21.86        28.41        74.56        13.41 
TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RL TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4R 
        3.48        52.73        82.49        20.22         2.89        34.06 
TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA51 TCGA-ZF-AA52 
       19.69         8.61        59.38        60.16        38.73        35.41 
TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5N TCGA-ZF-AA5P 
       57.90        19.40         8.52        47.15         5.52        10.13 

  2P LOSS MUTATED 2P LOSS WILD-TYPE 
             0.49              0.10 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
            66.02            166.03 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
           12.760            16.225 
[1] "0.5 - 66.0 (12.8)"  "0.1 - 166.0 (16.2)"
[1] "hr=" "1.2"
D44V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  2P LOSS MUTATED         1       13        14       15
  2P LOSS WILD-TYPE       3      111       113      114
D44V3, multiclass
           clus
vv          2P LOSS MUTATED 2P LOSS WILD-TYPE
  STAGE I                 1                 3
  STAGE II               13               111
  STAGE III              14               113
  STAGE IV               15               114
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1+T2  T3  T4
  2P LOSS MUTATED         15  19   6
  2P LOSS WILD-TYPE      106 165  47
D44V4, multiclass
          clus
vv         2P LOSS MUTATED 2P LOSS WILD-TYPE
  T0+T1+T2              15               106
  T3                    19               165
  T4                     6                47
[1] 3 2
[1] TRUE
[1] "dimension of 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    22   4  10   1
  2P LOSS WILD-TYPE 202  38  65   7
D44V5, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  N0              22               202
  N1               4                38
  N2              10                65
  N3               1                 7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V6, binary
                   cls
clus                  0   1
  2P LOSS MUTATED    22   2
  2P LOSS WILD-TYPE 163   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED     22    2
  2P LOSS WILD-TYPE  163    8
   clus
vv  2P LOSS MUTATED 2P LOSS WILD-TYPE
  0              22               163
  1               2                 8
[1] 2 2
[1] FALSE
D44V7, binary
                   cls
clus                  0   1
  2P LOSS MUTATED     7  36
  2P LOSS WILD-TYPE  94 252
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      7   36
  2P LOSS WILD-TYPE   94  252
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  FEMALE               7                94
  MALE                36               252
[1] 2 2
[1] FALSE
D44V8, continuous
D44V9, continuous
D44V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  2P LOSS MUTATED       3                         3    33
  2P LOSS WILD-TYPE    39                        18   278
D44V11, multiclass
                           clus
vv                          2P LOSS MUTATED 2P LOSS WILD-TYPE
  ASIAN                                   3                39
  BLACK OR AFRICAN AMERICAN               3                18
  WHITE                                  33               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"
D44V12, binary
                   cls
clus                  0   1
  2P LOSS MUTATED     1  39
  2P LOSS WILD-TYPE   8 313
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      1   39
  2P LOSS WILD-TYPE    8  313
                        clus
vv                       2P LOSS MUTATED 2P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 8
  NOT HISPANIC OR LATINO              39               313
[1] 2 2
[1] FALSE

Clustering(45) Variable = 2Q LOSS MUTATION ANALYSIS
D45V1, survival
                   sevent
clus2                 0   1
  2Q LOSS MUTATED    50  33
  2Q LOSS WILD-TYPE 180 120
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               83               300 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               33               120 
$`2Q LOSS MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KQ TCGA-2F-A9KW TCGA-4Z-AA7S TCGA-BL-A0C8 TCGA-BL-A13J 
       22.29        91.63         8.35        34.98        40.08         2.66 
TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A20V TCGA-BT-A2LA TCGA-BT-A3PH TCGA-C4-A0EZ 
       32.84        14.89         5.06        17.16         4.67         8.98 
TCGA-CF-A1HS TCGA-CF-A47X TCGA-CF-A7I0 TCGA-CU-A0YN TCGA-CU-A3KJ TCGA-CU-A3QU 
        0.43        12.62        12.10        12.92         5.46         5.19 
TCGA-DK-A2HX TCGA-DK-A3IK TCGA-DK-A3IS TCGA-DK-A3IV TCGA-DK-A3X2 TCGA-DK-A6AV 
        1.81         2.20        50.27         9.67        17.98        64.18 
TCGA-DK-A6B1 TCGA-DK-A6B6 TCGA-DK-AA77 TCGA-E5-A4U1 TCGA-E7-A541 TCGA-E7-A7DU 
       67.36        30.67        10.62        38.83        17.39         0.92 
TCGA-E7-A7PW TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3SJ 
       13.68        14.37         8.09        16.77         8.94        24.30 
TCGA-FD-A3SR TCGA-FD-A5BR TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A62N TCGA-FD-A6TE 
       19.79        26.73         5.36        27.45         2.70        12.36 
TCGA-FD-A6TF TCGA-FD-A6TH TCGA-FT-A61P TCGA-G2-A2EL TCGA-G2-AA3B TCGA-GC-A3OO 
        2.27         4.31         6.48        26.93        66.02        15.81 
TCGA-GC-A3RD TCGA-GC-A4ZW TCGA-GD-A3OP TCGA-GU-AATO TCGA-GV-A3JV TCGA-GV-A3JW 
       14.07         0.49         2.10        10.65        14.27        21.34 
TCGA-GV-A3QK TCGA-HQ-A2OE TCGA-HQ-A5NE TCGA-K4-A3WU TCGA-K4-A4AC TCGA-K4-A5RJ 
       27.35        38.60         8.22         3.45         9.14         1.74 
TCGA-K4-AAQO TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-S5-AA26 TCGA-UY-A78N TCGA-UY-A9PD 
       11.80        15.58        13.48         3.75        86.83        17.82 
TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A9SV TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAMT 
       15.35         1.87        12.76        10.82       110.60         2.96 
TCGA-YF-AA3L TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R9 TCGA-ZF-A9RF TCGA-ZF-A9RG 
       11.97        21.11        24.13        28.41        52.73        52.60 
TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4X TCGA-ZF-AA53 TCGA-ZF-AA5H 
       47.84        20.22        63.02        57.90        19.17 

$`2Q LOSS WILD-TYPE`
TCGA-2F-A9KP TCGA-2F-A9KR TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7O 
       11.97       103.50       105.70        16.27        44.94        16.83 
TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 
       16.77        17.16        27.62        49.12         0.62        41.75 
TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 
       51.16        66.54        15.12        10.22        47.80        33.83 
TCGA-BL-A13I TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J 
        7.33         6.74        12.39         6.58        13.15        19.04 
TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20W 
       12.16        17.88        19.50         5.06        14.96         8.35 
TCGA-BT-A20X TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B 
        8.25        16.18        20.48        12.82         9.96        17.56 
TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR 
       28.70        24.26        28.41         1.94        23.01         0.46 
TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47Y 
        0.69        10.95        12.66        12.46        12.10        12.26 
TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A8HX TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CF-A9FM 
       13.12        12.00        11.34        11.34        11.87        13.08 
TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 
        4.90         7.20        16.31         1.84        13.58        21.86 
TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC 
        2.14        66.41        18.41        19.00        16.70       130.88 
TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A2I2 
      112.44        16.14        17.62        15.62        10.59         7.79 
TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ 
      123.85        87.32        13.58         7.82         8.22        17.72 
TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 
       21.30        23.21        20.81        10.55       140.81        48.00 
TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-AA6L TCGA-DK-AA6P 
       41.56        76.60        15.68        41.06        38.24        15.02 
TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X 
       13.58       166.03        12.36        10.49         8.65         7.53 
TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E7-A3X6 
       13.64        43.50        12.03        43.59        15.35        24.66 
TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KE TCGA-E7-A5KF 
        0.10         0.49         2.24        16.70         0.56         0.66 
TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DV TCGA-E7-A7XN 
       14.56        13.97        12.99        14.33         1.22        14.07 
TCGA-E7-A85H TCGA-E7-A8O7 TCGA-FD-A3B3 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 
       12.95        15.32        32.02        33.04         4.01        12.62 
TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN 
       22.52        27.98        60.66        23.41        17.98        29.16 
TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P 
        5.52        25.74        46.78        12.85        22.98        27.35 
TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BS TCGA-FD-A5BT 
       14.96        20.91         3.62        15.58        53.88        11.01 
TCGA-FD-A5BU TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62O 
       19.33         5.69         8.25        18.08        58.92         7.10 
TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD 
        6.28        13.35        62.86        18.81         6.15        12.69 
TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE 
        3.06         9.67        10.85        31.07         7.13        10.65 
TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK 
       17.23         8.94         3.25        61.94        30.61        15.95 
TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3C 
       35.24        33.01         7.23        20.12        17.62         6.94 
TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3RB TCGA-GC-A3RC 
       64.44        19.46        21.40         2.24         4.50        15.91 
TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OQ 
       17.75        24.92         8.94        13.91         7.73         3.12 
TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R 
       20.98         2.20         7.36        10.92        11.31        11.31 
TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATP 
        7.63        27.09        20.05         5.62         4.73        32.98 
TCGA-GU-AATQ TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI 
        7.00        19.10        19.82        20.28         8.48        10.59 
TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OF 
        8.58        19.07        22.72         1.51        19.40         3.06 
TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A54R TCGA-K4-A5RH 
        9.01        25.02        21.24         2.76        27.68         9.07 
TCGA-K4-A5RI TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-LC-A66R TCGA-LT-A8JT 
       11.70         1.81        15.42         6.38        15.32        21.07 
TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-SY-A9G5 
       12.23        16.67        14.24         1.84        12.43        31.56 
TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OB 
       17.62        37.05        22.68        76.01        67.79        65.75 
TCGA-UY-A8OC TCGA-UY-A8OD TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PE TCGA-UY-A9PF 
        3.58       112.83        35.24        29.56         4.54         1.64 
TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HI 
       45.04         6.58        97.45       125.49        97.12        17.88 
TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SW 
       48.62        64.80        79.66         3.22        66.41        11.90 
TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 
       23.64        21.04        28.24        26.27        18.90         2.24 
TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMH 
       16.27        66.64         2.10        13.74        92.98        11.31 
TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMW TCGA-XF-AAMX 
       54.90         7.63        71.57        91.73         8.32         6.77 
TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 
       98.99        44.32        56.48        30.94        61.45        86.30 
TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 
       27.06        75.39        18.81         3.88        18.84         9.63 
TCGA-YC-A9TC TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R4 TCGA-ZF-A9R5 
        0.66        13.64        18.64         7.36        30.28        27.19 
TCGA-ZF-A9R7 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RL TCGA-ZF-AA4N 
       21.86        74.56        13.41         3.48        82.49         2.89 
TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA51 
       34.06        19.69         8.61        59.38        60.16        38.73 
TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5N TCGA-ZF-AA5P 
       35.41        19.40         8.52        47.15         5.52        10.13 

  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
             0.43              0.10 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
           110.60            166.03 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
           14.270            16.225 
[1] "0.4 - 110.6 (14.3)" "0.1 - 166.0 (16.2)"
[1] "hr=" "1.1"
D45V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  2Q LOSS MUTATED         1       27        25       30
  2Q LOSS WILD-TYPE       3       97       102       99
D45V3, multiclass
           clus
vv          2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  STAGE I                 1                 3
  STAGE II               27                97
  STAGE III              25               102
  STAGE IV               30                99
[1] 4 2
[1] TRUE
[1] "dimension of contingency 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         29  39  13
  2Q LOSS WILD-TYPE       92 145  40
D45V4, multiclass
          clus
vv         2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  T0+T1+T2              29                92
  T3                    39               145
  T4                    13                40
[1] 3 2
[1] TRUE
[1] "dimension of 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    42   8  22   1
  2Q LOSS WILD-TYPE 182  34  53   7
D45V5, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  N0              42               182
  N1               8                34
  N2              22                53
  N3               1                 7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V6, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED    44   3
  2Q LOSS WILD-TYPE 141   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED     44    3
  2Q LOSS WILD-TYPE  141    7
   clus
vv  2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  0              44               141
  1               3                 7
[1] 2 2
[1] FALSE
D45V7, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED    22  63
  2Q LOSS WILD-TYPE  79 225
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED     22   63
  2Q LOSS WILD-TYPE   79  225
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  FEMALE              22                79
  MALE                63               225
[1] 2 2
[1] FALSE
D45V8, continuous
D45V9, continuous
D45V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  2Q LOSS MUTATED       9                         5    65
  2Q LOSS WILD-TYPE    33                        16   246
D45V11, multiclass
                           clus
vv                          2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  ASIAN                                   9                33
  BLACK OR AFRICAN AMERICAN               5                16
  WHITE                                  65               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"
D45V12, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED     2  78
  2Q LOSS WILD-TYPE   7 274
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      2   78
  2Q LOSS WILD-TYPE    7  274
                        clus
vv                       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                 7
  NOT HISPANIC OR LATINO              78               274
[1] 2 2
[1] FALSE

Clustering(46) Variable = 3P LOSS MUTATION ANALYSIS
D46V1, survival
                   sevent
clus2                 0   1
  3P LOSS MUTATED    27  24
  3P LOSS WILD-TYPE 203 129
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               51               332 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               24               129 
$`3P LOSS MUTATED`
TCGA-2F-A9KR TCGA-4Z-AA7R TCGA-4Z-AA82 TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BT-A20V 
      103.50        17.16        51.16        40.08         2.66         5.06 
TCGA-BT-A20X TCGA-BT-A42C TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-CF-A1HS TCGA-CF-A5UA 
        8.25        28.70         8.98         1.94         0.43        12.00 
TCGA-CU-A0YN TCGA-CU-A3KJ TCGA-DK-A1A6 TCGA-DK-A1AB TCGA-DK-A2I2 TCGA-DK-A3IM 
       12.92         5.46        66.41        16.70         7.79         7.82 
TCGA-DK-A3WX TCGA-DK-A6B5 TCGA-DK-AA6Q TCGA-E7-A4IJ TCGA-E7-A7DV TCGA-FD-A3B4 
       10.55        41.06        13.58         0.49         1.22        16.77 
TCGA-FD-A3B6 TCGA-FD-A3N5 TCGA-FD-A43Y TCGA-FD-A5C1 TCGA-G2-A3IB TCGA-G2-AA3B 
       33.04        22.52        15.58        58.92         7.23        66.02 
TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GU-A767 TCGA-K4-A4AC TCGA-K4-A5RI 
        4.50        17.75        24.92         4.73         9.14        11.70 
TCGA-UY-A78O TCGA-XF-A8HD TCGA-XF-A9T0 TCGA-XF-A9T5 TCGA-XF-AAMQ TCGA-XF-AAMT 
       76.01        97.45        26.27        66.64        71.57         2.96 
TCGA-XF-AAMW TCGA-XF-AAN3 TCGA-YF-AA3M TCGA-ZF-A9RE TCGA-ZF-A9RG TCGA-ZF-A9RN 
        8.32        86.30        13.64         3.48        52.60        20.22 
TCGA-ZF-AA4W TCGA-ZF-AA56 TCGA-ZF-AA5H 
       60.16         8.52        19.17 

$`3P LOSS WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KT TCGA-2F-A9KW TCGA-4Z-AA7M 
       22.29        11.97        91.63       105.70         8.35        16.27 
TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA7Y 
       44.94        16.83        16.77        34.98        27.62        49.12 
TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA83 TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-4Z-AA87 
        0.62        41.75        66.54        15.12        10.22        47.80 
TCGA-4Z-AA89 TCGA-BL-A13I TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX 
       33.83         7.33         6.74        12.39         6.58        13.15 
TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R 
       19.04        32.84        12.16        17.88        19.50         5.06 
TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20W TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD 
       14.89        14.96         8.35        17.16        16.18        20.48 
TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F 
        4.67        12.82         9.96        17.56        24.26        28.41 
TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V 
       23.01         0.46         0.69        10.95        12.66        12.46 
TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A7I0 TCGA-CF-A8HX 
       12.10        12.62        12.26        13.12        12.10        11.34 
TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3QU 
       11.34        11.87        13.08         4.90         7.20         5.19 
TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A7 
       16.31         1.84        13.58        21.86         2.14        18.41 
TCGA-DK-A1AA TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG 
       19.00       130.88       112.44        16.14        17.62        15.62 
TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL 
        1.81        10.59       123.85        87.32         2.20        13.58 
TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV 
        8.22        17.72        50.27        21.30        23.21         9.67 
TCGA-DK-A3WW TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW 
       20.81       140.81        48.00        17.98        64.18        41.56 
TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6P 
       76.60        67.36        15.68        30.67        38.24        15.02 
TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 
      166.03        12.36        10.49         8.65         7.53        13.64 
TCGA-DK-AA74 TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 
       43.50        12.03        10.62        43.59        15.35        38.83 
TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE 
       24.66         0.10         2.24        16.70        17.39         0.56 
TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU 
        0.66        14.56        13.97        12.99        14.33         0.92 
TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A8O7 TCGA-E7-A97P TCGA-E7-A97Q 
       13.68        14.07        12.95        15.32        14.37         8.09 
TCGA-FD-A3B3 TCGA-FD-A3B5 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N6 TCGA-FD-A3NA 
       32.02         8.94         4.01        12.62        27.98        60.66 
TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP 
       24.30        23.41        17.98        29.16         5.52        25.74 
TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S 
       46.78        19.79        12.85        22.98        27.35        14.96 
TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU 
       20.91         3.62        26.73        53.88        11.01        19.33 
TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A62N 
        5.36         5.69         8.25        27.45        18.08         2.70 
TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC 
        7.10         6.28        13.35        62.86        18.81         6.15 
TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI 
       12.69        12.36         2.27         3.06         4.31         9.67 
TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FJ-A871 
       10.85        31.07         7.13        10.65        17.23         8.94 
TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL 
        3.25         6.48        61.94        30.61        15.95        26.93 
TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3C TCGA-G2-AA3D 
       35.24        33.01        20.12        17.62         6.94        64.44 
TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A3RD 
       19.46        21.40         2.24        15.81        15.91        14.07 
TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ 
        0.49         8.94        13.91         7.73         2.10         3.12 
TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R 
       20.98         2.20         7.36        10.92        11.31        11.31 
TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-AATO TCGA-GU-AATP 
        7.63        27.09        20.05         5.62        10.65        32.98 
TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF 
        7.00        14.27        21.34        19.10        19.82        20.28 
TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA 
        8.48        10.59        27.35         8.58        19.07        22.72 
TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE 
        1.51        19.40        38.60         3.06         9.01         8.22 
TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A54R TCGA-K4-A5RH 
       25.02         3.45        21.24         2.76        27.68         9.07 
TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-LC-A66R 
        1.74         1.81        15.42         6.38        11.80        15.32 
TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X 
       15.58        21.07        13.48        12.23        16.67        14.24 
TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L 
        1.84         3.75        12.43        31.56        17.62        37.05 
TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A78P TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A8OD 
       22.68        86.83        67.79        65.75         3.58       112.83 
TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HB 
       35.24        29.56        17.82         4.54         1.64        45.04 
TCGA-XF-A8HC TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A8HI 
        6.58       125.49        97.12        15.35         1.87        17.88 
TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SV 
       48.62        64.80        79.66         3.22        66.41        12.76 
TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T2 TCGA-XF-A9T3 
       11.90        23.64        21.04        28.24        18.90         2.24 
TCGA-XF-A9T4 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMG 
       16.27         2.10        13.74        92.98        10.82       110.60 
TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMR TCGA-XF-AAMX TCGA-XF-AAMY 
       11.31        54.90         7.63        91.73         6.77        98.99 
TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN4 TCGA-XF-AAN5 
       44.32        56.48        30.94        61.45        27.06        75.39 
TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L 
       18.81         3.88        18.84         9.63         0.66        11.97 
TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 
       18.64         7.36        21.11        24.13        30.28        27.19 
TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RF TCGA-ZF-A9RL 
       21.86        28.41        74.56        13.41        52.73        82.49 
TCGA-ZF-A9RM TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4V 
       47.84         2.89        34.06        19.69         8.61        59.38 
TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA58 
       63.02        38.73        35.41        57.90        19.40        47.15 
TCGA-ZF-AA5N TCGA-ZF-AA5P 
        5.52        10.13 

  3P LOSS MUTATED 3P LOSS WILD-TYPE 
             0.43              0.10 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
           103.50            166.03 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
           15.580            15.745 
[1] "0.4 - 103.5 (15.6)" "0.1 - 166.0 (15.7)"
[1] "hr=" "1.2"
D46V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  3P LOSS MUTATED         1       13        17       19
  3P LOSS WILD-TYPE       3      111       110      110
D46V3, multiclass
           clus
vv          3P LOSS MUTATED 3P LOSS WILD-TYPE
  STAGE I                 1                 3
  STAGE II               13               111
  STAGE III              17               110
  STAGE IV               19               110
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1+T2  T3  T4
  3P LOSS MUTATED         14  24  10
  3P LOSS WILD-TYPE      107 160  43
D46V4, multiclass
          clus
vv         3P LOSS MUTATED 3P LOSS WILD-TYPE
  T0+T1+T2              14               107
  T3                    24               160
  T4                    10                43
[1] 3 2
[1] TRUE
[1] "dimension of 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    28   6   9   2
  3P LOSS WILD-TYPE 196  36  66   6
D46V5, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  N0              28               196
  N1               6                36
  N2               9                66
  N3               2                 6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V6, binary
                   cls
clus                  0   1
  3P LOSS MUTATED    25   1
  3P LOSS WILD-TYPE 160   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     25    1
  3P LOSS WILD-TYPE  160    9
   clus
vv  3P LOSS MUTATED 3P LOSS WILD-TYPE
  0              25               160
  1               1                 9
[1] 2 2
[1] FALSE
D46V7, binary
                   cls
clus                  0   1
  3P LOSS MUTATED    23  28
  3P LOSS WILD-TYPE  78 260
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     23   28
  3P LOSS WILD-TYPE   78  260
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  FEMALE              23                78
  MALE                28               260
[1] 2 2
[1] FALSE
D46V8, continuous
D46V9, continuous
D46V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3P LOSS MUTATED       3                         6    38
  3P LOSS WILD-TYPE    39                        15   273
D46V11, multiclass
                           clus
vv                          3P LOSS MUTATED 3P LOSS WILD-TYPE
  ASIAN                                   3                39
  BLACK OR AFRICAN AMERICAN               6                15
  WHITE                                  38               273
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V12, binary
                   cls
clus                  0   1
  3P LOSS MUTATED     1  44
  3P LOSS WILD-TYPE   8 308
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      1   44
  3P LOSS WILD-TYPE    8  308
                        clus
vv                       3P LOSS MUTATED 3P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 8
  NOT HISPANIC OR LATINO              44               308
[1] 2 2
[1] FALSE

Clustering(47) Variable = 3Q LOSS MUTATION ANALYSIS
D47V1, survival
                   sevent
clus2                 0   1
  3Q LOSS MUTATED    13  10
  3Q LOSS WILD-TYPE 217 143
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               23               360 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               10               143 
$`3Q LOSS MUTATED`
TCGA-4Z-AA7R TCGA-BL-A0C8 TCGA-BL-A13J TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-CF-A5UA 
       17.16        40.08         2.66         8.98         1.94        12.00 
TCGA-CU-A0YN TCGA-DK-A3WX TCGA-DK-A6B5 TCGA-DK-AA6Q TCGA-E7-A7DV TCGA-FD-A43Y 
       12.92        10.55        41.06        13.58         1.22        15.58 
TCGA-FD-A5C1 TCGA-G2-AA3B TCGA-GU-A767 TCGA-K4-A4AC TCGA-UY-A78O TCGA-XF-A8HD 
       58.92        66.02         4.73         9.14        76.01        97.45 
TCGA-XF-A9T0 TCGA-ZF-A9R9 TCGA-ZF-A9RG TCGA-ZF-AA4W TCGA-ZF-AA5H 
       26.27        28.41        52.60        60.16        19.17 

$`3Q LOSS WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        91.63       103.50       105.70         8.35 
TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7S TCGA-4Z-AA7W 
       16.27        44.94        16.83        16.77        34.98        27.62 
TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA84 
       49.12         0.62        41.75        51.16        66.54        15.12 
TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A13I TCGA-BL-A3JM TCGA-BL-A5ZZ 
       10.22        47.80        33.83         7.33         6.74        12.39 
TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P 
        6.58        13.15        19.04        32.84        12.16        17.88 
TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W 
       19.50         5.06        14.89        14.96         5.06         8.35 
TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ 
        8.25        17.16        16.18        20.48         4.67        12.82 
TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F6 
        9.96        17.56        28.70        24.26        28.41        23.01 
TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V 
        0.46         0.43         0.69        10.95        12.66        12.46 
TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A7I0 TCGA-CF-A8HX 
       12.10        12.62        12.26        13.12        12.10        11.34 
TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ 
       11.34        11.87        13.08         4.90         7.20         5.46 
TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 
        5.19        16.31         1.84        13.58        21.86         2.14 
TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD 
       66.41        18.41        19.00        16.70       130.88       112.44 
TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 
       16.14        17.62        15.62         1.81        10.59         7.79 
TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN 
      123.85        87.32         2.20        13.58         7.82         8.22 
TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW 
       17.72        50.27        21.30        23.21         9.67        20.81 
TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 
      140.81        48.00        17.98        64.18        41.56        76.60 
TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6P TCGA-DK-AA6S 
       67.36        15.68        30.67        38.24        15.02       166.03 
TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 
       12.36        10.49         8.65         7.53        13.64        43.50 
TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 
       12.03        10.62        43.59        15.35        38.83        24.66 
TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE 
        0.10         0.49         2.24        16.70        17.39         0.56 
TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU 
        0.66        14.56        13.97        12.99        14.33         0.92 
TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A8O7 TCGA-E7-A97P TCGA-E7-A97Q 
       13.68        14.07        12.95        15.32        14.37         8.09 
TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 
       32.02        16.77         8.94        33.04         4.01        12.62 
TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM 
       22.52        27.98        60.66        24.30        23.41        17.98 
TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS 
       29.16         5.52        25.74        46.78        19.79        12.85 
TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BR 
       22.98        27.35        14.96        20.91         3.62        26.73 
TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY 
       53.88        11.01        19.33         5.36         5.69         8.25 
TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S 
       27.45        18.08         2.70         7.10         6.28        13.35 
TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF 
       62.86        18.81         6.15        12.69        12.36         2.27 
TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 
        3.06         4.31         9.67        10.85        31.07         7.13 
TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EF 
       10.65        17.23         8.94         3.25         6.48        61.94 
TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB 
       30.61        15.95        26.93        35.24        33.01         7.23 
TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM 
       20.12        17.62         6.94        64.44        19.46        21.40 
TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC 
        2.24        15.81         4.50        15.91        14.07        17.75 
TCGA-GC-A3YS TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP 
       24.92         0.49         8.94        13.91         7.73         2.10 
TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q 
        3.12        20.98         2.20         7.36        10.92        11.31 
TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-AATO 
       11.31         7.63        27.09        20.05         5.62        10.65 
TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ 
       32.98         7.00        14.27        21.34        19.10        19.82 
TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G 
       20.28         8.48        10.59        27.35         8.58        19.07 
TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND 
       22.72         1.51        19.40        38.60         3.06         9.01 
TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A54R 
        8.22        25.02         3.45        21.24         2.76        27.68 
TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P 
        9.07        11.70         1.74         1.81        15.42         6.38 
TCGA-K4-AAQO TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FI 
       11.80        15.32        15.58        21.07        13.48        12.23 
TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-SY-A9G5 
       16.67        14.24         1.84         3.75        12.43        31.56 
TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A78P TCGA-UY-A8OB 
       17.62        37.05        22.68        86.83        67.79        65.75 
TCGA-UY-A8OC TCGA-UY-A8OD TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE 
        3.58       112.83        35.24        29.56        17.82         4.54 
TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG 
        1.64        45.04         6.58       125.49        97.12        15.35 
TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ 
        1.87        17.88        48.62        64.80        79.66         3.22 
TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ 
       66.41        12.76        11.90        23.64        21.04        28.24 
TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 
       18.90         2.24        16.27        66.64         2.10        13.74 
TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML 
       92.98        10.82       110.60        11.31        54.90         7.63 
TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMY 
       71.57        91.73         2.96         8.32         6.77        98.99 
TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN4 
       44.32        56.48        30.94        61.45        86.30        27.06 
TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC 
       75.39        18.81         3.88        18.84         9.63         0.66 
TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 
       11.97        13.64        18.64         7.36        21.11        24.13 
TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE 
       30.28        27.19        21.86        74.56        13.41         3.48 
TCGA-ZF-A9RF TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4R 
       52.73        82.49        47.84        20.22         2.89        34.06 
TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 
       19.69         8.61        59.38        63.02        38.73        35.41 
TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5N TCGA-ZF-AA5P 
       57.90        19.40         8.52        47.15         5.52        10.13 

  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
             1.22              0.10 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
            97.45            166.03 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
            17.16             15.65 
[1] "1.2 - 97.5 (17.2)"  "0.1 - 166.0 (15.6)"
[1] "hr=" "1.1"
D47V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  3Q LOSS MUTATED         1        5         8        9
  3Q LOSS WILD-TYPE       3      119       119      120
D47V3, multiclass
           clus
vv          3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  STAGE I                 1                 3
  STAGE II                5               119
  STAGE III               8               119
  STAGE IV                9               120
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1+T2  T3  T4
  3Q LOSS MUTATED          6  12   5
  3Q LOSS WILD-TYPE      115 172  48
D47V4, multiclass
          clus
vv         3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  T0+T1+T2               6               115
  T3                    12               172
  T4                     5                48
[1] 3 2
[1] TRUE
[1] "dimension of 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    14   2   5   1
  3Q LOSS WILD-TYPE 210  40  70   7
D47V5, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  N0              14               210
  N1               2                40
  N2               5                70
  N3               1                 7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V6, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED    11   1
  3Q LOSS WILD-TYPE 174   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED     11    1
  3Q LOSS WILD-TYPE  174    9
   clus
vv  3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  0              11               174
  1               1                 9
[1] 2 2
[1] FALSE
D47V7, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED     8  15
  3Q LOSS WILD-TYPE  93 273
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      8   15
  3Q LOSS WILD-TYPE   93  273
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  FEMALE               8                93
  MALE                15               273
[1] 2 2
[1] FALSE
D47V8, continuous
D47V9, continuous
D47V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3Q LOSS MUTATED       1                         1    19
  3Q LOSS WILD-TYPE    41                        20   292
D47V11, multiclass
                           clus
vv                          3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  ASIAN                                   1                41
  BLACK OR AFRICAN AMERICAN               1                20
  WHITE                                  19               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"
D47V12, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED     0  20
  3Q LOSS WILD-TYPE   9 332
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      0   20
  3Q LOSS WILD-TYPE    9  332
                        clus
vv                       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 9
  NOT HISPANIC OR LATINO              20               332
[1] 2 2
[1] FALSE

Clustering(48) Variable = 4P LOSS MUTATION ANALYSIS
D48V1, survival
                   sevent
clus2                 0   1
  4P LOSS MUTATED    70  64
  4P LOSS WILD-TYPE 160  89
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
              134               249 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               64                89 
$`4P LOSS MUTATED`
TCGA-2F-A9KO TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7W TCGA-4Z-AA80 TCGA-4Z-AA82 
       22.29        16.77        17.16        27.62         0.62        51.16 
TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BT-A20J TCGA-BT-A20N 
       15.12        10.22        40.08         2.66        19.04        32.84 
TCGA-BT-A20R TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LB TCGA-BT-A2LD 
        5.06         5.06         8.35         8.25        16.18        20.48 
TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42E TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CU-A0YN 
        4.67        17.56        24.26         0.46         0.43        12.92 
TCGA-CU-A0YO TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I6 
        4.90        18.41       112.44         1.81        10.59        87.32 
TCGA-DK-A3IK TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IT TCGA-DK-A3IV TCGA-DK-A3X2 
        2.20         7.82         8.22        21.30         9.67        17.98 
TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6W 
       15.68        41.06        30.67        13.58       166.03         8.65 
TCGA-E5-A4TZ TCGA-E7-A3X6 TCGA-E7-A4IJ TCGA-FD-A3B3 TCGA-FD-A3B5 TCGA-FD-A3B6 
       15.35        24.66         0.49        32.02         8.94        33.04 
TCGA-FD-A3B7 TCGA-FD-A3SL TCGA-FD-A3SO TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A5BR 
        4.01        23.41         5.52        12.85        22.98        26.73 
TCGA-FD-A5BU TCGA-FD-A5BY TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P 
       19.33         8.25        58.92         2.70         7.10         6.28 
TCGA-FD-A62S TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-G2-A3IB 
       13.35         3.06         4.31        31.07        17.23         7.23 
TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3YS TCGA-GC-A6I3 
       19.46        21.40        15.81         4.50        24.92        13.91 
TCGA-GD-A2C5 TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-AATP 
        7.73         2.20        11.31         7.63        20.05        32.98 
TCGA-GV-A3JV TCGA-GV-A40G TCGA-H4-A2HQ TCGA-HQ-A2OF TCGA-K4-A3WS TCGA-K4-A3WV 
       14.27        19.07        19.40         3.06        25.02        21.24 
TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6MB TCGA-K4-AAQO 
        9.14        27.68        11.70         1.74        15.42        11.80 
TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G0 
       12.23        16.67        14.24         1.84         3.75        12.43 
TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78M TCGA-UY-A8OB TCGA-UY-A8OD TCGA-UY-A9PB 
       31.56        17.62        22.68        65.75       112.83        29.56 
TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HC TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A9SJ 
        4.54         1.64         6.58        97.12        15.35         3.22 
TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9T5 TCGA-XF-AAMG TCGA-XF-AAMJ TCGA-XF-AAMT 
       23.64        21.04        66.64       110.60        54.90         2.96 
TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN7 TCGA-YF-AA3M 
       44.32        56.48        61.45        86.30        18.81        13.64 
TCGA-ZF-A9R0 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE 
       18.64        21.86        28.41        74.56        13.41         3.48 
TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4T TCGA-ZF-AA4W 
       52.73        52.60        20.22         2.89        19.69        60.16 
TCGA-ZF-AA4X TCGA-ZF-AA53 
       63.02        57.90 

$`4P LOSS WILD-TYPE`
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW TCGA-4Z-AA7M 
       11.97        91.63       103.50       105.70         8.35        16.27 
TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7S TCGA-4Z-AA7Y TCGA-4Z-AA81 TCGA-4Z-AA83 
       44.94        16.83        34.98        49.12        41.75        66.54 
TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A13I TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 
       47.80        33.83         7.33         6.74        12.39         6.58 
TCGA-BT-A0YX TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20T TCGA-BT-A20U 
       13.15        12.16        17.88        19.50        14.89        14.96 
TCGA-BT-A2LA TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42C TCGA-BT-A42F TCGA-C4-A0EZ 
       17.16        12.82         9.96        28.70        28.41         8.98 
TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V 
        1.94        23.01         0.69        10.95        12.66        12.46 
TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 
       12.10        12.62        12.26        13.12        12.00        12.10 
TCGA-CF-A8HX TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YR TCGA-CU-A3KJ 
       11.34        11.34        11.87        13.08         7.20         5.46 
TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 
        5.19        16.31         1.84        13.58        21.86         2.14 
TCGA-DK-A1A6 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AE TCGA-DK-A1AF 
       66.41        19.00        16.70       130.88        16.14        17.62 
TCGA-DK-A1AG TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IL TCGA-DK-A3IQ TCGA-DK-A3IS 
       15.62         7.79       123.85        13.58        17.72        50.27 
TCGA-DK-A3IU TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A6AV 
       23.21        20.81        10.55       140.81        48.00        64.18 
TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-AA6L TCGA-DK-AA6P TCGA-DK-AA6T 
       41.56        76.60        67.36        38.24        15.02        12.36 
TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA76 TCGA-DK-AA77 
       10.49         7.53        13.64        43.50        12.03        10.62 
TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 
       43.59        38.83         0.10         2.24        16.70        17.39 
TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF 
        0.56         0.66        14.56        13.97        12.99        14.33 
TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A8O7 
        0.92         1.22        13.68        14.07        12.95        15.32 
TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B4 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 
       14.37         8.09        16.77        12.62        22.52        27.98 
TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SP TCGA-FD-A3SQ 
       60.66        24.30        17.98        29.16        25.74        46.78 
TCGA-FD-A3SR TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A43Y 
       19.79        27.35        14.96        20.91         3.62        15.58 
TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BZ TCGA-FD-A5C0 
       53.88        11.01         5.36         5.69        27.45        18.08 
TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF 
       62.86        18.81         6.15        12.69        12.36         2.27 
TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-FT-A3EE 
        9.67        10.85         7.13        10.65         8.94         3.25 
TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO 
        6.48        61.94        30.61        15.95        26.93        35.24 
TCGA-G2-A2ES TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3D 
       33.01        20.12        17.62        66.02         6.94        64.44 
TCGA-GC-A3I6 TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A4ZW TCGA-GC-A6I1 
        2.24        15.91        14.07        17.75         0.49         8.94 
TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42R 
        2.10         3.12        20.98         7.36        10.92        11.31 
TCGA-GU-A763 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATQ TCGA-GV-A3JW 
       27.09         5.62         4.73        10.65         7.00        21.34 
TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK 
       19.10        19.82        20.28         8.48        10.59        27.35 
TCGA-GV-A40E TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-HQ-A2OE TCGA-HQ-A5ND TCGA-HQ-A5NE 
        8.58        22.72         1.51        38.60         9.01         8.22 
TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A5RH TCGA-K4-A6FZ TCGA-K4-A83P TCGA-LC-A66R 
        3.45         2.76         9.07         1.81         6.38        15.32 
TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-MV-A51V TCGA-UY-A78L TCGA-UY-A78N TCGA-UY-A78O 
       15.58        21.07        13.48        37.05        86.83        76.01 
TCGA-UY-A78P TCGA-UY-A8OC TCGA-UY-A9PA TCGA-UY-A9PD TCGA-XF-A8HB TCGA-XF-A8HD 
       67.79         3.58        35.24        17.82        45.04        97.45 
TCGA-XF-A8HE TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI 
      125.49         1.87        17.88        48.62        64.80        79.66 
TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 
       66.41        12.76        11.90        28.24        26.27        18.90 
TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF 
        2.24        16.27         2.10        13.74        92.98        10.82 
TCGA-XF-AAMH TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMW TCGA-XF-AAMX 
       11.31         7.63        71.57        91.73         8.32         6.77 
TCGA-XF-AAMY TCGA-XF-AAN1 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN8 TCGA-YC-A89H 
       98.99        30.94        27.06        75.39         3.88        18.84 
TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 
        9.63         0.66        11.97         7.36        21.11        24.13 
TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-AA4R TCGA-ZF-AA4U 
       30.28        27.19        82.49        47.84        34.06         8.61 
TCGA-ZF-AA4V TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 
       59.38        38.73        35.41        19.40         8.52        47.15 
TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
       19.17         5.52        10.13 

  4P LOSS MUTATED 4P LOSS WILD-TYPE 
             0.43              0.10 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
           166.03            140.81 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
            16.72             15.32 
[1] "0.4 - 166.0 (16.7)" "0.1 - 140.8 (15.3)"
[1] "hr=" "1.4"
D48V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  4P LOSS MUTATED         1       35        38       60
  4P LOSS WILD-TYPE       3       89        89       69
D48V3, multiclass
           clus
vv          4P LOSS MUTATED 4P LOSS WILD-TYPE
  STAGE I                 1                 3
  STAGE II               35                89
  STAGE III              38                89
  STAGE IV               60                69
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1+T2  T3  T4
  4P LOSS MUTATED         36  74  17
  4P LOSS WILD-TYPE       85 110  36
D48V4, multiclass
          clus
vv         4P LOSS MUTATED 4P LOSS WILD-TYPE
  T0+T1+T2              36                85
  T3                    74               110
  T4                    17                36
[1] 3 2
[1] TRUE
[1] "dimension of 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    61  20  37   1
  4P LOSS WILD-TYPE 163  22  38   7
D48V5, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  N0              61               163
  N1              20                22
  N2              37                38
  N3               1                 7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V6, binary
                   cls
clus                  0   1
  4P LOSS MUTATED    58   3
  4P LOSS WILD-TYPE 127   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     58    3
  4P LOSS WILD-TYPE  127    7
   clus
vv  4P LOSS MUTATED 4P LOSS WILD-TYPE
  0              58               127
  1               3                 7
[1] 2 2
[1] FALSE
D48V7, binary
                   cls
clus                  0   1
  4P LOSS MUTATED    33 103
  4P LOSS WILD-TYPE  68 185
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     33  103
  4P LOSS WILD-TYPE   68  185
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  FEMALE              33                68
  MALE               103               185
[1] 2 2
[1] FALSE
D48V8, continuous
D48V9, continuous
D48V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  4P LOSS MUTATED       9                        13   111
  4P LOSS WILD-TYPE    33                         8   200
D48V11, multiclass
                           clus
vv                          4P LOSS MUTATED 4P LOSS WILD-TYPE
  ASIAN                                   9                33
  BLACK OR AFRICAN AMERICAN              13                 8
  WHITE                                 111               200
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V12, binary
                   cls
clus                  0   1
  4P LOSS MUTATED     4 122
  4P LOSS WILD-TYPE   5 230
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      4  122
  4P LOSS WILD-TYPE    5  230
                        clus
vv                       4P LOSS MUTATED 4P LOSS WILD-TYPE
  HISPANIC OR LATINO                   4                 5
  NOT HISPANIC OR LATINO             122               230
[1] 2 2
[1] FALSE

Clustering(49) Variable = 4Q LOSS MUTATION ANALYSIS
D49V1, survival
                   sevent
clus2                 0   1
  4Q LOSS MUTATED    69  58
  4Q LOSS WILD-TYPE 161  95
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
              127               256 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               58                95 
$`4Q LOSS MUTATED`
TCGA-2F-A9KT TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA80 TCGA-4Z-AA82 TCGA-4Z-AA84 
      105.70        16.77        17.16         0.62        51.16        15.12 
TCGA-4Z-AA86 TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BT-A20N TCGA-BT-A20R TCGA-BT-A20V 
       10.22        40.08         2.66        32.84         5.06         5.06 
TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F 
       16.18        20.48         4.67        17.56        24.26        28.41 
TCGA-C4-A0F0 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR 
        1.94         0.46         0.43        12.92         4.90         7.20 
TCGA-DK-A1AD TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I6 TCGA-DK-A3IK 
      112.44         1.81        10.59         7.79        87.32         2.20 
TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IT TCGA-DK-A6AV TCGA-DK-A6B2 TCGA-DK-A6B5 
        7.82         8.22        21.30        64.18        15.68        41.06 
TCGA-DK-A6B6 TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6W TCGA-E5-A4TZ TCGA-E7-A541 
       30.67        13.58       166.03         8.65        15.35        17.39 
TCGA-E7-A7DU TCGA-FD-A3B3 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3SL TCGA-FD-A3SO 
        0.92        32.02        33.04         4.01        23.41         5.52 
TCGA-FD-A43N TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C1 
       22.98        15.58        26.73         8.25        27.45        58.92 
TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TG TCGA-FD-A6TH 
        2.70         7.10         6.28        13.35         3.06         4.31 
TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-G2-A2EF TCGA-G2-A2EL TCGA-G2-A3IB TCGA-GC-A3BM 
       31.07        17.23        61.94        26.93         7.23        21.40 
TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A6C6 TCGA-GU-A42Q 
       15.81         4.50        13.91         7.73         2.20        11.31 
TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-AATP TCGA-GV-A3JV TCGA-GV-A40G TCGA-H4-A2HQ 
        7.63        20.05        32.98        14.27        19.07        19.40 
TCGA-HQ-A2OF TCGA-K4-A3WS TCGA-K4-A3WV TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RI 
        3.06        25.02        21.24         9.14        27.68        11.70 
TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN 
        1.74         1.81        15.42        13.48        12.23        16.67 
TCGA-R3-A69X TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78M TCGA-UY-A78N 
       14.24        12.43        31.56        17.62        22.68        86.83 
TCGA-UY-A8OB TCGA-UY-A8OD TCGA-UY-A9PB TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HC 
       65.75       112.83        29.56         4.54         1.64         6.58 
TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9T5 TCGA-XF-AAMG 
       97.12        15.35        23.64        21.04        66.64       110.60 
TCGA-XF-AAMJ TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAN0 TCGA-XF-AAN2 TCGA-XF-AAN3 
       54.90         2.96         8.32        56.48        61.45        86.30 
TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R4 TCGA-ZF-A9R7 TCGA-ZF-A9RC TCGA-ZF-A9RD 
       13.64        18.64        30.28        21.86        74.56        13.41 
TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-AA4N TCGA-ZF-AA4T TCGA-ZF-AA4X 
        3.48        52.73        52.60         2.89        19.69        63.02 
TCGA-ZF-AA54 
       19.40 

$`4Q LOSS WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7M 
       22.29        11.97        91.63       103.50         8.35        16.27 
TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA81 
       44.94        16.83        34.98        27.62        49.12        41.75 
TCGA-4Z-AA83 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A13I TCGA-BL-A3JM TCGA-BL-A5ZZ 
       66.54        47.80        33.83         7.33         6.74        12.39 
TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q 
        6.58        13.15        19.04        12.16        17.88        19.50 
TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A3PJ 
       14.89        14.96         8.35         8.25        17.16        12.82 
TCGA-BT-A3PK TCGA-BT-A42C TCGA-C4-A0EZ TCGA-C4-A0F6 TCGA-CF-A27C TCGA-CF-A47S 
        9.96        28.70         8.98        23.01         0.69        10.95 
TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 
       12.66        12.46        12.10        12.62        12.26        13.12 
TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CF-A9FM 
       12.00        12.10        11.34        11.34        11.87        13.08 
TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 
        5.46         5.19        16.31         1.84        13.58        21.86 
TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC 
        2.14        66.41        18.41        19.00        16.70       130.88 
TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I4 TCGA-DK-A3IL TCGA-DK-A3IQ 
       16.14        17.62        15.62       123.85        13.58        17.72 
TCGA-DK-A3IS TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY 
       50.27        23.21         9.67        20.81        10.55       140.81 
TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-AA6L 
       48.00        17.98        41.56        76.60        67.36        38.24 
TCGA-DK-AA6P TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 
       15.02        12.36        10.49         7.53        13.64        43.50 
TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 
       12.03        10.62        43.59        38.83        24.66         0.10 
TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 
        0.49         2.24        16.70         0.56         0.66        14.56 
TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A7XN 
       13.97        12.99        14.33         1.22        13.68        14.07 
TCGA-E7-A85H TCGA-E7-A8O7 TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B4 TCGA-FD-A3B5 
       12.95        15.32        14.37         8.09        16.77         8.94 
TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SM 
       12.62        22.52        27.98        60.66        24.30        17.98 
TCGA-FD-A3SN TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43P 
       29.16        25.74        46.78        19.79        12.85        27.35 
TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU 
       14.96        20.91         3.62        53.88        11.01        19.33 
TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5C0 TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC 
        5.36         5.69        18.08        62.86        18.81         6.15 
TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z9 
       12.69        12.36         2.27         9.67        10.85         7.13 
TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EJ TCGA-G2-A2EK 
       10.65         8.94         3.25         6.48        30.61        15.95 
TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C 
       35.24        33.01        20.12        17.62        66.02         6.94 
TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC 
       64.44        19.46         2.24        15.91        14.07        17.75 
TCGA-GC-A3YS TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS 
       24.92         0.49         8.94         2.10         3.12        20.98 
TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42R TCGA-GU-A763 TCGA-GU-A766 TCGA-GU-A767 
        7.36        10.92        11.31        27.09         5.62         4.73 
TCGA-GU-AATO TCGA-GU-AATQ TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF 
       10.65         7.00        21.34        19.10        19.82        20.28 
TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A6ZA TCGA-H4-A2HO 
        8.48        10.59        27.35         8.58        22.72         1.51 
TCGA-HQ-A2OE TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A5RH 
       38.60         9.01         8.22         3.45         2.76         9.07 
TCGA-K4-A83P TCGA-K4-AAQO TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-S5-A6DX 
        6.38        11.80        15.32        15.58        21.07         1.84 
TCGA-S5-AA26 TCGA-UY-A78L TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OC TCGA-UY-A9PA 
        3.75        37.05        76.01        67.79         3.58        35.24 
TCGA-UY-A9PD TCGA-XF-A8HB TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HH TCGA-XF-A8HI 
       17.82        45.04        97.45       125.49         1.87        17.88 
TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SV 
       48.62        64.80        79.66         3.22        66.41        12.76 
TCGA-XF-A9SW TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 
       11.90        28.24        26.27        18.90         2.24        16.27 
TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAML 
        2.10        13.74        92.98        10.82        11.31         7.63 
TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN1 
       71.57        91.73         6.77        98.99        44.32        30.94 
TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 
       27.06        75.39        18.81         3.88        18.84         9.63 
TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R5 
        0.66        11.97         7.36        21.11        24.13        27.19 
TCGA-ZF-A9R9 TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4R TCGA-ZF-AA4U 
       28.41        82.49        47.84        20.22        34.06         8.61 
TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA56 
       59.38        60.16        38.73        35.41        57.90         8.52 
TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
       47.15        19.17         5.52        10.13 

  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
             0.43              0.10 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
           166.03            140.81 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
            16.18             15.45 
[1] "0.4 - 166.0 (16.2)" "0.1 - 140.8 (15.4)"
[1] "hr=" "1.2"
D49V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  4Q LOSS MUTATED         1       34        39       53
  4Q LOSS WILD-TYPE       3       90        88       76
D49V3, multiclass
           clus
vv          4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  STAGE I                 1                 3
  STAGE II               34                90
  STAGE III              39                88
  STAGE IV               53                76
[1] 4 2
[1] TRUE
[1] "dimension of contingency 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         36  67  16
  4Q LOSS WILD-TYPE       85 117  37
D49V4, multiclass
          clus
vv         4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  T0+T1+T2              36                85
  T3                    67               117
  T4                    16                37
[1] 3 2
[1] TRUE
[1] "dimension of 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    65  18  31   1
  4Q LOSS WILD-TYPE 159  24  44   7
D49V5, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  N0              65               159
  N1              18                24
  N2              31                44
  N3               1                 7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V6, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED    56   3
  4Q LOSS WILD-TYPE 129   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     56    3
  4Q LOSS WILD-TYPE  129    7
   clus
vv  4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  0              56               129
  1               3                 7
[1] 2 2
[1] FALSE
D49V7, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED    34  95
  4Q LOSS WILD-TYPE  67 193
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     34   95
  4Q LOSS WILD-TYPE   67  193
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  FEMALE              34                67
  MALE                95               193
[1] 2 2
[1] FALSE
D49V8, continuous
D49V9, continuous
D49V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  4Q LOSS MUTATED       9                        10   106
  4Q LOSS WILD-TYPE    33                        11   205
D49V11, multiclass
                           clus
vv                          4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  ASIAN                                   9                33
  BLACK OR AFRICAN AMERICAN              10                11
  WHITE                                 106               205
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V12, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED     4 115
  4Q LOSS WILD-TYPE   5 237
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      4  115
  4Q LOSS WILD-TYPE    5  237
                        clus
vv                       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   4                 5
  NOT HISPANIC OR LATINO             115               237
[1] 2 2
[1] FALSE

Clustering(50) Variable = 5P LOSS MUTATION ANALYSIS
D50V1, survival
                   sevent
clus2                 0   1
  5P LOSS MUTATED    28  23
  5P LOSS WILD-TYPE 202 130
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               51               332 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               23               130 
$`5P LOSS MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KW TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-BL-A0C8 TCGA-BL-A13J 
       22.29         8.35        16.77        17.16        40.08         2.66 
TCGA-BT-A0S7 TCGA-BT-A20J TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-C4-A0F6 
        6.58        19.04        16.18        20.48         4.67        23.01 
TCGA-CF-A1HR TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A2I1 TCGA-DK-A3IL TCGA-DK-A3IM 
        0.46        18.41       112.44        10.59        13.58         7.82 
TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3X1 TCGA-E5-A2PC TCGA-E7-A6ME TCGA-E7-A7DU 
       50.27        21.30        48.00        43.59        12.99         0.92 
TCGA-FD-A3B6 TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A43U TCGA-FD-A5BZ TCGA-FJ-A3ZE 
       33.04        24.30        23.41        20.91        27.45        10.65 
TCGA-G2-A2EF TCGA-G2-A3VY TCGA-GC-A6I1 TCGA-GD-A6C6 TCGA-GV-A3JW TCGA-GV-A6ZA 
       61.94        17.62         8.94         2.20        21.34        22.72 
TCGA-HQ-A5ND TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-R3-A69X TCGA-UY-A8OD 
        9.01         3.45        21.24         2.76        14.24       112.83 
TCGA-UY-A9PD TCGA-UY-A9PF TCGA-XF-A8HG TCGA-XF-A9SI TCGA-XF-A9SV TCGA-XF-AAMX 
       17.82         1.64        15.35        79.66        12.76         6.77 
TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-ZF-A9R0 
       44.32        56.48        18.64 

$`5P LOSS WILD-TYPE`
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7N 
       11.97        91.63       103.50       105.70        16.27        44.94 
TCGA-4Z-AA7O TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 
       16.83        34.98        27.62        49.12         0.62        41.75 
TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 
       51.16        66.54        15.12        10.22        47.80        33.83 
TCGA-BL-A13I TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0YX TCGA-BT-A20N TCGA-BT-A20O 
        7.33         6.74        12.39        13.15        32.84        12.16 
TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V 
       17.88        19.50         5.06        14.89        14.96         5.06 
TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B 
        8.35         8.25        17.16        12.82         9.96        17.56 
TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-CF-A1HS 
       28.70        24.26        28.41         8.98         1.94         0.43 
TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X 
        0.69        10.95        12.66        12.46        12.10        12.62 
TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A8HY 
       12.26        13.12        12.00        12.10        11.34        11.34 
TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ 
       11.87        13.08        12.92         4.90         7.20         5.46 
TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 
        5.19        16.31         1.84        13.58        21.86         2.14 
TCGA-DK-A1A6 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AE TCGA-DK-A1AF 
       66.41        19.00        16.70       130.88        16.14        17.62 
TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK 
       15.62         1.81         7.79       123.85        87.32         2.20 
TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX 
        8.22        17.72        23.21         9.67        20.81        10.55 
TCGA-DK-A3WY TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 
      140.81        17.98        64.18        41.56        76.60        67.36 
TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6P TCGA-DK-AA6Q 
       15.68        41.06        30.67        38.24        15.02        13.58 
TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 
      166.03        12.36        10.49         8.65         7.53        13.64 
TCGA-DK-AA74 TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 
       43.50        12.03        10.62        15.35        38.83        24.66 
TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE 
        0.10         0.49         2.24        16.70        17.39         0.56 
TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MF TCGA-E7-A7DV TCGA-E7-A7PW 
        0.66        14.56        13.97        14.33         1.22        13.68 
TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A8O7 TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 
       14.07        12.95        15.32        14.37         8.09        32.02 
TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 
       16.77         8.94         4.01        12.62        22.52        27.98 
TCGA-FD-A3NA TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ 
       60.66        17.98        29.16         5.52        25.74        46.78 
TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43X 
       19.79        12.85        22.98        27.35        14.96         3.62 
TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV 
       15.58        26.73        53.88        11.01        19.33         5.36 
TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O 
        5.69         8.25        18.08        58.92         2.70         7.10 
TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD 
        6.28        13.35        62.86        18.81         6.15        12.69 
TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK 
       12.36         2.27         3.06         4.31         9.67        10.85 
TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A3EE TCGA-FT-A61P 
       31.07         7.13        17.23         8.94         3.25         6.48 
TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB 
       30.61        15.95        26.93        35.24        33.01         7.23 
TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM 
       20.12        66.02         6.94        64.44        19.46        21.40 
TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC 
        2.24        15.81         4.50        15.91        14.07        17.75 
TCGA-GC-A3YS TCGA-GC-A4ZW TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ 
       24.92         0.49        13.91         7.73         2.10         3.12 
TCGA-GD-A3OS TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 
       20.98         7.36        10.92        11.31        11.31         7.63 
TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATP 
       27.09        20.05         5.62         4.73        10.65        32.98 
TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH 
        7.00        14.27        19.10        19.82        20.28         8.48 
TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-H4-A2HO TCGA-H4-A2HQ 
       10.59        27.35         8.58        19.07         1.51        19.40 
TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A4AC TCGA-K4-A54R 
       38.60         3.06         8.22        25.02         9.14        27.68 
TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P 
        9.07        11.70         1.74         1.81        15.42         6.38 
TCGA-K4-AAQO TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FI 
       11.80        15.32        15.58        21.07        13.48        12.23 
TCGA-PQ-A6FN TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78K 
       16.67         1.84         3.75        12.43        31.56        17.62 
TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OB 
       37.05        22.68        86.83        76.01        67.79        65.75 
TCGA-UY-A8OC TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PE TCGA-XF-A8HB TCGA-XF-A8HC 
        3.58        35.24        29.56         4.54        45.04         6.58 
TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG 
       97.45       125.49        97.12         1.87        17.88        48.62 
TCGA-XF-A9SH TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY 
       64.80         3.22        66.41        11.90        23.64        21.04 
TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 
       28.24        26.27        18.90         2.24        16.27        66.64 
TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAMH 
        2.10        13.74        92.98        10.82       110.60        11.31 
TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW 
       54.90         7.63        71.57        91.73         2.96         8.32 
TCGA-XF-AAMY TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 
       98.99        30.94        61.45        86.30        27.06        75.39 
TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L 
       18.81         3.88        18.84         9.63         0.66        11.97 
TCGA-YF-AA3M TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 
       13.64         7.36        21.11        24.13        30.28        27.19 
TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF 
       21.86        28.41        74.56        13.41         3.48        52.73 
TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4R 
       52.60        82.49        47.84        20.22         2.89        34.06 
TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 
       19.69         8.61        59.38        60.16        63.02        38.73 
TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H 
       35.41        57.90        19.40         8.52        47.15        19.17 
TCGA-ZF-AA5N TCGA-ZF-AA5P 
        5.52        10.13 

  5P LOSS MUTATED 5P LOSS WILD-TYPE 
             0.46              0.10 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
           112.83            166.03 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
           17.820            15.385 
[1] "0.5 - 112.8 (17.8)" "0.1 - 166.0 (15.4)"
[1] "hr=" "1.1"
D50V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  5P LOSS MUTATED         1       14        17       20
  5P LOSS WILD-TYPE       3      110       110      109
D50V3, multiclass
           clus
vv          5P LOSS MUTATED 5P LOSS WILD-TYPE
  STAGE I                 1                 3
  STAGE II               14               110
  STAGE III              17               110
  STAGE IV               20               109
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1+T2  T3  T4
  5P LOSS MUTATED         15  26   9
  5P LOSS WILD-TYPE      106 158  44
D50V4, multiclass
          clus
vv         5P LOSS MUTATED 5P LOSS WILD-TYPE
  T0+T1+T2              15               106
  T3                    26               158
  T4                     9                44
[1] 3 2
[1] TRUE
[1] "dimension of 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    28   5  12   2
  5P LOSS WILD-TYPE 196  37  63   6
D50V5, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  N0              28               196
  N1               5                37
  N2              12                63
  N3               2                 6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V6, binary
                   cls
clus                  0   1
  5P LOSS MUTATED    25   3
  5P LOSS WILD-TYPE 160   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED     25    3
  5P LOSS WILD-TYPE  160    7
   clus
vv  5P LOSS MUTATED 5P LOSS WILD-TYPE
  0              25               160
  1               3                 7
[1] 2 2
[1] FALSE
D50V7, binary
                   cls
clus                  0   1
  5P LOSS MUTATED    16  37
  5P LOSS WILD-TYPE  85 251
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED     16   37
  5P LOSS WILD-TYPE   85  251
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  FEMALE              16                85
  MALE                37               251
[1] 2 2
[1] FALSE
D50V8, continuous
D50V9, continuous
D50V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  5P LOSS MUTATED       5                         3    43
  5P LOSS WILD-TYPE    37                        18   268
D50V11, multiclass
                           clus
vv                          5P LOSS MUTATED 5P LOSS WILD-TYPE
  ASIAN                                   5                37
  BLACK OR AFRICAN AMERICAN               3                18
  WHITE                                  43               268
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V12, binary
                   cls
clus                  0   1
  5P LOSS MUTATED     1  47
  5P LOSS WILD-TYPE   8 305
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      1   47
  5P LOSS WILD-TYPE    8  305
                        clus
vv                       5P LOSS MUTATED 5P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 8
  NOT HISPANIC OR LATINO              47               305
[1] 2 2
[1] FALSE

Clustering(51) Variable = 5Q LOSS MUTATION ANALYSIS
D51V1, survival
                   sevent
clus2                 0   1
  5Q LOSS MUTATED    81  66
  5Q LOSS WILD-TYPE 149  87
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
              147               236 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               66                87 
$`5Q LOSS MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KT TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R 
       22.29        11.97       105.70        16.83        16.77        17.16 
TCGA-4Z-AA7W TCGA-4Z-AA86 TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BT-A0S7 TCGA-BT-A20J 
       27.62        10.22        40.08         2.66         6.58        19.04 
TCGA-BT-A20R TCGA-BT-A20V TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A42B 
        5.06         5.06        20.48         4.67        12.82        17.56 
TCGA-BT-A42E TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CU-A3QU TCGA-DK-A1A5 TCGA-DK-A1AD 
       24.26        23.01         0.46         5.19         2.14       112.44 
TCGA-DK-A2I1 TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS 
       10.59        13.58         7.82         8.22        17.72        50.27 
TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3WX TCGA-DK-A3X1 TCGA-DK-A6B2 TCGA-DK-A6B5 
       21.30        23.21        10.55        48.00        15.68        41.06 
TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA76 
       15.02        13.58       166.03        10.49         8.65        12.03 
TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E7-A3X6 TCGA-E7-A4IJ TCGA-E7-A6ME TCGA-E7-A7DU 
       43.59        15.35        24.66         0.49        12.99         0.92 
TCGA-E7-A7PW TCGA-E7-A97Q TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3N5 TCGA-FD-A3SJ 
       13.68         8.09         8.94        33.04        22.52        24.30 
TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SP TCGA-FD-A3SR TCGA-FD-A3SS 
       23.41        17.98        29.16        25.74        19.79        12.85 
TCGA-FD-A43U TCGA-FD-A5BR TCGA-FD-A5BV TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 
       20.91        26.73         5.36         8.25        27.45        18.08 
TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD 
        7.10        13.35        62.86        18.81         6.15        12.69 
TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TK TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FT-A61P 
        2.27         3.06        10.85        10.65        17.23         6.48 
TCGA-G2-A2EF TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B TCGA-GC-A4ZW 
       61.94         7.23        20.12        17.62        66.02         0.49 
TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A6C6 TCGA-GU-A42P 
        8.94        13.91         7.73         2.10         2.20        10.92 
TCGA-GU-AATO TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ 
       10.65        32.98         7.00        21.34        19.10        19.82 
TCGA-GV-A3QF TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HQ TCGA-HQ-A2OF TCGA-HQ-A5ND 
       20.28        19.07        22.72        19.40         3.06         9.01 
TCGA-HQ-A5NE TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A54R TCGA-PQ-A6FN TCGA-R3-A69X 
        8.22         3.45         2.76        27.68        16.67        14.24 
TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78M TCGA-UY-A78P TCGA-UY-A8OB TCGA-UY-A8OD 
       31.56        17.62        22.68        67.79        65.75       112.83 
TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PF TCGA-XF-A8HC TCGA-XF-A8HF TCGA-XF-A8HG 
       29.56        17.82         1.64         6.58        97.12        15.35 
TCGA-XF-A9SI TCGA-XF-A9SV TCGA-XF-A9SZ TCGA-XF-A9T3 TCGA-XF-AAML TCGA-XF-AAMT 
       79.66        12.76        28.24         2.24         7.63         2.96 
TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN7 TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R0 
        6.77        56.48        18.81        11.97        13.64        18.64 
TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RL 
        7.36        24.13        21.86        28.41        74.56        82.49 
TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4X 
       47.84        20.22         2.89        34.06        19.69        63.02 
TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA5H 
       38.73        35.41        19.17 

$`5Q LOSS WILD-TYPE`
TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7S 
       91.63       103.50         8.35        16.27        44.94        34.98 
TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA84 
       49.12         0.62        41.75        51.16        66.54        15.12 
TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A13I TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0YX 
       47.80        33.83         7.33         6.74        12.39        13.15 
TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20T TCGA-BT-A20U 
       32.84        12.16        17.88        19.50        14.89        14.96 
TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A3PK TCGA-BT-A42C 
        8.35         8.25        17.16        16.18         9.96        28.70 
TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S 
       28.41         8.98         1.94         0.43         0.69        10.95 
TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 
       12.66        12.46        12.10        12.62        12.26        13.12 
TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CF-A9FM 
       12.00        12.10        11.34        11.34        11.87        13.08 
TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3YL TCGA-CU-A5W6 
       12.92         4.90         7.20         5.46        16.31         1.84 
TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB 
       13.58        21.86        66.41        18.41        19.00        16.70 
TCGA-DK-A1AC TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I2 
      130.88        16.14        17.62        15.62         1.81         7.79 
TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WY 
      123.85        87.32         2.20         9.67        20.81       140.81 
TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B6 
       17.98        64.18        41.56        76.60        67.36        30.67 
TCGA-DK-AA6L TCGA-DK-AA6T TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA77 
       38.24        12.36         7.53        13.64        43.50        10.62 
TCGA-E5-A4U1 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE 
       38.83         0.10         2.24        16.70        17.39         0.56 
TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MF TCGA-E7-A7DV TCGA-E7-A7XN 
        0.66        14.56        13.97        14.33         1.22        14.07 
TCGA-E7-A85H TCGA-E7-A8O7 TCGA-E7-A97P TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B7 
       12.95        15.32        14.37        32.02        16.77         4.01 
TCGA-FD-A3B8 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SO TCGA-FD-A3SQ TCGA-FD-A43N 
       12.62        27.98        60.66         5.52        46.78        22.98 
TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BS TCGA-FD-A5BT 
       27.35        14.96         3.62        15.58        53.88        11.01 
TCGA-FD-A5BU TCGA-FD-A5BX TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62P TCGA-FD-A6TE 
       19.33         5.69        58.92         2.70         6.28        12.36 
TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A871 TCGA-FT-A3EE 
        4.31         9.67        31.07         7.13         8.94         3.25 
TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-AA3C 
       30.61        15.95        26.93        35.24        33.01         6.94 
TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB 
       64.44        19.46        21.40         2.24        15.81         4.50 
TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GD-A3OQ TCGA-GD-A3OS 
       15.91        14.07        17.75        24.92         3.12        20.98 
TCGA-GD-A76B TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 
        7.36        11.31        11.31         7.63        27.09        20.05 
TCGA-GU-A766 TCGA-GU-A767 TCGA-GV-A3JV TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK 
        5.62         4.73        14.27         8.48        10.59        27.35 
TCGA-GV-A40E TCGA-H4-A2HO TCGA-HQ-A2OE TCGA-K4-A3WS TCGA-K4-A3WV TCGA-K4-A4AC 
        8.58         1.51        38.60        25.02        21.24         9.14 
TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P 
        9.07        11.70         1.74         1.81        15.42         6.38 
TCGA-K4-AAQO TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FI 
       11.80        15.32        15.58        21.07        13.48        12.23 
TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-UY-A78L TCGA-UY-A78N TCGA-UY-A78O 
        1.84         3.75        12.43        37.05        86.83        76.01 
TCGA-UY-A8OC TCGA-UY-A9PA TCGA-UY-A9PE TCGA-XF-A8HB TCGA-XF-A8HD TCGA-XF-A8HE 
        3.58        35.24         4.54        45.04        97.45       125.49 
TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SJ TCGA-XF-A9SL 
        1.87        17.88        48.62        64.80         3.22        66.41 
TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T4 
       11.90        23.64        21.04        26.27        18.90        16.27 
TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMG 
       66.64         2.10        13.74        92.98        10.82       110.60 
TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMW TCGA-XF-AAMY 
       11.31        54.90        71.57        91.73         8.32        98.99 
TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 
       44.32        30.94        61.45        86.30        27.06        75.39 
TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-ZF-A9R2 TCGA-ZF-A9R4 
        3.88        18.84         9.63         0.66        21.11        30.28 
TCGA-ZF-A9R5 TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-AA4U 
       27.19        13.41         3.48        52.73        52.60         8.61 
TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 
       59.38        60.16        57.90        19.40         8.52        47.15 
TCGA-ZF-AA5N TCGA-ZF-AA5P 
        5.52        10.13 

  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
             0.46              0.10 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
           166.03            140.81 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
            17.23             15.32 
[1] "0.5 - 166.0 (17.2)" "0.1 - 140.8 (15.3)"
[1] "hr=" "1.3"
D51V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  5Q LOSS MUTATED         2       41        44       61
  5Q LOSS WILD-TYPE       2       83        83       68
D51V3, multiclass
           clus
vv          5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  STAGE I                 2                 2
  STAGE II               41                83
  STAGE III              44                83
  STAGE IV               61                68
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1+T2  T3  T4
  5Q LOSS MUTATED         39  74  22
  5Q LOSS WILD-TYPE       82 110  31
D51V4, multiclass
          clus
vv         5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  T0+T1+T2              39                82
  T3                    74               110
  T4                    22                31
[1] 3 2
[1] TRUE
[1] "dimension of 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    68  18  36   6
  5Q LOSS WILD-TYPE 156  24  39   2
D51V5, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  N0              68               156
  N1              18                24
  N2              36                39
  N3               6                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V6, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED    63   6
  5Q LOSS WILD-TYPE 122   4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     63    6
  5Q LOSS WILD-TYPE  122    4
   clus
vv  5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  0              63               122
  1               6                 4
[1] 2 2
[1] FALSE
D51V7, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED    40 109
  5Q LOSS WILD-TYPE  61 179
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     40  109
  5Q LOSS WILD-TYPE   61  179
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  FEMALE              40                61
  MALE               109               179
[1] 2 2
[1] FALSE
D51V8, continuous
D51V9, continuous
D51V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  5Q LOSS MUTATED       9                        12   122
  5Q LOSS WILD-TYPE    33                         9   189
D51V11, multiclass
                           clus
vv                          5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  ASIAN                                   9                33
  BLACK OR AFRICAN AMERICAN              12                 9
  WHITE                                 122               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"
D51V12, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED     4 135
  5Q LOSS WILD-TYPE   5 217
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      4  135
  5Q LOSS WILD-TYPE    5  217
                        clus
vv                       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   4                 5
  NOT HISPANIC OR LATINO             135               217
[1] 2 2
[1] FALSE

Clustering(52) Variable = 6P LOSS MUTATION ANALYSIS
D52V1, survival
                   sevent
clus2                 0   1
  6P LOSS MUTATED    59  34
  6P LOSS WILD-TYPE 171 119
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               93               290 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               34               119 
$`6P LOSS MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KT TCGA-2F-A9KW TCGA-4Z-AA7R TCGA-4Z-AA7W TCGA-4Z-AA82 
       22.29       105.70         8.35        17.16        27.62        51.16 
TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BT-A20N TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LB 
       40.08         2.66        32.84         5.06         8.25        16.18 
TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A42C TCGA-CF-A1HR TCGA-CU-A3QU TCGA-CU-A5W6 
       20.48         4.67        28.70         0.46         5.19         1.84 
TCGA-DK-A1AB TCGA-DK-A2HX TCGA-DK-A2I4 TCGA-DK-A3IL TCGA-DK-A3IQ TCGA-DK-A3IS 
       16.70         1.81       123.85        13.58        17.72        50.27 
TCGA-DK-A3IT TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6P 
       21.30        17.98        64.18        41.06        30.67        15.02 
TCGA-DK-AA6S TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA76 TCGA-E5-A4TZ 
      166.03        10.49         8.65        13.64        12.03        15.35 
TCGA-E5-A4U1 TCGA-E7-A5KE TCGA-E7-A7PW TCGA-E7-A97Q TCGA-FD-A3SL TCGA-FD-A3SN 
       38.83         0.56        13.68         8.09        23.41        29.16 
TCGA-FD-A3SQ TCGA-FD-A43U TCGA-FD-A43Y TCGA-FD-A5BV TCGA-FD-A62O TCGA-FD-A6TE 
       46.78        20.91        15.58         5.36         7.10        12.36 
TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-G2-A2EO TCGA-G2-A3IE TCGA-G2-AA3D TCGA-G2-AA3F 
       31.07        17.23        35.24        20.12        64.44        19.46 
TCGA-GC-A3RB TCGA-GC-A3RD TCGA-GD-A3OP TCGA-GU-A767 TCGA-GV-A3JW TCGA-GV-A3JZ 
        4.50        14.07         2.10         4.73        21.34        19.82 
TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-K4-A4AB TCGA-K4-A5RI TCGA-K4-A6FZ 
       19.40        38.60         3.06         2.76        11.70         1.81 
TCGA-MV-A51V TCGA-PQ-A6FN TCGA-R3-A69X TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A8OD 
       13.48        16.67        14.24        31.56        17.62       112.83 
TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A9SG TCGA-XF-A9T0 TCGA-XF-A9T3 TCGA-XF-AAMJ 
       15.35         1.87        48.62        26.27         2.24        54.90 
TCGA-XF-AAMW TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN3 TCGA-XF-AAN5 TCGA-YF-AA3L 
        8.32        44.32        56.48        86.30        75.39        11.97 
TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R7 TCGA-ZF-A9R9 
       13.64        18.64         7.36        21.11        21.86        28.41 
TCGA-ZF-AA4N TCGA-ZF-AA51 TCGA-ZF-AA53 
        2.89        38.73        57.90 

$`6P LOSS WILD-TYPE`
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7O 
       11.97        91.63       103.50        16.27        44.94        16.83 
TCGA-4Z-AA7Q TCGA-4Z-AA7S TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA83 
       16.77        34.98        49.12         0.62        41.75        66.54 
TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A13I TCGA-BL-A3JM 
       15.12        10.22        47.80        33.83         7.33         6.74 
TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P 
       12.39         6.58        13.15        19.04        12.16        17.88 
TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20W TCGA-BT-A2LA 
       19.50         5.06        14.89        14.96         8.35        17.16 
TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ 
       12.82         9.96        17.56        24.26        28.41         8.98 
TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T 
        1.94        23.01         0.43         0.69        10.95        12.66 
TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA 
       12.46        12.10        12.62        12.26        13.12        12.00 
TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YN 
       12.10        11.34        11.34        11.87        13.08        12.92 
TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3YL TCGA-CU-A72E TCGA-DK-A1A3 
        4.90         7.20         5.46        16.31        13.58        21.86 
TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AC TCGA-DK-A1AD 
        2.14        66.41        18.41        19.00       130.88       112.44 
TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I6 
       16.14        17.62        15.62        10.59         7.79        87.32 
TCGA-DK-A3IK TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW 
        2.20         7.82         8.22        23.21         9.67        20.81 
TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 
       10.55       140.81        48.00        41.56        76.60        67.36 
TCGA-DK-A6B2 TCGA-DK-AA6L TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6X TCGA-DK-AA74 
       15.68        38.24        13.58        12.36         7.53        43.50 
TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ 
       10.62        43.59        24.66         0.10         0.49         2.24 
TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME 
       16.70        17.39         0.66        14.56        13.97        12.99 
TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A8O7 
       14.33         0.92         1.22        14.07        12.95        15.32 
TCGA-E7-A97P TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 
       14.37        32.02        16.77         8.94        33.04         4.01 
TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SM 
       12.62        22.52        27.98        60.66        24.30        17.98 
TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P 
        5.52        25.74        19.79        12.85        22.98        27.35 
TCGA-FD-A43S TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU 
       14.96         3.62        26.73        53.88        11.01        19.33 
TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N 
        5.69         8.25        27.45        18.08        58.92         2.70 
TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD 
        6.28        13.35        62.86        18.81         6.15        12.69 
TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z9 
        2.27         3.06         4.31         9.67        10.85         7.13 
TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ 
       10.65         8.94         3.25         6.48        61.94        30.61 
TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3VY TCGA-G2-AA3B 
       15.95        26.93        33.01         7.23        17.62        66.02 
TCGA-G2-AA3C TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A3WC 
        6.94        21.40         2.24        15.81        15.91        17.75 
TCGA-GC-A3YS TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OQ 
       24.92         0.49         8.94        13.91         7.73         3.12 
TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R 
       20.98         2.20         7.36        10.92        11.31        11.31 
TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-AATO TCGA-GU-AATP 
        7.63        27.09        20.05         5.62        10.65        32.98 
TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JX TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI 
        7.00        14.27        19.10        20.28         8.48        10.59 
TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-HQ-A5ND 
       27.35         8.58        19.07        22.72         1.51         9.01 
TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AC TCGA-K4-A54R 
        8.22        25.02         3.45        21.24         9.14        27.68 
TCGA-K4-A5RH TCGA-K4-A5RJ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-LC-A66R 
        9.07         1.74        15.42         6.38        11.80        15.32 
TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-PQ-A6FI TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G0 
       15.58        21.07        12.23         1.84         3.75        12.43 
TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OB 
       37.05        22.68        86.83        76.01        67.79        65.75 
TCGA-UY-A8OC TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF 
        3.58        35.24        29.56        17.82         4.54         1.64 
TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HI 
       45.04         6.58        97.45       125.49        97.12        17.88 
TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SW 
       64.80        79.66         3.22        66.41        12.76        11.90 
TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T2 TCGA-XF-A9T4 TCGA-XF-A9T5 
       23.64        21.04        28.24        18.90        16.27        66.64 
TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAMH 
        2.10        13.74        92.98        10.82       110.60        11.31 
TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMX TCGA-XF-AAMY 
        7.63        71.57        91.73         2.96         6.77        98.99 
TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN4 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A89H 
       30.94        61.45        27.06        18.81         3.88        18.84 
TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9RC 
        9.63         0.66        24.13        30.28        27.19        74.56 
TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM 
       13.41         3.48        52.73        52.60        82.49        47.84 
TCGA-ZF-A9RN TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W 
       20.22        34.06        19.69         8.61        59.38        60.16 
TCGA-ZF-AA4X TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H 
       63.02        35.41        19.40         8.52        47.15        19.17 
TCGA-ZF-AA5N TCGA-ZF-AA5P 
        5.52        10.13 

  6P LOSS MUTATED 6P LOSS WILD-TYPE 
             0.46              0.10 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
           166.03            140.81 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
            17.62             15.22 
[1] "0.5 - 166.0 (17.6)" "0.1 - 140.8 (15.2)"
[1] "hr=" "1.2"
D52V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  6P LOSS MUTATED         2       24        29       37
  6P LOSS WILD-TYPE       2      100        98       92
D52V3, multiclass
           clus
vv          6P LOSS MUTATED 6P LOSS WILD-TYPE
  STAGE I                 2                 2
  STAGE II               24               100
  STAGE III              29                98
  STAGE IV               37                92
[1] 4 2
[1] TRUE
[1] "dimension of contingency 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         22  43  18
  6P LOSS WILD-TYPE       99 141  35
D52V4, multiclass
          clus
vv         6P LOSS MUTATED 6P LOSS WILD-TYPE
  T0+T1+T2              22                99
  T3                    43               141
  T4                    18                35
[1] 3 2
[1] TRUE
[1] "dimension of 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    47   6  27   2
  6P LOSS WILD-TYPE 177  36  48   6
D52V5, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  N0              47               177
  N1               6                36
  N2              27                48
  N3               2                 6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V6, binary
                   cls
clus                  0   1
  6P LOSS MUTATED    54   2
  6P LOSS WILD-TYPE 131   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     54    2
  6P LOSS WILD-TYPE  131    8
   clus
vv  6P LOSS MUTATED 6P LOSS WILD-TYPE
  0              54               131
  1               2                 8
[1] 2 2
[1] FALSE
D52V7, binary
                   cls
clus                  0   1
  6P LOSS MUTATED    29  65
  6P LOSS WILD-TYPE  72 223
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     29   65
  6P LOSS WILD-TYPE   72  223
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  FEMALE              29                72
  MALE                65               223
[1] 2 2
[1] FALSE
D52V8, continuous
D52V9, continuous
D52V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  6P LOSS MUTATED       6                         5    76
  6P LOSS WILD-TYPE    36                        16   235
D52V11, multiclass
                           clus
vv                          6P LOSS MUTATED 6P LOSS WILD-TYPE
  ASIAN                                   6                36
  BLACK OR AFRICAN AMERICAN               5                16
  WHITE                                  76               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"
D52V12, binary
                   cls
clus                  0   1
  6P LOSS MUTATED     4  84
  6P LOSS WILD-TYPE   5 268
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      4   84
  6P LOSS WILD-TYPE    5  268
                        clus
vv                       6P LOSS MUTATED 6P LOSS WILD-TYPE
  HISPANIC OR LATINO                   4                 5
  NOT HISPANIC OR LATINO              84               268
[1] 2 2
[1] FALSE

Clustering(53) Variable = 6Q LOSS MUTATION ANALYSIS
D53V1, survival
                   sevent
clus2                 0   1
  6Q LOSS MUTATED    85  61
  6Q LOSS WILD-TYPE 145  92
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
              146               237 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               61                92 
$`6Q LOSS MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KT TCGA-2F-A9KW TCGA-4Z-AA7M TCGA-4Z-AA7R TCGA-4Z-AA7W 
       22.29       105.70         8.35        16.27        17.16        27.62 
TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA86 TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BT-A20N 
       41.75        51.16        10.22        40.08         2.66        32.84 
TCGA-BT-A20V TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A42C TCGA-C4-A0F0 
        5.06        16.18        20.48         4.67        28.70         1.94 
TCGA-CF-A1HR TCGA-CU-A3QU TCGA-CU-A5W6 TCGA-DK-A1A6 TCGA-DK-A1AB TCGA-DK-A2HX 
        0.46         5.19         1.84        66.41        16.70         1.81 
TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IQ 
       10.59         7.79       123.85         2.20        13.58        17.72 
TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6B5 TCGA-DK-A6B6 
       50.27        21.30        17.98        64.18        41.06        30.67 
TCGA-DK-AA6L TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U 
       38.24        15.02        13.58       166.03        12.36        10.49 
TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 
        8.65        13.64        12.03        43.59        15.35        38.83 
TCGA-E7-A4IJ TCGA-E7-A5KE TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A97Q TCGA-FD-A3B5 
        0.49         0.56         1.22        13.68         8.09         8.94 
TCGA-FD-A3SL TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A43U TCGA-FD-A43Y 
       23.41        29.16        46.78        19.79        20.91        15.58 
TCGA-FD-A5BR TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 
       26.73        19.33         5.36         8.25        27.45        18.08 
TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TC TCGA-FD-A6TE TCGA-FD-A6TG 
        7.10         6.28        13.35         6.15        12.36         3.06 
TCGA-FD-A6TH TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2EO TCGA-G2-A2ES 
        4.31        31.07        17.23         6.48        35.24        33.01 
TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3RB 
       20.12        66.02        64.44        19.46         2.24         4.50 
TCGA-GC-A3RD TCGA-GC-A6I1 TCGA-GD-A3OP TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A767 
       14.07         8.94         2.10        11.31         7.63         4.73 
TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF 
       32.98         7.00        21.34        19.10        19.82        20.28 
TCGA-GV-A3QH TCGA-GV-A6ZA TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-K4-A4AB 
        8.48        22.72        19.40        38.60         3.06         2.76 
TCGA-K4-A5RI TCGA-K4-A6FZ TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FN TCGA-R3-A69X 
       11.70         1.81        15.58        13.48        16.67        14.24 
TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78M TCGA-UY-A8OB TCGA-UY-A8OD 
       12.43        31.56        17.62        22.68        65.75       112.83 
TCGA-UY-A9PB TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A9SG 
       29.56         1.64        45.04        15.35         1.87        48.62 
TCGA-XF-A9SJ TCGA-XF-A9SW TCGA-XF-A9T0 TCGA-XF-A9T3 TCGA-XF-AAMJ TCGA-XF-AAML 
        3.22        11.90        26.27         2.24        54.90         7.63 
TCGA-XF-AAMR TCGA-XF-AAMW TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN3 TCGA-XF-AAN5 
       91.73         8.32        44.32        56.48        86.30        75.39 
TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R7 
       11.97        13.64        18.64         7.36        21.11        21.86 
TCGA-ZF-A9R9 TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA53 
       28.41         2.89        34.06        38.73        35.41        57.90 
TCGA-ZF-AA54 TCGA-ZF-AA5H 
       19.40        19.17 

$`6Q LOSS WILD-TYPE`
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q 
       11.97        91.63       103.50        44.94        16.83        16.77 
TCGA-4Z-AA7S TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA83 TCGA-4Z-AA84 TCGA-4Z-AA87 
       34.98        49.12         0.62        66.54        15.12        47.80 
TCGA-4Z-AA89 TCGA-BL-A13I TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX 
       33.83         7.33         6.74        12.39         6.58        13.15 
TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T 
       19.04        12.16        17.88        19.50         5.06        14.89 
TCGA-BT-A20U TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A3PJ TCGA-BT-A3PK 
       14.96         8.35         8.25        17.16        12.82         9.96 
TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F6 TCGA-CF-A1HS 
       17.56        24.26        28.41         8.98        23.01         0.43 
TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X 
        0.69        10.95        12.66        12.46        12.10        12.62 
TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A8HY 
       12.26        13.12        12.00        12.10        11.34        11.34 
TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ 
       11.87        13.08        12.92         4.90         7.20         5.46 
TCGA-CU-A3YL TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A7 TCGA-DK-A1AA 
       16.31        13.58        21.86         2.14        18.41        19.00 
TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I6 
      130.88       112.44        16.14        17.62        15.62        87.32 
TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX 
        7.82         8.22        23.21         9.67        20.81        10.55 
TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 
      140.81        48.00        41.56        76.60        67.36        15.68 
TCGA-DK-AA6X TCGA-DK-AA74 TCGA-DK-AA77 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ 
        7.53        43.50        10.62        24.66         0.10         2.24 
TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME 
       16.70        17.39         0.66        14.56        13.97        12.99 
TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A8O7 TCGA-E7-A97P 
       14.33         0.92        14.07        12.95        15.32        14.37 
TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 
       32.02        16.77        33.04         4.01        12.62        22.52 
TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SM TCGA-FD-A3SO TCGA-FD-A3SP 
       27.98        60.66        24.30        17.98         5.52        25.74 
TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43X TCGA-FD-A5BS 
       12.85        22.98        27.35        14.96         3.62        53.88 
TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A6TA TCGA-FD-A6TB 
       11.01         5.69        58.92         2.70        62.86        18.81 
TCGA-FD-A6TD TCGA-FD-A6TF TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE 
       12.69         2.27         9.67        10.85         7.13        10.65 
TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL 
        8.94         3.25        61.94        30.61        15.95        26.93 
TCGA-G2-A3IB TCGA-G2-A3VY TCGA-G2-AA3C TCGA-GC-A3BM TCGA-GC-A3OO TCGA-GC-A3RC 
        7.23        17.62         6.94        21.40        15.81        15.91 
TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A4ZW TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OQ 
       17.75        24.92         0.49        13.91         7.73         3.12 
TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A763 
       20.98         2.20         7.36        10.92        11.31        27.09 
TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-AATO TCGA-GV-A3JV TCGA-GV-A3QI TCGA-GV-A3QK 
       20.05         5.62        10.65        14.27        10.59        27.35 
TCGA-GV-A40E TCGA-GV-A40G TCGA-H4-A2HO TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS 
        8.58        19.07         1.51         9.01         8.22        25.02 
TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RJ 
        3.45        21.24         9.14        27.68         9.07         1.74 
TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-LC-A66R TCGA-LT-A8JT TCGA-PQ-A6FI 
       15.42         6.38        11.80        15.32        21.07        12.23 
TCGA-S5-A6DX TCGA-S5-AA26 TCGA-UY-A78L TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A78P 
        1.84         3.75        37.05        86.83        76.01        67.79 
TCGA-UY-A8OC TCGA-UY-A9PA TCGA-UY-A9PD TCGA-UY-A9PE TCGA-XF-A8HC TCGA-XF-A8HD 
        3.58        35.24        17.82         4.54         6.58        97.45 
TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SL 
      125.49        97.12        17.88        64.80        79.66        66.41 
TCGA-XF-A9SV TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T2 TCGA-XF-A9T4 
       12.76        23.64        21.04        28.24        18.90        16.27 
TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMG 
       66.64         2.10        13.74        92.98        10.82       110.60 
TCGA-XF-AAMH TCGA-XF-AAMQ TCGA-XF-AAMT TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAN1 
       11.31        71.57         2.96         6.77        98.99        30.94 
TCGA-XF-AAN2 TCGA-XF-AAN4 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 
       61.45        27.06        18.81         3.88        18.84         9.63 
TCGA-YC-A9TC TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9RC TCGA-ZF-A9RD 
        0.66        24.13        30.28        27.19        74.56        13.41 
TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN 
        3.48        52.73        52.60        82.49        47.84        20.22 
TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA56 
       19.69         8.61        59.38        60.16        63.02         8.52 
TCGA-ZF-AA58 TCGA-ZF-AA5N TCGA-ZF-AA5P 
       47.15         5.52        10.13 

  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
             0.46              0.10 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
           166.03            140.81 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
            16.93             15.32 
[1] "0.5 - 166.0 (16.9)" "0.1 - 140.8 (15.3)"
[1] "hr=" "1.1"
D53V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  6Q LOSS MUTATED         2       40        40       63
  6Q LOSS WILD-TYPE       2       84        87       66
D53V3, multiclass
           clus
vv          6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  STAGE I                 2                 2
  STAGE II               40                84
  STAGE III              40                87
  STAGE IV               63                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                T0+T1+T2  T3  T4
  6Q LOSS MUTATED         40  71  23
  6Q LOSS WILD-TYPE       81 113  30
D53V4, multiclass
          clus
vv         6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  T0+T1+T2              40                81
  T3                    71               113
  T4                    23                30
[1] 3 2
[1] TRUE
[1] "dimension of 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    70  16  41   4
  6Q LOSS WILD-TYPE 154  26  34   4
D53V5, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  N0              70               154
  N1              16                26
  N2              41                34
  N3               4                 4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V6, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED    70   2
  6Q LOSS WILD-TYPE 115   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     70    2
  6Q LOSS WILD-TYPE  115    8
   clus
vv  6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  0              70               115
  1               2                 8
[1] 2 2
[1] FALSE
D53V7, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED    43 105
  6Q LOSS WILD-TYPE  58 183
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     43  105
  6Q LOSS WILD-TYPE   58  183
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  FEMALE              43                58
  MALE               105               183
[1] 2 2
[1] FALSE
D53V8, continuous
D53V9, continuous
D53V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  6Q LOSS MUTATED       9                         9   121
  6Q LOSS WILD-TYPE    33                        12   190
D53V11, multiclass
                           clus
vv                          6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  ASIAN                                   9                33
  BLACK OR AFRICAN AMERICAN               9                12
  WHITE                                 121               190
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V12, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED     6 131
  6Q LOSS WILD-TYPE   3 221
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      6  131
  6Q LOSS WILD-TYPE    3  221
                        clus
vv                       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   6                 3
  NOT HISPANIC OR LATINO             131               221
[1] 2 2
[1] FALSE

Clustering(54) Variable = 7P LOSS MUTATION ANALYSIS
D54V1, survival
                   sevent
clus2                 0   1
  7P LOSS MUTATED    10   9
  7P LOSS WILD-TYPE 220 144
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               19               364 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                9               144 
$`7P LOSS MUTATED`
TCGA-4Z-AA7S TCGA-BL-A0C8 TCGA-BL-A13J TCGA-CF-A47X TCGA-DK-A1A5 TCGA-DK-A6B5 
       34.98        40.08         2.66        12.62         2.14        41.06 
TCGA-DK-AA6W TCGA-DK-AA77 TCGA-FD-A5BY TCGA-FD-A6TA TCGA-GU-AATO TCGA-GV-A3QF 
        8.65        10.62         8.25        62.86        10.65        20.28 
TCGA-K4-A3WS TCGA-XF-AAML TCGA-XF-AAMZ TCGA-ZF-A9RL TCGA-ZF-AA4T TCGA-ZF-AA54 
       25.02         7.63        44.32        82.49        19.69        19.40 
TCGA-ZF-AA58 
       47.15 

$`7P LOSS WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        91.63       103.50       105.70         8.35 
TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7W 
       16.27        44.94        16.83        16.77        17.16        27.62 
TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA84 
       49.12         0.62        41.75        51.16        66.54        15.12 
TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A13I TCGA-BL-A3JM TCGA-BL-A5ZZ 
       10.22        47.80        33.83         7.33         6.74        12.39 
TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P 
        6.58        13.15        19.04        32.84        12.16        17.88 
TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W 
       19.50         5.06        14.89        14.96         5.06         8.35 
TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ 
        8.25        17.16        16.18        20.48         4.67        12.82 
TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ 
        9.96        17.56        28.70        24.26        28.41         8.98 
TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S 
        1.94        23.01         0.46         0.43         0.69        10.95 
TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA 
       12.66        12.46        12.10        12.26        13.12        12.00 
TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YN 
       12.10        11.34        11.34        11.87        13.08        12.92 
TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 
        4.90         7.20         5.46         5.19        16.31         1.84 
TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB 
       13.58        21.86        66.41        18.41        19.00        16.70 
TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX 
      130.88       112.44        16.14        17.62        15.62         1.81 
TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL 
       10.59         7.79       123.85        87.32         2.20        13.58 
TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU 
        7.82         8.22        17.72        50.27        21.30        23.21 
TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 
        9.67        20.81        10.55       140.81        48.00        17.98 
TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B6 
       64.18        41.56        76.60        67.36        15.68        30.67 
TCGA-DK-AA6L TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U 
       38.24        15.02        13.58       166.03        12.36        10.49 
TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E5-A4TZ 
        7.53        13.64        43.50        12.03        43.59        15.35 
TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 
       38.83        24.66         0.10         0.49         2.24        16.70 
TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME 
       17.39         0.56         0.66        14.56        13.97        12.99 
TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H 
       14.33         0.92         1.22        13.68        14.07        12.95 
TCGA-E7-A8O7 TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 
       15.32        14.37         8.09        32.02        16.77         8.94 
TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA 
       33.04         4.01        12.62        22.52        27.98        60.66 
TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP 
       24.30        23.41        17.98        29.16         5.52        25.74 
TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S 
       46.78        19.79        12.85        22.98        27.35        14.96 
TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT 
       20.91         3.62        15.58        26.73        53.88        11.01 
TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 
       19.33         5.36         5.69        27.45        18.08        58.92 
TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TB TCGA-FD-A6TC 
        2.70         7.10         6.28        13.35        18.81         6.15 
TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI 
       12.69        12.36         2.27         3.06         4.31         9.67 
TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FJ-A871 
       10.85        31.07         7.13        10.65        17.23         8.94 
TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL 
        3.25         6.48        61.94        30.61        15.95        26.93 
TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B 
       35.24        33.01         7.23        20.12        17.62        66.02 
TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO 
        6.94        64.44        19.46        21.40         2.24        15.81 
TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A4ZW 
        4.50        15.91        14.07        17.75        24.92         0.49 
TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS 
        8.94        13.91         7.73         2.10         3.12        20.98 
TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 
        2.20         7.36        10.92        11.31        11.31         7.63 
TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATP TCGA-GU-AATQ 
       27.09        20.05         5.62         4.73        32.98         7.00 
TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QH TCGA-GV-A3QI 
       14.27        21.34        19.10        19.82         8.48        10.59 
TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ 
       27.35         8.58        19.07        22.72         1.51        19.40 
TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WU TCGA-K4-A3WV 
       38.60         3.06         9.01         8.22         3.45        21.24 
TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ 
        2.76         9.14        27.68         9.07        11.70         1.74 
TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-LC-A66R TCGA-LT-A5Z6 
        1.81        15.42         6.38        11.80        15.32        15.58 
TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX 
       21.07        13.48        12.23        16.67        14.24         1.84 
TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M 
        3.75        12.43        31.56        17.62        37.05        22.68 
TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A8OD 
       86.83        76.01        67.79        65.75         3.58       112.83 
TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HB 
       35.24        29.56        17.82         4.54         1.64        45.04 
TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A8HH 
        6.58        97.45       125.49        97.12        15.35         1.87 
TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SL 
       17.88        48.62        64.80        79.66         3.22        66.41 
TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 
       12.76        11.90        23.64        21.04        28.24        26.27 
TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 
       18.90         2.24        16.27        66.64         2.10        13.74 
TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAMQ 
       92.98        10.82       110.60        11.31        54.90        71.57 
TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAN0 
       91.73         2.96         8.32         6.77        98.99        56.48 
TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 
       30.94        61.45        86.30        27.06        75.39        18.81 
TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M 
        3.88        18.84         9.63         0.66        11.97        13.64 
TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 
       18.64         7.36        21.11        24.13        30.28        27.19 
TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF 
       21.86        28.41        74.56        13.41         3.48        52.73 
TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4U 
       52.60        47.84        20.22         2.89        34.06         8.61 
TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA53 
       59.38        60.16        63.02        38.73        35.41        57.90 
TCGA-ZF-AA56 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
        8.52        19.17         5.52        10.13 

  7P LOSS MUTATED 7P LOSS WILD-TYPE 
             2.14              0.10 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
            82.49            166.03 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
            19.69             15.60 
[1] "2.1 - 82.5 (19.7)"  "0.1 - 166.0 (15.6)"
[1] "hr=" "1.1"
D54V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  7P LOSS MUTATED         1        6         4        9
  7P LOSS WILD-TYPE       3      118       123      120
D54V3, multiclass
           clus
vv          7P LOSS MUTATED 7P LOSS WILD-TYPE
  STAGE I                 1                 3
  STAGE II                6               118
  STAGE III               4               123
  STAGE IV                9               120
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1+T2  T3  T4
  7P LOSS MUTATED          6   8   5
  7P LOSS WILD-TYPE      115 176  48
D54V4, multiclass
          clus
vv         7P LOSS MUTATED 7P LOSS WILD-TYPE
  T0+T1+T2               6               115
  T3                     8               176
  T4                     5                48
[1] 3 2
[1] TRUE
[1] "dimension of 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     8   0   8   1
  7P LOSS WILD-TYPE 216  42  67   7
D54V5, multiclass
    clus
vv   7P LOSS MUTATED 7P LOSS WILD-TYPE
  N0               8               216
  N1               0                42
  N2               8                67
  N3               1                 7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V6, binary
                   cls
clus                  0   1
  7P LOSS MUTATED     8   0
  7P LOSS WILD-TYPE 177  10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      8    0
  7P LOSS WILD-TYPE  177   10
   clus
vv  7P LOSS MUTATED 7P LOSS WILD-TYPE
  0               8               177
  1               0                10
[1] 2 2
[1] FALSE
D54V7, binary
                   cls
clus                  0   1
  7P LOSS MUTATED     3  17
  7P LOSS WILD-TYPE  98 271
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      3   17
  7P LOSS WILD-TYPE   98  271
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  FEMALE               3                98
  MALE                17               271
[1] 2 2
[1] FALSE
D54V8, continuous
D54V9, continuous
D54V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  7P LOSS MUTATED       1                         1    18
  7P LOSS WILD-TYPE    41                        20   293
D54V11, multiclass
                           clus
vv                          7P LOSS MUTATED 7P LOSS WILD-TYPE
  ASIAN                                   1                41
  BLACK OR AFRICAN AMERICAN               1                20
  WHITE                                  18               293
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V12, binary
                   cls
clus                  0   1
  7P LOSS MUTATED     0  19
  7P LOSS WILD-TYPE   9 333
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      0   19
  7P LOSS WILD-TYPE    9  333
                        clus
vv                       7P LOSS MUTATED 7P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 9
  NOT HISPANIC OR LATINO              19               333
[1] 2 2
[1] FALSE

Clustering(55) Variable = 7Q LOSS MUTATION ANALYSIS
D55V1, survival
                   sevent
clus2                 0   1
  7Q LOSS MUTATED    15  10
  7Q LOSS WILD-TYPE 215 143
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               25               358 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               10               143 
$`7Q LOSS MUTATED`
TCGA-BL-A0C8 TCGA-BL-A13J TCGA-CF-A47X TCGA-DK-A1A5 TCGA-DK-A2I4 TCGA-DK-A3IK 
       40.08         2.66        12.62         2.14       123.85         2.20 
TCGA-DK-A3IM TCGA-DK-AA6P TCGA-E7-A6ME TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A6TE 
        7.82        15.02        12.99         8.25        18.08        12.36 
TCGA-GC-A4ZW TCGA-GU-A766 TCGA-GU-AATO TCGA-GU-AATQ TCGA-K4-A3WS TCGA-UY-A8OB 
        0.49         5.62        10.65         7.00        25.02        65.75 
TCGA-XF-AAML TCGA-XF-AAMT TCGA-XF-AAMZ TCGA-YF-AA3M TCGA-ZF-A9RF TCGA-ZF-A9RL 
        7.63         2.96        44.32        13.64        52.73        82.49 
TCGA-ZF-AA4T 
       19.69 

$`7Q LOSS WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        91.63       103.50       105.70         8.35 
TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S 
       16.27        44.94        16.83        16.77        17.16        34.98 
TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 
       27.62        49.12         0.62        41.75        51.16        66.54 
TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A13I TCGA-BL-A3JM 
       15.12        10.22        47.80        33.83         7.33         6.74 
TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O 
       12.39         6.58        13.15        19.04        32.84        12.16 
TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V 
       17.88        19.50         5.06        14.89        14.96         5.06 
TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH 
        8.35         8.25        17.16        16.18        20.48         4.67 
TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F 
       12.82         9.96        17.56        28.70        24.26        28.41 
TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C 
        8.98         1.94        23.01         0.46         0.43         0.69 
TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47Y TCGA-CF-A5U8 
       10.95        12.66        12.46        12.10        12.26        13.12 
TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CF-A9FM 
       12.00        12.10        11.34        11.34        11.87        13.08 
TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL 
       12.92         4.90         7.20         5.46         5.19        16.31 
TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA 
        1.84        13.58        21.86        66.41        18.41        19.00 
TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG 
       16.70       130.88       112.44        16.14        17.62        15.62 
TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I6 TCGA-DK-A3IL TCGA-DK-A3IN 
        1.81        10.59         7.79        87.32        13.58         8.22 
TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW 
       17.72        50.27        21.30        23.21         9.67        20.81 
TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW 
       10.55       140.81        48.00        17.98        64.18        41.56 
TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L 
       76.60        67.36        15.68        41.06        30.67        38.24 
TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X 
       13.58       166.03        12.36        10.49         8.65         7.53 
TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4TZ 
       13.64        43.50        12.03        10.62        43.59        15.35 
TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 
       38.83        24.66         0.10         0.49         2.24        16.70 
TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MF 
       17.39         0.56         0.66        14.56        13.97        14.33 
TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A8O7 
        0.92         1.22        13.68        14.07        12.95        15.32 
TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 
       14.37         8.09        32.02        16.77         8.94        33.04 
TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ 
        4.01        12.62        22.52        27.98        60.66        24.30 
TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ 
       23.41        17.98        29.16         5.52        25.74        46.78 
TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U 
       19.79        12.85        22.98        27.35        14.96        20.91 
TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU 
        3.62        15.58        26.73        53.88        11.01        19.33 
TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BZ TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O 
        5.36         5.69        27.45        58.92         2.70         7.10 
TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD 
        6.28        13.35        62.86        18.81         6.15        12.69 
TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 
        2.27         3.06         4.31         9.67        10.85        31.07 
TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A3EE TCGA-FT-A61P 
        7.13        10.65        17.23         8.94         3.25         6.48 
TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES 
       61.94        30.61        15.95        26.93        35.24        33.01 
TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3D 
        7.23        20.12        17.62        66.02         6.94        64.44 
TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC 
       19.46        21.40         2.24        15.81         4.50        15.91 
TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 
       14.07        17.75        24.92         8.94        13.91         7.73 
TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P 
        2.10         3.12        20.98         2.20         7.36        10.92 
TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A767 
       11.31        11.31         7.63        27.09        20.05         4.73 
TCGA-GU-AATP TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF 
       32.98        14.27        21.34        19.10        19.82        20.28 
TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA 
        8.48        10.59        27.35         8.58        19.07        22.72 
TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE 
        1.51        19.40        38.60         3.06         9.01         8.22 
TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH 
        3.45        21.24         2.76         9.14        27.68         9.07 
TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO 
       11.70         1.74         1.81        15.42         6.38        11.80 
TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN 
       15.32        15.58        21.07        13.48        12.23        16.67 
TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78K 
       14.24         1.84         3.75        12.43        31.56        17.62 
TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OC 
       37.05        22.68        86.83        76.01        67.79         3.58 
TCGA-UY-A8OD TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF 
      112.83        35.24        29.56        17.82         4.54         1.64 
TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG 
       45.04         6.58        97.45       125.49        97.12        15.35 
TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ 
        1.87        17.88        48.62        64.80        79.66         3.22 
TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ 
       66.41        12.76        11.90        23.64        21.04        28.24 
TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 
       26.27        18.90         2.24        16.27        66.64         2.10 
TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAMJ 
       13.74        92.98        10.82       110.60        11.31        54.90 
TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAN0 
       71.57        91.73         8.32         6.77        98.99        56.48 
TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 
       30.94        61.45        86.30        27.06        75.39        18.81 
TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R0 
        3.88        18.84         9.63         0.66        11.97        18.64 
TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 
        7.36        21.11        24.13        30.28        27.19        21.86 
TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RG TCGA-ZF-A9RM 
       28.41        74.56        13.41         3.48        52.60        47.84 
TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W 
       20.22         2.89        34.06         8.61        59.38        60.16 
TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 
       63.02        38.73        35.41        57.90        19.40         8.52 
TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
       47.15        19.17         5.52        10.13 

  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
             0.49              0.10 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
           123.85            166.03 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
           12.620            16.045 
[1] "0.5 - 123.8 (12.6)" "0.1 - 166.0 (16.0)"
[1] "hr=" "1.1"
D55V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  7Q LOSS MUTATED         1        9         6        9
  7Q LOSS WILD-TYPE       3      115       121      120
D55V3, multiclass
           clus
vv          7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  STAGE I                 1                 3
  STAGE II                9               115
  STAGE III               6               121
  STAGE IV                9               120
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1+T2  T3  T4
  7Q LOSS MUTATED          8  12   3
  7Q LOSS WILD-TYPE      113 172  50
D55V4, multiclass
          clus
vv         7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  T0+T1+T2               8               113
  T3                    12               172
  T4                     3                50
[1] 3 2
[1] TRUE
[1] "dimension of 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    11   1   8   0
  7Q LOSS WILD-TYPE 213  41  67   8
D55V5, multiclass
    clus
vv   7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  N0              11               213
  N1               1                41
  N2               8                67
  N3               0                 8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V6, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED    11   0
  7Q LOSS WILD-TYPE 174  10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED     11    0
  7Q LOSS WILD-TYPE  174   10
   clus
vv  7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  0              11               174
  1               0                10
[1] 2 2
[1] FALSE
D55V7, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED     4  21
  7Q LOSS WILD-TYPE  97 267
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      4   21
  7Q LOSS WILD-TYPE   97  267
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  FEMALE               4                97
  MALE                21               267
[1] 2 2
[1] FALSE
D55V8, continuous
D55V9, continuous
D55V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  7Q LOSS MUTATED       2                         0    22
  7Q LOSS WILD-TYPE    40                        21   289
D55V11, multiclass
                           clus
vv                          7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  ASIAN                                   2                40
  BLACK OR AFRICAN AMERICAN               0                21
  WHITE                                  22               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"
D55V12, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED     2  23
  7Q LOSS WILD-TYPE   7 329
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      2   23
  7Q LOSS WILD-TYPE    7  329
                        clus
vv                       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                 7
  NOT HISPANIC OR LATINO              23               329
[1] 2 2
[1] FALSE

Clustering(56) Variable = 8P LOSS MUTATION ANALYSIS
D56V1, survival
                   sevent
clus2                 0   1
  8P LOSS MUTATED   110  66
  8P LOSS WILD-TYPE 120  87
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
              176               207 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               66                87 
$`8P LOSS MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW TCGA-4Z-AA7Q 
       22.29        11.97       103.50       105.70         8.35        16.77 
TCGA-4Z-AA7R TCGA-4Z-AA7W TCGA-4Z-AA80 TCGA-4Z-AA86 TCGA-BL-A0C8 TCGA-BL-A13J 
       17.16        27.62         0.62        10.22        40.08         2.66 
TCGA-BT-A20W TCGA-BT-A2LB TCGA-BT-A3PK TCGA-BT-A42C TCGA-BT-A42F TCGA-C4-A0EZ 
        8.35        16.18         9.96        28.70        28.41         8.98 
TCGA-CF-A1HS TCGA-CF-A47S TCGA-CF-A8HX TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CU-A0YN 
        0.43        10.95        11.34        11.34        11.87        12.92 
TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-DK-A1A3 TCGA-DK-A1A7 TCGA-DK-A1AC TCGA-DK-A1AD 
        5.46         5.19        21.86        18.41       130.88       112.44 
TCGA-DK-A2HX TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM 
        1.81       123.85        87.32         2.20        13.58         7.82 
TCGA-DK-A3IN TCGA-DK-A3IT TCGA-DK-A3IV TCGA-DK-A6AV TCGA-DK-A6B2 TCGA-DK-A6B5 
        8.22        21.30         9.67        64.18        15.68        41.06 
TCGA-DK-AA6L TCGA-DK-AA6P TCGA-DK-AA6S TCGA-DK-AA6W TCGA-DK-AA76 TCGA-DK-AA77 
       38.24        15.02       166.03         8.65        12.03        10.62 
TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A677 TCGA-E7-A7DU 
       15.35        38.83        17.39         0.56        14.56         0.92 
TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A97Q TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 
        1.22        13.68         8.09        16.77         8.94        33.04 
TCGA-FD-A3B7 TCGA-FD-A3N5 TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SO 
        4.01        22.52        24.30        23.41        17.98         5.52 
TCGA-FD-A3SR TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BU 
       19.79        22.98        27.35        15.58        26.73        19.33 
TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A62N TCGA-FD-A62P TCGA-FD-A62S 
        8.25        27.45        18.08         2.70         6.28        13.35 
TCGA-FD-A6TA TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TH TCGA-FD-A6TK 
       62.86        12.69        12.36         2.27         4.31        10.85 
TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EK TCGA-G2-A3IE 
       31.07        17.23         6.48        61.94        15.95        20.12 
TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD 
        6.94        64.44        19.46         4.50        15.91        14.07 
TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A4ZW TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP 
       17.75        24.92         0.49        13.91         7.73         2.10 
TCGA-GD-A3OQ TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-A766 
        3.12         7.36        10.92         7.63        20.05         5.62 
TCGA-GU-AATO TCGA-GU-AATP TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF 
       10.65        32.98        21.34        19.10        19.82        20.28 
TCGA-GV-A3QH TCGA-GV-A40E TCGA-GV-A40G TCGA-H4-A2HQ TCGA-HQ-A5ND TCGA-HQ-A5NE 
        8.48         8.58        19.07        19.40         9.01         8.22 
TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R 
       25.02         3.45        21.24         2.76         9.14        27.68 
TCGA-K4-A5RH TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-AAQO TCGA-LT-A5Z6 
        9.07         1.74         1.81        15.42        11.80        15.58 
TCGA-LT-A8JT TCGA-PQ-A6FI TCGA-R3-A69X TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A8OB 
       21.07        12.23        14.24        17.62        37.05        65.75 
TCGA-UY-A8OD TCGA-UY-A9PB TCGA-UY-A9PD TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HH 
      112.83        29.56        17.82        45.04         6.58         1.87 
TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9T0 TCGA-XF-A9T3 
       79.66         3.22        12.76        11.90        26.27         2.24 
TCGA-XF-A9T5 TCGA-XF-AAMG TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMT 
       66.64       110.60        54.90         7.63        71.57         2.96 
TCGA-XF-AAMW TCGA-XF-AAN0 TCGA-XF-AAN2 TCGA-XF-AAN5 TCGA-YC-A89H TCGA-ZF-A9R0 
        8.32        56.48        61.45        75.39        18.84        18.64 
TCGA-ZF-A9R4 TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RL TCGA-ZF-AA4R TCGA-ZF-AA4T 
       30.28        13.41         3.48        82.49        34.06        19.69 
TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA53 TCGA-ZF-AA56 TCGA-ZF-AA58 
        8.61        59.38        60.16        57.90         8.52        47.15 
TCGA-ZF-AA5H TCGA-ZF-AA5P 
       19.17        10.13 

$`8P LOSS WILD-TYPE`
TCGA-2F-A9KQ TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7S TCGA-4Z-AA7Y 
       91.63        16.27        44.94        16.83        34.98        49.12 
TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA84 TCGA-4Z-AA87 TCGA-4Z-AA89 
       41.75        51.16        66.54        15.12        47.80        33.83 
TCGA-BL-A13I TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J 
        7.33         6.74        12.39         6.58        13.15        19.04 
TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T 
       32.84        12.16        17.88        19.50         5.06        14.89 
TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LD TCGA-BT-A3PH 
       14.96         5.06         8.25        17.16        20.48         4.67 
TCGA-BT-A3PJ TCGA-BT-A42B TCGA-BT-A42E TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR 
       12.82        17.56        24.26         1.94        23.01         0.46 
TCGA-CF-A27C TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y 
        0.69        12.66        12.46        12.10        12.62        12.26 
TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A9FM TCGA-CU-A0YO TCGA-CU-A0YR 
       13.12        12.00        12.10        13.08         4.90         7.20 
TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1AA 
       16.31         1.84        13.58         2.14        66.41        19.00 
TCGA-DK-A1AB TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A2I2 
       16.70        16.14        17.62        15.62        10.59         7.79 
TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IU TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY 
       17.72        50.27        23.21        20.81        10.55       140.81 
TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B6 
       48.00        17.98        41.56        76.60        67.36        30.67 
TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 
       13.58        12.36        10.49         7.53        13.64        43.50 
TCGA-E5-A2PC TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 
       43.59        24.66         0.10         0.49         2.24        16.70 
TCGA-E7-A5KF TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7XN TCGA-E7-A85H 
        0.66        13.97        12.99        14.33        14.07        12.95 
TCGA-E7-A8O7 TCGA-E7-A97P TCGA-FD-A3B3 TCGA-FD-A3B8 TCGA-FD-A3N6 TCGA-FD-A3NA 
       15.32        14.37        32.02        12.62        27.98        60.66 
TCGA-FD-A3SN TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SS TCGA-FD-A43S TCGA-FD-A43U 
       29.16        25.74        46.78        12.85        14.96        20.91 
TCGA-FD-A43X TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5C1 
        3.62        53.88        11.01         5.36         5.69        58.92 
TCGA-FD-A62O TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FJ-A3Z9 
        7.10        18.81         6.15         3.06         9.67         7.13 
TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EJ TCGA-G2-A2EL TCGA-G2-A2EO 
       10.65         8.94         3.25        30.61        26.93        35.24 
TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3VY TCGA-G2-AA3B TCGA-GC-A3BM TCGA-GC-A3I6 
       33.01         7.23        17.62        66.02        21.40         2.24 
TCGA-GC-A3OO TCGA-GC-A6I1 TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A42R 
       15.81         8.94        20.98         2.20        11.31        11.31 
TCGA-GU-A763 TCGA-GU-A767 TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3QI TCGA-GV-A3QK 
       27.09         4.73         7.00        14.27        10.59        27.35 
TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-K4-A5RI TCGA-K4-A83P 
       22.72         1.51        38.60         3.06        11.70         6.38 
TCGA-LC-A66R TCGA-MV-A51V TCGA-PQ-A6FN TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G0 
       15.32        13.48        16.67         1.84         3.75        12.43 
TCGA-SY-A9G5 TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OC 
       31.56        22.68        86.83        76.01        67.79         3.58 
TCGA-UY-A9PA TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF 
       35.24         4.54         1.64        97.45       125.49        97.12 
TCGA-XF-A8HG TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SL TCGA-XF-A9SX 
       15.35        17.88        48.62        64.80        66.41        23.64 
TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T2 TCGA-XF-A9T4 TCGA-XF-A9T6 TCGA-XF-A9T8 
       21.04        28.24        18.90        16.27         2.10        13.74 
TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMR TCGA-XF-AAMX TCGA-XF-AAMY 
       92.98        10.82        11.31        91.73         6.77        98.99 
TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN7 TCGA-XF-AAN8 
       44.32        30.94        86.30        27.06        18.81         3.88 
TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R1 TCGA-ZF-A9R2 
        9.63         0.66        11.97        13.64         7.36        21.11 
TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RF 
       24.13        27.19        21.86        28.41        74.56        52.73 
TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4X TCGA-ZF-AA51 
       52.60        47.84        20.22         2.89        63.02        38.73 
TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA5N 
       35.41        19.40         5.52 

  8P LOSS MUTATED 8P LOSS WILD-TYPE 
             0.43              0.10 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
           166.03            140.81 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
            15.58             16.14 
[1] "0.4 - 166.0 (15.6)" "0.1 - 140.8 (16.1)"
[1] "hr=" "1.1"
D56V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  8P LOSS MUTATED         1       55        48       71
  8P LOSS WILD-TYPE       3       69        79       58
D56V3, multiclass
           clus
vv          8P LOSS MUTATED 8P LOSS WILD-TYPE
  STAGE I                 1                 3
  STAGE II               55                69
  STAGE III              48                79
  STAGE IV               71                58
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1+T2  T3  T4
  8P LOSS MUTATED         50  84  26
  8P LOSS WILD-TYPE       71 100  27
D56V4, multiclass
          clus
vv         8P LOSS MUTATED 8P LOSS WILD-TYPE
  T0+T1+T2              50                71
  T3                    84               100
  T4                    26                27
[1] 3 2
[1] TRUE
[1] "dimension of 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    91  23  42   4
  8P LOSS WILD-TYPE 133  19  33   4
D56V5, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  N0              91               133
  N1              23                19
  N2              42                33
  N3               4                 4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V6, binary
                   cls
clus                  0   1
  8P LOSS MUTATED    71   6
  8P LOSS WILD-TYPE 114   4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     71    6
  8P LOSS WILD-TYPE  114    4
   clus
vv  8P LOSS MUTATED 8P LOSS WILD-TYPE
  0              71               114
  1               6                 4
[1] 2 2
[1] FALSE
D56V7, binary
                   cls
clus                  0   1
  8P LOSS MUTATED    46 131
  8P LOSS WILD-TYPE  55 157
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     46  131
  8P LOSS WILD-TYPE   55  157
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  FEMALE              46                55
  MALE               131               157
[1] 2 2
[1] FALSE
D56V8, continuous
D56V9, continuous
D56V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  8P LOSS MUTATED      13                        12   146
  8P LOSS WILD-TYPE    29                         9   165
D56V11, multiclass
                           clus
vv                          8P LOSS MUTATED 8P LOSS WILD-TYPE
  ASIAN                                  13                29
  BLACK OR AFRICAN AMERICAN              12                 9
  WHITE                                 146               165
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V12, binary
                   cls
clus                  0   1
  8P LOSS MUTATED     4 162
  8P LOSS WILD-TYPE   5 190
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      4  162
  8P LOSS WILD-TYPE    5  190
                        clus
vv                       8P LOSS MUTATED 8P LOSS WILD-TYPE
  HISPANIC OR LATINO                   4                 5
  NOT HISPANIC OR LATINO             162               190
[1] 2 2
[1] FALSE

Clustering(57) Variable = 8Q LOSS MUTATION ANALYSIS
D57V1, survival
                   sevent
clus2                 0   1
  8Q LOSS MUTATED    23  11
  8Q LOSS WILD-TYPE 207 142
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               34               349 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               11               142 
$`8Q LOSS MUTATED`
TCGA-2F-A9KT TCGA-2F-A9KW TCGA-BL-A0C8 TCGA-BL-A13J TCGA-CF-A1HS TCGA-CF-A8HX 
      105.70         8.35        40.08         2.66         0.43        11.34 
TCGA-DK-A2HX TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A6B5 TCGA-DK-AA76 TCGA-DK-AA77 
        1.81        13.58         7.82        41.06        12.03        10.62 
TCGA-E7-A5KE TCGA-E7-A677 TCGA-E7-A7DV TCGA-FD-A3B7 TCGA-FD-A3SL TCGA-FD-A3SR 
        0.56        14.56         1.22         4.01        23.41        19.79 
TCGA-FD-A5BU TCGA-FD-A5BZ TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-G2-AA3F TCGA-GU-A42P 
       19.33        27.45        10.85        31.07        19.46        10.92 
TCGA-GU-A762 TCGA-GU-AATO TCGA-H4-A2HQ TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A5RJ 
        7.63        10.65        19.40        25.02         3.45         1.74 
TCGA-LT-A5Z6 TCGA-UY-A78L TCGA-XF-AAMQ TCGA-XF-AAN0 
       15.58        37.05        71.57        56.48 

$`8Q LOSS WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-4Z-AA7M TCGA-4Z-AA7N 
       22.29        11.97        91.63       103.50        16.27        44.94 
TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA7Y 
       16.83        16.77        17.16        34.98        27.62        49.12 
TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA84 TCGA-4Z-AA86 
        0.62        41.75        51.16        66.54        15.12        10.22 
TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A13I TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 
       47.80        33.83         7.33         6.74        12.39         6.58 
TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q 
       13.15        19.04        32.84        12.16        17.88        19.50 
TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X 
        5.06        14.89        14.96         5.06         8.35         8.25 
TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK 
       17.16        16.18        20.48         4.67        12.82         9.96 
TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 
       17.56        28.70        24.26        28.41         8.98         1.94 
TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V 
       23.01         0.46         0.69        10.95        12.66        12.46 
TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 
       12.10        12.62        12.26        13.12        12.00        12.10 
TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR 
       11.34        11.87        13.08        12.92         4.90         7.20 
TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 
        5.46         5.19        16.31         1.84        13.58        21.86 
TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC 
        2.14        66.41        18.41        19.00        16.70       130.88 
TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A2I2 
      112.44        16.14        17.62        15.62        10.59         7.79 
TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS 
      123.85        87.32         2.20         8.22        17.72        50.27 
TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY 
       21.30        23.21         9.67        20.81        10.55       140.81 
TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 
       48.00        17.98        64.18        41.56        76.60        67.36 
TCGA-DK-A6B2 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6S 
       15.68        30.67        38.24        15.02        13.58       166.03 
TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 
       12.36        10.49         8.65         7.53        13.64        43.50 
TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ 
       43.59        15.35        38.83        24.66         0.10         0.49 
TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KF TCGA-E7-A678 TCGA-E7-A6ME 
        2.24        16.70        17.39         0.66        13.97        12.99 
TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A8O7 
       14.33         0.92        13.68        14.07        12.95        15.32 
TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 
       14.37         8.09        32.02        16.77         8.94        33.04 
TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SM 
       12.62        22.52        27.98        60.66        24.30        17.98 
TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SS TCGA-FD-A43N 
       29.16         5.52        25.74        46.78        12.85        22.98 
TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR 
       27.35        14.96        20.91         3.62        15.58        26.73 
TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C0 
       53.88        11.01         5.36         5.69         8.25        18.08 
TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA 
       58.92         2.70         7.10         6.28        13.35        62.86 
TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG 
       18.81         6.15        12.69        12.36         2.27         3.06 
TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FJ-A871 
        4.31         9.67         7.13        10.65        17.23         8.94 
TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL 
        3.25         6.48        61.94        30.61        15.95        26.93 
TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B 
       35.24        33.01         7.23        20.12        17.62        66.02 
TCGA-G2-AA3C TCGA-G2-AA3D TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB 
        6.94        64.44        21.40         2.24        15.81         4.50 
TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A4ZW TCGA-GC-A6I1 
       15.91        14.07        17.75        24.92         0.49         8.94 
TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 
       13.91         7.73         2.10         3.12        20.98         2.20 
TCGA-GD-A76B TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 
        7.36        11.31        11.31        27.09        20.05         5.62 
TCGA-GU-A767 TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX 
        4.73        32.98         7.00        14.27        21.34        19.10 
TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E 
       19.82        20.28         8.48        10.59        27.35         8.58 
TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND 
       19.07        22.72         1.51        38.60         3.06         9.01 
TCGA-HQ-A5NE TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH 
        8.22        21.24         2.76         9.14        27.68         9.07 
TCGA-K4-A5RI TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-LC-A66R 
       11.70         1.81        15.42         6.38        11.80        15.32 
TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX 
       21.07        13.48        12.23        16.67        14.24         1.84 
TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78M TCGA-UY-A78N 
        3.75        12.43        31.56        17.62        22.68        86.83 
TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A8OD TCGA-UY-A9PA 
       76.01        67.79        65.75         3.58       112.83        35.24 
TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HC 
       29.56        17.82         4.54         1.64        45.04         6.58 
TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A8HI 
       97.45       125.49        97.12        15.35         1.87        17.88 
TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SV 
       48.62        64.80        79.66         3.22        66.41        12.76 
TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 
       11.90        23.64        21.04        28.24        26.27        18.90 
TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME 
        2.24        16.27        66.64         2.10        13.74        92.98 
TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMR 
       10.82       110.60        11.31        54.90         7.63        91.73 
TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN1 
        2.96         8.32         6.77        98.99        44.32        30.94 
TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-XF-AAN8 
       61.45        86.30        27.06        75.39        18.81         3.88 
TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R0 
       18.84         9.63         0.66        11.97        13.64        18.64 
TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 
        7.36        21.11        24.13        30.28        27.19        21.86 
TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG 
       28.41        74.56        13.41         3.48        52.73        52.60 
TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4T 
       82.49        47.84        20.22         2.89        34.06        19.69 
TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 
        8.61        59.38        60.16        63.02        38.73        35.41 
TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N 
       57.90        19.40         8.52        47.15        19.17         5.52 
TCGA-ZF-AA5P 
       10.13 

  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
             0.43              0.10 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
           105.70            166.03 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
           12.805            15.950 
[1] "0.4 - 105.7 (12.8)" "0.1 - 166.0 (15.9)"
[1] "hr=" "1.1"
D57V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  8Q LOSS MUTATED         1       10         6       16
  8Q LOSS WILD-TYPE       3      114       121      113
D57V3, multiclass
           clus
vv          8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  STAGE I                 1                 3
  STAGE II               10               114
  STAGE III               6               121
  STAGE IV               16               113
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1+T2  T3  T4
  8Q LOSS MUTATED          9  11  10
  8Q LOSS WILD-TYPE      112 173  43
D57V4, multiclass
          clus
vv         8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  T0+T1+T2               9               112
  T3                    11               173
  T4                    10                43
[1] 3 2
[1] TRUE
[1] "dimension of 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   4  10   1
  8Q LOSS WILD-TYPE 208  38  65   7
D57V5, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  N0              16               208
  N1               4                38
  N2              10                65
  N3               1                 7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V6, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED    16   2
  8Q LOSS WILD-TYPE 169   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED     16    2
  8Q LOSS WILD-TYPE  169    8
   clus
vv  8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  0              16               169
  1               2                 8
[1] 2 2
[1] FALSE
D57V7, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED    11  23
  8Q LOSS WILD-TYPE  90 265
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED     11   23
  8Q LOSS WILD-TYPE   90  265
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  FEMALE              11                90
  MALE                23               265
[1] 2 2
[1] FALSE
D57V8, continuous
D57V9, continuous
D57V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  8Q LOSS MUTATED       4                         3    27
  8Q LOSS WILD-TYPE    38                        18   284
D57V11, multiclass
                           clus
vv                          8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  ASIAN                                   4                38
  BLACK OR AFRICAN AMERICAN               3                18
  WHITE                                  27               284
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V12, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED     0  34
  8Q LOSS WILD-TYPE   9 318
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      0   34
  8Q LOSS WILD-TYPE    9  318
                        clus
vv                       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 9
  NOT HISPANIC OR LATINO              34               318
[1] 2 2
[1] FALSE

Clustering(58) Variable = 9P LOSS MUTATION ANALYSIS
D58V1, survival
                   sevent
clus2                 0   1
  9P LOSS MUTATED    97  62
  9P LOSS WILD-TYPE 133  91
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              159               224 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               62                91 
$`9P LOSS MUTATED`
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW TCGA-4Z-AA7M 
       11.97        91.63       103.50       105.70         8.35        16.27 
TCGA-4Z-AA7O TCGA-4Z-AA7S TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-BL-A0C8 TCGA-BT-A0S7 
       16.83        34.98        49.12         0.62        40.08         6.58 
TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20T TCGA-BT-A20W 
       19.04        32.84        17.88        19.50        14.89         8.35 
TCGA-BT-A2LB TCGA-BT-A42E TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A27C TCGA-CF-A47V 
       16.18        24.26        23.01         0.46         0.69        12.46 
TCGA-CF-A47X TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CU-A0YO 
       12.62        13.12        12.00        11.34        11.87         4.90 
TCGA-CU-A3KJ TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1AA 
        5.46         1.84        13.58        21.86         2.14        19.00 
TCGA-DK-A1AB TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A3IK TCGA-DK-A3IN TCGA-DK-A3IQ 
       16.70        17.62        15.62         2.20         8.22        17.72 
TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3WX TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV 
       50.27        21.30        10.55        48.00        17.98        64.18 
TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6U 
       15.68        41.06        15.02        13.58       166.03        10.49 
TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A2PC 
        8.65         7.53        13.64        12.03        10.62        43.59 
TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A7DU 
       38.83        24.66        17.39         0.56         0.66         0.92 
TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A97Q TCGA-FD-A3B5 TCGA-FD-A3SM TCGA-FD-A3SN 
        1.22        13.68         8.09         8.94        17.98        29.16 
TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43X TCGA-FD-A43Y 
       46.78        19.79        12.85        22.98         3.62        15.58 
TCGA-FD-A5BR TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62O 
       26.73         5.36        27.45        18.08        58.92         7.10 
TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TD TCGA-FD-A6TG TCGA-FD-A6TK 
        6.28        62.86        18.81        12.69         3.06        10.85 
TCGA-FT-A61P TCGA-G2-A2EO TCGA-G2-A3IB TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3F 
        6.48        35.24         7.23        17.62        66.02        19.46 
TCGA-GC-A3BM TCGA-GC-A3RD TCGA-GC-A3YS TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GD-A6C6 
       21.40        14.07        24.92         0.49         8.94         2.20 
TCGA-GD-A76B TCGA-GU-A42Q TCGA-GU-A762 TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATP 
        7.36        11.31         7.63         4.73        10.65        32.98 
TCGA-GU-AATQ TCGA-GV-A3JW TCGA-GV-A3QH TCGA-GV-A3QK TCGA-GV-A6ZA TCGA-H4-A2HQ 
        7.00        21.34         8.48        27.35        22.72        19.40 
TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB 
       38.60         3.06        25.02         3.45        21.24         2.76 
TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A6MB TCGA-K4-AAQO TCGA-LT-A8JT TCGA-PQ-A6FI 
        9.07        11.70        15.42        11.80        21.07        12.23 
TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G5 TCGA-UY-A8OB 
       16.67        14.24         1.84         3.75        31.56        65.75 
TCGA-UY-A8OD TCGA-UY-A9PD TCGA-UY-A9PE TCGA-XF-A8HF TCGA-XF-A8HI TCGA-XF-A9SV 
      112.83        17.82         4.54        97.12        17.88        12.76 
TCGA-XF-A9T0 TCGA-XF-A9T4 TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMX TCGA-XF-AAMY 
       26.27        16.27        71.57        91.73         6.77        98.99 
TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN7 TCGA-YF-AA3L TCGA-ZF-A9R1 TCGA-ZF-A9R2 
       44.32        30.94        18.81        11.97         7.36        21.11 
TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-A9RL TCGA-ZF-AA4U TCGA-ZF-AA4W 
       28.41        74.56         3.48        82.49         8.61        60.16 
TCGA-ZF-AA51 TCGA-ZF-AA54 TCGA-ZF-AA56 
       38.73        19.40         8.52 

$`9P LOSS WILD-TYPE`
TCGA-2F-A9KO TCGA-4Z-AA7N TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7W TCGA-4Z-AA81 
       22.29        44.94        16.77        17.16        27.62        41.75 
TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 
       51.16        66.54        15.12        10.22        47.80        33.83 
TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0YX TCGA-BT-A20O 
        7.33         2.66         6.74        12.39        13.15        12.16 
TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LD 
        5.06        14.96         5.06         8.25        17.16        20.48 
TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42F 
        4.67        12.82         9.96        17.56        28.70        28.41 
TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-CF-A1HS TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47W 
        8.98         1.94         0.43        10.95        12.66        12.10 
TCGA-CF-A47Y TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YR 
       12.26        12.10        11.34        13.08        12.92         7.20 
TCGA-CU-A3QU TCGA-CU-A3YL TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AC TCGA-DK-A1AD 
        5.19        16.31        66.41        18.41       130.88       112.44 
TCGA-DK-A1AE TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 
       16.14         1.81        10.59         7.79       123.85        87.32 
TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WY 
       13.58         7.82        23.21         9.67        20.81       140.81 
TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6T 
       41.56        76.60        67.36        30.67        38.24        12.36 
TCGA-DK-AA74 TCGA-E5-A4TZ TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 
       43.50        15.35         0.10         0.49         2.24        16.70 
TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7XN TCGA-E7-A85H 
       14.56        13.97        12.99        14.33        14.07        12.95 
TCGA-E7-A8O7 TCGA-E7-A97P TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B6 TCGA-FD-A3B7 
       15.32        14.37        32.02        16.77        33.04         4.01 
TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL 
       12.62        22.52        27.98        60.66        24.30        23.41 
TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BS 
        5.52        25.74        27.35        14.96        20.91        53.88 
TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A62N TCGA-FD-A62S 
       11.01        19.33         5.69         8.25         2.70        13.35 
TCGA-FD-A6TC TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z7 
        6.15        12.36         2.27         4.31         9.67        31.07 
TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EF 
        7.13        10.65        17.23         8.94         3.25        61.94 
TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2ES TCGA-G2-A3IE TCGA-G2-AA3C 
       30.61        15.95        26.93        33.01        20.12         6.94 
TCGA-G2-AA3D TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3WC 
       64.44         2.24        15.81         4.50        15.91        17.75 
TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GU-A42P 
       13.91         7.73         2.10         3.12        20.98        10.92 
TCGA-GU-A42R TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GV-A3JV TCGA-GV-A3JX 
       11.31        27.09        20.05         5.62        14.27        19.10 
TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QI TCGA-GV-A40E TCGA-GV-A40G TCGA-H4-A2HO 
       19.82        20.28        10.59         8.58        19.07         1.51 
TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6FZ 
        9.01         8.22         9.14        27.68         1.74         1.81 
TCGA-K4-A83P TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-SY-A9G0 TCGA-UY-A78K 
        6.38        15.32        15.58        13.48        12.43        17.62 
TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OC 
       37.05        22.68        86.83        76.01        67.79         3.58 
TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HD 
       35.24        29.56         1.64        45.04         6.58        97.45 
TCGA-XF-A8HE TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI 
      125.49        15.35         1.87        48.62        64.80        79.66 
TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ 
        3.22        66.41        11.90        23.64        21.04        28.24 
TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME 
       18.90         2.24        66.64         2.10        13.74        92.98 
TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMT 
       10.82       110.60        11.31        54.90         7.63         2.96 
TCGA-XF-AAMW TCGA-XF-AAN0 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 
        8.32        56.48        61.45        86.30        27.06        75.39 
TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3M TCGA-ZF-A9R0 
        3.88        18.84         9.63         0.66        13.64        18.64 
TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9RD TCGA-ZF-A9RF 
       24.13        30.28        27.19        21.86        13.41        52.73 
TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4T 
       52.60        47.84        20.22         2.89        34.06        19.69 
TCGA-ZF-AA4V TCGA-ZF-AA4X TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA58 TCGA-ZF-AA5H 
       59.38        63.02        35.41        57.90        47.15        19.17 
TCGA-ZF-AA5N TCGA-ZF-AA5P 
        5.52        10.13 

  9P LOSS MUTATED 9P LOSS WILD-TYPE 
             0.46              0.10 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
           166.03            140.81 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
           15.680            15.695 
[1] "0.5 - 166.0 (15.7)" "0.1 - 140.8 (15.7)"
[1] "hr=" "1"  
D58V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  9P LOSS MUTATED         2       52        61       46
  9P LOSS WILD-TYPE       2       72        66       83
D58V3, multiclass
           clus
vv          9P LOSS MUTATED 9P LOSS WILD-TYPE
  STAGE I                 2                 2
  STAGE II               52                72
  STAGE III              61                66
  STAGE IV               46                83
[1] 4 2
[1] TRUE
[1] "dimension of contingency 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         52  80  22
  9P LOSS WILD-TYPE       69 104  31
D58V4, multiclass
          clus
vv         9P LOSS MUTATED 9P LOSS WILD-TYPE
  T0+T1+T2              52                69
  T3                    80               104
  T4                    22                31
[1] 3 2
[1] TRUE
[1] "dimension of 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   105  13  30   3
  9P LOSS WILD-TYPE 119  29  45   5
D58V5, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  N0             105               119
  N1              13                29
  N2              30                45
  N3               3                 5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V6, binary
                   cls
clus                  0   1
  9P LOSS MUTATED    81   3
  9P LOSS WILD-TYPE 104   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     81    3
  9P LOSS WILD-TYPE  104    7
   clus
vv  9P LOSS MUTATED 9P LOSS WILD-TYPE
  0              81               104
  1               3                 7
[1] 2 2
[1] FALSE
D58V7, binary
                   cls
clus                  0   1
  9P LOSS MUTATED    40 124
  9P LOSS WILD-TYPE  61 164
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     40  124
  9P LOSS WILD-TYPE   61  164
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  FEMALE              40                61
  MALE               124               164
[1] 2 2
[1] FALSE
D58V8, continuous
D58V9, continuous
D58V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  9P LOSS MUTATED      18                         8   130
  9P LOSS WILD-TYPE    24                        13   181
D58V11, multiclass
                           clus
vv                          9P LOSS MUTATED 9P LOSS WILD-TYPE
  ASIAN                                  18                24
  BLACK OR AFRICAN AMERICAN               8                13
  WHITE                                 130               181
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V12, binary
                   cls
clus                  0   1
  9P LOSS MUTATED     4 150
  9P LOSS WILD-TYPE   5 202
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      4  150
  9P LOSS WILD-TYPE    5  202
                        clus
vv                       9P LOSS MUTATED 9P LOSS WILD-TYPE
  HISPANIC OR LATINO                   4                 5
  NOT HISPANIC OR LATINO             150               202
[1] 2 2
[1] FALSE

Clustering(59) Variable = 9Q LOSS MUTATION ANALYSIS
D59V1, survival
                   sevent
clus2                 0   1
  9Q LOSS MUTATED   101  55
  9Q LOSS WILD-TYPE 129  98
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
              156               227 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               55                98 
$`9Q LOSS MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        91.63       103.50       105.70         8.35 
TCGA-4Z-AA7M TCGA-4Z-AA7O TCGA-4Z-AA7S TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA83 
       16.27        16.83        34.98        49.12         0.62        66.54 
TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BT-A0S7 TCGA-BT-A20N TCGA-BT-A20P TCGA-BT-A20Q 
       33.83        40.08         6.58        32.84        17.88        19.50 
TCGA-BT-A20T TCGA-BT-A2LB TCGA-BT-A42C TCGA-BT-A42E TCGA-C4-A0F6 TCGA-CF-A1HR 
       14.89        16.18        28.70        24.26        23.01         0.46 
TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47V TCGA-CF-A47X TCGA-CF-A5U8 TCGA-CF-A8HX 
        0.69        10.95        12.46        12.62        13.12        11.34 
TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YO TCGA-CU-A3KJ TCGA-CU-A3QU 
       11.34        11.87        13.08         4.90         5.46         5.19 
TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AD TCGA-DK-A1AF 
        1.84        13.58         2.14        19.00       112.44        17.62 
TCGA-DK-A1AG TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3WX TCGA-DK-A3X2 
       15.62        17.72        50.27        21.30        10.55        17.98 
TCGA-DK-A6AV TCGA-DK-A6B5 TCGA-DK-AA6P TCGA-DK-AA6S TCGA-DK-AA6U TCGA-DK-AA6W 
       64.18        41.06        15.02       166.03        10.49         8.65 
TCGA-DK-AA6X TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A3X6 
        7.53        12.03        10.62        43.59        38.83        24.66 
TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A7DU TCGA-E7-A7DV 
       16.70        17.39         0.56         0.66         0.92         1.22 
TCGA-E7-A7PW TCGA-E7-A97Q TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3SM TCGA-FD-A3SQ 
       13.68         8.09         8.94        33.04        17.98        46.78 
TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR 
       19.79        12.85        22.98         3.62        15.58        26.73 
TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A6TA 
       27.45        18.08        58.92         7.10         6.28        62.86 
TCGA-FD-A6TB TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FT-A61P TCGA-G2-A2EK TCGA-G2-A2EL 
       18.81         2.27         3.06         6.48        15.95        26.93 
TCGA-G2-A2EO TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3RD 
       35.24        17.62        66.02        19.46        21.40        14.07 
TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A6C6 TCGA-GU-A763 
        0.49         8.94         7.73         2.10         2.20        27.09 
TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW 
        4.73        10.65        32.98         7.00        14.27        21.34 
TCGA-GV-A3QH TCGA-GV-A40G TCGA-GV-A6ZA TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-K4-A3WS 
        8.48        19.07        22.72        38.60         3.06        25.02 
TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A5RI TCGA-K4-AAQO TCGA-LT-A8JT 
        3.45        21.24         2.76        11.70        11.80        21.07 
TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-SY-A9G5 
       16.67        14.24         1.84         3.75        12.43        31.56 
TCGA-UY-A78O TCGA-UY-A8OD TCGA-UY-A9PD TCGA-XF-A8HF TCGA-XF-A8HI TCGA-XF-A9SV 
       76.01       112.83        17.82        97.12        17.88        12.76 
TCGA-XF-A9T0 TCGA-XF-A9T4 TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMW TCGA-XF-AAMX 
       26.27        16.27        71.57        91.73         8.32         6.77 
TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN7 TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R0 
       44.32        30.94        18.81        11.97        13.64        18.64 
TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RE 
        7.36        21.11        24.13        28.41        74.56         3.48 
TCGA-ZF-A9RL TCGA-ZF-A9RN TCGA-ZF-AA4U TCGA-ZF-AA4W TCGA-ZF-AA51 TCGA-ZF-AA54 
       82.49        20.22         8.61        60.16        38.73        19.40 

$`9Q LOSS WILD-TYPE`
TCGA-4Z-AA7N TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7W TCGA-4Z-AA81 TCGA-4Z-AA82 
       44.94        16.77        17.16        27.62        41.75        51.16 
TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM 
       15.12        10.22        47.80         7.33         2.66         6.74 
TCGA-BL-A5ZZ TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20R TCGA-BT-A20U 
       12.39        13.15        19.04        12.16         5.06        14.96 
TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LD TCGA-BT-A3PH 
        5.06         8.35         8.25        17.16        20.48         4.67 
TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 
       12.82         9.96        17.56        28.41         8.98         1.94 
TCGA-CF-A1HS TCGA-CF-A47T TCGA-CF-A47W TCGA-CF-A47Y TCGA-CF-A5UA TCGA-CF-A7I0 
        0.43        12.66        12.10        12.26        12.00        12.10 
TCGA-CU-A0YN TCGA-CU-A0YR TCGA-CU-A3YL TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 
       12.92         7.20        16.31        21.86        66.41        18.41 
TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AE TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 
       16.70       130.88        16.14         1.81        10.59         7.79 
TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN 
      123.85        87.32         2.20        13.58         7.82         8.22 
TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A6AW 
       23.21         9.67        20.81       140.81        48.00        41.56 
TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6Q 
       76.60        67.36        15.68        30.67        38.24        13.58 
TCGA-DK-AA6T TCGA-DK-AA71 TCGA-DK-AA74 TCGA-E5-A4TZ TCGA-E7-A3Y1 TCGA-E7-A4IJ 
       12.36        13.64        43.50        15.35         0.10         0.49 
TCGA-E7-A4XJ TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7XN 
        2.24        14.56        13.97        12.99        14.33        14.07 
TCGA-E7-A85H TCGA-E7-A8O7 TCGA-E7-A97P TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B7 
       12.95        15.32        14.37        32.02        16.77         4.01 
TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL 
       12.62        22.52        27.98        60.66        24.30        23.41 
TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U 
       29.16         5.52        25.74        27.35        14.96        20.91 
TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY 
       53.88        11.01        19.33         5.36         5.69         8.25 
TCGA-FD-A62N TCGA-FD-A62S TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TH 
        2.70        13.35         6.15        12.69        12.36         4.31 
TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF 
        9.67        10.85        31.07         7.13        10.65        17.23 
TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2ES TCGA-G2-A3IB 
        8.94         3.25        61.94        30.61        33.01         7.23 
TCGA-G2-A3IE TCGA-G2-AA3C TCGA-G2-AA3D TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB 
       20.12         6.94        64.44         2.24        15.81         4.50 
TCGA-GC-A3RC TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I3 TCGA-GD-A3OQ TCGA-GD-A3OS 
       15.91        17.75        24.92        13.91         3.12        20.98 
TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A764 
        7.36        10.92        11.31        11.31         7.63        20.05 
TCGA-GU-A766 TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QI TCGA-GV-A3QK 
        5.62        19.10        19.82        20.28        10.59        27.35 
TCGA-GV-A40E TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A4AC 
        8.58         1.51        19.40         9.01         8.22         9.14 
TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P 
       27.68         9.07         1.74         1.81        15.42         6.38 
TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI TCGA-UY-A78K TCGA-UY-A78L 
       15.32        15.58        13.48        12.23        17.62        37.05 
TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A78P TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A9PA 
       22.68        86.83        67.79        65.75         3.58        35.24 
TCGA-UY-A9PB TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HD 
       29.56         4.54         1.64        45.04         6.58        97.45 
TCGA-XF-A8HE TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI 
      125.49        15.35         1.87        48.62        64.80        79.66 
TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ 
        3.22        66.41        11.90        23.64        21.04        28.24 
TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME 
       18.90         2.24        66.64         2.10        13.74        92.98 
TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMT 
       10.82       110.60        11.31        54.90         7.63         2.96 
TCGA-XF-AAMY TCGA-XF-AAN0 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 
       98.99        56.48        61.45        86.30        27.06        75.39 
TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-ZF-A9R4 TCGA-ZF-A9R5 
        3.88        18.84         9.63         0.66        30.28        27.19 
TCGA-ZF-A9R7 TCGA-ZF-A9RD TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-AA4N 
       21.86        13.41        52.73        52.60        47.84         2.89 
TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4V TCGA-ZF-AA4X TCGA-ZF-AA52 TCGA-ZF-AA53 
       34.06        19.69        59.38        63.02        35.41        57.90 
TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
        8.52        47.15        19.17         5.52        10.13 

  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
             0.46              0.10 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
           166.03            140.81 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
           16.765            15.320 
[1] "0.5 - 166.0 (16.8)" "0.1 - 140.8 (15.3)"
[1] "hr=" "1.2"
D59V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  9Q LOSS MUTATED         3       56        54       44
  9Q LOSS WILD-TYPE       1       68        73       85
D59V3, multiclass
           clus
vv          9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  STAGE I                 3                 1
  STAGE II               56                68
  STAGE III              54                73
  STAGE IV               44                85
[1] 4 2
[1] TRUE
[1] "dimension of contingency 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         56  72  21
  9Q LOSS WILD-TYPE       65 112  32
D59V4, multiclass
          clus
vv         9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  T0+T1+T2              56                65
  T3                    72               112
  T4                    21                32
[1] 3 2
[1] TRUE
[1] "dimension of 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   101  12  28   3
  9Q LOSS WILD-TYPE 123  30  47   5
D59V5, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  N0             101               123
  N1              12                30
  N2              28                47
  N3               3                 5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V6, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED    85   3
  9Q LOSS WILD-TYPE 100   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     85    3
  9Q LOSS WILD-TYPE  100    7
   clus
vv  9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  0              85               100
  1               3                 7
[1] 2 2
[1] FALSE
D59V7, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED    40 120
  9Q LOSS WILD-TYPE  61 168
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     40  120
  9Q LOSS WILD-TYPE   61  168
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  FEMALE              40                61
  MALE               120               168
[1] 2 2
[1] FALSE
D59V8, continuous
D59V9, continuous
D59V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  9Q LOSS MUTATED      19                         6   126
  9Q LOSS WILD-TYPE    23                        15   185
D59V11, multiclass
                           clus
vv                          9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  ASIAN                                  19                23
  BLACK OR AFRICAN AMERICAN               6                15
  WHITE                                 126               185
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V12, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED     3 144
  9Q LOSS WILD-TYPE   6 208
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      3  144
  9Q LOSS WILD-TYPE    6  208
                        clus
vv                       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   3                 6
  NOT HISPANIC OR LATINO             144               208
[1] 2 2
[1] FALSE

Clustering(60) Variable = 10P LOSS MUTATION ANALYSIS
D60V1, survival
                    sevent
clus2                  0   1
  10P LOSS MUTATED    42  29
  10P LOSS WILD-TYPE 188 124
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                71                312 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                29                124 
$`10P LOSS MUTATED`
TCGA-2F-A9KP TCGA-2F-A9KR TCGA-4Z-AA82 TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BT-A20U 
       11.97       103.50        51.16        40.08         2.66        14.96 
TCGA-BT-A2LA TCGA-BT-A2LD TCGA-BT-A42C TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A27C 
       17.16        20.48        28.70         1.94        23.01         0.69 
TCGA-CF-A8HY TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-DK-A2I2 TCGA-DK-A3IS 
       11.34         4.90         7.20         5.46         7.79        50.27 
TCGA-DK-A6B1 TCGA-DK-AA6L TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA76 
       67.36        38.24        10.49         8.65         7.53        12.03 
TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E7-A541 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B7 
       43.59        15.35        17.39        16.77         8.94         4.01 
TCGA-FD-A3N5 TCGA-FD-A3SR TCGA-FD-A43N TCGA-FD-A43Y TCGA-FD-A5BY TCGA-FD-A6TD 
       22.52        19.79        22.98        15.58         8.25        12.69 
TCGA-FJ-A3Z7 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-G2-A2EL TCGA-G2-A3IB TCGA-GC-A3BM 
       31.07        10.65        17.23        26.93         7.23        21.40 
TCGA-GC-A3RC TCGA-GC-A6I3 TCGA-GV-A3JX TCGA-GV-A40G TCGA-H4-A2HQ TCGA-K4-A3WU 
       15.91        13.91        19.10        19.07        19.40         3.45 
TCGA-K4-A5RH TCGA-K4-A5RI TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI TCGA-UY-A78O 
        9.07        11.70        15.58        13.48        12.23        76.01 
TCGA-UY-A9PB TCGA-UY-A9PE TCGA-XF-A8HE TCGA-XF-A8HH TCGA-XF-A9SG TCGA-XF-A9SI 
       29.56         4.54       125.49         1.87        48.62        79.66 
TCGA-XF-A9SV TCGA-XF-AAMF TCGA-XF-AAMJ TCGA-XF-AAMX TCGA-YF-AA3L TCGA-ZF-A9R1 
       12.76        10.82        54.90         6.77        11.97         7.36 
TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-AA4N TCGA-ZF-AA4W TCGA-ZF-AA4X 
       13.41         3.48         2.89        60.16        63.02 

$`10P LOSS WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KQ TCGA-2F-A9KT TCGA-2F-A9KW TCGA-4Z-AA7M TCGA-4Z-AA7N 
       22.29        91.63       105.70         8.35        16.27        44.94 
TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA7Y 
       16.83        16.77        17.16        34.98        27.62        49.12 
TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA83 TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-4Z-AA87 
        0.62        41.75        66.54        15.12        10.22        47.80 
TCGA-4Z-AA89 TCGA-BL-A13I TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX 
       33.83         7.33         6.74        12.39         6.58        13.15 
TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R 
       19.04        32.84        12.16        17.88        19.50         5.06 
TCGA-BT-A20T TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LB TCGA-BT-A3PH 
       14.89         5.06         8.35         8.25        16.18         4.67 
TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ 
       12.82         9.96        17.56        24.26        28.41         8.98 
TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W 
        0.46         0.43        10.95        12.66        12.46        12.10 
TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A8HX 
       12.62        12.26        13.12        12.00        12.10        11.34 
TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 
       11.87        13.08        12.92         5.19        16.31         1.84 
TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA 
       13.58        21.86         2.14        66.41        18.41        19.00 
TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG 
       16.70       130.88       112.44        16.14        17.62        15.62 
TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL 
        1.81        10.59       123.85        87.32         2.20        13.58 
TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV 
        7.82         8.22        17.72        21.30        23.21         9.67 
TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV 
       20.81        10.55       140.81        48.00        17.98        64.18 
TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6P 
       41.56        76.60        15.68        41.06        30.67        15.02 
TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA77 
       13.58       166.03        12.36        13.64        43.50        10.62 
TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 
       38.83        24.66         0.10         0.49         2.24        16.70 
TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF 
        0.56         0.66        14.56        13.97        12.99        14.33 
TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A8O7 
        0.92         1.22        13.68        14.07        12.95        15.32 
TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B6 TCGA-FD-A3B8 TCGA-FD-A3N6 
       14.37         8.09        32.02        33.04        12.62        27.98 
TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO 
       60.66        24.30        23.41        17.98        29.16         5.52 
TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U 
       25.74        46.78        12.85        27.35        14.96        20.91 
TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV 
        3.62        26.73        53.88        11.01        19.33         5.36 
TCGA-FD-A5BX TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O 
        5.69        27.45        18.08        58.92         2.70         7.10 
TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TE 
        6.28        13.35        62.86        18.81         6.15        12.36 
TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z9 
        2.27         3.06         4.31         9.67        10.85         7.13 
TCGA-FJ-A871 TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK 
        8.94         3.25         6.48        61.94        30.61        15.95 
TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C 
       35.24        33.01        20.12        17.62        66.02         6.94 
TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RD 
       64.44        19.46         2.24        15.81         4.50        14.07 
TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OP 
       17.75        24.92         0.49         8.94         7.73         2.10 
TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q 
        3.12        20.98         2.20         7.36        10.92        11.31 
TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 
       11.31         7.63        27.09        20.05         5.62         4.73 
TCGA-GU-AATO TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JZ 
       10.65        32.98         7.00        14.27        21.34        19.82 
TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A6ZA 
       20.28         8.48        10.59        27.35         8.58        22.72 
TCGA-H4-A2HO TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS 
        1.51        38.60         3.06         9.01         8.22        25.02 
TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6FZ 
       21.24         2.76         9.14        27.68         1.74         1.81 
TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-LC-A66R TCGA-LT-A8JT TCGA-PQ-A6FN 
       15.42         6.38        11.80        15.32        21.07        16.67 
TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78K 
       14.24         1.84         3.75        12.43        31.56        17.62 
TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A78P TCGA-UY-A8OB TCGA-UY-A8OC 
       37.05        22.68        86.83        67.79        65.75         3.58 
TCGA-UY-A8OD TCGA-UY-A9PA TCGA-UY-A9PD TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HC 
      112.83        35.24        17.82         1.64        45.04         6.58 
TCGA-XF-A8HD TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SJ 
       97.45        97.12        15.35        17.88        64.80         3.22 
TCGA-XF-A9SL TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 
       66.41        11.90        23.64        21.04        28.24        26.27 
TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 
       18.90         2.24        16.27        66.64         2.10        13.74 
TCGA-XF-AAME TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR 
       92.98       110.60        11.31         7.63        71.57        91.73 
TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN1 
        2.96         8.32        98.99        44.32        56.48        30.94 
TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-XF-AAN8 
       61.45        86.30        27.06        75.39        18.81         3.88 
TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R2 
       18.84         9.63         0.66        13.64        18.64        21.11 
TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RC 
       24.13        30.28        27.19        21.86        28.41        74.56 
TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4R 
       52.73        52.60        82.49        47.84        20.22        34.06 
TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA53 
       19.69         8.61        59.38        38.73        35.41        57.90 
TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
       19.40         8.52        47.15        19.17         5.52        10.13 

  10P LOSS MUTATED 10P LOSS WILD-TYPE 
              0.69               0.10 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
            125.49             166.03 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
             14.96              16.16 
[1] "0.7 - 125.5 (15.0)" "0.1 - 166.0 (16.2)"
[1] "hr=" "1.1"
D60V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  10P LOSS MUTATED         2       24        22       21
  10P LOSS WILD-TYPE       2      100       105      108
D60V3, multiclass
           clus
vv          10P LOSS MUTATED 10P LOSS WILD-TYPE
  STAGE I                  2                  2
  STAGE II                24                100
  STAGE III               22                105
  STAGE IV                21                108
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1+T2  T3  T4
  10P LOSS MUTATED         22  28   9
  10P LOSS WILD-TYPE       99 156  44
D60V4, multiclass
          clus
vv         10P LOSS MUTATED 10P LOSS WILD-TYPE
  T0+T1+T2               22                 99
  T3                     28                156
  T4                      9                 44
[1] 3 2
[1] TRUE
[1] "dimension of 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    43   7  12   2
  10P LOSS WILD-TYPE 181  35  63   6
D60V5, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  N0               43                181
  N1                7                 35
  N2               12                 63
  N3                2                  6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V6, binary
                    cls
clus                   0   1
  10P LOSS MUTATED    30   3
  10P LOSS WILD-TYPE 155   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     30    3
  10P LOSS WILD-TYPE  155    7
   clus
vv  10P LOSS MUTATED 10P LOSS WILD-TYPE
  0               30                155
  1                3                  7
[1] 2 2
[1] FALSE
D60V7, binary
                    cls
clus                   0   1
  10P LOSS MUTATED    19  52
  10P LOSS WILD-TYPE  82 236
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     19   52
  10P LOSS WILD-TYPE   82  236
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  FEMALE               19                 82
  MALE                 52                236
[1] 2 2
[1] FALSE
D60V8, continuous
D60V9, continuous
D60V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  10P LOSS MUTATED       4                         9    53
  10P LOSS WILD-TYPE    38                        12   258
D60V11, multiclass
                           clus
vv                          10P LOSS MUTATED 10P LOSS WILD-TYPE
  ASIAN                                    4                 38
  BLACK OR AFRICAN AMERICAN                9                 12
  WHITE                                   53                258
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V12, binary
                    cls
clus                   0   1
  10P LOSS MUTATED     2  65
  10P LOSS WILD-TYPE   7 287
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      2   65
  10P LOSS WILD-TYPE    7  287
                        clus
vv                       10P LOSS MUTATED 10P LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  7
  NOT HISPANIC OR LATINO               65                287
[1] 2 2
[1] FALSE

Clustering(61) Variable = 10Q LOSS MUTATION ANALYSIS
D61V1, survival
                    sevent
clus2                  0   1
  10Q LOSS MUTATED    72  49
  10Q LOSS WILD-TYPE 158 104
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
               121                262 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                49                104 
$`10Q LOSS MUTATED`
TCGA-2F-A9KP TCGA-2F-A9KR TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-BL-A0C8 TCGA-BL-A13J 
       11.97       103.50        16.77        17.16        40.08         2.66 
TCGA-BT-A20N TCGA-BT-A20U TCGA-BT-A20W TCGA-BT-A2LA TCGA-BT-A2LD TCGA-BT-A42B 
       32.84        14.96         8.35        17.16        20.48        17.56 
TCGA-BT-A42C TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A27C TCGA-CF-A8HY TCGA-CU-A0YO 
       28.70         1.94        23.01         0.69        11.34         4.90 
TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-DK-A1A5 TCGA-DK-A2HX TCGA-DK-A2I2 
        7.20         5.46         5.19         2.14         1.81         7.79 
TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IS TCGA-DK-A3X1 
       87.32         2.20        13.58         7.82        50.27        48.00 
TCGA-DK-A6B1 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6P TCGA-DK-AA6S TCGA-DK-AA6U 
       67.36        30.67        38.24        15.02       166.03        10.49 
TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E7-A3X6 
        8.65         7.53        12.03        43.59        15.35        24.66 
TCGA-E7-A4IJ TCGA-E7-A541 TCGA-E7-A6ME TCGA-E7-A7DV TCGA-FD-A3B7 TCGA-FD-A3N5 
        0.49        17.39        12.99         1.22         4.01        22.52 
TCGA-FD-A3SR TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43U TCGA-FD-A43Y TCGA-FD-A5BY 
       19.79        22.98        27.35        20.91        15.58         8.25 
TCGA-FD-A5C1 TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FJ-A3Z7 TCGA-FJ-A3ZE 
       58.92        12.69        12.36         2.27        31.07        10.65 
TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-GC-A3BM 
       17.23         6.48         7.23        20.12        17.62        21.40 
TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A4ZW TCGA-GC-A6I3 TCGA-GD-A3OP 
       15.91        14.07        17.75         0.49        13.91         2.10 
TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A764 TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QF 
        7.36        10.92        20.05        21.34        19.10        20.28 
TCGA-GV-A3QH TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HQ TCGA-K4-A3WS TCGA-K4-A3WU 
        8.48        19.07        22.72        19.40        25.02         3.45 
TCGA-K4-A4AC TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A6FZ TCGA-LT-A5Z6 TCGA-MV-A51V 
        9.14         9.07        11.70         1.81        15.58        13.48 
TCGA-PQ-A6FI TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PD TCGA-UY-A9PE 
       12.23        76.01        65.75        35.24        17.82         4.54 
TCGA-XF-A8HC TCGA-XF-A8HF TCGA-XF-A8HH TCGA-XF-A9SG TCGA-XF-A9SI TCGA-XF-A9SJ 
        6.58        97.12         1.87        48.62        79.66         3.22 
TCGA-XF-A9SV TCGA-XF-AAMF TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMW TCGA-XF-AAMX 
       12.76        10.82        54.90         7.63         8.32         6.77 
TCGA-XF-AAN7 TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R2 TCGA-ZF-A9RE TCGA-ZF-A9RN 
       18.81        11.97        13.64        21.11         3.48        20.22 
TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4X TCGA-ZF-AA51 
        2.89        34.06        19.69         8.61        63.02        38.73 
TCGA-ZF-AA52 
       35.41 

$`10Q LOSS WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KQ TCGA-2F-A9KT TCGA-2F-A9KW TCGA-4Z-AA7M TCGA-4Z-AA7N 
       22.29        91.63       105.70         8.35        16.27        44.94 
TCGA-4Z-AA7O TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 
       16.83        34.98        27.62        49.12         0.62        41.75 
TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 
       51.16        66.54        15.12        10.22        47.80        33.83 
TCGA-BL-A13I TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J 
        7.33         6.74        12.39         6.58        13.15        19.04 
TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20V 
       12.16        17.88        19.50         5.06        14.89         5.06 
TCGA-BT-A20X TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42E 
        8.25        16.18         4.67        12.82         9.96        24.26 
TCGA-BT-A42F TCGA-C4-A0EZ TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A47S TCGA-CF-A47T 
       28.41         8.98         0.46         0.43        10.95        12.66 
TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA 
       12.46        12.10        12.62        12.26        13.12        12.00 
TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A3YL 
       12.10        11.34        11.87        13.08        12.92        16.31 
TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA 
        1.84        13.58        21.86        66.41        18.41        19.00 
TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG 
       16.70       130.88       112.44        16.14        17.62        15.62 
TCGA-DK-A2I1 TCGA-DK-A2I4 TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3IU 
       10.59       123.85         8.22        17.72        21.30        23.21 
TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X2 TCGA-DK-A6AV 
        9.67        20.81        10.55       140.81        17.98        64.18 
TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-AA6Q TCGA-DK-AA6T 
       41.56        76.60        15.68        41.06        13.58        12.36 
TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA77 TCGA-E5-A4U1 TCGA-E7-A3Y1 TCGA-E7-A4XJ 
       13.64        43.50        10.62        38.83         0.10         2.24 
TCGA-E7-A519 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MF 
       16.70         0.56         0.66        14.56        13.97        14.33 
TCGA-E7-A7DU TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A8O7 TCGA-E7-A97P 
        0.92        13.68        14.07        12.95        15.32        14.37 
TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B8 
        8.09        32.02        16.77         8.94        33.04        12.62 
TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN 
       27.98        60.66        24.30        23.41        17.98        29.16 
TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SS TCGA-FD-A43S TCGA-FD-A43X 
        5.52        25.74        46.78        12.85        14.96         3.62 
TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX 
       26.73        53.88        11.01        19.33         5.36         5.69 
TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S 
       27.45        18.08         2.70         7.10         6.28        13.35 
TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI 
       62.86        18.81         6.15         3.06         4.31         9.67 
TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EF TCGA-G2-A2EJ 
       10.85         7.13         8.94         3.25        61.94        30.61 
TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-AA3B TCGA-G2-AA3C 
       15.95        26.93        35.24        33.01        66.02         6.94 
TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3YS 
       64.44        19.46         2.24        15.81         4.50        24.92 
TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42Q 
        8.94         7.73         3.12        20.98         2.20        11.31 
TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO 
       11.31         7.63        27.09         5.62         4.73        10.65 
TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JZ TCGA-GV-A3QI TCGA-GV-A3QK 
       32.98         7.00        14.27        19.82        10.59        27.35 
TCGA-GV-A40E TCGA-H4-A2HO TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE 
        8.58         1.51        38.60         3.06         9.01         8.22 
TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6MB TCGA-K4-A83P 
       21.24         2.76        27.68         1.74        15.42         6.38 
TCGA-K4-AAQO TCGA-LC-A66R TCGA-LT-A8JT TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX 
       11.80        15.32        21.07        16.67        14.24         1.84 
TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M 
        3.75        12.43        31.56        17.62        37.05        22.68 
TCGA-UY-A78N TCGA-UY-A78P TCGA-UY-A8OC TCGA-UY-A8OD TCGA-UY-A9PB TCGA-UY-A9PF 
       86.83        67.79         3.58       112.83        29.56         1.64 
TCGA-XF-A8HB TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HG TCGA-XF-A8HI TCGA-XF-A9SH 
       45.04        97.45       125.49        15.35        17.88        64.80 
TCGA-XF-A9SL TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 
       66.41        11.90        23.64        21.04        28.24        26.27 
TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 
       18.90         2.24        16.27        66.64         2.10        13.74 
TCGA-XF-AAME TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMT 
       92.98       110.60        11.31        71.57        91.73         2.96 
TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 
       98.99        44.32        56.48        30.94        61.45        86.30 
TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC 
       27.06        75.39         3.88        18.84         9.63         0.66 
TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 
       18.64         7.36        24.13        30.28        27.19        21.86 
TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL 
       28.41        74.56        13.41        52.73        52.60        82.49 
TCGA-ZF-A9RM TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 
       47.84        59.38        60.16        57.90        19.40         8.52 
TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
       47.15        19.17         5.52        10.13 

  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
              0.49               0.10 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
            166.03             140.81 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
             15.02              16.16 
[1] "0.5 - 166.0 (15.0)" "0.1 - 140.8 (16.2)"
[1] "hr=" "1.2"
D61V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  10Q LOSS MUTATED         2       43        35       39
  10Q LOSS WILD-TYPE       2       81        92       90
D61V3, multiclass
           clus
vv          10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  STAGE I                  2                  2
  STAGE II                43                 81
  STAGE III               35                 92
  STAGE IV                39                 90
[1] 4 2
[1] TRUE
[1] "dimension of contingency 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         38  53  14
  10Q LOSS WILD-TYPE       83 131  39
D61V4, multiclass
          clus
vv         10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  T0+T1+T2               38                 83
  T3                     53                131
  T4                     14                 39
[1] 3 2
[1] TRUE
[1] "dimension of 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    63  11  23   3
  10Q LOSS WILD-TYPE 161  31  52   5
D61V5, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  N0               63                161
  N1               11                 31
  N2               23                 52
  N3                3                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V6, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED    50   4
  10Q LOSS WILD-TYPE 135   6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     50    4
  10Q LOSS WILD-TYPE  135    6
   clus
vv  10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  0               50                135
  1                4                  6
[1] 2 2
[1] FALSE
D61V7, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED    31  90
  10Q LOSS WILD-TYPE  70 198
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     31   90
  10Q LOSS WILD-TYPE   70  198
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  FEMALE               31                 70
  MALE                 90                198
[1] 2 2
[1] FALSE
D61V8, continuous
D61V9, continuous
D61V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  10Q LOSS MUTATED       8                         8    98
  10Q LOSS WILD-TYPE    34                        13   213
D61V11, multiclass
                           clus
vv                          10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  ASIAN                                    8                 34
  BLACK OR AFRICAN AMERICAN                8                 13
  WHITE                                   98                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"
D61V12, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED     4 111
  10Q LOSS WILD-TYPE   5 241
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      4  111
  10Q LOSS WILD-TYPE    5  241
                        clus
vv                       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                  5
  NOT HISPANIC OR LATINO              111                241
[1] 2 2
[1] FALSE

Clustering(62) Variable = 11P LOSS MUTATION ANALYSIS
D62V1, survival
                    sevent
clus2                  0   1
  11P LOSS MUTATED   100  64
  11P LOSS WILD-TYPE 130  89
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
               164                219 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                64                 89 
$`11P LOSS MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KR TCGA-2F-A9KT TCGA-4Z-AA7O TCGA-4Z-AA7S TCGA-4Z-AA80 
       22.29       103.50       105.70        16.83        34.98         0.62 
TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BT-A20N TCGA-BT-A20T 
       15.12        33.83        40.08         2.66        32.84        14.89 
TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A2LA TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42C 
        5.06         8.35        17.16         4.67        17.56        28.70 
TCGA-C4-A0EZ TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47X 
        8.98        23.01         0.46         0.43         0.69        12.62 
TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CU-A3KJ 
       13.12        12.00        12.10        11.34        11.87         5.46 
TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1AB TCGA-DK-A1AD 
        1.84        13.58         2.14        66.41        16.70       112.44 
TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM 
        1.81        10.59        87.32         2.20        13.58         7.82 
TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-AA6L 
       17.72        50.27        21.30        17.98        64.18        38.24 
TCGA-DK-AA6P TCGA-DK-AA6S TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA76 TCGA-DK-AA77 
       15.02       166.03        10.49         8.65        12.03        10.62 
TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A4IJ TCGA-E7-A541 
       43.59        15.35        38.83        24.66         0.49        17.39 
TCGA-E7-A5KE TCGA-E7-A6ME TCGA-E7-A7DU TCGA-E7-A7PW TCGA-E7-A85H TCGA-E7-A97P 
        0.56        12.99         0.92        13.68        12.95        14.37 
TCGA-E7-A97Q TCGA-FD-A3B5 TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SN TCGA-FD-A3SS 
        8.09         8.94        24.30        23.41        29.16        12.85 
TCGA-FD-A43N TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 
       22.98        15.58        26.73        27.45        18.08        58.92 
TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TC TCGA-FD-A6TF 
        2.70         7.10        13.35        62.86         6.15         2.27 
TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FJ-A3Z7 TCGA-FJ-A3ZE TCGA-FT-A61P TCGA-G2-A2EO 
        3.06         4.31        31.07        10.65         6.48        35.24 
TCGA-G2-A2ES TCGA-G2-AA3B TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3RD 
       33.01        66.02        64.44        19.46        21.40        14.07 
TCGA-GC-A3YS TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42Q 
       24.92         7.73         2.10         2.20         7.36        11.31 
TCGA-GU-A42R TCGA-GU-A767 TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW 
       11.31         4.73        32.98         7.00        14.27        21.34 
TCGA-GV-A3QF TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF 
       20.28        19.07        22.72        19.40        38.60         3.06 
TCGA-HQ-A5ND TCGA-K4-A5RI TCGA-K4-A6MB TCGA-K4-AAQO TCGA-LT-A8JT TCGA-R3-A69X 
        9.01        11.70        15.42        11.80        21.07        14.24 
TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78M TCGA-UY-A78O 
        1.84         3.75        12.43        31.56        22.68        76.01 
TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A9PD TCGA-UY-A9PE TCGA-XF-A8HG TCGA-XF-A9SG 
       65.75         3.58        17.82         4.54        15.35        48.62 
TCGA-XF-A9SH TCGA-XF-A9SJ TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9T5 TCGA-XF-A9T6 
       64.80         3.22        12.76        11.90        66.64         2.10 
TCGA-XF-AAMG TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMT 
      110.60        54.90         7.63        71.57        91.73         2.96 
TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN7 TCGA-YF-AA3L 
        8.32         6.77        44.32        56.48        18.81        11.97 
TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R4 TCGA-ZF-A9RC TCGA-ZF-A9RD 
       18.64         7.36        21.11        30.28        74.56        13.41 
TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4U 
       82.49        47.84        20.22        34.06        19.69         8.61 
TCGA-ZF-AA4X TCGA-ZF-AA5H 
       63.02        19.17 

$`11P LOSS WILD-TYPE`
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KW TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7Q 
       11.97        91.63         8.35        16.27        44.94        16.77 
TCGA-4Z-AA7R TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 
       17.16        27.62        49.12        41.75        51.16        66.54 
TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-BL-A13I TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 
       10.22        47.80         7.33         6.74        12.39         6.58 
TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R 
       13.15        19.04        12.16        17.88        19.50         5.06 
TCGA-BT-A20U TCGA-BT-A20X TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK 
       14.96         8.25        16.18        20.48        12.82         9.96 
TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F0 TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V 
       24.26        28.41         1.94        10.95        12.66        12.46 
TCGA-CF-A47W TCGA-CF-A47Y TCGA-CF-A8HX TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO 
       12.10        12.26        11.34        13.08        12.92         4.90 
TCGA-CU-A0YR TCGA-CU-A3QU TCGA-CU-A3YL TCGA-DK-A1A3 TCGA-DK-A1A7 TCGA-DK-A1AA 
        7.20         5.19        16.31        21.86        18.41        19.00 
TCGA-DK-A1AC TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I2 TCGA-DK-A2I4 
      130.88        16.14        17.62        15.62         7.79       123.85 
TCGA-DK-A3IN TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY 
        8.22        23.21         9.67        20.81        10.55       140.81 
TCGA-DK-A3X1 TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 
       48.00        41.56        76.60        67.36        15.68        41.06 
TCGA-DK-A6B6 TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 
       30.67        13.58        12.36         7.53        13.64        43.50 
TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 
        0.10         2.24        16.70         0.66        14.56        13.97 
TCGA-E7-A6MF TCGA-E7-A7DV TCGA-E7-A7XN TCGA-E7-A8O7 TCGA-FD-A3B3 TCGA-FD-A3B4 
       14.33         1.22        14.07        15.32        32.02        16.77 
TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA 
       33.04         4.01        12.62        22.52        27.98        60.66 
TCGA-FD-A3SM TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A43P 
       17.98         5.52        25.74        46.78        19.79        27.35 
TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU 
       14.96        20.91         3.62        53.88        11.01        19.33 
TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A62P TCGA-FD-A6TB TCGA-FD-A6TD 
        5.36         5.69         8.25         6.28        18.81        12.69 
TCGA-FD-A6TE TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZF TCGA-FJ-A871 
       12.36         9.67        10.85         7.13        17.23         8.94 
TCGA-FT-A3EE TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A3IB 
        3.25        61.94        30.61        15.95        26.93         7.23 
TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3C TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB 
       20.12        17.62         6.94         2.24        15.81         4.50 
TCGA-GC-A3RC TCGA-GC-A3WC TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A3OQ 
       15.91        17.75         0.49         8.94        13.91         3.12 
TCGA-GD-A3OS TCGA-GU-A42P TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 
       20.98        10.92         7.63        27.09        20.05         5.62 
TCGA-GU-AATO TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK 
       10.65        19.10        19.82         8.48        10.59        27.35 
TCGA-GV-A40E TCGA-H4-A2HO TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV 
        8.58         1.51         8.22        25.02         3.45        21.24 
TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RJ TCGA-K4-A6FZ 
        2.76         9.14        27.68         9.07         1.74         1.81 
TCGA-K4-A83P TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN 
        6.38        15.32        15.58        13.48        12.23        16.67 
TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78N TCGA-UY-A78P TCGA-UY-A8OD TCGA-UY-A9PA 
       17.62        37.05        86.83        67.79       112.83        35.24 
TCGA-UY-A9PB TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HE 
       29.56         1.64        45.04         6.58        97.45       125.49 
TCGA-XF-A8HF TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SX 
       97.12         1.87        17.88        79.66        66.41        23.64 
TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 
       21.04        28.24        26.27        18.90         2.24        16.27 
TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMY TCGA-XF-AAN1 
       13.74        92.98        10.82        11.31        98.99        30.94 
TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN8 TCGA-YC-A89H 
       61.45        86.30        27.06        75.39         3.88        18.84 
TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3M TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 
        9.63         0.66        13.64        24.13        27.19        21.86 
TCGA-ZF-A9R9 TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-AA4N TCGA-ZF-AA4V 
       28.41         3.48        52.73        52.60         2.89        59.38 
TCGA-ZF-AA4W TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 
       60.16        38.73        35.41        57.90        19.40         8.52 
TCGA-ZF-AA58 TCGA-ZF-AA5N TCGA-ZF-AA5P 
       47.15         5.52        10.13 

  11P LOSS MUTATED 11P LOSS WILD-TYPE 
              0.43               0.10 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
            166.03             140.81 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
            15.235             16.140 
[1] "0.4 - 166.0 (15.2)" "0.1 - 140.8 (16.1)"
[1] "hr=" "1"  
D62V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  11P LOSS MUTATED         2       50        44       68
  11P LOSS WILD-TYPE       2       74        83       61
D62V3, multiclass
           clus
vv          11P LOSS MUTATED 11P LOSS WILD-TYPE
  STAGE I                  2                  2
  STAGE II                50                 74
  STAGE III               44                 83
  STAGE IV                68                 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                 T0+T1+T2  T3  T4
  11P LOSS MUTATED         56  82  24
  11P LOSS WILD-TYPE       65 102  29
D62V4, multiclass
          clus
vv         11P LOSS MUTATED 11P LOSS WILD-TYPE
  T0+T1+T2               56                 65
  T3                     82                102
  T4                     24                 29
[1] 3 2
[1] TRUE
[1] "dimension of 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    88  22  42   3
  11P LOSS WILD-TYPE 136  20  33   5
D62V5, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  N0               88                136
  N1               22                 20
  N2               42                 33
  N3                3                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V6, binary
                    cls
clus                  0  1
  11P LOSS MUTATED   86  7
  11P LOSS WILD-TYPE 99  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     86    7
  11P LOSS WILD-TYPE   99    3
   clus
vv  11P LOSS MUTATED 11P LOSS WILD-TYPE
  0               86                 99
  1                7                  3
[1] 2 2
[1] FALSE
D62V7, binary
                    cls
clus                   0   1
  11P LOSS MUTATED    43 126
  11P LOSS WILD-TYPE  58 162
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     43  126
  11P LOSS WILD-TYPE   58  162
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  FEMALE               43                 58
  MALE                126                162
[1] 2 2
[1] FALSE
D62V8, continuous
D62V9, continuous
D62V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  11P LOSS MUTATED      25                         8   126
  11P LOSS WILD-TYPE    17                        13   185
D62V11, multiclass
                           clus
vv                          11P LOSS MUTATED 11P LOSS WILD-TYPE
  ASIAN                                   25                 17
  BLACK OR AFRICAN AMERICAN                8                 13
  WHITE                                  126                185
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V12, binary
                    cls
clus                   0   1
  11P LOSS MUTATED     5 150
  11P LOSS WILD-TYPE   4 202
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      5  150
  11P LOSS WILD-TYPE    4  202
                        clus
vv                       11P LOSS MUTATED 11P LOSS WILD-TYPE
  HISPANIC OR LATINO                    5                  4
  NOT HISPANIC OR LATINO              150                202
[1] 2 2
[1] FALSE

Clustering(63) Variable = 11Q LOSS MUTATION ANALYSIS
D63V1, survival
                    sevent
clus2                  0   1
  11Q LOSS MUTATED    68  50
  11Q LOSS WILD-TYPE 162 103
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
               118                265 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                50                103 
$`11Q LOSS MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KR TCGA-2F-A9KT TCGA-4Z-AA7O TCGA-4Z-AA7S TCGA-4Z-AA89 
       22.29       103.50       105.70        16.83        34.98        33.83 
TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A20V TCGA-BT-A20W 
       40.08         2.66        32.84        14.89         5.06         8.35 
TCGA-BT-A2LA TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42C TCGA-C4-A0EZ TCGA-CF-A1HS 
       17.16         4.67        17.56        28.70         8.98         0.43 
TCGA-CF-A27C TCGA-CF-A47X TCGA-CF-A5U8 TCGA-CF-A7I0 TCGA-CF-A8HY TCGA-CU-A3KJ 
        0.69        12.62        13.12        12.10        11.34         5.46 
TCGA-CU-A5W6 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1AB TCGA-DK-A1AD TCGA-DK-A2I1 
        1.84         2.14        66.41        16.70       112.44        10.59 
TCGA-DK-A2I6 TCGA-DK-A3IL TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A6AV 
       87.32        13.58         8.22        17.72        50.27        64.18 
TCGA-DK-A6B6 TCGA-DK-AA6P TCGA-DK-AA6S TCGA-DK-AA6W TCGA-E5-A2PC TCGA-E5-A4TZ 
       30.67        15.02       166.03         8.65        43.59        15.35 
TCGA-E7-A4IJ TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A6ME TCGA-E7-A7DU TCGA-E7-A7PW 
        0.49        17.39         0.56        12.99         0.92        13.68 
TCGA-E7-A85H TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B5 TCGA-FD-A3SJ TCGA-FD-A43N 
       12.95        14.37         8.09         8.94        24.30        22.98 
TCGA-FD-A43Y TCGA-FD-A5BV TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N 
       15.58         5.36         8.25        18.08        58.92         2.70 
TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TC TCGA-FD-A6TH TCGA-FT-A61P TCGA-G2-A2EO 
        7.10        13.35         6.15         4.31         6.48        35.24 
TCGA-G2-A2ES TCGA-GC-A3BM TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OP 
       33.01        21.40        24.92         8.94         7.73         2.10 
TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42Q TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW 
        2.20         7.36        11.31         7.00        14.27        21.34 
TCGA-GV-A3QK TCGA-GV-A40G TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND 
       27.35        19.07        19.40        38.60         3.06         9.01 
TCGA-K4-A5RI TCGA-SY-A9G5 TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A8OD TCGA-UY-A9PB 
       11.70        31.56        76.01        65.75       112.83        29.56 
TCGA-UY-A9PE TCGA-XF-A8HG TCGA-XF-A9SG TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9T5 
        4.54        15.35        48.62        12.76        11.90        66.64 
TCGA-XF-A9T6 TCGA-XF-AAMG TCGA-XF-AAMJ TCGA-XF-AAMQ TCGA-XF-AAMT TCGA-XF-AAMW 
        2.10       110.60        54.90        71.57         2.96         8.32 
TCGA-XF-AAN0 TCGA-XF-AAN2 TCGA-XF-AAN7 TCGA-ZF-A9R0 TCGA-ZF-A9R2 TCGA-ZF-A9R4 
       56.48        61.45        18.81        18.64        21.11        30.28 
TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RN TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4U 
       74.56        13.41        20.22        34.06        19.69         8.61 
TCGA-ZF-AA4X TCGA-ZF-AA54 TCGA-ZF-AA58 TCGA-ZF-AA5H 
       63.02        19.40        47.15        19.17 

$`11Q LOSS WILD-TYPE`
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KW TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7Q 
       11.97        91.63         8.35        16.27        44.94        16.77 
TCGA-4Z-AA7R TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 
       17.16        27.62        49.12         0.62        41.75        51.16 
TCGA-4Z-AA83 TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-BL-A13I TCGA-BL-A3JM 
       66.54        15.12        10.22        47.80         7.33         6.74 
TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P 
       12.39         6.58        13.15        19.04        12.16        17.88 
TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20X TCGA-BT-A2LB TCGA-BT-A2LD 
       19.50         5.06        14.96         8.25        16.18        20.48 
TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F6 
       12.82         9.96        24.26        28.41         1.94        23.01 
TCGA-CF-A1HR TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47Y 
        0.46        10.95        12.66        12.46        12.10        12.26 
TCGA-CF-A5UA TCGA-CF-A8HX TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO 
       12.00        11.34        11.87        13.08        12.92         4.90 
TCGA-CU-A0YR TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A7 
        7.20         5.19        16.31        13.58        21.86        18.41 
TCGA-DK-A1AA TCGA-DK-A1AC TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX 
       19.00       130.88        16.14        17.62        15.62         1.81 
TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IM TCGA-DK-A3IT TCGA-DK-A3IU 
        7.79       123.85         2.20         7.82        21.30        23.21 
TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 
        9.67        20.81        10.55       140.81        48.00        17.98 
TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-AA6L 
       41.56        76.60        67.36        15.68        41.06        38.24 
TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 
       13.58        12.36        10.49         7.53        13.64        43.50 
TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ 
       12.03        10.62        38.83        24.66         0.10         2.24 
TCGA-E7-A519 TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MF TCGA-E7-A7DV 
       16.70         0.66        14.56        13.97        14.33         1.22 
TCGA-E7-A7XN TCGA-E7-A8O7 TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B6 TCGA-FD-A3B7 
       14.07        15.32        32.02        16.77        33.04         4.01 
TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SL TCGA-FD-A3SM 
       12.62        22.52        27.98        60.66        23.41        17.98 
TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS 
       29.16         5.52        25.74        46.78        19.79        12.85 
TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS 
       27.35        14.96        20.91         3.62        26.73        53.88 
TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BX TCGA-FD-A5BZ TCGA-FD-A62P TCGA-FD-A6TA 
       11.01        19.33         5.69        27.45         6.28        62.86 
TCGA-FD-A6TB TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TI 
       18.81        12.69        12.36         2.27         3.06         9.67 
TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FJ-A871 
       10.85        31.07         7.13        10.65        17.23         8.94 
TCGA-FT-A3EE TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A3IB 
        3.25        61.94        30.61        15.95        26.93         7.23 
TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F 
       20.12        17.62        66.02         6.94        64.44        19.46 
TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC 
        2.24        15.81         4.50        15.91        14.07        17.75 
TCGA-GC-A4ZW TCGA-GC-A6I3 TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GU-A42P TCGA-GU-A42R 
        0.49        13.91         3.12        20.98        10.92        11.31 
TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO 
        7.63        27.09        20.05         5.62         4.73        10.65 
TCGA-GU-AATP TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI 
       32.98        19.10        19.82        20.28         8.48        10.59 
TCGA-GV-A40E TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU 
        8.58        22.72         1.51         8.22        25.02         3.45 
TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RJ 
       21.24         2.76         9.14        27.68         9.07         1.74 
TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-LC-A66R TCGA-LT-A5Z6 
        1.81        15.42         6.38        11.80        15.32        15.58 
TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX 
       21.07        13.48        12.23        16.67        14.24         1.84 
TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78N 
        3.75        12.43        17.62        37.05        22.68        86.83 
TCGA-UY-A78P TCGA-UY-A8OC TCGA-UY-A9PA TCGA-UY-A9PD TCGA-UY-A9PF TCGA-XF-A8HB 
       67.79         3.58        35.24        17.82         1.64        45.04 
TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HH TCGA-XF-A8HI 
        6.58        97.45       125.49        97.12         1.87        17.88 
TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SX TCGA-XF-A9SY 
       64.80        79.66         3.22        66.41        23.64        21.04 
TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T8 
       28.24        26.27        18.90         2.24        16.27        13.74 
TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAML TCGA-XF-AAMR TCGA-XF-AAMX 
       92.98        10.82        11.31         7.63        91.73         6.77 
TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 
       98.99        44.32        30.94        86.30        27.06        75.39 
TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M 
        3.88        18.84         9.63         0.66        11.97        13.64 
TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RE 
        7.36        24.13        27.19        21.86        28.41         3.48 
TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-AA4N TCGA-ZF-AA4V 
       52.73        52.60        82.49        47.84         2.89        59.38 
TCGA-ZF-AA4W TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA56 TCGA-ZF-AA5N 
       60.16        38.73        35.41        57.90         8.52         5.52 
TCGA-ZF-AA5P 
       10.13 

  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
              0.43               0.10 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
            166.03             140.81 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
             16.14              15.68 
[1] "0.4 - 166.0 (16.1)" "0.1 - 140.8 (15.7)"
[1] "hr=" "1"  
D63V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  11Q LOSS MUTATED         1       36        38       43
  11Q LOSS WILD-TYPE       3       88        89       86
D63V3, multiclass
           clus
vv          11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  STAGE I                  1                  3
  STAGE II                36                 88
  STAGE III               38                 89
  STAGE IV                43                 86
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1+T2  T3  T4
  11Q LOSS MUTATED         41  57  19
  11Q LOSS WILD-TYPE       80 127  34
D63V4, multiclass
          clus
vv         11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  T0+T1+T2               41                 80
  T3                     57                127
  T4                     19                 34
[1] 3 2
[1] TRUE
[1] "dimension of 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  15  25   1
  11Q LOSS WILD-TYPE 158  27  50   7
D63V5, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  N0               66                158
  N1               15                 27
  N2               25                 50
  N3                1                  7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V6, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED    61   3
  11Q LOSS WILD-TYPE 124   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     61    3
  11Q LOSS WILD-TYPE  124    7
   clus
vv  11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  0               61                124
  1                3                  7
[1] 2 2
[1] FALSE
D63V7, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED    36  85
  11Q LOSS WILD-TYPE  65 203
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     36   85
  11Q LOSS WILD-TYPE   65  203
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  FEMALE               36                 65
  MALE                 85                203
[1] 2 2
[1] FALSE
D63V8, continuous
D63V9, continuous
D63V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  11Q LOSS MUTATED      18                         7    89
  11Q LOSS WILD-TYPE    24                        14   222
D63V11, multiclass
                           clus
vv                          11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  ASIAN                                   18                 24
  BLACK OR AFRICAN AMERICAN                7                 14
  WHITE                                   89                222
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V12, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED     3 107
  11Q LOSS WILD-TYPE   6 245
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      3  107
  11Q LOSS WILD-TYPE    6  245
                        clus
vv                       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  6
  NOT HISPANIC OR LATINO              107                245
[1] 2 2
[1] FALSE

Clustering(64) Variable = 12P LOSS MUTATION ANALYSIS
D64V1, survival
                    sevent
clus2                  0   1
  12P LOSS MUTATED    26  24
  12P LOSS WILD-TYPE 204 129
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                50                333 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                24                129 
$`12P LOSS MUTATED`
TCGA-2F-A9KW TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BT-A2LA TCGA-C4-A0F0 TCGA-CF-A47X 
        8.35        40.08         2.66        17.16         1.94        12.62 
TCGA-CU-A3QU TCGA-CU-A5W6 TCGA-DK-A1AC TCGA-DK-A3IV TCGA-E5-A2PC TCGA-E7-A97Q 
        5.19         1.84       130.88         9.67        43.59         8.09 
TCGA-FD-A3SL TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A43N TCGA-FD-A43X TCGA-FD-A5C0 
       23.41        46.78        19.79        22.98         3.62        18.08 
TCGA-FD-A6TE TCGA-FD-A6TH TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3YS TCGA-GD-A76B 
       12.36         4.31        64.44        19.46        24.92         7.36 
TCGA-GV-A3JW TCGA-LC-A66R TCGA-PQ-A6FN TCGA-SY-A9G0 TCGA-UY-A78M TCGA-UY-A8OD 
       21.34        15.32        16.67        12.43        22.68       112.83 
TCGA-UY-A9PD TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A9SH TCGA-XF-A9SJ 
       17.82        97.12        15.35         1.87        64.80         3.22 
TCGA-XF-A9T3 TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAMJ TCGA-XF-AAMW TCGA-XF-AAN0 
        2.24        10.82       110.60        54.90         8.32        56.48 
TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9RF TCGA-ZF-A9RN TCGA-ZF-AA4T TCGA-ZF-AA4U 
       11.97        18.64        52.73        20.22        19.69         8.61 
TCGA-ZF-AA4W TCGA-ZF-AA52 
       60.16        35.41 

$`12P LOSS WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-4Z-AA7M 
       22.29        11.97        91.63       103.50       105.70        16.27 
TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W 
       44.94        16.83        16.77        17.16        34.98        27.62 
TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA84 
       49.12         0.62        41.75        51.16        66.54        15.12 
TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A13I TCGA-BL-A3JM TCGA-BL-A5ZZ 
       10.22        47.80        33.83         7.33         6.74        12.39 
TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P 
        6.58        13.15        19.04        32.84        12.16        17.88 
TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W 
       19.50         5.06        14.89        14.96         5.06         8.35 
TCGA-BT-A20X TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK 
        8.25        16.18        20.48         4.67        12.82         9.96 
TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F6 
       17.56        28.70        24.26        28.41         8.98        23.01 
TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V 
        0.46         0.43         0.69        10.95        12.66        12.46 
TCGA-CF-A47W TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A8HX 
       12.10        12.26        13.12        12.00        12.10        11.34 
TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR 
       11.34        11.87        13.08        12.92         4.90         7.20 
TCGA-CU-A3KJ TCGA-CU-A3YL TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 
        5.46        16.31        13.58        21.86         2.14        66.41 
TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF 
       18.41        19.00        16.70       112.44        16.14        17.62 
TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 
       15.62         1.81        10.59         7.79       123.85        87.32 
TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS 
        2.20        13.58         7.82         8.22        17.72        50.27 
TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 
       21.30        23.21        20.81        10.55       140.81        48.00 
TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 
       17.98        64.18        41.56        76.60        67.36        15.68 
TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6S 
       41.06        30.67        38.24        15.02        13.58       166.03 
TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 
       12.36        10.49         8.65         7.53        13.64        43.50 
TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 
       12.03        10.62        15.35        38.83        24.66         0.10 
TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF 
        0.49         2.24        16.70        17.39         0.56         0.66 
TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV 
       14.56        13.97        12.99        14.33         0.92         1.22 
TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A8O7 TCGA-E7-A97P TCGA-FD-A3B3 
       13.68        14.07        12.95        15.32        14.37        32.02 
TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 
       16.77         8.94        33.04         4.01        12.62        22.52 
TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO 
       27.98        60.66        24.30        17.98        29.16         5.52 
TCGA-FD-A3SP TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43Y 
       25.74        12.85        27.35        14.96        20.91        15.58 
TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX 
       26.73        53.88        11.01        19.33         5.36         5.69 
TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P 
        8.25        27.45        58.92         2.70         7.10         6.28 
TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TF 
       13.35        62.86        18.81         6.15        12.69         2.27 
TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE 
        3.06         9.67        10.85        31.07         7.13        10.65 
TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ 
       17.23         8.94         3.25         6.48        61.94        30.61 
TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE 
       15.95        26.93        35.24        33.01         7.23        20.12 
TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO 
       17.62        66.02         6.94        21.40         2.24        15.81 
TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A4ZW TCGA-GC-A6I1 
        4.50        15.91        14.07        17.75         0.49         8.94 
TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 
       13.91         7.73         2.10         3.12        20.98         2.20 
TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 
       10.92        11.31        11.31         7.63        27.09        20.05 
TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JV 
        5.62         4.73        10.65        32.98         7.00        14.27 
TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK 
       19.10        19.82        20.28         8.48        10.59        27.35 
TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE 
        8.58        19.07        22.72         1.51        19.40        38.60 
TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV 
        3.06         9.01         8.22        25.02         3.45        21.24 
TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ 
        2.76         9.14        27.68         9.07        11.70         1.74 
TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-LT-A5Z6 TCGA-LT-A8JT 
        1.81        15.42         6.38        11.80        15.58        21.07 
TCGA-MV-A51V TCGA-PQ-A6FI TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G5 
       13.48        12.23        14.24         1.84         3.75        31.56 
TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OB 
       17.62        37.05        86.83        76.01        67.79        65.75 
TCGA-UY-A8OC TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HB 
        3.58        35.24        29.56         4.54         1.64        45.04 
TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SI 
        6.58        97.45       125.49        17.88        48.62        79.66 
TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ 
       66.41        12.76        11.90        23.64        21.04        28.24 
TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 
       26.27        18.90        16.27        66.64         2.10        13.74 
TCGA-XF-AAME TCGA-XF-AAMH TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMT 
       92.98        11.31         7.63        71.57        91.73         2.96 
TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 
        6.77        98.99        44.32        30.94        61.45        86.30 
TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 
       27.06        75.39        18.81         3.88        18.84         9.63 
TCGA-YC-A9TC TCGA-YF-AA3M TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R4 
        0.66        13.64         7.36        21.11        24.13        30.28 
TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE 
       27.19        21.86        28.41        74.56        13.41         3.48 
TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4V 
       52.60        82.49        47.84         2.89        34.06        59.38 
TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 
       63.02        38.73        57.90        19.40         8.52        47.15 
TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
       19.17         5.52        10.13 

  12P LOSS MUTATED 12P LOSS WILD-TYPE 
              1.84               0.10 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
            130.88             166.03 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
             17.95              15.58 
[1] "1.8 - 130.9 (17.9)" "0.1 - 166.0 (15.6)"
[1] "hr=" "1.1"
D64V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  12P LOSS MUTATED         1       11        16       23
  12P LOSS WILD-TYPE       3      113       111      106
D64V3, multiclass
           clus
vv          12P LOSS MUTATED 12P LOSS WILD-TYPE
  STAGE I                  1                  3
  STAGE II                11                113
  STAGE III               16                111
  STAGE IV                23                106
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1+T2  T3  T4
  12P LOSS MUTATED         15  23  12
  12P LOSS WILD-TYPE      106 161  41
D64V4, multiclass
          clus
vv         12P LOSS MUTATED 12P LOSS WILD-TYPE
  T0+T1+T2               15                106
  T3                     23                161
  T4                     12                 41
[1] 3 2
[1] TRUE
[1] "dimension of 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    21   5  16   1
  12P LOSS WILD-TYPE 203  37  59   7
D64V5, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  N0               21                203
  N1                5                 37
  N2               16                 59
  N3                1                  7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V6, binary
                    cls
clus                   0   1
  12P LOSS MUTATED    21   1
  12P LOSS WILD-TYPE 164   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     21    1
  12P LOSS WILD-TYPE  164    9
   clus
vv  12P LOSS MUTATED 12P LOSS WILD-TYPE
  0               21                164
  1                1                  9
[1] 2 2
[1] FALSE
D64V7, binary
                    cls
clus                   0   1
  12P LOSS MUTATED    13  38
  12P LOSS WILD-TYPE  88 250
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     13   38
  12P LOSS WILD-TYPE   88  250
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  FEMALE               13                 88
  MALE                 38                250
[1] 2 2
[1] FALSE
D64V8, continuous
D64V9, continuous
D64V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  12P LOSS MUTATED       5                         1    43
  12P LOSS WILD-TYPE    37                        20   268
D64V11, multiclass
                           clus
vv                          12P LOSS MUTATED 12P LOSS WILD-TYPE
  ASIAN                                    5                 37
  BLACK OR AFRICAN AMERICAN                1                 20
  WHITE                                   43                268
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V12, binary
                    cls
clus                   0   1
  12P LOSS MUTATED     2  47
  12P LOSS WILD-TYPE   7 305
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      2   47
  12P LOSS WILD-TYPE    7  305
                        clus
vv                       12P LOSS MUTATED 12P LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  7
  NOT HISPANIC OR LATINO               47                305
[1] 2 2
[1] FALSE

Clustering(65) Variable = 12Q LOSS MUTATION ANALYSIS
D65V1, survival
                    sevent
clus2                  0   1
  12Q LOSS MUTATED    31  22
  12Q LOSS WILD-TYPE 199 131
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                53                330 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                22                131 
$`12Q LOSS MUTATED`
TCGA-4Z-AA86 TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BT-A2LD TCGA-C4-A0F0 TCGA-CF-A47X 
       10.22        40.08         2.66        20.48         1.94        12.62 
TCGA-CU-A3QU TCGA-DK-A2I6 TCGA-DK-A3IV TCGA-E5-A2PC TCGA-E7-A97Q TCGA-FD-A3SL 
        5.19        87.32         9.67        43.59         8.09        23.41 
TCGA-FD-A3SO TCGA-FD-A3SQ TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43X TCGA-FD-A6TE 
        5.52        46.78        12.85        22.98         3.62        12.36 
TCGA-FD-A6TH TCGA-FT-A61P TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3RD TCGA-GC-A3YS 
        4.31         6.48        64.44        19.46        14.07        24.92 
TCGA-GC-A4ZW TCGA-GD-A76B TCGA-GV-A3JW TCGA-HQ-A5NE TCGA-K4-A4AC TCGA-K4-A5RJ 
        0.49         7.36        21.34         8.22         9.14         1.74 
TCGA-LC-A66R TCGA-PQ-A6FN TCGA-SY-A9G0 TCGA-UY-A78M TCGA-UY-A8OD TCGA-UY-A9PD 
       15.32        16.67        12.43        22.68       112.83        17.82 
TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A9SH TCGA-XF-A9SJ TCGA-XF-A9T3 TCGA-XF-AAMF 
       97.12        15.35        64.80         3.22         2.24        10.82 
TCGA-XF-AAMG TCGA-XF-AAMJ TCGA-XF-AAMW TCGA-XF-AAN0 TCGA-ZF-A9R0 TCGA-ZF-A9RF 
      110.60        54.90         8.32        56.48        18.64        52.73 
TCGA-ZF-AA4U TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA52 TCGA-ZF-AA5H 
        8.61        60.16        63.02        35.41        19.17 

$`12Q LOSS WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        91.63       103.50       105.70         8.35 
TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S 
       16.27        44.94        16.83        16.77        17.16        34.98 
TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 
       27.62        49.12         0.62        41.75        51.16        66.54 
TCGA-4Z-AA84 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A13I TCGA-BL-A3JM TCGA-BL-A5ZZ 
       15.12        47.80        33.83         7.33         6.74        12.39 
TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P 
        6.58        13.15        19.04        32.84        12.16        17.88 
TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W 
       19.50         5.06        14.89        14.96         5.06         8.35 
TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK 
        8.25        17.16        16.18         4.67        12.82         9.96 
TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F6 
       17.56        28.70        24.26        28.41         8.98        23.01 
TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V 
        0.46         0.43         0.69        10.95        12.66        12.46 
TCGA-CF-A47W TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A8HX 
       12.10        12.26        13.12        12.00        12.10        11.34 
TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR 
       11.34        11.87        13.08        12.92         4.90         7.20 
TCGA-CU-A3KJ TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 
        5.46        16.31         1.84        13.58        21.86         2.14 
TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD 
       66.41        18.41        19.00        16.70       130.88       112.44 
TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 
       16.14        17.62        15.62         1.81        10.59         7.79 
TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ 
      123.85         2.20        13.58         7.82         8.22        17.72 
TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY 
       50.27        21.30        23.21        20.81        10.55       140.81 
TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 
       48.00        17.98        64.18        41.56        76.60        67.36 
TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6P TCGA-DK-AA6Q 
       15.68        41.06        30.67        38.24        15.02        13.58 
TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 
      166.03        12.36        10.49         8.65         7.53        13.64 
TCGA-DK-AA74 TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 
       43.50        12.03        10.62        15.35        38.83        24.66 
TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE 
        0.10         0.49         2.24        16.70        17.39         0.56 
TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU 
        0.66        14.56        13.97        12.99        14.33         0.92 
TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A8O7 TCGA-E7-A97P 
        1.22        13.68        14.07        12.95        15.32        14.37 
TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 
       32.02        16.77         8.94        33.04         4.01        12.62 
TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SM TCGA-FD-A3SN 
       22.52        27.98        60.66        24.30        17.98        29.16 
TCGA-FD-A3SP TCGA-FD-A3SR TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43Y 
       25.74        19.79        27.35        14.96        20.91        15.58 
TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX 
       26.73        53.88        11.01        19.33         5.36         5.69 
TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O 
        8.25        27.45        18.08        58.92         2.70         7.10 
TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD 
        6.28        13.35        62.86        18.81         6.15        12.69 
TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 
        2.27         3.06         9.67        10.85        31.07         7.13 
TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EF TCGA-G2-A2EJ 
       10.65        17.23         8.94         3.25        61.94        30.61 
TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE 
       15.95        26.93        35.24        33.01         7.23        20.12 
TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO 
       17.62        66.02         6.94        21.40         2.24        15.81 
TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3WC TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 
        4.50        15.91        17.75         8.94        13.91         7.73 
TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42P TCGA-GU-A42Q 
        2.10         3.12        20.98         2.20        10.92        11.31 
TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 
       11.31         7.63        27.09        20.05         5.62         4.73 
TCGA-GU-AATO TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JX TCGA-GV-A3JZ 
       10.65        32.98         7.00        14.27        19.10        19.82 
TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G 
       20.28         8.48        10.59        27.35         8.58        19.07 
TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND 
       22.72         1.51        19.40        38.60         3.06         9.01 
TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A54R TCGA-K4-A5RH 
       25.02         3.45        21.24         2.76        27.68         9.07 
TCGA-K4-A5RI TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-LT-A5Z6 
       11.70         1.81        15.42         6.38        11.80        15.58 
TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FI TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 
       21.07        13.48        12.23        14.24         1.84         3.75 
TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A78P 
       31.56        17.62        37.05        86.83        76.01        67.79 
TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PE TCGA-UY-A9PF 
       65.75         3.58        35.24        29.56         4.54         1.64 
TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HH TCGA-XF-A8HI 
       45.04         6.58        97.45       125.49         1.87        17.88 
TCGA-XF-A9SG TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX 
       48.62        79.66        66.41        12.76        11.90        23.64 
TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T4 TCGA-XF-A9T5 
       21.04        28.24        26.27        18.90        16.27        66.64 
TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMH TCGA-XF-AAML TCGA-XF-AAMQ 
        2.10        13.74        92.98        11.31         7.63        71.57 
TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN1 
       91.73         2.96         6.77        98.99        44.32        30.94 
TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-XF-AAN8 
       61.45        86.30        27.06        75.39        18.81         3.88 
TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R1 
       18.84         9.63         0.66        11.97        13.64         7.36 
TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 
       21.11        24.13        30.28        27.19        21.86        28.41 
TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM 
       74.56        13.41         3.48        52.60        82.49        47.84 
TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4V TCGA-ZF-AA51 
       20.22         2.89        34.06        19.69        59.38        38.73 
TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5N TCGA-ZF-AA5P 
       57.90        19.40         8.52        47.15         5.52        10.13 

  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
              0.49               0.10 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
            112.83             166.03 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
            15.350             15.745 
[1] "0.5 - 112.8 (15.3)" "0.1 - 166.0 (15.7)"
[1] "hr=" "1"  
D65V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  12Q LOSS MUTATED         1       13        14       26
  12Q LOSS WILD-TYPE       3      111       113      103
D65V3, multiclass
           clus
vv          12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  STAGE I                  1                  3
  STAGE II                13                111
  STAGE III               14                113
  STAGE IV                26                103
[1] 4 2
[1] TRUE
[1] "dimension of contingency 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         18  25  10
  12Q LOSS WILD-TYPE      103 159  43
D65V4, multiclass
          clus
vv         12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  T0+T1+T2               18                103
  T3                     25                159
  T4                     10                 43
[1] 3 2
[1] TRUE
[1] "dimension of 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    21   9  14   2
  12Q LOSS WILD-TYPE 203  33  61   6
D65V5, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  N0               21                203
  N1                9                 33
  N2               14                 61
  N3                2                  6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V6, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED    24   1
  12Q LOSS WILD-TYPE 161   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED     24    1
  12Q LOSS WILD-TYPE  161    9
   clus
vv  12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  0               24                161
  1                1                  9
[1] 2 2
[1] FALSE
D65V7, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED    12  42
  12Q LOSS WILD-TYPE  89 246
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED     12   42
  12Q LOSS WILD-TYPE   89  246
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  FEMALE               12                 89
  MALE                 42                246
[1] 2 2
[1] FALSE
D65V8, continuous
D65V9, continuous
D65V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  12Q LOSS MUTATED       5                         2    45
  12Q LOSS WILD-TYPE    37                        19   266
D65V11, multiclass
                           clus
vv                          12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  ASIAN                                    5                 37
  BLACK OR AFRICAN AMERICAN                2                 19
  WHITE                                   45                266
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V12, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED     1  50
  12Q LOSS WILD-TYPE   8 302
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      1   50
  12Q LOSS WILD-TYPE    8  302
                        clus
vv                       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  8
  NOT HISPANIC OR LATINO               50                302
[1] 2 2
[1] FALSE

Clustering(66) Variable = 13Q LOSS MUTATION ANALYSIS
D66V1, survival
                    sevent
clus2                  0   1
  13Q LOSS MUTATED    45  36
  13Q LOSS WILD-TYPE 185 117
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                81                302 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                36                117 
$`13Q LOSS MUTATED`
TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7W TCGA-4Z-AA82 TCGA-4Z-AA84 TCGA-BL-A0C8 
       16.77        17.16        27.62        51.16        15.12        40.08 
TCGA-BL-A13J TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA 
        2.66        32.84        14.89         5.06         8.25        17.16 
TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E TCGA-C4-A0F0 TCGA-CU-A5W6 
        4.67        17.56        28.70        24.26         1.94         1.84 
TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1AC TCGA-DK-A2I2 TCGA-DK-A2I6 TCGA-DK-A3IM 
       21.86         2.14       130.88         7.79        87.32         7.82 
TCGA-DK-A3IN TCGA-DK-A6B6 TCGA-DK-AA6W TCGA-E7-A3X6 TCGA-E7-A4IJ TCGA-E7-A5KE 
        8.22        30.67         8.65        24.66         0.49         0.56 
TCGA-E7-A7DV TCGA-E7-A85H TCGA-FD-A3B5 TCGA-FD-A3B7 TCGA-FD-A3SJ TCGA-FD-A3SN 
        1.22        12.95         8.94         4.01        24.30        29.16 
TCGA-FD-A43P TCGA-FD-A5BV TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FJ-A3ZF TCGA-G2-A2EO 
       27.35         5.36        58.92         2.70        17.23        35.24 
TCGA-G2-A2ES TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GC-A6I3 
       33.01        19.46        21.40        24.92         8.94        13.91 
TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GV-A3JW TCGA-GV-A3QI TCGA-HQ-A2OE TCGA-HQ-A5ND 
        2.20        11.31        21.34        10.59        38.60         9.01 
TCGA-K4-A3WV TCGA-K4-A4AC TCGA-K4-A6FZ TCGA-UY-A78N TCGA-UY-A8OB TCGA-UY-A9PB 
       21.24         9.14         1.81        86.83        65.75        29.56 
TCGA-UY-A9PD TCGA-UY-A9PF TCGA-XF-A9SY TCGA-XF-A9T5 TCGA-XF-AAMG TCGA-XF-AAMJ 
       17.82         1.64        21.04        66.64       110.60        54.90 
TCGA-XF-AAMX TCGA-XF-AAMZ TCGA-ZF-A9R2 TCGA-ZF-A9R9 TCGA-ZF-A9RE TCGA-ZF-A9RF 
        6.77        44.32        21.11        28.41         3.48        52.73 
TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4W TCGA-ZF-AA51 
       52.60        47.84        20.22         2.89        60.16        38.73 
TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA58 
       57.90        19.40        47.15 

$`13Q LOSS WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        91.63       103.50       105.70         8.35 
TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7S TCGA-4Z-AA7Y TCGA-4Z-AA80 
       16.27        44.94        16.83        34.98        49.12         0.62 
TCGA-4Z-AA81 TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A13I 
       41.75        66.54        10.22        47.80        33.83         7.33 
TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O 
        6.74        12.39         6.58        13.15        19.04        12.16 
TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20W TCGA-BT-A2LB 
       17.88        19.50         5.06        14.96         8.35        16.18 
TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F6 
       20.48        12.82         9.96        28.41         8.98        23.01 
TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V 
        0.46         0.43         0.69        10.95        12.66        12.46 
TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 
       12.10        12.62        12.26        13.12        12.00        12.10 
TCGA-CF-A8HX TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO 
       11.34        11.34        11.87        13.08        12.92         4.90 
TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A72E TCGA-DK-A1A6 
        7.20         5.46         5.19        16.31        13.58        66.41 
TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF 
       18.41        19.00        16.70       112.44        16.14        17.62 
TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IL 
       15.62         1.81        10.59       123.85         2.20        13.58 
TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW 
       17.72        50.27        21.30        23.21         9.67        20.81 
TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW 
       10.55       140.81        48.00        17.98        64.18        41.56 
TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-AA6L TCGA-DK-AA6P 
       76.60        67.36        15.68        41.06        38.24        15.02 
TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA71 
       13.58       166.03        12.36        10.49         7.53        13.64 
TCGA-DK-AA74 TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 
       43.50        12.03        10.62        43.59        15.35        38.83 
TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KF TCGA-E7-A677 
        0.10         2.24        16.70        17.39         0.66        14.56 
TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7PW TCGA-E7-A7XN 
       13.97        12.99        14.33         0.92        13.68        14.07 
TCGA-E7-A8O7 TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B6 
       15.32        14.37         8.09        32.02        16.77        33.04 
TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SL TCGA-FD-A3SM 
       12.62        22.52        27.98        60.66        23.41        17.98 
TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N 
        5.52        25.74        46.78        19.79        12.85        22.98 
TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS 
       14.96        20.91         3.62        15.58        26.73        53.88 
TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 
       11.01        19.33         5.69         8.25        27.45        18.08 
TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC 
        7.10         6.28        13.35        62.86        18.81         6.15 
TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI 
       12.69        12.36         2.27         3.06         4.31         9.67 
TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-FT-A3EE 
       10.85        31.07         7.13        10.65         8.94         3.25 
TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A3IB 
        6.48        61.94        30.61        15.95        26.93         7.23 
TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3D TCGA-GC-A3I6 
       20.12        17.62        66.02         6.94        64.44         2.24 
TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A4ZW 
       15.81         4.50        15.91        14.07        17.75         0.49 
TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A76B TCGA-GU-A42P 
        7.73         2.10         3.12        20.98         7.36        10.92 
TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 
       11.31         7.63        27.09        20.05         5.62         4.73 
TCGA-GU-AATO TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JX TCGA-GV-A3JZ 
       10.65        32.98         7.00        14.27        19.10        19.82 
TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA 
       20.28         8.48        27.35         8.58        19.07        22.72 
TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OF TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU 
        1.51        19.40         3.06         8.22        25.02         3.45 
TCGA-K4-A4AB TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6MB 
        2.76        27.68         9.07        11.70         1.74        15.42 
TCGA-K4-A83P TCGA-K4-AAQO TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-MV-A51V 
        6.38        11.80        15.32        15.58        21.07        13.48 
TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G0 
       12.23        16.67        14.24         1.84         3.75        12.43 
TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78O TCGA-UY-A78P 
       31.56        17.62        37.05        22.68        76.01        67.79 
TCGA-UY-A8OC TCGA-UY-A8OD TCGA-UY-A9PA TCGA-UY-A9PE TCGA-XF-A8HB TCGA-XF-A8HC 
        3.58       112.83        35.24         4.54        45.04         6.58 
TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A8HI 
       97.45       125.49        97.12        15.35         1.87        17.88 
TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SV 
       48.62        64.80        79.66         3.22        66.41        12.76 
TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 
       11.90        23.64        28.24        26.27        18.90         2.24 
TCGA-XF-A9T4 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMH 
       16.27         2.10        13.74        92.98        10.82        11.31 
TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMY 
        7.63        71.57        91.73         2.96         8.32        98.99 
TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 
       56.48        30.94        61.45        86.30        27.06        75.39 
TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L 
       18.81         3.88        18.84         9.63         0.66        11.97 
TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 
       13.64        18.64         7.36        24.13        30.28        27.19 
TCGA-ZF-A9R7 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RL TCGA-ZF-AA4R TCGA-ZF-AA4T 
       21.86        74.56        13.41        82.49        34.06        19.69 
TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4X TCGA-ZF-AA52 TCGA-ZF-AA56 TCGA-ZF-AA5H 
        8.61        59.38        63.02        35.41         8.52        19.17 
TCGA-ZF-AA5N TCGA-ZF-AA5P 
        5.52        10.13 

  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
              0.49               0.10 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
            130.88             166.03 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
             19.46              15.32 
[1] "0.5 - 130.9 (19.5)" "0.1 - 166.0 (15.3)"
[1] "hr=" "1.1"
D66V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  13Q LOSS MUTATED         1       23        29       27
  13Q LOSS WILD-TYPE       3      101        98      102
D66V3, multiclass
           clus
vv          13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  STAGE I                  1                  3
  STAGE II                23                101
  STAGE III               29                 98
  STAGE IV                27                102
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1+T2  T3  T4
  13Q LOSS MUTATED         25  43   8
  13Q LOSS WILD-TYPE       96 141  45
D66V4, multiclass
          clus
vv         13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  T0+T1+T2               25                 96
  T3                     43                141
  T4                      8                 45
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  13Q LOSS MUTATED    41  12  13   2
  13Q LOSS WILD-TYPE 183  30  62   6
D66V5, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  N0               41                183
  N1               12                 30
  N2               13                 62
  N3                2                  6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V6, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED    39   1
  13Q LOSS WILD-TYPE 146   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     39    1
  13Q LOSS WILD-TYPE  146    9
   clus
vv  13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  0               39                146
  1                1                  9
[1] 2 2
[1] FALSE
D66V7, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED    18  63
  13Q LOSS WILD-TYPE  83 225
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     18   63
  13Q LOSS WILD-TYPE   83  225
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  FEMALE               18                 83
  MALE                 63                225
[1] 2 2
[1] FALSE
D66V8, continuous
D66V9, continuous
D66V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  13Q LOSS MUTATED       5                         8    64
  13Q LOSS WILD-TYPE    37                        13   247
D66V11, multiclass
                           clus
vv                          13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  ASIAN                                    5                 37
  BLACK OR AFRICAN AMERICAN                8                 13
  WHITE                                   64                247
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V12, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED     4  67
  13Q LOSS WILD-TYPE   5 285
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      4   67
  13Q LOSS WILD-TYPE    5  285
                        clus
vv                       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                  5
  NOT HISPANIC OR LATINO               67                285
[1] 2 2
[1] FALSE

Clustering(67) Variable = 14Q LOSS MUTATION ANALYSIS
D67V1, survival
                    sevent
clus2                  0   1
  14Q LOSS MUTATED    69  45
  14Q LOSS WILD-TYPE 161 108
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               114                269 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                45                108 
$`14Q LOSS MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW TCGA-4Z-AA7M 
       22.29        11.97       103.50       105.70         8.35        16.27 
TCGA-4Z-AA7Q TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA84 TCGA-4Z-AA87 
       16.77         0.62        41.75        51.16        15.12        47.80 
TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BT-A20J TCGA-BT-A20T TCGA-BT-A20V TCGA-BT-A2LB 
       40.08         2.66        19.04        14.89         5.06        16.18 
TCGA-BT-A3PK TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A47X TCGA-CF-A5U8 TCGA-CF-A8HY 
        9.96         0.46         0.43        12.62        13.12        11.34 
TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1AC 
        4.90         7.20         1.84        21.86         2.14       130.88 
TCGA-DK-A1AD TCGA-DK-A2I1 TCGA-DK-A2I6 TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3X1 
      112.44        10.59        87.32        17.72        50.27        48.00 
TCGA-DK-A6AV TCGA-DK-A6B5 TCGA-DK-AA6S TCGA-DK-AA6U TCGA-E5-A4TZ TCGA-E5-A4U1 
       64.18        41.06       166.03        10.49        15.35        38.83 
TCGA-E7-A4IJ TCGA-E7-A6ME TCGA-E7-A7DU TCGA-FD-A3SN TCGA-FD-A3SP TCGA-FD-A3SQ 
        0.49        12.99         0.92        29.16        25.74        46.78 
TCGA-FD-A43N TCGA-FD-A43U TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A6TA 
       22.98        20.91        18.08        58.92         6.28        62.86 
TCGA-FD-A6TC TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-FT-A61P 
        6.15         3.06         4.31        31.07        17.23         6.48 
TCGA-G2-A2EF TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3D TCGA-GC-A3RB 
       61.94        20.12        17.62        66.02        64.44         4.50 
TCGA-GC-A3RD TCGA-GC-A4ZW TCGA-GD-A76B TCGA-GU-A42Q TCGA-GU-AATP TCGA-GV-A3JZ 
       14.07         0.49         7.36        11.31        32.98        19.82 
TCGA-GV-A3QF TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HQ TCGA-HQ-A2OE 
       20.28         8.58        19.07        22.72        19.40        38.60 
TCGA-HQ-A2OF TCGA-K4-A3WU TCGA-K4-A6MB TCGA-PQ-A6FI TCGA-R3-A69X TCGA-S5-A6DX 
        3.06         3.45        15.42        12.23        14.24         1.84 
TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A8OB 
       12.43        31.56        17.62        37.05        22.68        65.75 
TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HH TCGA-XF-A9SG TCGA-XF-A9SX 
       17.82         4.54         1.64         1.87        48.62        23.64 
TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMX TCGA-XF-AAMY 
       28.24        26.27        54.90         7.63         6.77        98.99 
TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-YF-AA3M TCGA-ZF-A9RC 
       44.32        56.48        61.45        86.30        13.64        74.56 
TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4T TCGA-ZF-AA51 TCGA-ZF-AA52 
       47.84        20.22         2.89        19.69        38.73        35.41 

$`14Q LOSS WILD-TYPE`
TCGA-2F-A9KQ TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W 
       91.63        44.94        16.83        17.16        34.98        27.62 
TCGA-4Z-AA7Y TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-4Z-AA89 TCGA-BL-A13I TCGA-BL-A3JM 
       49.12        66.54        10.22        33.83         7.33         6.74 
TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P 
       12.39         6.58        13.15        32.84        12.16        17.88 
TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA 
       19.50         5.06        14.96         8.35         8.25        17.16 
TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E 
       20.48         4.67        12.82        17.56        28.70        24.26 
TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A27C TCGA-CF-A47S 
       28.41         8.98         1.94        23.01         0.69        10.95 
TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47Y TCGA-CF-A5UA TCGA-CF-A7I0 
       12.66        12.46        12.10        12.26        12.00        12.10 
TCGA-CF-A8HX TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A3KJ TCGA-CU-A3QU 
       11.34        11.87        13.08        12.92         5.46         5.19 
TCGA-CU-A3YL TCGA-CU-A72E TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB 
       16.31        13.58        66.41        18.41        19.00        16.70 
TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I2 TCGA-DK-A2I4 
       16.14        17.62        15.62         1.81         7.79       123.85 
TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IT TCGA-DK-A3IU 
        2.20        13.58         7.82         8.22        21.30        23.21 
TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X2 TCGA-DK-A6AW 
        9.67        20.81        10.55       140.81        17.98        41.56 
TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6P 
       76.60        67.36        15.68        30.67        38.24        15.02 
TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 
       13.58        12.36         8.65         7.53        13.64        43.50 
TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ 
       12.03        10.62        43.59        24.66         0.10         2.24 
TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 
       16.70        17.39         0.56         0.66        14.56        13.97 
TCGA-E7-A6MF TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A8O7 
       14.33         1.22        13.68        14.07        12.95        15.32 
TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 
       14.37         8.09        32.02        16.77         8.94        33.04 
TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ 
        4.01        12.62        22.52        27.98        60.66        24.30 
TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SO TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43P 
       23.41        17.98         5.52        19.79        12.85        27.35 
TCGA-FD-A43S TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT 
       14.96         3.62        15.58        26.73        53.88        11.01 
TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A62N 
       19.33         5.36         5.69         8.25        27.45         2.70 
TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TB TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF 
        7.10        13.35        18.81        12.69        12.36         2.27 
TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-FT-A3EE 
        9.67        10.85         7.13        10.65         8.94         3.25 
TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB 
       30.61        15.95        26.93        35.24        33.01         7.23 
TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RC 
        6.94        19.46        21.40         2.24        15.81        15.91 
TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP 
       17.75        24.92         8.94        13.91         7.73         2.10 
TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42P TCGA-GU-A42R TCGA-GU-A762 
        3.12        20.98         2.20        10.92        11.31         7.63 
TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATQ 
       27.09        20.05         5.62         4.73        10.65         7.00 
TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK 
       14.27        21.34        19.10         8.48        10.59        27.35 
TCGA-H4-A2HO TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WV TCGA-K4-A4AB 
        1.51         9.01         8.22        25.02        21.24         2.76 
TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ 
        9.14        27.68         9.07        11.70         1.74         1.81 
TCGA-K4-A83P TCGA-K4-AAQO TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-MV-A51V 
        6.38        11.80        15.32        15.58        21.07        13.48 
TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OC 
       16.67         3.75        86.83        76.01        67.79         3.58 
TCGA-UY-A8OD TCGA-UY-A9PA TCGA-UY-A9PB TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HD 
      112.83        35.24        29.56        45.04         6.58        97.45 
TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SI 
      125.49        97.12        15.35        17.88        64.80        79.66 
TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9T2 
        3.22        66.41        12.76        11.90        21.04        18.90 
TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME 
        2.24        16.27        66.64         2.10        13.74        92.98 
TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMT 
       10.82       110.60        11.31        71.57        91.73         2.96 
TCGA-XF-AAMW TCGA-XF-AAN1 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-XF-AAN8 
        8.32        30.94        27.06        75.39        18.81         3.88 
TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R1 
       18.84         9.63         0.66        11.97        18.64         7.36 
TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 
       21.11        24.13        30.28        27.19        21.86        28.41 
TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-AA4R 
       13.41         3.48        52.73        52.60        82.49        34.06 
TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA53 TCGA-ZF-AA54 
        8.61        59.38        60.16        63.02        57.90        19.40 
TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
        8.52        47.15        19.17         5.52        10.13 

  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
              0.43               0.10 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
            166.03             140.81 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
             18.56              14.96 
[1] "0.4 - 166.0 (18.6)" "0.1 - 140.8 (15.0)"
[1] "hr=" "1.2"
D67V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  14Q LOSS MUTATED         2       33        34       43
  14Q LOSS WILD-TYPE       2       91        93       86
D67V3, multiclass
           clus
vv          14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  STAGE I                  2                  2
  STAGE II                33                 91
  STAGE III               34                 93
  STAGE IV                43                 86
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1+T2  T3  T4
  14Q LOSS MUTATED         36  53  16
  14Q LOSS WILD-TYPE       85 131  37
D67V4, multiclass
          clus
vv         14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  T0+T1+T2               36                 85
  T3                     53                131
  T4                     16                 37
[1] 3 2
[1] TRUE
[1] "dimension of 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    59   8  34   1
  14Q LOSS WILD-TYPE 165  34  41   7
D67V5, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  N0               59                165
  N1                8                 34
  N2               34                 41
  N3                1                  7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V6, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED    56   2
  14Q LOSS WILD-TYPE 129   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     56    2
  14Q LOSS WILD-TYPE  129    8
   clus
vv  14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  0               56                129
  1                2                  8
[1] 2 2
[1] FALSE
D67V7, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED    22  93
  14Q LOSS WILD-TYPE  79 195
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     22   93
  14Q LOSS WILD-TYPE   79  195
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  FEMALE               22                 79
  MALE                 93                195
[1] 2 2
[1] FALSE
D67V8, continuous
D67V9, continuous
D67V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  14Q LOSS MUTATED      12                         5    92
  14Q LOSS WILD-TYPE    30                        16   219
D67V11, multiclass
                           clus
vv                          14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  ASIAN                                   12                 30
  BLACK OR AFRICAN AMERICAN                5                 16
  WHITE                                   92                219
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V12, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED     4  99
  14Q LOSS WILD-TYPE   5 253
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      4   99
  14Q LOSS WILD-TYPE    5  253
                        clus
vv                       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                  5
  NOT HISPANIC OR LATINO               99                253
[1] 2 2
[1] FALSE

Clustering(68) Variable = 15Q LOSS MUTATION ANALYSIS
D68V1, survival
                    sevent
clus2                  0   1
  15Q LOSS MUTATED    85  49
  15Q LOSS WILD-TYPE 145 104
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
               134                249 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                49                104 
$`15Q LOSS MUTATED`
TCGA-2F-A9KW TCGA-4Z-AA7M TCGA-4Z-AA7W TCGA-4Z-AA80 TCGA-4Z-AA82 TCGA-4Z-AA84 
        8.35        16.27        27.62         0.62        51.16        15.12 
TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BT-A0S7 TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20W 
       40.08         2.66         6.58        19.04        32.84         8.35 
TCGA-BT-A20X TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E 
        8.25        16.18        20.48        17.56        28.70        24.26 
TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-CF-A1HS TCGA-CF-A47X TCGA-CU-A3KJ TCGA-DK-A1A7 
        8.98         1.94         0.43        12.62         5.46        18.41 
TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A6B2 
        7.79       123.85        87.32         7.82         8.22        15.68 
TCGA-DK-A6B5 TCGA-DK-AA6P TCGA-DK-AA6S TCGA-DK-AA6W TCGA-DK-AA74 TCGA-DK-AA76 
       41.06        15.02       166.03         8.65        43.50        12.03 
TCGA-E5-A2PC TCGA-E7-A4IJ TCGA-E7-A541 TCGA-E7-A7DV TCGA-E7-A7PW TCGA-FD-A3B3 
       43.59         0.49        17.39         1.22        13.68        32.02 
TCGA-FD-A3NA TCGA-FD-A3SN TCGA-FD-A3SP TCGA-FD-A43N TCGA-FD-A5BV TCGA-FD-A5BY 
       60.66        29.16        25.74        22.98         5.36         8.25 
TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62S TCGA-FD-A6TD 
       27.45        18.08        58.92         2.70        13.35        12.69 
TCGA-FD-A6TH TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2EF 
        4.31        10.85        31.07        17.23         6.48        61.94 
TCGA-G2-A2EL TCGA-G2-A3IE TCGA-G2-AA3B TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3YS 
       26.93        20.12        66.02        15.81         4.50        24.92 
TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GD-A3OP TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P 
        0.49         8.94         2.10         2.20         7.36        10.92 
TCGA-GU-A762 TCGA-GU-A766 TCGA-GU-AATO TCGA-GV-A3JX TCGA-GV-A3QF TCGA-GV-A3QH 
        7.63         5.62        10.65        19.10        20.28         8.48 
TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A5NE 
        8.58        19.07        22.72        19.40        38.60         8.22 
TCGA-K4-A3WS TCGA-K4-A4AB TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-LC-A66R 
       25.02         2.76         9.07        11.70         1.74        15.32 
TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FN TCGA-R3-A69X TCGA-SY-A9G0 TCGA-UY-A78L 
       15.58        13.48        16.67        14.24        12.43        37.05 
TCGA-UY-A78M TCGA-UY-A78O TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE 
       22.68        76.01        35.24        29.56        17.82         4.54 
TCGA-UY-A9PF TCGA-XF-A8HD TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A9SG 
        1.64        97.45        97.12        15.35         1.87        48.62 
TCGA-XF-A9SJ TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9T0 TCGA-XF-A9T3 TCGA-XF-A9T5 
        3.22        11.90        23.64        26.27         2.24        66.64 
TCGA-XF-AAMG TCGA-XF-AAML TCGA-XF-AAMT TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAN2 
      110.60         7.63         2.96         6.77        98.99        61.45 
TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R4 TCGA-ZF-A9R9 TCGA-ZF-A9RG TCGA-ZF-A9RL 
       11.97        13.64        30.28        28.41        52.60        82.49 
TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4T TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 
       20.22         2.89        19.69        63.02        38.73        35.41 
TCGA-ZF-AA58 TCGA-ZF-AA5H 
       47.15        19.17 

$`15Q LOSS WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-4Z-AA7N 
       22.29        11.97        91.63       103.50       105.70        44.94 
TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7Y TCGA-4Z-AA81 
       16.83        16.77        17.16        34.98        49.12        41.75 
TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A13I TCGA-BL-A3JM 
       66.54        10.22        47.80        33.83         7.33         6.74 
TCGA-BL-A5ZZ TCGA-BT-A0YX TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R 
       12.39        13.15        12.16        17.88        19.50         5.06 
TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A2LA TCGA-BT-A3PH TCGA-BT-A3PJ 
       14.89        14.96         5.06        17.16         4.67        12.82 
TCGA-BT-A3PK TCGA-BT-A42F TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A27C TCGA-CF-A47S 
        9.96        28.41        23.01         0.46         0.69        10.95 
TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA 
       12.66        12.46        12.10        12.26        13.12        12.00 
TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YN 
       12.10        11.34        11.34        11.87        13.08        12.92 
TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E 
        4.90         7.20         5.19        16.31         1.84        13.58 
TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC 
       21.86         2.14        66.41        19.00        16.70       130.88 
TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 
      112.44        16.14        17.62        15.62         1.81        10.59 
TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU 
        2.20        13.58        17.72        50.27        21.30        23.21 
TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 
        9.67        20.81        10.55       140.81        48.00        17.98 
TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B6 TCGA-DK-AA6L 
       64.18        41.56        76.60        67.36        30.67        38.24 
TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA77 
       13.58        12.36        10.49         7.53        13.64        10.62 
TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A519 
       15.35        38.83        24.66         0.10         2.24        16.70 
TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF 
        0.56         0.66        14.56        13.97        12.99        14.33 
TCGA-E7-A7DU TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A8O7 TCGA-E7-A97P TCGA-E7-A97Q 
        0.92        14.07        12.95        15.32        14.37         8.09 
TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 
       16.77         8.94        33.04         4.01        12.62        22.52 
TCGA-FD-A3N6 TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SO TCGA-FD-A3SQ 
       27.98        24.30        23.41        17.98         5.52        46.78 
TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X 
       19.79        12.85        27.35        14.96        20.91         3.62 
TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BX 
       15.58        26.73        53.88        11.01        19.33         5.69 
TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TE 
        7.10         6.28        62.86        18.81         6.15        12.36 
TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 
        2.27         3.06         9.67         7.13        10.65         8.94 
TCGA-FT-A3EE TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB 
        3.25        30.61        15.95        35.24        33.01         7.23 
TCGA-G2-A3VY TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 
       17.62         6.94        64.44        19.46        21.40         2.24 
TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OQ 
       15.91        14.07        17.75        13.91         7.73         3.12 
TCGA-GD-A3OS TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A767 
       20.98        11.31        11.31        27.09        20.05         4.73 
TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JZ TCGA-GV-A3QI 
       32.98         7.00        14.27        21.34        19.82        10.59 
TCGA-GV-A3QK TCGA-H4-A2HO TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-K4-A3WU TCGA-K4-A3WV 
       27.35         1.51         3.06         9.01         3.45        21.24 
TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO 
        9.14        27.68         1.81        15.42         6.38        11.80 
TCGA-LT-A8JT TCGA-PQ-A6FI TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G5 TCGA-UY-A78K 
       21.07        12.23         1.84         3.75        31.56        17.62 
TCGA-UY-A78N TCGA-UY-A78P TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A8OD TCGA-XF-A8HB 
       86.83        67.79        65.75         3.58       112.83        45.04 
TCGA-XF-A8HC TCGA-XF-A8HE TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SL 
        6.58       125.49        17.88        64.80        79.66        66.41 
TCGA-XF-A9SV TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T2 TCGA-XF-A9T4 TCGA-XF-A9T6 
       12.76        21.04        28.24        18.90        16.27         2.10 
TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAMQ 
       13.74        92.98        10.82        11.31        54.90        71.57 
TCGA-XF-AAMR TCGA-XF-AAMW TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN3 
       91.73         8.32        44.32        56.48        30.94        86.30 
TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 
       27.06        75.39        18.81         3.88        18.84         9.63 
TCGA-YC-A9TC TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R5 
        0.66        18.64         7.36        21.11        24.13        27.19 
TCGA-ZF-A9R7 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RM 
       21.86        74.56        13.41         3.48        52.73        47.84 
TCGA-ZF-AA4R TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA53 TCGA-ZF-AA54 
       34.06         8.61        59.38        60.16        57.90        19.40 
TCGA-ZF-AA56 TCGA-ZF-AA5N TCGA-ZF-AA5P 
        8.52         5.52        10.13 

  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
              0.43               0.10 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
            166.03             140.81 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
            16.225             15.420 
[1] "0.4 - 166.0 (16.2)" "0.1 - 140.8 (15.4)"
[1] "hr=" "1.2"
D68V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  15Q LOSS MUTATED         1       38        50       43
  15Q LOSS WILD-TYPE       3       86        77       86
D68V3, multiclass
           clus
vv          15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  STAGE I                  1                  3
  STAGE II                38                 86
  STAGE III               50                 77
  STAGE IV                43                 86
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1+T2  T3  T4
  15Q LOSS MUTATED         34  71  15
  15Q LOSS WILD-TYPE       87 113  38
D68V4, multiclass
          clus
vv         15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  T0+T1+T2               34                 87
  T3                     71                113
  T4                     15                 38
[1] 3 2
[1] TRUE
[1] "dimension of 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    75  13  28   2
  15Q LOSS WILD-TYPE 149  29  47   6
D68V5, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  N0               75                149
  N1               13                 29
  N2               28                 47
  N3                2                  6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V6, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED    50   3
  15Q LOSS WILD-TYPE 135   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED     50    3
  15Q LOSS WILD-TYPE  135    7
   clus
vv  15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  0               50                135
  1                3                  7
[1] 2 2
[1] FALSE
D68V7, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED    37  97
  15Q LOSS WILD-TYPE  64 191
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED     37   97
  15Q LOSS WILD-TYPE   64  191
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  FEMALE               37                 64
  MALE                 97                191
[1] 2 2
[1] FALSE
D68V8, continuous
D68V9, continuous
D68V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  15Q LOSS MUTATED       6                         4   116
  15Q LOSS WILD-TYPE    36                        17   195
D68V11, multiclass
                           clus
vv                          15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  ASIAN                                    6                 36
  BLACK OR AFRICAN AMERICAN                4                 17
  WHITE                                  116                195
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V12, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED     5 119
  15Q LOSS WILD-TYPE   4 233
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      5  119
  15Q LOSS WILD-TYPE    4  233
                        clus
vv                       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    5                  4
  NOT HISPANIC OR LATINO              119                233
[1] 2 2
[1] FALSE

Clustering(69) Variable = 16P LOSS MUTATION ANALYSIS
D69V1, survival
                    sevent
clus2                  0   1
  16P LOSS MUTATED    60  40
  16P LOSS WILD-TYPE 170 113
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
               100                283 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                40                113 
$`16P LOSS MUTATED`
TCGA-2F-A9KO TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-BL-A0C8 
       22.29        16.27        16.77        15.12        10.22        40.08 
TCGA-BL-A13J TCGA-BT-A20N TCGA-BT-A20R TCGA-BT-A3PJ TCGA-BT-A42E TCGA-CF-A1HS 
        2.66        32.84         5.06        12.82        24.26         0.43 
TCGA-CU-A0YN TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1AC 
       12.92         5.46         5.19         1.84        21.86       130.88 
TCGA-DK-A2HX TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3WX TCGA-DK-A3X2 TCGA-DK-A6B1 
        1.81       123.85        87.32        10.55        17.98        67.36 
TCGA-DK-A6B6 TCGA-DK-AA6P TCGA-DK-AA76 TCGA-E7-A541 TCGA-FD-A3B3 TCGA-FD-A3B6 
       30.67        15.02        12.03        17.39        32.02        33.04 
TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43N TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BZ 
        5.52        25.74        22.98        15.58        26.73        27.45 
TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TH 
        2.70         7.10        13.35        12.69        12.36         4.31 
TCGA-FJ-A3Z7 TCGA-G2-A2EF TCGA-G2-A3IE TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3YS 
       31.07        61.94        20.12        15.91        14.07        24.92 
TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A6C6 TCGA-GU-A42P TCGA-GV-A3JX 
        8.94         7.73         2.10         2.20        10.92        19.10 
TCGA-GV-A3JZ TCGA-GV-A3QH TCGA-GV-A6ZA TCGA-HQ-A2OE TCGA-K4-A4AC TCGA-K4-A54R 
       19.82         8.48        22.72        38.60         9.14        27.68 
TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-LT-A5Z6 TCGA-MV-A51V 
        9.07        11.70         1.74         1.81        15.58        13.48 
TCGA-PQ-A6FI TCGA-SY-A9G0 TCGA-UY-A78N TCGA-UY-A8OB TCGA-UY-A8OD TCGA-UY-A9PA 
       12.23        12.43        86.83        65.75       112.83        35.24 
TCGA-UY-A9PB TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HC TCGA-XF-A8HF TCGA-XF-A8HG 
       29.56         4.54         1.64         6.58        97.12        15.35 
TCGA-XF-A9SI TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-AAN0 TCGA-XF-AAN2 
       79.66        11.90        23.64        21.04        56.48        61.45 
TCGA-XF-AAN3 TCGA-XF-AAN7 TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9RC TCGA-ZF-A9RF 
       86.30        18.81        11.97        13.64        74.56        52.73 
TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4U TCGA-ZF-AA4X 
       82.49        47.84        20.22         2.89         8.61        63.02 
TCGA-ZF-AA51 TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA58 
       38.73        57.90        19.40        47.15 

$`16P LOSS WILD-TYPE`
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW TCGA-4Z-AA7N 
       11.97        91.63       103.50       105.70         8.35        44.94 
TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 
       16.83        17.16        34.98        27.62        49.12         0.62 
TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A13I 
       41.75        51.16        66.54        47.80        33.83         7.33 
TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O 
        6.74        12.39         6.58        13.15        19.04        12.16 
TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W 
       17.88        19.50        14.89        14.96         5.06         8.35 
TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PK 
        8.25        17.16        16.18        20.48         4.67         9.96 
TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F6 
       17.56        28.70        28.41         8.98         1.94        23.01 
TCGA-CF-A1HR TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W 
        0.46         0.69        10.95        12.66        12.46        12.10 
TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A8HX 
       12.62        12.26        13.12        12.00        12.10        11.34 
TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3YL 
       11.34        11.87        13.08         4.90         7.20        16.31 
TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB 
       13.58         2.14        66.41        18.41        19.00        16.70 
TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A2I2 
      112.44        16.14        17.62        15.62        10.59         7.79 
TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS 
        2.20        13.58         7.82         8.22        17.72        50.27 
TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WY TCGA-DK-A3X1 
       21.30        23.21         9.67        20.81       140.81        48.00 
TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-AA6L 
       64.18        41.56        76.60        15.68        41.06        38.24 
TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X 
       13.58       166.03        12.36        10.49         8.65         7.53 
TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 
       13.64        43.50        10.62        43.59        15.35        38.83 
TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KE 
       24.66         0.10         0.49         2.24        16.70         0.56 
TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU 
        0.66        14.56        13.97        12.99        14.33         0.92 
TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A8O7 TCGA-E7-A97P 
        1.22        13.68        14.07        12.95        15.32        14.37 
TCGA-E7-A97Q TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 
        8.09        16.77         8.94         4.01        12.62        22.52 
TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN 
       27.98        60.66        24.30        23.41        17.98        29.16 
TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U 
       46.78        19.79        12.85        27.35        14.96        20.91 
TCGA-FD-A43X TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX 
        3.62        53.88        11.01        19.33         5.36         5.69 
TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TB 
        8.25        18.08        58.92         6.28        62.86        18.81 
TCGA-FD-A6TC TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z9 
        6.15         2.27         3.06         9.67        10.85         7.13 
TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EJ 
       10.65        17.23         8.94         3.25         6.48        30.61 
TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3VY 
       15.95        26.93        35.24        33.01         7.23        17.62 
TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 
       66.02         6.94        64.44        19.46        21.40         2.24 
TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GC-A4ZW TCGA-GC-A6I3 TCGA-GD-A3OQ 
       15.81         4.50        17.75         0.49        13.91         3.12 
TCGA-GD-A3OS TCGA-GD-A76B TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 
       20.98         7.36        11.31        11.31         7.63        27.09 
TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATP TCGA-GU-AATQ 
       20.05         5.62         4.73        10.65        32.98         7.00 
TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3QF TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E 
       14.27        21.34        20.28        10.59        27.35         8.58 
TCGA-GV-A40G TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE 
       19.07         1.51        19.40         3.06         9.01         8.22 
TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A6MB TCGA-K4-A83P 
       25.02         3.45        21.24         2.76        15.42         6.38 
TCGA-K4-AAQO TCGA-LC-A66R TCGA-LT-A8JT TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX 
       11.80        15.32        21.07        16.67        14.24         1.84 
TCGA-S5-AA26 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78O 
        3.75        31.56        17.62        37.05        22.68        76.01 
TCGA-UY-A78P TCGA-UY-A8OC TCGA-UY-A9PD TCGA-XF-A8HB TCGA-XF-A8HD TCGA-XF-A8HE 
       67.79         3.58        17.82        45.04        97.45       125.49 
TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SJ TCGA-XF-A9SL 
        1.87        17.88        48.62        64.80         3.22        66.41 
TCGA-XF-A9SV TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 
       12.76        28.24        26.27        18.90         2.24        16.27 
TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMG 
       66.64         2.10        13.74        92.98        10.82       110.60 
TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMT 
       11.31        54.90         7.63        71.57        91.73         2.96 
TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN4 
        8.32         6.77        98.99        44.32        30.94        27.06 
TCGA-XF-AAN5 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-ZF-A9R0 
       75.39         3.88        18.84         9.63         0.66        18.64 
TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 
        7.36        21.11        24.13        30.28        27.19        21.86 
TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RG TCGA-ZF-AA4R TCGA-ZF-AA4T 
       28.41        13.41         3.48        52.60        34.06        19.69 
TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA52 TCGA-ZF-AA56 TCGA-ZF-AA5H TCGA-ZF-AA5N 
       59.38        60.16        35.41         8.52        19.17         5.52 
TCGA-ZF-AA5P 
       10.13 

  16P LOSS MUTATED 16P LOSS WILD-TYPE 
              0.43               0.10 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
            130.88             166.03 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
             17.08              15.35 
[1] "0.4 - 130.9 (17.1)" "0.1 - 166.0 (15.3)"
[1] "hr=" "1.1"
D69V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  16P LOSS MUTATED         1       30        33       34
  16P LOSS WILD-TYPE       3       94        94       95
D69V3, multiclass
           clus
vv          16P LOSS MUTATED 16P LOSS WILD-TYPE
  STAGE I                  1                  3
  STAGE II                30                 94
  STAGE III               33                 94
  STAGE IV                34                 95
[1] 4 2
[1] TRUE
[1] "dimension of contingency 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         27  55   9
  16P LOSS WILD-TYPE       94 129  44
D69V4, multiclass
          clus
vv         16P LOSS MUTATED 16P LOSS WILD-TYPE
  T0+T1+T2               27                 94
  T3                     55                129
  T4                      9                 44
[1] 3 2
[1] TRUE
[1] "dimension of 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    48  13  21   2
  16P LOSS WILD-TYPE 176  29  54   6
D69V5, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  N0               48                176
  N1               13                 29
  N2               21                 54
  N3                2                  6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V6, binary
                    cls
clus                   0   1
  16P LOSS MUTATED    37   1
  16P LOSS WILD-TYPE 148   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED     37    1
  16P LOSS WILD-TYPE  148    9
   clus
vv  16P LOSS MUTATED 16P LOSS WILD-TYPE
  0               37                148
  1                1                  9
[1] 2 2
[1] FALSE
D69V7, binary
                    cls
clus                   0   1
  16P LOSS MUTATED    23  77
  16P LOSS WILD-TYPE  78 211
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED     23   77
  16P LOSS WILD-TYPE   78  211
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  FEMALE               23                 78
  MALE                 77                211
[1] 2 2
[1] FALSE
D69V8, continuous
D69V9, continuous
D69V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16P LOSS MUTATED       4                         3    89
  16P LOSS WILD-TYPE    38                        18   222
D69V11, multiclass
                           clus
vv                          16P LOSS MUTATED 16P LOSS WILD-TYPE
  ASIAN                                    4                 38
  BLACK OR AFRICAN AMERICAN                3                 18
  WHITE                                   89                222
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V12, binary
                    cls
clus                   0   1
  16P LOSS MUTATED     3  90
  16P LOSS WILD-TYPE   6 262
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      3   90
  16P LOSS WILD-TYPE    6  262
                        clus
vv                       16P LOSS MUTATED 16P LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  6
  NOT HISPANIC OR LATINO               90                262
[1] 2 2
[1] FALSE

Clustering(70) Variable = 16Q LOSS MUTATION ANALYSIS
D70V1, survival
                    sevent
clus2                  0   1
  16Q LOSS MUTATED    57  38
  16Q LOSS WILD-TYPE 173 115
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                95                288 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                38                115 
$`16Q LOSS MUTATED`
TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA81 TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-BL-A0C8 
       16.27        16.77        41.75        15.12        10.22        40.08 
TCGA-BL-A13J TCGA-BT-A42E TCGA-CF-A1HS TCGA-CU-A0YN TCGA-CU-A3KJ TCGA-CU-A3QU 
        2.66        24.26         0.43        12.92         5.46         5.19 
TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1AC TCGA-DK-A2HX TCGA-DK-A2I4 TCGA-DK-A2I6 
        1.84        21.86       130.88         1.81       123.85        87.32 
TCGA-DK-A3IV TCGA-DK-A3X2 TCGA-DK-A6B1 TCGA-DK-A6B6 TCGA-DK-AA6P TCGA-DK-AA6W 
        9.67        17.98        67.36        30.67        15.02         8.65 
TCGA-DK-AA76 TCGA-E5-A4TZ TCGA-E7-A4IJ TCGA-E7-A541 TCGA-FD-A3SO TCGA-FD-A3SS 
       12.03        15.35         0.49        17.39         5.52        12.85 
TCGA-FD-A43N TCGA-FD-A43U TCGA-FD-A5BR TCGA-FD-A5BZ TCGA-FD-A62N TCGA-FD-A62O 
       22.98        20.91        26.73        27.45         2.70         7.10 
TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FJ-A3Z7 TCGA-FT-A61P TCGA-G2-A3IE TCGA-GC-A3RC 
       12.69        12.36        31.07         6.48        20.12        15.91 
TCGA-GC-A3RD TCGA-GD-A3OP TCGA-GD-A6C6 TCGA-GU-A42P TCGA-GV-A3JV TCGA-GV-A3JX 
       14.07         2.10         2.20        10.92        14.27        19.10 
TCGA-GV-A3JZ TCGA-GV-A3QH TCGA-HQ-A2OE TCGA-K4-A3WV TCGA-K4-A4AC TCGA-K4-A5RH 
       19.82         8.48        38.60        21.24         9.14         9.07 
TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI 
       11.70         1.74         1.81        15.58        13.48        12.23 
TCGA-SY-A9G0 TCGA-UY-A78N TCGA-UY-A8OB TCGA-UY-A8OD TCGA-UY-A9PA TCGA-UY-A9PF 
       12.43        86.83        65.75       112.83        35.24         1.64 
TCGA-XF-A8HC TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A9SI TCGA-XF-A9SJ 
        6.58       125.49        97.12        15.35        79.66         3.22 
TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-AAMG TCGA-XF-AAML TCGA-XF-AAN0 
       11.90        23.64        21.04       110.60         7.63        56.48 
TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN7 TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R4 
       61.45        86.30        18.81        11.97        13.64        30.28 
TCGA-ZF-A9RC TCGA-ZF-A9RF TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4T 
       74.56        52.73        47.84        20.22         2.89        19.69 
TCGA-ZF-AA4U TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA53 TCGA-ZF-AA58 
        8.61        63.02        38.73        57.90        47.15 

$`16Q LOSS WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        91.63       103.50       105.70         8.35 
TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA7Y 
       44.94        16.83        17.16        34.98        27.62        49.12 
TCGA-4Z-AA80 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A13I 
        0.62        51.16        66.54        47.80        33.83         7.33 
TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N 
        6.74        12.39         6.58        13.15        19.04        32.84 
TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U 
       12.16        17.88        19.50         5.06        14.89        14.96 
TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD 
        5.06         8.35         8.25        17.16        16.18        20.48 
TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42F 
        4.67        12.82         9.96        17.56        28.70        28.41 
TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A27C TCGA-CF-A47S 
        8.98         1.94        23.01         0.46         0.69        10.95 
TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 
       12.66        12.46        12.10        12.62        12.26        13.12 
TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CF-A9FM 
       12.00        12.10        11.34        11.34        11.87        13.08 
TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3YL TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1A6 
        4.90         7.20        16.31        13.58         2.14        66.41 
TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF 
       18.41        19.00        16.70       112.44        16.14        17.62 
TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM 
       15.62        10.59         7.79         2.20        13.58         7.82 
TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3WW 
        8.22        17.72        50.27        21.30        23.21        20.81 
TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 
       10.55       140.81        48.00        64.18        41.56        76.60 
TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-AA6L TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6T 
       15.68        41.06        38.24        13.58       166.03        12.36 
TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA77 TCGA-E5-A2PC 
       10.49         7.53        13.64        43.50        10.62        43.59 
TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KE 
       38.83        24.66         0.10         2.24        16.70         0.56 
TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU 
        0.66        14.56        13.97        12.99        14.33         0.92 
TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A8O7 TCGA-E7-A97P 
        1.22        13.68        14.07        12.95        15.32        14.37 
TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 
        8.09        32.02        16.77         8.94        33.04         4.01 
TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL 
       12.62        22.52        27.98        60.66        24.30        23.41 
TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A43P 
       17.98        29.16        25.74        46.78        19.79        27.35 
TCGA-FD-A43S TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU 
       14.96         3.62        15.58        53.88        11.01        19.33 
TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62P 
        5.36         5.69         8.25        18.08        58.92         6.28 
TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TF TCGA-FD-A6TG 
       13.35        62.86        18.81         6.15         2.27         3.06 
TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF 
        4.31         9.67        10.85         7.13        10.65        17.23 
TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL 
        8.94         3.25        61.94        30.61        15.95        26.93 
TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C 
       35.24        33.01         7.23        17.62        66.02         6.94 
TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB 
       64.44        19.46        21.40         2.24        15.81         4.50 
TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 
       17.75        24.92         0.49         8.94        13.91         7.73 
TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A76B TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 
        3.12        20.98         7.36        11.31        11.31         7.63 
TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATP 
       27.09        20.05         5.62         4.73        10.65        32.98 
TCGA-GU-AATQ TCGA-GV-A3JW TCGA-GV-A3QF TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E 
        7.00        21.34        20.28        10.59        27.35         8.58 
TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OF TCGA-HQ-A5ND 
       19.07        22.72         1.51        19.40         3.06         9.01 
TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A54R TCGA-K4-A6MB 
        8.22        25.02         3.45         2.76        27.68        15.42 
TCGA-K4-A83P TCGA-K4-AAQO TCGA-LC-A66R TCGA-LT-A8JT TCGA-PQ-A6FN TCGA-R3-A69X 
        6.38        11.80        15.32        21.07        16.67        14.24 
TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M 
        1.84         3.75        31.56        17.62        37.05        22.68 
TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OC TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE 
       76.01        67.79         3.58        29.56        17.82         4.54 
TCGA-XF-A8HB TCGA-XF-A8HD TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH 
       45.04        97.45         1.87        17.88        48.62        64.80 
TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 
       66.41        12.76        28.24        26.27        18.90         2.24 
TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF 
       16.27        66.64         2.10        13.74        92.98        10.82 
TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW 
       11.31        54.90        71.57        91.73         2.96         8.32 
TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN4 TCGA-XF-AAN5 
        6.77        98.99        44.32        30.94        27.06        75.39 
TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-ZF-A9R0 TCGA-ZF-A9R1 
        3.88        18.84         9.63         0.66        18.64         7.36 
TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RD 
       21.11        24.13        27.19        21.86        28.41        13.41 
TCGA-ZF-A9RE TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-AA4R TCGA-ZF-AA4V TCGA-ZF-AA4W 
        3.48        52.60        82.49        34.06        59.38        60.16 
TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
       35.41        19.40         8.52        19.17         5.52        10.13 

  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
              0.43               0.10 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
            130.88             166.03 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
             15.91              15.65 
[1] "0.4 - 130.9 (15.9)" "0.1 - 166.0 (15.6)"
[1] "hr=" "1.1"
D70V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  16Q LOSS MUTATED         1       31        26       35
  16Q LOSS WILD-TYPE       3       93       101       94
D70V3, multiclass
           clus
vv          16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  STAGE I                  1                  3
  STAGE II                31                 93
  STAGE III               26                101
  STAGE IV                35                 94
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1+T2  T3  T4
  16Q LOSS MUTATED         28  46  13
  16Q LOSS WILD-TYPE       93 138  40
D70V4, multiclass
          clus
vv         16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  T0+T1+T2               28                 93
  T3                     46                138
  T4                     13                 40
[1] 3 2
[1] TRUE
[1] "dimension of 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    42  11  23   2
  16Q LOSS WILD-TYPE 182  31  52   6
D70V5, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  N0               42                182
  N1               11                 31
  N2               23                 52
  N3                2                  6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V6, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED    37   1
  16Q LOSS WILD-TYPE 148   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED     37    1
  16Q LOSS WILD-TYPE  148    9
   clus
vv  16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  0               37                148
  1                1                  9
[1] 2 2
[1] FALSE
D70V7, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED    18  77
  16Q LOSS WILD-TYPE  83 211
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED     18   77
  16Q LOSS WILD-TYPE   83  211
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  FEMALE               18                 83
  MALE                 77                211
[1] 2 2
[1] FALSE
D70V8, continuous
D70V9, continuous
D70V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16Q LOSS MUTATED       5                         2    85
  16Q LOSS WILD-TYPE    37                        19   226
D70V11, multiclass
                           clus
vv                          16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  ASIAN                                    5                 37
  BLACK OR AFRICAN AMERICAN                2                 19
  WHITE                                   85                226
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V12, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED     5  83
  16Q LOSS WILD-TYPE   4 269
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      5   83
  16Q LOSS WILD-TYPE    4  269
                        clus
vv                       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    5                  4
  NOT HISPANIC OR LATINO               83                269
[1] 2 2
[1] FALSE

Clustering(71) Variable = 17P LOSS MUTATION ANALYSIS
D71V1, survival
                    sevent
clus2                  0   1
  17P LOSS MUTATED    96  70
  17P LOSS WILD-TYPE 134  83
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               166                217 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                70                 83 
$`17P LOSS MUTATED`
TCGA-2F-A9KR TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA82 TCGA-BL-A0C8 TCGA-BL-A13J 
      103.50       105.70        16.27        51.16        40.08         2.66 
TCGA-BL-A5ZZ TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20T 
       12.39        19.04        32.84        17.88        19.50        14.89 
TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A3PK TCGA-BT-A42E 
        8.25        17.16        16.18         4.67         9.96        24.26 
TCGA-C4-A0F0 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47X TCGA-CU-A3KJ 
        1.94         0.46         0.43         0.69        12.62         5.46 
TCGA-CU-A5W6 TCGA-DK-A1AB TCGA-DK-A1AD TCGA-DK-A2HX TCGA-DK-A2I6 TCGA-DK-A3IL 
        1.84        16.70       112.44         1.81        87.32        13.58 
TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IV TCGA-DK-A3X1 
        8.22        17.72        50.27        21.30         9.67        48.00 
TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6B5 TCGA-DK-AA6L TCGA-DK-AA6Q TCGA-DK-AA6S 
       17.98        64.18        41.06        38.24        13.58       166.03 
TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 
       10.49         7.53        12.03        43.59        15.35        38.83 
TCGA-E7-A4IJ TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A677 TCGA-E7-A6ME TCGA-E7-A7DU 
        0.49        17.39         0.56        14.56        12.99         0.92 
TCGA-E7-A7PW TCGA-E7-A85H TCGA-E7-A97Q TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3NA 
       13.68        12.95         8.09        16.77         8.94        60.66 
TCGA-FD-A3SJ TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SQ TCGA-FD-A3SS TCGA-FD-A43N 
       24.30        29.16         5.52        46.78        12.85        22.98 
TCGA-FD-A43P TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BV TCGA-FD-A5BY 
       27.35        20.91         3.62        26.73         5.36         8.25 
TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TD 
        7.10         6.28        13.35        62.86        18.81        12.69 
TCGA-FD-A6TG TCGA-FD-A6TK TCGA-FJ-A3ZE TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EL 
        3.06        10.85        10.65        61.94        30.61        26.93 
TCGA-G2-A2EO TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3D TCGA-GC-A3BM TCGA-GC-A3RD 
       35.24        20.12        17.62        64.44        21.40        14.07 
TCGA-GC-A3YS TCGA-GC-A4ZW TCGA-GC-A6I3 TCGA-GD-A3OP TCGA-GD-A6C6 TCGA-GU-A42Q 
       24.92         0.49        13.91         2.10         2.20        11.31 
TCGA-GU-A42R TCGA-GU-A767 TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JW TCGA-GV-A3QF 
       11.31         4.73        32.98         7.00        21.34        20.28 
TCGA-H4-A2HQ TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A4AC TCGA-K4-A5RI 
       19.40         3.06         9.01         8.22         9.14        11.70 
TCGA-K4-A5RJ TCGA-K4-A6MB TCGA-K4-AAQO TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X 
        1.74        15.42        11.80        12.23        16.67        14.24 
TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78M TCGA-UY-A78O TCGA-UY-A78P 
        1.84        12.43        31.56        22.68        76.01        67.79 
TCGA-UY-A8OC TCGA-UY-A8OD TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HD 
        3.58       112.83        17.82         4.54         1.64        97.45 
TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A9SG TCGA-XF-A9SI 
      125.49        97.12        15.35         1.87        48.62        79.66 
TCGA-XF-A9SJ TCGA-XF-A9SV TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T3 TCGA-XF-AAMF 
        3.22        12.76        23.64        28.24         2.24        10.82 
TCGA-XF-AAMJ TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMZ 
       54.90        91.73         2.96         8.32         6.77        44.32 
TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN3 TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R0 
       56.48        30.94        86.30        11.97        13.64        18.64 
TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RE TCGA-ZF-A9RG 
        7.36        24.13        21.86        28.41         3.48        52.60 
TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4T TCGA-ZF-AA4W 
       82.49        47.84        20.22         2.89        19.69        60.16 
TCGA-ZF-AA51 TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 
       38.73        57.90        19.40         8.52 

$`17P LOSS WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KW TCGA-4Z-AA7N TCGA-4Z-AA7O 
       22.29        11.97        91.63         8.35        44.94        16.83 
TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 
       16.77        17.16        34.98        27.62        49.12         0.62 
TCGA-4Z-AA81 TCGA-4Z-AA83 TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 
       41.75        66.54        15.12        10.22        47.80        33.83 
TCGA-BL-A13I TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20O TCGA-BT-A20R 
        7.33         6.74         6.58        13.15        12.16         5.06 
TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A42B 
       14.96         5.06         8.35        20.48        12.82        17.56 
TCGA-BT-A42C TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F6 TCGA-CF-A47S TCGA-CF-A47T 
       28.70        28.41         8.98        23.01        10.95        12.66 
TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 
       12.46        12.10        12.26        13.12        12.00        12.10 
TCGA-CF-A8HX TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO 
       11.34        11.34        11.87        13.08        12.92         4.90 
TCGA-CU-A0YR TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 
        7.20         5.19        16.31        13.58        21.86         2.14 
TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AC TCGA-DK-A1AE TCGA-DK-A1AF 
       66.41        18.41        19.00       130.88        16.14        17.62 
TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IM 
       15.62        10.59         7.79       123.85         2.20         7.82 
TCGA-DK-A3IU TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A6AW TCGA-DK-A6B0 
       23.21        20.81        10.55       140.81        41.56        76.60 
TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B6 TCGA-DK-AA6P TCGA-DK-AA6T TCGA-DK-AA6W 
       67.36        15.68        30.67        15.02        12.36         8.65 
TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA77 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ 
       13.64        43.50        10.62        24.66         0.10         2.24 
TCGA-E7-A519 TCGA-E7-A5KF TCGA-E7-A678 TCGA-E7-A6MF TCGA-E7-A7DV TCGA-E7-A7XN 
       16.70         0.66        13.97        14.33         1.22        14.07 
TCGA-E7-A8O7 TCGA-E7-A97P TCGA-FD-A3B3 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 
       15.32        14.37        32.02        33.04         4.01        12.62 
TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SP TCGA-FD-A3SR 
       22.52        27.98        23.41        17.98        25.74        19.79 
TCGA-FD-A43S TCGA-FD-A43Y TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BX 
       14.96        15.58        53.88        11.01        19.33         5.69 
TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A6TC TCGA-FD-A6TE 
       27.45        18.08        58.92         2.70         6.15        12.36 
TCGA-FD-A6TF TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZF 
        2.27         4.31         9.67        31.07         7.13        17.23 
TCGA-FJ-A871 TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EK TCGA-G2-A2ES TCGA-G2-A3IB 
        8.94         3.25         6.48        15.95        33.01         7.23 
TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB 
       66.02         6.94        19.46         2.24        15.81         4.50 
TCGA-GC-A3RC TCGA-GC-A3WC TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OQ TCGA-GD-A3OS 
       15.91        17.75         8.94         7.73         3.12        20.98 
TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 
        7.36        10.92         7.63        27.09        20.05         5.62 
TCGA-GU-AATO TCGA-GV-A3JV TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QH TCGA-GV-A3QI 
       10.65        14.27        19.10        19.82         8.48        10.59 
TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-HQ-A2OE 
       27.35         8.58        19.07        22.72         1.51        38.60 
TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A54R TCGA-K4-A5RH 
       25.02         3.45        21.24         2.76        27.68         9.07 
TCGA-K4-A6FZ TCGA-K4-A83P TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-MV-A51V 
        1.81         6.38        15.32        15.58        21.07        13.48 
TCGA-S5-AA26 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78N TCGA-UY-A8OB TCGA-UY-A9PA 
        3.75        17.62        37.05        86.83        65.75        35.24 
TCGA-UY-A9PB TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SL 
       29.56        45.04         6.58        17.88        64.80        66.41 
TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T4 TCGA-XF-A9T5 
       11.90        21.04        26.27        18.90        16.27        66.64 
TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAML 
        2.10        13.74        92.98       110.60        11.31         7.63 
TCGA-XF-AAMQ TCGA-XF-AAMY TCGA-XF-AAN2 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 
       71.57        98.99        61.45        27.06        75.39        18.81 
TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-ZF-A9R2 TCGA-ZF-A9R4 
        3.88        18.84         9.63         0.66        21.11        30.28 
TCGA-ZF-A9R5 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RF TCGA-ZF-AA4R TCGA-ZF-AA4U 
       27.19        74.56        13.41        52.73        34.06         8.61 
TCGA-ZF-AA4V TCGA-ZF-AA4X TCGA-ZF-AA52 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N 
       59.38        63.02        35.41        47.15        19.17         5.52 
TCGA-ZF-AA5P 
       10.13 

  17P LOSS MUTATED 17P LOSS WILD-TYPE 
              0.43               0.10 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
            166.03             140.81 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
            16.225             15.620 
[1] "0.4 - 166.0 (16.2)" "0.1 - 140.8 (15.6)"
[1] "hr=" "1.1"
D71V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  17P LOSS MUTATED         2       48        55       59
  17P LOSS WILD-TYPE       2       76        72       70
D71V3, multiclass
           clus
vv          17P LOSS MUTATED 17P LOSS WILD-TYPE
  STAGE I                  2                  2
  STAGE II                48                 76
  STAGE III               55                 72
  STAGE IV                59                 70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1+T2  T3  T4
  17P LOSS MUTATED         46  83  24
  17P LOSS WILD-TYPE       75 101  29
D71V4, multiclass
          clus
vv         17P LOSS MUTATED 17P LOSS WILD-TYPE
  T0+T1+T2               46                 75
  T3                     83                101
  T4                     24                 29
[1] 3 2
[1] TRUE
[1] "dimension of 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    90  15  40   3
  17P LOSS WILD-TYPE 134  27  35   5
D71V5, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  N0               90                134
  N1               15                 27
  N2               40                 35
  N3                3                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V6, binary
                    cls
clus                   0   1
  17P LOSS MUTATED    76   3
  17P LOSS WILD-TYPE 109   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     76    3
  17P LOSS WILD-TYPE  109    7
   clus
vv  17P LOSS MUTATED 17P LOSS WILD-TYPE
  0               76                109
  1                3                  7
[1] 2 2
[1] FALSE
D71V7, binary
                    cls
clus                   0   1
  17P LOSS MUTATED    48 120
  17P LOSS WILD-TYPE  53 168
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     48  120
  17P LOSS WILD-TYPE   53  168
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  FEMALE               48                 53
  MALE                120                168
[1] 2 2
[1] FALSE
D71V8, continuous
D71V9, continuous
D71V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  17P LOSS MUTATED      17                         9   131
  17P LOSS WILD-TYPE    25                        12   180
D71V11, multiclass
                           clus
vv                          17P LOSS MUTATED 17P LOSS WILD-TYPE
  ASIAN                                   17                 25
  BLACK OR AFRICAN AMERICAN                9                 12
  WHITE                                  131                180
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V12, binary
                    cls
clus                   0   1
  17P LOSS MUTATED     4 155
  17P LOSS WILD-TYPE   5 197
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      4  155
  17P LOSS WILD-TYPE    5  197
                        clus
vv                       17P LOSS MUTATED 17P LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                  5
  NOT HISPANIC OR LATINO              155                197
[1] 2 2
[1] FALSE

Clustering(72) Variable = 17Q LOSS MUTATION ANALYSIS
D72V1, survival
                    sevent
clus2                  0   1
  17Q LOSS MUTATED    23  18
  17Q LOSS WILD-TYPE 207 135
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                41                342 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                18                135 
$`17Q LOSS MUTATED`
TCGA-4Z-AA82 TCGA-BL-A0C8 TCGA-BT-A20P TCGA-BT-A2LA TCGA-CF-A1HR TCGA-CF-A1HS 
       51.16        40.08        17.88        17.16         0.46         0.43 
TCGA-DK-A1AB TCGA-DK-A3IN TCGA-DK-A6AV TCGA-DK-AA6Q TCGA-DK-AA76 TCGA-E5-A4TZ 
       16.70         8.22        64.18        13.58        12.03        15.35 
TCGA-E5-A4U1 TCGA-E7-A97Q TCGA-FD-A3NA TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43U 
       38.83         8.09        60.66        12.85        27.35        20.91 
TCGA-FD-A43X TCGA-FD-A62S TCGA-FD-A6TK TCGA-FJ-A3ZE TCGA-G2-A3IE TCGA-GC-A3YS 
        3.62        13.35        10.85        10.65        20.12        24.92 
TCGA-GD-A3OP TCGA-GU-AATQ TCGA-GV-A3JW TCGA-K4-A4AC TCGA-PQ-A6FN TCGA-SY-A9G0 
        2.10         7.00        21.34         9.14        16.67        12.43 
TCGA-SY-A9G5 TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A9SI TCGA-XF-AAMX 
       31.56        17.82         4.54         1.64        79.66         6.77 
TCGA-ZF-A9R3 TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4T 
       24.13        47.84        20.22         2.89        19.69 

$`17Q LOSS WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        91.63       103.50       105.70         8.35 
TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S 
       16.27        44.94        16.83        16.77        17.16        34.98 
TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA83 TCGA-4Z-AA84 
       27.62        49.12         0.62        41.75        66.54        15.12 
TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM 
       10.22        47.80        33.83         7.33         2.66         6.74 
TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O 
       12.39         6.58        13.15        19.04        32.84        12.16 
TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W 
       19.50         5.06        14.89        14.96         5.06         8.35 
TCGA-BT-A20X TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK 
        8.25        16.18        20.48         4.67        12.82         9.96 
TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 
       17.56        28.70        24.26        28.41         8.98         1.94 
TCGA-C4-A0F6 TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W 
       23.01         0.69        10.95        12.66        12.46        12.10 
TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A8HX 
       12.62        12.26        13.12        12.00        12.10        11.34 
TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR 
       11.34        11.87        13.08        12.92         4.90         7.20 
TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 
        5.46         5.19        16.31         1.84        13.58        21.86 
TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AC TCGA-DK-A1AD 
        2.14        66.41        18.41        19.00       130.88       112.44 
TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 
       16.14        17.62        15.62         1.81        10.59         7.79 
TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IQ 
      123.85        87.32         2.20        13.58         7.82        17.72 
TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX 
       50.27        21.30        23.21         9.67        20.81        10.55 
TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 
      140.81        48.00        17.98        41.56        76.60        67.36 
TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6P TCGA-DK-AA6S 
       15.68        41.06        30.67        38.24        15.02       166.03 
TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 
       12.36        10.49         8.65         7.53        13.64        43.50 
TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ 
       10.62        43.59        24.66         0.10         0.49         2.24 
TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 
       16.70        17.39         0.56         0.66        14.56        13.97 
TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A7XN 
       12.99        14.33         0.92         1.22        13.68        14.07 
TCGA-E7-A85H TCGA-E7-A8O7 TCGA-E7-A97P TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 
       12.95        15.32        14.37        32.02        16.77         8.94 
TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SJ 
       33.04         4.01        12.62        22.52        27.98        24.30 
TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ 
       23.41        17.98        29.16         5.52        25.74        46.78 
TCGA-FD-A3SR TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS 
       19.79        22.98        14.96        15.58        26.73        53.88 
TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ 
       11.01        19.33         5.36         5.69         8.25        27.45 
TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A6TA 
       18.08        58.92         2.70         7.10         6.28        62.86 
TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG 
       18.81         6.15        12.69        12.36         2.27         3.06 
TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZF TCGA-FJ-A871 
        4.31         9.67        31.07         7.13        17.23         8.94 
TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL 
        3.25         6.48        61.94        30.61        15.95        26.93 
TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C 
       35.24        33.01         7.23        17.62        66.02         6.94 
TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB 
       64.44        19.46        21.40         2.24        15.81         4.50 
TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GC-A6I3 
       15.91        14.07        17.75         0.49         8.94        13.91 
TCGA-GD-A2C5 TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P 
        7.73         3.12        20.98         2.20         7.36        10.92 
TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 
       11.31        11.31         7.63        27.09        20.05         5.62 
TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATP TCGA-GV-A3JV TCGA-GV-A3JX TCGA-GV-A3JZ 
        4.73        10.65        32.98        14.27        19.10        19.82 
TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G 
       20.28         8.48        10.59        27.35         8.58        19.07 
TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND 
       22.72         1.51        19.40        38.60         3.06         9.01 
TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A54R 
        8.22        25.02         3.45        21.24         2.76        27.68 
TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P 
        9.07        11.70         1.74         1.81        15.42         6.38 
TCGA-K4-AAQO TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FI 
       11.80        15.32        15.58        21.07        13.48        12.23 
TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M 
       14.24         1.84         3.75        17.62        37.05        22.68 
TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A8OD 
       86.83        76.01        67.79        65.75         3.58       112.83 
TCGA-UY-A9PA TCGA-UY-A9PB TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HE 
       35.24        29.56        45.04         6.58        97.45       125.49 
TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH 
       97.12        15.35         1.87        17.88        48.62        64.80 
TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY 
        3.22        66.41        12.76        11.90        23.64        21.04 
TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 
       28.24        26.27        18.90         2.24        16.27        66.64 
TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAMH 
        2.10        13.74        92.98        10.82       110.60        11.31 
TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW 
       54.90         7.63        71.57        91.73         2.96         8.32 
TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 
       98.99        44.32        56.48        30.94        61.45        86.30 
TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 
       27.06        75.39        18.81         3.88        18.84         9.63 
TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R2 
        0.66        11.97        13.64        18.64         7.36        21.11 
TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RD 
       30.28        27.19        21.86        28.41        74.56        13.41 
TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-AA4R TCGA-ZF-AA4U 
        3.48        52.73        52.60        82.49        34.06         8.61 
TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA53 
       59.38        60.16        63.02        38.73        35.41        57.90 
TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
       19.40         8.52        47.15        19.17         5.52        10.13 

  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
              0.43               0.10 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
             79.66             166.03 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
             16.67              15.65 
[1] "0.4 - 79.7 (16.7)"  "0.1 - 166.0 (15.6)"
[1] "hr=" "1.2"
D72V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  17Q LOSS MUTATED         1       14        11       14
  17Q LOSS WILD-TYPE       3      110       116      115
D72V3, multiclass
           clus
vv          17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  STAGE I                  1                  3
  STAGE II                14                110
  STAGE III               11                116
  STAGE IV                14                115
[1] 4 2
[1] TRUE
[1] "dimension of contingency 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         14  14  10
  17Q LOSS WILD-TYPE      107 170  43
D72V4, multiclass
          clus
vv         17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  T0+T1+T2               14                107
  T3                     14                170
  T4                     10                 43
[1] 3 2
[1] TRUE
[1] "dimension of 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    22   4   7   3
  17Q LOSS WILD-TYPE 202  38  68   5
D72V5, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  N0               22                202
  N1                4                 38
  N2                7                 68
  N3                3                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V6, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED    17   1
  17Q LOSS WILD-TYPE 168   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     17    1
  17Q LOSS WILD-TYPE  168    9
   clus
vv  17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  0               17                168
  1                1                  9
[1] 2 2
[1] FALSE
D72V7, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED    14  28
  17Q LOSS WILD-TYPE  87 260
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     14   28
  17Q LOSS WILD-TYPE   87  260
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  FEMALE               14                 87
  MALE                 28                260
[1] 2 2
[1] FALSE
D72V8, continuous
D72V9, continuous
D72V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  17Q LOSS MUTATED       5                         4    32
  17Q LOSS WILD-TYPE    37                        17   279
D72V11, multiclass
                           clus
vv                          17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  ASIAN                                    5                 37
  BLACK OR AFRICAN AMERICAN                4                 17
  WHITE                                   32                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"
D72V12, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED     0  41
  17Q LOSS WILD-TYPE   9 311
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      0   41
  17Q LOSS WILD-TYPE    9  311
                        clus
vv                       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  9
  NOT HISPANIC OR LATINO               41                311
[1] 2 2
[1] FALSE

Clustering(73) Variable = 18P LOSS MUTATION ANALYSIS
D73V1, survival
                    sevent
clus2                  0   1
  18P LOSS MUTATED    52  42
  18P LOSS WILD-TYPE 178 111
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                94                289 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                42                111 
$`18P LOSS MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7S TCGA-4Z-AA7W 
       22.29        91.63       103.50         8.35        34.98        27.62 
TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BT-A20J TCGA-BT-A20N 
       51.16        66.54        40.08         2.66        19.04        32.84 
TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A42B TCGA-CF-A1HR 
        5.06        14.89         8.25        17.16        17.56         0.46 
TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A8HY TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 
       10.95        12.66        11.34         1.84        13.58        21.86 
TCGA-DK-A1A5 TCGA-DK-A1A7 TCGA-DK-A1AB TCGA-DK-A1AD TCGA-DK-A1AF TCGA-DK-A2HX 
        2.14        18.41        16.70       112.44        17.62         1.81 
TCGA-DK-A2I1 TCGA-DK-A3IL TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3X2 
       10.59        13.58        17.72        50.27        21.30        17.98 
TCGA-DK-A6AV TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-AA6L TCGA-DK-AA6P TCGA-DK-AA6S 
       64.18        15.68        41.06        38.24        15.02       166.03 
TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E7-A3X6 TCGA-E7-A5KE TCGA-E7-A7DV TCGA-E7-A85H 
       10.62        43.59        24.66         0.56         1.22        12.95 
TCGA-E7-A97Q TCGA-FD-A3B7 TCGA-FD-A3SJ TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A62O 
        8.09         4.01        24.30        29.16        46.78         7.10 
TCGA-FD-A62S TCGA-FD-A6TA TCGA-G2-A3IE TCGA-G2-AA3B TCGA-GC-A3BM TCGA-GC-A3RD 
       13.35        62.86        20.12        66.02        21.40        14.07 
TCGA-GC-A3YS TCGA-GU-A764 TCGA-GU-A767 TCGA-GU-AATO TCGA-GV-A3JW TCGA-GV-A40E 
       24.92        20.05         4.73        10.65        21.34         8.58 
TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-K4-A5RI TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-SY-A9G0 
       38.60         3.06        11.70        12.23        16.67        12.43 
TCGA-SY-A9G5 TCGA-UY-A78M TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A9SW TCGA-XF-A9T5 
       31.56        22.68         4.54         1.64        11.90        66.64 
TCGA-XF-AAMR TCGA-XF-AAMW TCGA-XF-AAMZ TCGA-XF-AAN3 TCGA-YC-A89H TCGA-YF-AA3L 
       91.73         8.32        44.32        86.30        18.84        11.97 
TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R2 TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RG 
       13.64        18.64        21.11        28.41        13.41        52.60 
TCGA-ZF-A9RM TCGA-ZF-AA4N TCGA-ZF-AA4T TCGA-ZF-AA4U 
       47.84         2.89        19.69         8.61 

$`18P LOSS WILD-TYPE`
TCGA-2F-A9KP TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q 
       11.97       105.70        16.27        44.94        16.83        16.77 
TCGA-4Z-AA7R TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA84 TCGA-4Z-AA86 
       17.16        49.12         0.62        41.75        15.12        10.22 
TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A13I TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 
       47.80        33.83         7.33         6.74        12.39         6.58 
TCGA-BT-A0YX TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20U TCGA-BT-A20V 
       13.15        12.16        17.88        19.50        14.96         5.06 
TCGA-BT-A20W TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK 
        8.35        16.18        20.48         4.67        12.82         9.96 
TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F6 
       28.70        24.26        28.41         8.98         1.94        23.01 
TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y 
        0.43         0.69        12.46        12.10        12.62        12.26 
TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A9FF TCGA-CF-A9FM 
       13.12        12.00        12.10        11.34        11.87        13.08 
TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL 
       12.92         4.90         7.20         5.46         5.19        16.31 
TCGA-DK-A1A6 TCGA-DK-A1AA TCGA-DK-A1AC TCGA-DK-A1AE TCGA-DK-A1AG TCGA-DK-A2I2 
       66.41        19.00       130.88        16.14        15.62         7.79 
TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IU 
      123.85        87.32         2.20         7.82         8.22        23.21 
TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A6AW 
        9.67        20.81        10.55       140.81        48.00        41.56 
TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B6 TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6U 
       76.60        67.36        30.67        13.58        12.36        10.49 
TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA76 TCGA-E5-A4TZ 
        8.65         7.53        13.64        43.50        12.03        15.35 
TCGA-E5-A4U1 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 
       38.83         0.10         0.49         2.24        16.70        17.39 
TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU 
        0.66        14.56        13.97        12.99        14.33         0.92 
TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A8O7 TCGA-E7-A97P TCGA-FD-A3B3 TCGA-FD-A3B4 
       13.68        14.07        15.32        14.37        32.02        16.77 
TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA 
        8.94        33.04        12.62        22.52        27.98        60.66 
TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SR TCGA-FD-A3SS 
       23.41        17.98         5.52        25.74        19.79        12.85 
TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A43Y 
       22.98        27.35        14.96        20.91         3.62        15.58 
TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX 
       26.73        53.88        11.01        19.33         5.36         5.69 
TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62P 
        8.25        27.45        18.08        58.92         2.70         6.28 
TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG 
       18.81         6.15        12.69        12.36         2.27         3.06 
TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE 
        4.31         9.67        10.85        31.07         7.13        10.65 
TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ 
       17.23         8.94         3.25         6.48        61.94        30.61 
TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3VY 
       15.95        26.93        35.24        33.01         7.23        17.62 
TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB 
        6.94        64.44        19.46         2.24        15.81         4.50 
TCGA-GC-A3RC TCGA-GC-A3WC TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 
       15.91        17.75         0.49         8.94        13.91         7.73 
TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P 
        2.10         3.12        20.98         2.20         7.36        10.92 
TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A766 TCGA-GU-AATP 
       11.31        11.31         7.63        27.09         5.62        32.98 
TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH 
        7.00        14.27        19.10        19.82        20.28         8.48 
TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ 
       10.59        27.35        19.07        22.72         1.51        19.40 
TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB 
        9.01         8.22        25.02         3.45        21.24         2.76 
TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB 
        9.14        27.68         9.07         1.74         1.81        15.42 
TCGA-K4-A83P TCGA-K4-AAQO TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-MV-A51V 
        6.38        11.80        15.32        15.58        21.07        13.48 
TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78N 
       14.24         1.84         3.75        17.62        37.05        86.83 
TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A8OD TCGA-UY-A9PA 
       76.01        67.79        65.75         3.58       112.83        35.24 
TCGA-UY-A9PB TCGA-UY-A9PD TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HE 
       29.56        17.82        45.04         6.58        97.45       125.49 
TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH 
       97.12        15.35         1.87        17.88        48.62        64.80 
TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SX TCGA-XF-A9SY 
       79.66         3.22        66.41        12.76        23.64        21.04 
TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T6 
       28.24        26.27        18.90         2.24        16.27         2.10 
TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAMJ 
       13.74        92.98        10.82       110.60        11.31        54.90 
TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMT TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAN0 
        7.63        71.57         2.96         6.77        98.99        56.48 
TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-XF-AAN8 
       30.94        61.45        27.06        75.39        18.81         3.88 
TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 
        9.63         0.66         7.36        24.13        30.28        27.19 
TCGA-ZF-A9R7 TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RL TCGA-ZF-A9RN 
       21.86        74.56         3.48        52.73        82.49        20.22 
TCGA-ZF-AA4R TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 
       34.06        59.38        60.16        63.02        38.73        35.41 
TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N 
       57.90        19.40         8.52        47.15        19.17         5.52 
TCGA-ZF-AA5P 
       10.13 

  18P LOSS MUTATED 18P LOSS WILD-TYPE 
              0.46               0.10 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
            166.03             140.81 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
             17.67              15.35 
[1] "0.5 - 166.0 (17.7)" "0.1 - 140.8 (15.3)"
[1] "hr=" "1.1"
D73V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  18P LOSS MUTATED         1       30        23       40
  18P LOSS WILD-TYPE       3       94       104       89
D73V3, multiclass
           clus
vv          18P LOSS MUTATED 18P LOSS WILD-TYPE
  STAGE I                  1                  3
  STAGE II                30                 94
  STAGE III               23                104
  STAGE IV                40                 89
[1] 4 2
[1] TRUE
[1] "dimension of contingency 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         33  46  13
  18P LOSS WILD-TYPE       88 138  40
D73V4, multiclass
          clus
vv         18P LOSS MUTATED 18P LOSS WILD-TYPE
  T0+T1+T2               33                 88
  T3                     46                138
  T4                     13                 40
[1] 3 2
[1] TRUE
[1] "dimension of 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    46  11  28   2
  18P LOSS WILD-TYPE 178  31  47   6
D73V5, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  N0               46                178
  N1               11                 31
  N2               28                 47
  N3                2                  6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V6, binary
                    cls
clus                   0   1
  18P LOSS MUTATED    52   0
  18P LOSS WILD-TYPE 133  10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     52    0
  18P LOSS WILD-TYPE  133   10
   clus
vv  18P LOSS MUTATED 18P LOSS WILD-TYPE
  0               52                133
  1                0                 10
[1] 2 2
[1] FALSE
D73V7, binary
                    cls
clus                   0   1
  18P LOSS MUTATED    29  68
  18P LOSS WILD-TYPE  72 220
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     29   68
  18P LOSS WILD-TYPE   72  220
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  FEMALE               29                 72
  MALE                 68                220
[1] 2 2
[1] FALSE
D73V8, continuous
D73V9, continuous
D73V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18P LOSS MUTATED      11                         4    76
  18P LOSS WILD-TYPE    31                        17   235
D73V11, multiclass
                           clus
vv                          18P LOSS MUTATED 18P LOSS WILD-TYPE
  ASIAN                                   11                 31
  BLACK OR AFRICAN AMERICAN                4                 17
  WHITE                                   76                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"
D73V12, binary
                    cls
clus                   0   1
  18P LOSS MUTATED     3  85
  18P LOSS WILD-TYPE   6 267
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      3   85
  18P LOSS WILD-TYPE    6  267
                        clus
vv                       18P LOSS MUTATED 18P LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  6
  NOT HISPANIC OR LATINO               85                267
[1] 2 2
[1] FALSE

Clustering(74) Variable = 18Q LOSS MUTATION ANALYSIS
D74V1, survival
                    sevent
clus2                  0   1
  18Q LOSS MUTATED    86  50
  18Q LOSS WILD-TYPE 144 103
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               136                247 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                50                103 
$`18Q LOSS MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7M TCGA-4Z-AA7R 
       22.29        91.63       103.50         8.35        16.27        17.16 
TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-BL-A0C8 TCGA-BL-A13J 
       34.98        27.62        51.16        66.54        40.08         2.66 
TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A20X 
       19.04        32.84         5.06        14.89         8.35         8.25 
TCGA-BT-A2LA TCGA-BT-A42B TCGA-BT-A42C TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A47S 
       17.16        17.56        28.70         0.46         0.43        10.95 
TCGA-CF-A47T TCGA-CF-A8HX TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CU-A0YN TCGA-CU-A0YR 
       12.66        11.34        11.34        11.87        12.92         7.20 
TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1A7 TCGA-DK-A1AB TCGA-DK-A1AD 
        1.84        13.58         2.14        18.41        16.70       112.44 
TCGA-DK-A1AF TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL 
       17.62         1.81        10.59        87.32         2.20        13.58 
TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3X1 TCGA-DK-A6AV TCGA-DK-A6B2 
       17.72        50.27        21.30        48.00        64.18        15.68 
TCGA-DK-A6B5 TCGA-DK-AA6P TCGA-DK-AA6S TCGA-DK-AA6X TCGA-E5-A2PC TCGA-E7-A3X6 
       41.06        15.02       166.03         7.53        43.59        24.66 
TCGA-E7-A5KE TCGA-E7-A7DV TCGA-E7-A85H TCGA-E7-A97Q TCGA-FD-A3B4 TCGA-FD-A3B7 
        0.56         1.22        12.95         8.09        16.77         4.01 
TCGA-FD-A3NA TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SS 
       60.66        29.16         5.52        25.74        46.78        12.85 
TCGA-FD-A43N TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TA TCGA-FJ-A3ZF 
       22.98         2.70         7.10        13.35        62.86        17.23 
TCGA-G2-A2EF TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3RC 
       61.94        20.12        66.02        19.46        21.40        15.91 
TCGA-GC-A3RD TCGA-GC-A3YS TCGA-GC-A4ZW TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A762 
       14.07        24.92         0.49        20.98         2.20         7.63 
TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO TCGA-GV-A3JW TCGA-GV-A3JX 
       20.05         5.62         4.73        10.65        21.34        19.10 
TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF 
        8.58        19.07        22.72        19.40        38.60         3.06 
TCGA-K4-A3WS TCGA-K4-A3WV TCGA-K4-A5RI TCGA-LC-A66R TCGA-MV-A51V TCGA-PQ-A6FI 
       25.02        21.24        11.70        15.32        13.48        12.23 
TCGA-PQ-A6FN TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HC 
       16.67        12.43        31.56         4.54         1.64         6.58 
TCGA-XF-A8HF TCGA-XF-A9SJ TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9T5 TCGA-XF-AAMG 
       97.12         3.22        11.90        23.64        66.64       110.60 
TCGA-XF-AAMJ TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMZ TCGA-XF-AAN3 
       54.90        71.57        91.73         2.96        44.32        86.30 
TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R2 TCGA-ZF-A9R9 TCGA-ZF-A9RD 
       11.97        13.64        18.64        21.11        28.41        13.41 
TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-AA4N TCGA-ZF-AA4T TCGA-ZF-AA4U 
       52.60        82.49        47.84         2.89        19.69         8.61 
TCGA-ZF-AA4W TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA5H 
       60.16        38.73        35.41        19.17 

$`18Q LOSS WILD-TYPE`
TCGA-2F-A9KP TCGA-2F-A9KT TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7Y 
       11.97       105.70        44.94        16.83        16.77        49.12 
TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 
        0.62        41.75        15.12        10.22        47.80        33.83 
TCGA-BL-A13I TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20O 
        7.33         6.74        12.39         6.58        13.15        12.16 
TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A2LB TCGA-BT-A2LD 
       17.88        19.50        14.96         5.06        16.18        20.48 
TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ 
        4.67        12.82         9.96        24.26        28.41         8.98 
TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A27C TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X 
        1.94        23.01         0.69        12.46        12.10        12.62 
TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A9FM TCGA-CU-A0YO 
       12.26        13.12        12.00        12.10        13.08         4.90 
TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1AA 
        5.46         5.19        16.31        21.86        66.41        19.00 
TCGA-DK-A1AC TCGA-DK-A1AE TCGA-DK-A1AG TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IM 
      130.88        16.14        15.62         7.79       123.85         7.82 
TCGA-DK-A3IN TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY 
        8.22        23.21         9.67        20.81        10.55       140.81 
TCGA-DK-A3X2 TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B6 TCGA-DK-AA6L 
       17.98        41.56        76.60        67.36        30.67        38.24 
TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA74 
       13.58        12.36        10.49         8.65        13.64        43.50 
TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3Y1 TCGA-E7-A4IJ 
       12.03        10.62        15.35        38.83         0.10         0.49 
TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 
        2.24        16.70        17.39         0.66        14.56        13.97 
TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A8O7 
       12.99        14.33         0.92        13.68        14.07        15.32 
TCGA-E7-A97P TCGA-FD-A3B3 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B8 TCGA-FD-A3N5 
       14.37        32.02         8.94        33.04        12.62        22.52 
TCGA-FD-A3N6 TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SR TCGA-FD-A43P 
       27.98        24.30        23.41        17.98        19.79        27.35 
TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS 
       14.96        20.91         3.62        15.58        26.73        53.88 
TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ 
       11.01        19.33         5.36         5.69         8.25        27.45 
TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD 
       18.08        58.92         6.28        18.81         6.15        12.69 
TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK 
       12.36         2.27         3.06         4.31         9.67        10.85 
TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-FT-A3EE TCGA-FT-A61P 
       31.07         7.13        10.65         8.94         3.25         6.48 
TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB 
       30.61        15.95        26.93        35.24        33.01         7.23 
TCGA-G2-A3VY TCGA-G2-AA3C TCGA-G2-AA3D TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB 
       17.62         6.94        64.44         2.24        15.81         4.50 
TCGA-GC-A3WC TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ 
       17.75         8.94        13.91         7.73         2.10         3.12 
TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A763 TCGA-GU-AATP 
        7.36        10.92        11.31        11.31        27.09        32.98 
TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI 
        7.00        14.27        19.82        20.28         8.48        10.59 
TCGA-GV-A3QK TCGA-H4-A2HO TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WU TCGA-K4-A4AB 
       27.35         1.51         9.01         8.22         3.45         2.76 
TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB 
        9.14        27.68         9.07         1.74         1.81        15.42 
TCGA-K4-A83P TCGA-K4-AAQO TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-R3-A69X TCGA-S5-A6DX 
        6.38        11.80        15.58        21.07        14.24         1.84 
TCGA-S5-AA26 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A78O 
        3.75        17.62        37.05        22.68        86.83        76.01 
TCGA-UY-A78P TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A8OD TCGA-UY-A9PA TCGA-UY-A9PB 
       67.79        65.75         3.58       112.83        35.24        29.56 
TCGA-UY-A9PD TCGA-XF-A8HB TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HG TCGA-XF-A8HH 
       17.82        45.04        97.45       125.49        15.35         1.87 
TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SV 
       17.88        48.62        64.80        79.66        66.41        12.76 
TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 
       21.04        28.24        26.27        18.90         2.24        16.27 
TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAML 
        2.10        13.74        92.98        10.82        11.31         7.63 
TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN2 
        8.32         6.77        98.99        56.48        30.94        61.45 
TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 
       27.06        75.39        18.81         3.88        18.84         9.63 
TCGA-YC-A9TC TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 
        0.66         7.36        24.13        30.28        27.19        21.86 
TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RN TCGA-ZF-AA4R TCGA-ZF-AA4V 
       74.56         3.48        52.73        20.22        34.06        59.38 
TCGA-ZF-AA4X TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5N 
       63.02        57.90        19.40         8.52        47.15         5.52 
TCGA-ZF-AA5P 
       10.13 

  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
              0.43               0.10 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
            166.03             140.81 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
            17.395             14.960 
[1] "0.4 - 166.0 (17.4)" "0.1 - 140.8 (15.0)"
[1] "hr=" "1.3"
D74V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  18Q LOSS MUTATED         1       43        41       50
  18Q LOSS WILD-TYPE       3       81        86       79
D74V3, multiclass
           clus
vv          18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  STAGE I                  1                  3
  STAGE II                43                 81
  STAGE III               41                 86
  STAGE IV                50                 79
[1] 4 2
[1] TRUE
[1] "dimension of contingency 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         41  67  19
  18Q LOSS WILD-TYPE       80 117  34
D74V4, multiclass
          clus
vv         18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  T0+T1+T2               41                 80
  T3                     67                117
  T4                     19                 34
[1] 3 2
[1] TRUE
[1] "dimension of 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    75  13  33   3
  18Q LOSS WILD-TYPE 149  29  42   5
D74V5, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  N0               75                149
  N1               13                 29
  N2               33                 42
  N3                3                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V6, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED    71   1
  18Q LOSS WILD-TYPE 114   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     71    1
  18Q LOSS WILD-TYPE  114    9
   clus
vv  18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  0               71                114
  1                1                  9
[1] 2 2
[1] FALSE
D74V7, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED    38 100
  18Q LOSS WILD-TYPE  63 188
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     38  100
  18Q LOSS WILD-TYPE   63  188
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  FEMALE               38                 63
  MALE                100                188
[1] 2 2
[1] FALSE
D74V8, continuous
D74V9, continuous
D74V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18Q LOSS MUTATED      15                         7   110
  18Q LOSS WILD-TYPE    27                        14   201
D74V11, multiclass
                           clus
vv                          18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  ASIAN                                   15                 27
  BLACK OR AFRICAN AMERICAN                7                 14
  WHITE                                  110                201
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V12, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED     5 122
  18Q LOSS WILD-TYPE   4 230
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      5  122
  18Q LOSS WILD-TYPE    4  230
                        clus
vv                       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    5                  4
  NOT HISPANIC OR LATINO              122                230
[1] 2 2
[1] FALSE

Clustering(75) Variable = 19P LOSS MUTATION ANALYSIS
D75V1, survival
                    sevent
clus2                  0   1
  19P LOSS MUTATED    47  43
  19P LOSS WILD-TYPE 183 110
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                90                293 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                43                110 
$`19P LOSS MUTATED`
TCGA-2F-A9KW TCGA-4Z-AA7W TCGA-BT-A20J TCGA-BT-A20R TCGA-BT-A20V TCGA-BT-A2LB 
        8.35        27.62        19.04         5.06         5.06        16.18 
TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42E TCGA-C4-A0EZ 
       20.48         4.67         9.96        17.56        24.26         8.98 
TCGA-C4-A0F6 TCGA-CU-A0YN TCGA-DK-A1A5 TCGA-DK-A1AD TCGA-DK-A2I6 TCGA-DK-A3IL 
       23.01        12.92         2.14       112.44        87.32        13.58 
TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3X2 TCGA-DK-AA6X TCGA-E5-A2PC 
        8.22        17.72        21.30        17.98         7.53        43.59 
TCGA-E7-A4IJ TCGA-E7-A85H TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3SJ TCGA-FD-A3SM 
        0.49        12.95        14.37         8.09        24.30        17.98 
TCGA-FD-A3SO TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A5BV TCGA-FD-A5BY TCGA-FD-A5BZ 
        5.52        12.85        22.98         5.36         8.25        27.45 
TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A6TB TCGA-FD-A6TE TCGA-FJ-A3ZE TCGA-FJ-A3ZF 
       18.08        58.92        18.81        12.36        10.65        17.23 
TCGA-FJ-A871 TCGA-FT-A61P TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3C 
        8.94         6.48        33.01         7.23        20.12         6.94 
TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3RB TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GD-A6C6 
       19.46         2.24         4.50         0.49         8.94         2.20 
TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A762 TCGA-GU-AATO TCGA-GV-A3JZ TCGA-H4-A2HQ 
       10.92        11.31         7.63        10.65        19.82        19.40 
TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A54R TCGA-K4-A5RJ TCGA-LC-A66R TCGA-MV-A51V 
        9.01        25.02        27.68         1.74        15.32        13.48 
TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X TCGA-SY-A9G5 TCGA-UY-A78M TCGA-UY-A8OD 
       12.23        16.67        14.24        31.56        22.68       112.83 
TCGA-UY-A9PD TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A9SG TCGA-XF-A9SJ TCGA-XF-A9SW 
       17.82         1.64        45.04        48.62         3.22        11.90 
TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-AAMG TCGA-XF-AAMX TCGA-XF-AAN3 TCGA-YF-AA3M 
       66.64         2.10       110.60         6.77        86.30        13.64 
TCGA-ZF-A9R4 TCGA-ZF-A9RC TCGA-ZF-A9RL TCGA-ZF-AA4R TCGA-ZF-AA53 TCGA-ZF-AA5H 
       30.28        74.56        82.49        34.06        57.90        19.17 

$`19P LOSS WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-4Z-AA7M 
       22.29        11.97        91.63       103.50       105.70        16.27 
TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7Y 
       44.94        16.83        16.77        17.16        34.98        49.12 
TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA84 TCGA-4Z-AA86 
        0.62        41.75        51.16        66.54        15.12        10.22 
TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM 
       47.80        33.83        40.08         7.33         2.66         6.74 
TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P 
       12.39         6.58        13.15        32.84        12.16        17.88 
TCGA-BT-A20Q TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA 
       19.50        14.89        14.96         8.35         8.25        17.16 
TCGA-BT-A3PJ TCGA-BT-A42C TCGA-BT-A42F TCGA-C4-A0F0 TCGA-CF-A1HR TCGA-CF-A1HS 
       12.82        28.70        28.41         1.94         0.46         0.43 
TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X 
        0.69        10.95        12.66        12.46        12.10        12.62 
TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A8HY 
       12.26        13.12        12.00        12.10        11.34        11.34 
TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU 
       11.87        13.08         4.90         7.20         5.46         5.19 
TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 
       16.31         1.84        13.58        21.86        66.41        18.41 
TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG 
       19.00        16.70       130.88        16.14        17.62        15.62 
TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IM 
        1.81        10.59         7.79       123.85         2.20         7.82 
TCGA-DK-A3IS TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY 
       50.27        23.21         9.67        20.81        10.55       140.81 
TCGA-DK-A3X1 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 
       48.00        64.18        41.56        76.60        67.36        15.68 
TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6S 
       41.06        30.67        38.24        15.02        13.58       166.03 
TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA76 
       12.36        10.49         8.65        13.64        43.50        12.03 
TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ 
       10.62        15.35        38.83        24.66         0.10         2.24 
TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 
       16.70        17.39         0.56         0.66        14.56        13.97 
TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A7XN 
       12.99        14.33         0.92         1.22        13.68        14.07 
TCGA-E7-A8O7 TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 
       15.32        32.02        16.77         8.94        33.04         4.01 
TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SL TCGA-FD-A3SN 
       12.62        22.52        27.98        60.66        23.41        29.16 
TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U 
       25.74        46.78        19.79        27.35        14.96        20.91 
TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU 
        3.62        15.58        26.73        53.88        11.01        19.33 
TCGA-FD-A5BX TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA 
        5.69         2.70         7.10         6.28        13.35        62.86 
TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI 
        6.15        12.69         2.27         3.06         4.31         9.67 
TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FT-A3EE TCGA-G2-A2EF TCGA-G2-A2EJ 
       10.85        31.07         7.13         3.25        61.94        30.61 
TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3D 
       15.95        26.93        35.24        17.62        66.02        64.44 
TCGA-GC-A3BM TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS 
       21.40        15.81        15.91        14.07        17.75        24.92 
TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A76B 
       13.91         7.73         2.10         3.12        20.98         7.36 
TCGA-GU-A42R TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATP 
       11.31        27.09        20.05         5.62         4.73        32.98 
TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QF TCGA-GV-A3QH 
        7.00        14.27        21.34        19.10        20.28         8.48 
TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO 
       10.59        27.35         8.58        19.07        22.72         1.51 
TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5NE TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB 
       38.60         3.06         8.22         3.45        21.24         2.76 
TCGA-K4-A4AC TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P 
        9.14         9.07        11.70         1.81        15.42         6.38 
TCGA-K4-AAQO TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G0 
       11.80        15.58        21.07         1.84         3.75        12.43 
TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OB 
       17.62        37.05        86.83        76.01        67.79        65.75 
TCGA-UY-A8OC TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PE TCGA-XF-A8HC TCGA-XF-A8HD 
        3.58        35.24        29.56         4.54         6.58        97.45 
TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SH 
      125.49        97.12        15.35         1.87        17.88        64.80 
TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ 
       79.66        66.41        12.76        23.64        21.04        28.24 
TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T8 TCGA-XF-AAME 
       26.27        18.90         2.24        16.27        13.74        92.98 
TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR 
       10.82        11.31        54.90         7.63        71.57        91.73 
TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN1 
        2.96         8.32        98.99        44.32        56.48        30.94 
TCGA-XF-AAN2 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A89H 
       61.45        27.06        75.39        18.81         3.88        18.84 
TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R2 
        9.63         0.66        11.97        18.64         7.36        21.11 
TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RE 
       24.13        27.19        21.86        28.41        13.41         3.48 
TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4T 
       52.73        52.60        47.84        20.22         2.89        19.69 
TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 
        8.61        59.38        60.16        63.02        38.73        35.41 
TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5N TCGA-ZF-AA5P 
       19.40         8.52        47.15         5.52        10.13 

  19P LOSS MUTATED 19P LOSS WILD-TYPE 
              0.49               0.10 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
            112.83             166.03 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
            14.845             15.810 
[1] "0.5 - 112.8 (14.8)" "0.1 - 166.0 (15.8)"
[1] "hr=" "1.4"
D75V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  19P LOSS MUTATED         0       21        31       38
  19P LOSS WILD-TYPE       4      103        96       91
D75V3, multiclass
           clus
vv          19P LOSS MUTATED 19P LOSS WILD-TYPE
  STAGE I                  0                  4
  STAGE II                21                103
  STAGE III               31                 96
  STAGE IV                38                 91
[1] 4 2
[1] TRUE
[1] "dimension of contingency 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         20  53  10
  19P LOSS WILD-TYPE      101 131  43
D75V4, multiclass
          clus
vv         19P LOSS MUTATED 19P LOSS WILD-TYPE
  T0+T1+T2               20                101
  T3                     53                131
  T4                     10                 43
[1] 3 2
[1] TRUE
[1] "dimension of 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    43  14  19   4
  19P LOSS WILD-TYPE 181  28  56   4
D75V5, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  N0               43                181
  N1               14                 28
  N2               19                 56
  N3                4                  4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V6, binary
                    cls
clus                   0   1
  19P LOSS MUTATED    36   4
  19P LOSS WILD-TYPE 149   6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED     36    4
  19P LOSS WILD-TYPE  149    6
   clus
vv  19P LOSS MUTATED 19P LOSS WILD-TYPE
  0               36                149
  1                4                  6
[1] 2 2
[1] FALSE
D75V7, binary
                    cls
clus                   0   1
  19P LOSS MUTATED    24  66
  19P LOSS WILD-TYPE  77 222
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED     24   66
  19P LOSS WILD-TYPE   77  222
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  FEMALE               24                 77
  MALE                 66                222
[1] 2 2
[1] FALSE
D75V8, continuous
D75V9, continuous
D75V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  19P LOSS MUTATED       4                         5    75
  19P LOSS WILD-TYPE    38                        16   236
D75V11, multiclass
                           clus
vv                          19P LOSS MUTATED 19P LOSS WILD-TYPE
  ASIAN                                    4                 38
  BLACK OR AFRICAN AMERICAN                5                 16
  WHITE                                   75                236
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V12, binary
                    cls
clus                   0   1
  19P LOSS MUTATED     4  81
  19P LOSS WILD-TYPE   5 271
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      4   81
  19P LOSS WILD-TYPE    5  271
                        clus
vv                       19P LOSS MUTATED 19P LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                  5
  NOT HISPANIC OR LATINO               81                271
[1] 2 2
[1] FALSE

Clustering(76) Variable = 19Q LOSS MUTATION ANALYSIS
D76V1, survival
                    sevent
clus2                  0   1
  19Q LOSS MUTATED    29  25
  19Q LOSS WILD-TYPE 201 128
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                54                329 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                25                128 
$`19Q LOSS MUTATED`
TCGA-2F-A9KW TCGA-4Z-AA7W TCGA-BT-A20R TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PK 
        8.35        27.62         5.06        20.48         4.67         9.96 
TCGA-BT-A42B TCGA-C4-A0EZ TCGA-CU-A0YN TCGA-DK-A1AD TCGA-DK-A3IN TCGA-DK-A3IQ 
       17.56         8.98        12.92       112.44         8.22        17.72 
TCGA-DK-A3IT TCGA-DK-A3X2 TCGA-DK-AA6X TCGA-E7-A4IJ TCGA-E7-A85H TCGA-E7-A97P 
       21.30        17.98         7.53         0.49        12.95        14.37 
TCGA-E7-A97Q TCGA-FD-A3SO TCGA-FD-A5BV TCGA-FD-A5BY TCGA-FD-A5C1 TCGA-FD-A6TE 
        8.09         5.52         5.36         8.25        58.92        12.36 
TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-FT-A61P TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE 
       10.65         8.94         6.48        33.01         7.23        20.12 
TCGA-GC-A3I6 TCGA-GC-A3RB TCGA-GC-A4ZW TCGA-GD-A6C6 TCGA-GU-A762 TCGA-GU-AATO 
        2.24         4.50         0.49         2.20         7.63        10.65 
TCGA-K4-A54R TCGA-K4-A5RJ TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI 
       27.68         1.74        15.32        15.58        13.48        12.23 
TCGA-PQ-A6FN TCGA-SY-A9G5 TCGA-UY-A78M TCGA-UY-A8OD TCGA-XF-A9SG TCGA-XF-A9SW 
       16.67        31.56        22.68       112.83        48.62        11.90 
TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-AAMG TCGA-XF-AAML TCGA-ZF-A9R4 TCGA-ZF-AA5H 
       66.64         2.10       110.60         7.63        30.28        19.17 

$`19Q LOSS WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-4Z-AA7M 
       22.29        11.97        91.63       103.50       105.70        16.27 
TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7Y 
       44.94        16.83        16.77        17.16        34.98        49.12 
TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA84 TCGA-4Z-AA86 
        0.62        41.75        51.16        66.54        15.12        10.22 
TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM 
       47.80        33.83        40.08         7.33         2.66         6.74 
TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O 
       12.39         6.58        13.15        19.04        32.84        12.16 
TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W 
       17.88        19.50        14.89        14.96         5.06         8.35 
TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A3PJ TCGA-BT-A42C TCGA-BT-A42E 
        8.25        17.16        16.18        12.82        28.70        24.26 
TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C 
       28.41         1.94        23.01         0.46         0.43         0.69 
TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y 
       10.95        12.66        12.46        12.10        12.62        12.26 
TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A8HY TCGA-CF-A9FF 
       13.12        12.00        12.10        11.34        11.34        11.87 
TCGA-CF-A9FM TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL 
       13.08         4.90         7.20         5.46         5.19        16.31 
TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 
        1.84        13.58        21.86         2.14        66.41        18.41 
TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG 
       19.00        16.70       130.88        16.14        17.62        15.62 
TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK 
        1.81        10.59         7.79       123.85        87.32         2.20 
TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IS TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW 
       13.58         7.82        50.27        23.21         9.67        20.81 
TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 
       10.55       140.81        48.00        64.18        41.56        76.60 
TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6P 
       67.36        15.68        41.06        30.67        38.24        15.02 
TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA71 
       13.58       166.03        12.36        10.49         8.65        13.64 
TCGA-DK-AA74 TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 
       43.50        12.03        10.62        43.59        15.35        38.83 
TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE 
       24.66         0.10         2.24        16.70        17.39         0.56 
TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU 
        0.66        14.56        13.97        12.99        14.33         0.92 
TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A8O7 TCGA-FD-A3B3 TCGA-FD-A3B4 
        1.22        13.68        14.07        15.32        32.02        16.77 
TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 
        8.94        33.04         4.01        12.62        22.52        27.98 
TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SP 
       60.66        24.30        23.41        17.98        29.16        25.74 
TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S 
       46.78        19.79        12.85        22.98        27.35        14.96 
TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT 
       20.91         3.62        15.58        26.73        53.88        11.01 
TCGA-FD-A5BU TCGA-FD-A5BX TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A62N TCGA-FD-A62O 
       19.33         5.69        27.45        18.08         2.70         7.10 
TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD 
        6.28        13.35        62.86        18.81         6.15        12.69 
TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 
        2.27         3.06         4.31         9.67        10.85        31.07 
TCGA-FJ-A3Z9 TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK 
        7.13        17.23         3.25        61.94        30.61        15.95 
TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3D 
       26.93        35.24        17.62        66.02         6.94        64.44 
TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC 
       19.46        21.40        15.81        15.91        14.07        17.75 
TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ 
       24.92         8.94        13.91         7.73         2.10         3.12 
TCGA-GD-A3OS TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A763 
       20.98         7.36        10.92        11.31        11.31        27.09 
TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JV 
       20.05         5.62         4.73        32.98         7.00        14.27 
TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI 
       21.34        19.10        19.82        20.28         8.48        10.59 
TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ 
       27.35         8.58        19.07        22.72         1.51        19.40 
TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU 
       38.60         3.06         9.01         8.22        25.02         3.45 
TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A6FZ 
       21.24         2.76         9.14         9.07        11.70         1.81 
TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-LT-A8JT TCGA-R3-A69X TCGA-S5-A6DX 
       15.42         6.38        11.80        21.07        14.24         1.84 
TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78N TCGA-UY-A78O 
        3.75        12.43        17.62        37.05        86.83        76.01 
TCGA-UY-A78P TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD 
       67.79        65.75         3.58        35.24        29.56        17.82 
TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HE 
        4.54         1.64        45.04         6.58        97.45       125.49 
TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SI 
       97.12        15.35         1.87        17.88        64.80        79.66 
TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ 
        3.22        66.41        12.76        23.64        21.04        28.24 
TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T8 TCGA-XF-AAME 
       26.27        18.90         2.24        16.27        13.74        92.98 
TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMT 
       10.82        11.31        54.90        71.57        91.73         2.96 
TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN1 
        8.32         6.77        98.99        44.32        56.48        30.94 
TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-XF-AAN8 
       61.45        86.30        27.06        75.39        18.81         3.88 
TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R0 
       18.84         9.63         0.66        11.97        13.64        18.64 
TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 
        7.36        21.11        24.13        27.19        21.86        28.41 
TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL 
       74.56        13.41         3.48        52.73        52.60        82.49 
TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4U 
       47.84        20.22         2.89        34.06        19.69         8.61 
TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA53 
       59.38        60.16        63.02        38.73        35.41        57.90 
TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5N TCGA-ZF-AA5P 
       19.40         8.52        47.15         5.52        10.13 

  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
              0.49               0.10 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
            112.83             166.03 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
            12.295             16.270 
[1] "0.5 - 112.8 (12.3)" "0.1 - 166.0 (16.3)"
[1] "hr=" "1.5"
D76V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  19Q LOSS MUTATED         0       16        19       19
  19Q LOSS WILD-TYPE       4      108       108      110
D76V3, multiclass
           clus
vv          19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  STAGE I                  0                  4
  STAGE II                16                108
  STAGE III               19                108
  STAGE IV                19                110
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1+T2  T3  T4
  19Q LOSS MUTATED         12  30   7
  19Q LOSS WILD-TYPE      109 154  46
D76V4, multiclass
          clus
vv         19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  T0+T1+T2               12                109
  T3                     30                154
  T4                      7                 46
[1] 3 2
[1] TRUE
[1] "dimension of 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    28   6  11   2
  19Q LOSS WILD-TYPE 196  36  64   6
D76V5, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  N0               28                196
  N1                6                 36
  N2               11                 64
  N3                2                  6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V6, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED    21   2
  19Q LOSS WILD-TYPE 164   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED     21    2
  19Q LOSS WILD-TYPE  164    8
   clus
vv  19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  0               21                164
  1                2                  8
[1] 2 2
[1] FALSE
D76V7, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED    14  40
  19Q LOSS WILD-TYPE  87 248
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED     14   40
  19Q LOSS WILD-TYPE   87  248
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  FEMALE               14                 87
  MALE                 40                248
[1] 2 2
[1] FALSE
D76V8, continuous
D76V9, continuous
D76V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  19Q LOSS MUTATED       4                         2    46
  19Q LOSS WILD-TYPE    38                        19   265
D76V11, multiclass
                           clus
vv                          19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  ASIAN                                    4                 38
  BLACK OR AFRICAN AMERICAN                2                 19
  WHITE                                   46                265
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V12, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED     2  49
  19Q LOSS WILD-TYPE   7 303
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      2   49
  19Q LOSS WILD-TYPE    7  303
                        clus
vv                       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  7
  NOT HISPANIC OR LATINO               49                303
[1] 2 2
[1] FALSE

Clustering(77) Variable = 20P LOSS MUTATION ANALYSIS
D77V1, survival
                    sevent
clus2                  0   1
  20P LOSS MUTATED    15  17
  20P LOSS WILD-TYPE 215 136
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                32                351 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                17                136 
$`20P LOSS MUTATED`
TCGA-4Z-AA7W TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20P TCGA-CF-A47S TCGA-CF-A5U8 
       27.62        19.04        32.84        17.88        10.95        13.12 
TCGA-CF-A8HY TCGA-DK-A1A3 TCGA-DK-A3IM TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-DK-A6AV 
       11.34        21.86         7.82         9.67        48.00        64.18 
TCGA-E7-A85H TCGA-FD-A5C0 TCGA-FD-A6TB TCGA-G2-A3VY TCGA-G2-AA3D TCGA-GU-A42R 
       12.95        18.08        18.81        17.62        64.44        11.31 
TCGA-GU-AATQ TCGA-GV-A40E TCGA-HQ-A2OE TCGA-K4-A4AC TCGA-UY-A78K TCGA-UY-A78N 
        7.00         8.58        38.60         9.14        17.62        86.83 
TCGA-XF-A8HE TCGA-XF-A9SW TCGA-XF-AAML TCGA-XF-AAMX TCGA-XF-AAN7 TCGA-ZF-A9R9 
      125.49        11.90         7.63         6.77        18.81        28.41 
TCGA-ZF-A9RD TCGA-ZF-A9RF 
       13.41        52.73 

$`20P LOSS WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        91.63       103.50       105.70         8.35 
TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S 
       16.27        44.94        16.83        16.77        17.16        34.98 
TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA84 
       49.12         0.62        41.75        51.16        66.54        15.12 
TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J 
       10.22        47.80        33.83        40.08         7.33         2.66 
TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20O TCGA-BT-A20Q 
        6.74        12.39         6.58        13.15        12.16        19.50 
TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X 
        5.06        14.89        14.96         5.06         8.35         8.25 
TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK 
       17.16        16.18        20.48         4.67        12.82         9.96 
TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 
       17.56        28.70        24.26        28.41         8.98         1.94 
TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47T TCGA-CF-A47V 
       23.01         0.46         0.43         0.69        12.66        12.46 
TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A8HX 
       12.10        12.62        12.26        12.00        12.10        11.34 
TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ 
       11.87        13.08        12.92         4.90         7.20         5.46 
TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1A6 
        5.19        16.31         1.84        13.58         2.14        66.41 
TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE 
       18.41        19.00        16.70       130.88       112.44        16.14 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 
       17.62        15.62         1.81        10.59         7.79       123.85 
TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS 
       87.32         2.20        13.58         8.22        17.72        50.27 
TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X2 
       21.30        23.21        20.81        10.55       140.81        17.98 
TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 
       41.56        76.60        67.36        15.68        41.06        30.67 
TCGA-DK-AA6L TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U 
       38.24        15.02        13.58       166.03        12.36        10.49 
TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA76 TCGA-DK-AA77 
        8.65         7.53        13.64        43.50        12.03        10.62 
TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ 
       43.59        15.35        38.83        24.66         0.10         0.49 
TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 
        2.24        16.70        17.39         0.56         0.66        14.56 
TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW 
       13.97        12.99        14.33         0.92         1.22        13.68 
TCGA-E7-A7XN TCGA-E7-A8O7 TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 
       14.07        15.32        14.37         8.09        32.02        16.77 
TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 
        8.94        33.04         4.01        12.62        22.52        27.98 
TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO 
       60.66        24.30        23.41        17.98        29.16         5.52 
TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P 
       25.74        46.78        19.79        12.85        22.98        27.35 
TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS 
       14.96        20.91         3.62        15.58        26.73        53.88 
TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ 
       11.01        19.33         5.36         5.69         8.25        27.45 
TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA 
       58.92         2.70         7.10         6.28        13.35        62.86 
TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH 
        6.15        12.69        12.36         2.27         3.06         4.31 
TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF 
        9.67        10.85        31.07         7.13        10.65        17.23 
TCGA-FJ-A871 TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK 
        8.94         3.25         6.48        61.94        30.61        15.95 
TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3B 
       26.93        35.24        33.01         7.23        20.12        66.02 
TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB 
        6.94        19.46        21.40         2.24        15.81         4.50 
TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A4ZW TCGA-GC-A6I1 
       15.91        14.07        17.75        24.92         0.49         8.94 
TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 
       13.91         7.73         2.10         3.12        20.98         2.20 
TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 
        7.36        10.92        11.31         7.63        27.09        20.05 
TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATP TCGA-GV-A3JV TCGA-GV-A3JW 
        5.62         4.73        10.65        32.98        14.27        21.34 
TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK 
       19.10        19.82        20.28         8.48        10.59        27.35 
TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OF TCGA-HQ-A5ND 
       19.07        22.72         1.51        19.40         3.06         9.01 
TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A54R 
        8.22        25.02         3.45        21.24         2.76        27.68 
TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P 
        9.07        11.70         1.74         1.81        15.42         6.38 
TCGA-K4-AAQO TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FI 
       11.80        15.32        15.58        21.07        13.48        12.23 
TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-SY-A9G5 
       16.67        14.24         1.84         3.75        12.43        31.56 
TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OB TCGA-UY-A8OC 
       37.05        22.68        76.01        67.79        65.75         3.58 
TCGA-UY-A8OD TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF 
      112.83        35.24        29.56        17.82         4.54         1.64 
TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A8HH 
       45.04         6.58        97.45        97.12        15.35         1.87 
TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SL 
       17.88        48.62        64.80        79.66         3.22        66.41 
TCGA-XF-A9SV TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 
       12.76        23.64        21.04        28.24        26.27        18.90 
TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME 
        2.24        16.27        66.64         2.10        13.74        92.98 
TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAMQ TCGA-XF-AAMR 
       10.82       110.60        11.31        54.90        71.57        91.73 
TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN1 
        2.96         8.32        98.99        44.32        56.48        30.94 
TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN8 TCGA-YC-A89H 
       61.45        86.30        27.06        75.39         3.88        18.84 
TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R1 
        9.63         0.66        11.97        13.64        18.64         7.36 
TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9RC 
       21.11        24.13        30.28        27.19        21.86        74.56 
TCGA-ZF-A9RE TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N 
        3.48        52.60        82.49        47.84        20.22         2.89 
TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X 
       34.06        19.69         8.61        59.38        60.16        63.02 
TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 
       38.73        35.41        57.90        19.40         8.52        47.15 
TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
       19.17         5.52        10.13 

  20P LOSS MUTATED 20P LOSS WILD-TYPE 
              6.77               0.10 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
            125.49             166.03 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
             17.75              15.58 
[1] "6.8 - 125.5 (17.8)" "0.1 - 166.0 (15.6)"
[1] "hr=" "1.3"
D77V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  20P LOSS MUTATED         0       12         9       10
  20P LOSS WILD-TYPE       4      112       118      119
D77V3, multiclass
           clus
vv          20P LOSS MUTATED 20P LOSS WILD-TYPE
  STAGE I                  0                  4
  STAGE II                12                112
  STAGE III                9                118
  STAGE IV                10                119
[1] 4 2
[1] TRUE
[1] "dimension of contingency 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         11  16   1
  20P LOSS WILD-TYPE      110 168  52
D77V4, multiclass
          clus
vv         20P LOSS MUTATED 20P LOSS WILD-TYPE
  T0+T1+T2               11                110
  T3                     16                168
  T4                      1                 52
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  20P LOSS MUTATED    17   2   9   0
  20P LOSS WILD-TYPE 207  40  66   8
D77V5, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  N0               17                207
  N1                2                 40
  N2                9                 66
  N3                0                  8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V6, binary
                    cls
clus                   0   1
  20P LOSS MUTATED    13   0
  20P LOSS WILD-TYPE 172  10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED     13    0
  20P LOSS WILD-TYPE  172   10
   clus
vv  20P LOSS MUTATED 20P LOSS WILD-TYPE
  0               13                172
  1                0                 10
[1] 2 2
[1] FALSE
D77V7, binary
                    cls
clus                   0   1
  20P LOSS MUTATED     5  27
  20P LOSS WILD-TYPE  96 261
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      5   27
  20P LOSS WILD-TYPE   96  261
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  FEMALE                5                 96
  MALE                 27                261
[1] 2 2
[1] FALSE
D77V8, continuous
D77V9, continuous
D77V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  20P LOSS MUTATED       6                         1    23
  20P LOSS WILD-TYPE    36                        20   288
D77V11, multiclass
                           clus
vv                          20P LOSS MUTATED 20P LOSS WILD-TYPE
  ASIAN                                    6                 36
  BLACK OR AFRICAN AMERICAN                1                 20
  WHITE                                   23                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"
D77V12, binary
                    cls
clus                   0   1
  20P LOSS MUTATED     0  29
  20P LOSS WILD-TYPE   9 323
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      0   29
  20P LOSS WILD-TYPE    9  323
                        clus
vv                       20P LOSS MUTATED 20P LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  9
  NOT HISPANIC OR LATINO               29                323
[1] 2 2
[1] FALSE

Clustering(78) Variable = 20Q LOSS MUTATION ANALYSIS
D78V1, survival
                    sevent
clus2                  0   1
  20Q LOSS MUTATED     4   9
  20Q LOSS WILD-TYPE 226 144
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                13                370 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 9                144 
$`20Q LOSS MUTATED`
TCGA-4Z-AA7W TCGA-BT-A20P TCGA-BT-A20V TCGA-CF-A8HY TCGA-DK-A1A3 TCGA-DK-A2I6 
       27.62        17.88         5.06        11.34        21.86        87.32 
TCGA-DK-A3IV TCGA-UY-A78N TCGA-XF-A9SW TCGA-XF-AAML TCGA-XF-AAMW TCGA-XF-AAN7 
        9.67        86.83        11.90         7.63         8.32        18.81 
TCGA-ZF-A9RF 
       52.73 

$`20Q LOSS WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        91.63       103.50       105.70         8.35 
TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S 
       16.27        44.94        16.83        16.77        17.16        34.98 
TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA84 
       49.12         0.62        41.75        51.16        66.54        15.12 
TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J 
       10.22        47.80        33.83        40.08         7.33         2.66 
TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N 
        6.74        12.39         6.58        13.15        19.04        32.84 
TCGA-BT-A20O TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20W 
       12.16        19.50         5.06        14.89        14.96         8.35 
TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ 
        8.25        17.16        16.18        20.48         4.67        12.82 
TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ 
        9.96        17.56        28.70        24.26        28.41         8.98 
TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S 
        1.94        23.01         0.46         0.43         0.69        10.95 
TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 
       12.66        12.46        12.10        12.62        12.26        13.12 
TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YN 
       12.00        12.10        11.34        11.87        13.08        12.92 
TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 
        4.90         7.20         5.46         5.19        16.31         1.84 
TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB 
       13.58         2.14        66.41        18.41        19.00        16.70 
TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX 
      130.88       112.44        16.14        17.62        15.62         1.81 
TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM 
       10.59         7.79       123.85         2.20        13.58         7.82 
TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3WW 
        8.22        17.72        50.27        21.30        23.21        20.81 
TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW 
       10.55       140.81        48.00        17.98        64.18        41.56 
TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L 
       76.60        67.36        15.68        41.06        30.67        38.24 
TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W 
       15.02        13.58       166.03        12.36        10.49         8.65 
TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A2PC 
        7.53        13.64        43.50        12.03        10.62        43.59 
TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ 
       15.35        38.83        24.66         0.10         0.49         2.24 
TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 
       16.70        17.39         0.56         0.66        14.56        13.97 
TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A7XN 
       12.99        14.33         0.92         1.22        13.68        14.07 
TCGA-E7-A85H TCGA-E7-A8O7 TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 
       12.95        15.32        14.37         8.09        32.02        16.77 
TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 
        8.94        33.04         4.01        12.62        22.52        27.98 
TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO 
       60.66        24.30        23.41        17.98        29.16         5.52 
TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P 
       25.74        46.78        19.79        12.85        22.98        27.35 
TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS 
       14.96        20.91         3.62        15.58        26.73        53.88 
TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ 
       11.01        19.33         5.36         5.69         8.25        27.45 
TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S 
       18.08        58.92         2.70         7.10         6.28        13.35 
TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF 
       62.86        18.81         6.15        12.69        12.36         2.27 
TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 
        3.06         4.31         9.67        10.85        31.07         7.13 
TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EF 
       10.65        17.23         8.94         3.25         6.48        61.94 
TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB 
       30.61        15.95        26.93        35.24        33.01         7.23 
TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F 
       20.12        17.62        66.02         6.94        64.44        19.46 
TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD 
       21.40         2.24        15.81         4.50        15.91        14.07 
TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 
       17.75        24.92         0.49         8.94        13.91         7.73 
TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P 
        2.10         3.12        20.98         2.20         7.36        10.92 
TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 
       11.31        11.31         7.63        27.09        20.05         5.62 
TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW 
        4.73        10.65        32.98         7.00        14.27        21.34 
TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK 
       19.10        19.82        20.28         8.48        10.59        27.35 
TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE 
        8.58        19.07        22.72         1.51        19.40        38.60 
TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV 
        3.06         9.01         8.22        25.02         3.45        21.24 
TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ 
        2.76         9.14        27.68         9.07        11.70         1.74 
TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-LC-A66R TCGA-LT-A5Z6 
        1.81        15.42         6.38        11.80        15.32        15.58 
TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX 
       21.07        13.48        12.23        16.67        14.24         1.84 
TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M 
        3.75        12.43        31.56        17.62        37.05        22.68 
TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A8OD TCGA-UY-A9PA 
       76.01        67.79        65.75         3.58       112.83        35.24 
TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HC 
       29.56        17.82         4.54         1.64        45.04         6.58 
TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A8HI 
       97.45       125.49        97.12        15.35         1.87        17.88 
TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SV 
       48.62        64.80        79.66         3.22        66.41        12.76 
TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 
       23.64        21.04        28.24        26.27        18.90         2.24 
TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF 
       16.27        66.64         2.10        13.74        92.98        10.82 
TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMT 
      110.60        11.31        54.90        71.57        91.73         2.96 
TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN2 
        6.77        98.99        44.32        56.48        30.94        61.45 
TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 
       86.30        27.06        75.39         3.88        18.84         9.63 
TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R2 
        0.66        11.97        13.64        18.64         7.36        21.11 
TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RC 
       24.13        30.28        27.19        21.86        28.41        74.56 
TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN 
       13.41         3.48        52.60        82.49        47.84        20.22 
TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W 
        2.89        34.06        19.69         8.61        59.38        60.16 
TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 
       63.02        38.73        35.41        57.90        19.40         8.52 
TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
       47.15        19.17         5.52        10.13 

  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
              5.06               0.10 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
             87.32             166.03 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
             17.88              15.65 
[1] "5.1 - 87.3 (17.9)"  "0.1 - 166.0 (15.6)"
[1] "hr=" "1.6"
D78V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  20Q LOSS MUTATED         0        5         1        7
  20Q LOSS WILD-TYPE       4      119       126      122
D78V3, multiclass
           clus
vv          20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  STAGE I                  0                  4
  STAGE II                 5                119
  STAGE III                1                126
  STAGE IV                 7                122
[1] 4 2
[1] TRUE
[1] "dimension of contingency 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          7   4   1
  20Q LOSS WILD-TYPE      114 180  52
D78V4, multiclass
          clus
vv         20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  T0+T1+T2                7                114
  T3                      4                180
  T4                      1                 52
[1] 3 2
[1] TRUE
[1] "dimension of 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     5   3   3   0
  20Q LOSS WILD-TYPE 219  39  72   8
D78V5, multiclass
    clus
vv   20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  N0                5                219
  N1                3                 39
  N2                3                 72
  N3                0                  8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V6, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     8   0
  20Q LOSS WILD-TYPE 177  10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      8    0
  20Q LOSS WILD-TYPE  177   10
   clus
vv  20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  0                8                177
  1                0                 10
[1] 2 2
[1] FALSE
D78V7, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     3  10
  20Q LOSS WILD-TYPE  98 278
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      3   10
  20Q LOSS WILD-TYPE   98  278
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  FEMALE                3                 98
  MALE                 10                278
[1] 2 2
[1] FALSE
D78V8, continuous
D78V9, continuous
D78V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  20Q LOSS MUTATED       1                         1    11
  20Q LOSS WILD-TYPE    41                        20   300
D78V11, multiclass
                           clus
vv                          20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  ASIAN                                    1                 41
  BLACK OR AFRICAN AMERICAN                1                 20
  WHITE                                   11                300
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V12, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     0  12
  20Q LOSS WILD-TYPE   9 340
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      0   12
  20Q LOSS WILD-TYPE    9  340
                        clus
vv                       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  9
  NOT HISPANIC OR LATINO               12                340
[1] 2 2
[1] FALSE

Clustering(79) Variable = 21Q LOSS MUTATION ANALYSIS
D79V1, survival
                    sevent
clus2                  0   1
  21Q LOSS MUTATED    39  37
  21Q LOSS WILD-TYPE 191 116
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                76                307 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                37                116 
$`21Q LOSS MUTATED`
TCGA-2F-A9KO TCGA-4Z-AA80 TCGA-4Z-AA82 TCGA-4Z-AA86 TCGA-BL-A0C8 TCGA-BL-A13J 
       22.29         0.62        51.16        10.22        40.08         2.66 
TCGA-BT-A20T TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A42E TCGA-CF-A1HR TCGA-CF-A47X 
       14.89         5.06         8.25        24.26         0.46        12.62 
TCGA-CU-A0YN TCGA-CU-A3QU TCGA-CU-A5W6 TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A6B6 
       12.92         5.19         1.84         8.22        17.72        30.67 
TCGA-DK-AA6Q TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA76 TCGA-E5-A2PC 
       13.58         8.65         7.53        13.64        12.03        43.59 
TCGA-FD-A3B5 TCGA-FD-A3SL TCGA-FD-A3SO TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BV 
        8.94        23.41         5.52         3.62        15.58         5.36 
TCGA-FD-A5BY TCGA-FD-A6TA TCGA-FD-A6TD TCGA-FD-A6TF TCGA-FD-A6TK TCGA-G2-A2EJ 
        8.25        62.86        12.69         2.27        10.85        30.61 
TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GU-A767 TCGA-GV-A3JV 
       64.44        19.46        24.92         8.94         4.73        14.27 
TCGA-GV-A3QI TCGA-GV-A6ZA TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-K4-A4AB TCGA-K4-A4AC 
       10.59        22.72         3.06         9.01         2.76         9.14 
TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-LT-A5Z6 TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OB 
       11.70         1.74        15.58        76.01        67.79        65.75 
TCGA-UY-A8OD TCGA-UY-A9PA TCGA-UY-A9PB TCGA-XF-A8HG TCGA-XF-A9SI TCGA-XF-A9SX 
      112.83        35.24        29.56        15.35        79.66        23.64 
TCGA-XF-A9T5 TCGA-XF-A9T8 TCGA-XF-AAMG TCGA-XF-AAML TCGA-XF-AAN2 TCGA-XF-AAN7 
       66.64        13.74       110.60         7.63        61.45        18.81 
TCGA-ZF-A9R0 TCGA-ZF-A9R7 TCGA-ZF-A9RD TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4R 
       18.64        21.86        13.41        20.22         2.89        34.06 
TCGA-ZF-AA4W TCGA-ZF-AA53 TCGA-ZF-AA56 TCGA-ZF-AA5H 
       60.16        57.90         8.52        19.17 

$`21Q LOSS WILD-TYPE`
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW TCGA-4Z-AA7M 
       11.97        91.63       103.50       105.70         8.35        16.27 
TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W 
       44.94        16.83        16.77        17.16        34.98        27.62 
TCGA-4Z-AA7Y TCGA-4Z-AA81 TCGA-4Z-AA83 TCGA-4Z-AA84 TCGA-4Z-AA87 TCGA-4Z-AA89 
       49.12        41.75        66.54        15.12        47.80        33.83 
TCGA-BL-A13I TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J 
        7.33         6.74        12.39         6.58        13.15        19.04 
TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U 
       32.84        12.16        17.88        19.50         5.06        14.96 
TCGA-BT-A20W TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ 
        8.35        17.16        16.18        20.48         4.67        12.82 
TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 
        9.96        17.56        28.70        28.41         8.98         1.94 
TCGA-C4-A0F6 TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V 
       23.01         0.43         0.69        10.95        12.66        12.46 
TCGA-CF-A47W TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A8HX 
       12.10        12.26        13.12        12.00        12.10        11.34 
TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ 
       11.34        11.87        13.08         4.90         7.20         5.46 
TCGA-CU-A3YL TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 
       16.31        13.58        21.86         2.14        66.41        18.41 
TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF 
       19.00        16.70       130.88       112.44        16.14        17.62 
TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 
       15.62         1.81        10.59         7.79       123.85        87.32 
TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU 
        2.20        13.58         7.82        50.27        21.30        23.21 
TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 
        9.67        20.81        10.55       140.81        48.00        17.98 
TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 
       64.18        41.56        76.60        67.36        15.68        41.06 
TCGA-DK-AA6L TCGA-DK-AA6P TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA74 
       38.24        15.02       166.03        12.36        10.49        43.50 
TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ 
       10.62        15.35        38.83        24.66         0.10         0.49 
TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 
        2.24        16.70        17.39         0.56         0.66        14.56 
TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW 
       13.97        12.99        14.33         0.92         1.22        13.68 
TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A8O7 TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 
       14.07        12.95        15.32        14.37         8.09        32.02 
TCGA-FD-A3B4 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 
       16.77        33.04         4.01        12.62        22.52        27.98 
TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SP TCGA-FD-A3SQ 
       60.66        24.30        17.98        29.16        25.74        46.78 
TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U 
       19.79        12.85        22.98        27.35        14.96        20.91 
TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BX TCGA-FD-A5BZ 
       26.73        53.88        11.01        19.33         5.69        27.45 
TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S 
       18.08        58.92         2.70         7.10         6.28        13.35 
TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI 
       18.81         6.15        12.36         3.06         4.31         9.67 
TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A3EE 
       31.07         7.13        10.65        17.23         8.94         3.25 
TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES 
        6.48        61.94        15.95        26.93        35.24        33.01 
TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C TCGA-GC-A3BM 
        7.23        20.12        17.62        66.02         6.94        21.40 
TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC 
        2.24        15.81         4.50        15.91        14.07        17.75 
TCGA-GC-A4ZW TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS 
        0.49        13.91         7.73         2.10         3.12        20.98 
TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 
        2.20         7.36        10.92        11.31        11.31         7.63 
TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-AATO TCGA-GU-AATP TCGA-GU-AATQ 
       27.09        20.05         5.62        10.65        32.98         7.00 
TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QK 
       21.34        19.10        19.82        20.28         8.48        27.35 
TCGA-GV-A40E TCGA-GV-A40G TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A5NE 
        8.58        19.07         1.51        19.40        38.60         8.22 
TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A6FZ 
       25.02         3.45        21.24        27.68         9.07         1.81 
TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-LC-A66R TCGA-LT-A8JT TCGA-MV-A51V 
       15.42         6.38        11.80        15.32        21.07        13.48 
TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G0 
       12.23        16.67        14.24         1.84         3.75        12.43 
TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A8OC 
       31.56        17.62        37.05        22.68        86.83         3.58 
TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HD 
       17.82         4.54         1.64        45.04         6.58        97.45 
TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH 
      125.49        97.12         1.87        17.88        48.62        64.80 
TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9SZ 
        3.22        66.41        12.76        11.90        21.04        28.24 
TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T6 TCGA-XF-AAME 
       26.27        18.90         2.24        16.27         2.10        92.98 
TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMT 
       10.82        11.31        54.90        71.57        91.73         2.96 
TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN1 
        8.32         6.77        98.99        44.32        56.48        30.94 
TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 
       86.30        27.06        75.39         3.88        18.84         9.63 
TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 
        0.66        11.97        13.64         7.36        21.11        24.13 
TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-A9RF 
       30.28        27.19        28.41        74.56         3.48        52.73 
TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4V 
       52.60        82.49        47.84        19.69         8.61        59.38 
TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA58 TCGA-ZF-AA5N 
       63.02        38.73        35.41        19.40        47.15         5.52 
TCGA-ZF-AA5P 
       10.13 

  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
              0.46               0.10 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
            112.83             166.03 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
            14.005             16.180 
[1] "0.5 - 112.8 (14.0)" "0.1 - 166.0 (16.2)"
[1] "hr=" "1.3"
D79V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  21Q LOSS MUTATED         1       23        23       28
  21Q LOSS WILD-TYPE       3      101       104      101
D79V3, multiclass
           clus
vv          21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  STAGE I                  1                  3
  STAGE II                23                101
  STAGE III               23                104
  STAGE IV                28                101
[1] 4 2
[1] TRUE
[1] "dimension of contingency 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         21  38  10
  21Q LOSS WILD-TYPE      100 146  43
D79V4, multiclass
          clus
vv         21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  T0+T1+T2               21                100
  T3                     38                146
  T4                     10                 43
[1] 3 2
[1] TRUE
[1] "dimension of 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    40  17  11   0
  21Q LOSS WILD-TYPE 184  25  64   8
D79V5, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  N0               40                184
  N1               17                 25
  N2               11                 64
  N3                0                  8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V6, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED    32   2
  21Q LOSS WILD-TYPE 153   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     32    2
  21Q LOSS WILD-TYPE  153    8
   clus
vv  21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  0               32                153
  1                2                  8
[1] 2 2
[1] FALSE
D79V7, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED    22  54
  21Q LOSS WILD-TYPE  79 234
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     22   54
  21Q LOSS WILD-TYPE   79  234
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  FEMALE               22                 79
  MALE                 54                234
[1] 2 2
[1] FALSE
D79V8, continuous
D79V9, continuous
D79V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  21Q LOSS MUTATED       3                         5    66
  21Q LOSS WILD-TYPE    39                        16   245
D79V11, multiclass
                           clus
vv                          21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  ASIAN                                    3                 39
  BLACK OR AFRICAN AMERICAN                5                 16
  WHITE                                   66                245
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V12, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED     2  69
  21Q LOSS WILD-TYPE   7 283
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      2   69
  21Q LOSS WILD-TYPE    7  283
                        clus
vv                       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  7
  NOT HISPANIC OR LATINO               69                283
[1] 2 2
[1] FALSE

Clustering(80) Variable = 22Q LOSS MUTATION ANALYSIS
D80V1, survival
                    sevent
clus2                  0   1
  22Q LOSS MUTATED    86  65
  22Q LOSS WILD-TYPE 144  88
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
               151                232 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                65                 88 
$`22Q LOSS MUTATED`
TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA7W TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA86 
       16.27        16.77        27.62         0.62        41.75        10.22 
TCGA-4Z-AA87 TCGA-BL-A13J TCGA-BT-A20J TCGA-BT-A20R TCGA-BT-A42B TCGA-BT-A42C 
       47.80         2.66        19.04         5.06        17.56        28.70 
TCGA-BT-A42E TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A47X TCGA-CU-A0YN 
       24.26         8.98         1.94        23.01        12.62        12.92 
TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-DK-A1A7 TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 
        5.46         5.19        18.41         1.81        10.59         7.79 
TCGA-DK-A2I4 TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IT 
      123.85        13.58         7.82         8.22        17.72        21.30 
TCGA-DK-A3IV TCGA-DK-A3X2 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-AA6Q 
        9.67        17.98        67.36        15.68        41.06        13.58 
TCGA-DK-AA6S TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E5-A4TZ 
      166.03         8.65         7.53        12.03        43.59        15.35 
TCGA-E7-A5KE TCGA-E7-A6ME TCGA-E7-A7DV TCGA-E7-A7PW TCGA-FD-A3B3 TCGA-FD-A3B4 
        0.56        12.99         1.22        13.68        32.02        16.77 
TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3N5 TCGA-FD-A3SJ TCGA-FD-A3SN TCGA-FD-A3SO 
        8.94        33.04        22.52        24.30        29.16         5.52 
TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43U TCGA-FD-A43Y TCGA-FD-A5BV 
       19.79        12.85        22.98        20.91        15.58         5.36 
TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A62N TCGA-FD-A62P TCGA-FD-A6TB 
        8.25        27.45        18.08         2.70         6.28        18.81 
TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TK TCGA-FJ-A3Z7 
        6.15        12.69        12.36         2.27        10.85        31.07 
TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-GC-A3RC 
       17.23         6.48         7.23        20.12        17.62        15.91 
TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A6C6 
       24.92         8.94        13.91         7.73         2.10         2.20 
TCGA-GD-A76B TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-A766 
        7.36        11.31        11.31         7.63        20.05         5.62 
TCGA-GU-AATO TCGA-GU-AATP TCGA-GV-A3JX TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HQ 
       10.65        32.98        19.10        19.07        22.72        19.40 
TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ 
        8.22        25.02         3.45         9.07        11.70         1.74 
TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-LC-A66R TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN 
        1.81        15.42        15.32        13.48        12.23        16.67 
TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78N TCGA-UY-A8OB TCGA-UY-A9PA 
       31.56        17.62        37.05        86.83        65.75        35.24 
TCGA-UY-A9PB TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HF 
       29.56         4.54         1.64        45.04         6.58        97.12 
TCGA-XF-A8HG TCGA-XF-A9SG TCGA-XF-A9SJ TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY 
       15.35        48.62         3.22        11.90        23.64        21.04 
TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T3 TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAMT 
       28.24        26.27         2.24        10.82       110.60         2.96 
TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-YF-AA3L TCGA-YF-AA3M 
       44.32        56.48        61.45        86.30        11.97        13.64 
TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RM 
       21.86        28.41        74.56        13.41         3.48        47.84 
TCGA-ZF-A9RN TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4X TCGA-ZF-AA52 
       20.22        34.06        19.69         8.61        63.02        35.41 
TCGA-ZF-AA5H 
       19.17 

$`22Q LOSS WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        91.63       103.50       105.70         8.35 
TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7Y TCGA-4Z-AA82 
       44.94        16.83        17.16        34.98        49.12        51.16 
TCGA-4Z-AA83 TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A3JM 
       66.54        15.12        33.83        40.08         7.33         6.74 
TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P 
       12.39         6.58        13.15        32.84        12.16        17.88 
TCGA-BT-A20Q TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X 
       19.50        14.89        14.96         5.06         8.35         8.25 
TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK 
       17.16        16.18        20.48         4.67        12.82         9.96 
TCGA-BT-A42F TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T 
       28.41         0.46         0.43         0.69        10.95        12.66 
TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 
       12.46        12.10        12.26        13.12        12.00        12.10 
TCGA-CF-A8HX TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YO TCGA-CU-A0YR 
       11.34        11.34        11.87        13.08         4.90         7.20 
TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 
       16.31         1.84        13.58        21.86         2.14        66.41 
TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF 
       19.00        16.70       130.88       112.44        16.14        17.62 
TCGA-DK-A1AG TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IS TCGA-DK-A3IU TCGA-DK-A3WW 
       15.62        87.32         2.20        50.27        23.21        20.81 
TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 
       10.55       140.81        48.00        64.18        41.56        76.60 
TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6P TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA71 
       30.67        38.24        15.02        12.36        10.49        13.64 
TCGA-DK-AA74 TCGA-DK-AA77 TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ 
       43.50        10.62        38.83        24.66         0.10         0.49 
TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 
        2.24        16.70        17.39         0.66        14.56        13.97 
TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A8O7 TCGA-E7-A97P 
       14.33         0.92        14.07        12.95        15.32        14.37 
TCGA-E7-A97Q TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SL 
        8.09         4.01        12.62        27.98        60.66        23.41 
TCGA-FD-A3SM TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43X 
       17.98        25.74        46.78        27.35        14.96         3.62 
TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BX TCGA-FD-A5C1 
       26.73        53.88        11.01        19.33         5.69        58.92 
TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI 
        7.10        13.35        62.86         3.06         4.31         9.67 
TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EF TCGA-G2-A2EJ 
        7.13        10.65         8.94         3.25        61.94        30.61 
TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-AA3B TCGA-G2-AA3C 
       15.95        26.93        35.24        33.01        66.02         6.94 
TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB 
       64.44        19.46        21.40         2.24        15.81         4.50 
TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A4ZW TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GU-A42P 
       14.07        17.75         0.49         3.12        20.98        10.92 
TCGA-GU-A763 TCGA-GU-A767 TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JZ 
       27.09         4.73         7.00        14.27        21.34        19.82 
TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-H4-A2HO 
       20.28         8.48        10.59        27.35         8.58         1.51 
TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC 
       38.60         3.06         9.01        21.24         2.76         9.14 
TCGA-K4-A54R TCGA-K4-A83P TCGA-K4-AAQO TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-R3-A69X 
       27.68         6.38        11.80        15.58        21.07        14.24 
TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-UY-A78M TCGA-UY-A78O TCGA-UY-A78P 
        1.84         3.75        12.43        22.68        76.01        67.79 
TCGA-UY-A8OC TCGA-UY-A8OD TCGA-UY-A9PD TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HH 
        3.58       112.83        17.82        97.45       125.49         1.87 
TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9T2 
       17.88        64.80        79.66        66.41        12.76        18.90 
TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMH 
       16.27        66.64         2.10        13.74        92.98        11.31 
TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMW TCGA-XF-AAMX 
       54.90         7.63        71.57        91.73         8.32         6.77 
TCGA-XF-AAMY TCGA-XF-AAN1 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-XF-AAN8 
       98.99        30.94        27.06        75.39        18.81         3.88 
TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R2 
       18.84         9.63         0.66        18.64         7.36        21.11 
TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL 
       24.13        30.28        27.19        52.73        52.60        82.49 
TCGA-ZF-AA4N TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA51 TCGA-ZF-AA53 TCGA-ZF-AA54 
        2.89        59.38        60.16        38.73        57.90        19.40 
TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5N TCGA-ZF-AA5P 
        8.52        47.15         5.52        10.13 

  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
              0.56               0.10 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
            166.03             140.81 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
             15.58              15.88 
[1] "0.6 - 166.0 (15.6)" "0.1 - 140.8 (15.9)"
[1] "hr=" "1.3"
D80V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  22Q LOSS MUTATED         0       40        49       63
  22Q LOSS WILD-TYPE       4       84        78       66
D80V3, multiclass
           clus
vv          22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  STAGE I                  0                  4
  STAGE II                40                 84
  STAGE III               49                 78
  STAGE IV                63                 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                 T0+T1+T2  T3  T4
  22Q LOSS MUTATED         38  76  25
  22Q LOSS WILD-TYPE       83 108  28
D80V4, multiclass
          clus
vv         22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  T0+T1+T2               38                 83
  T3                     76                108
  T4                     25                 28
[1] 3 2
[1] TRUE
[1] "dimension of 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    75  18  41   3
  22Q LOSS WILD-TYPE 149  24  34   5
D80V5, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  N0               75                149
  N1               18                 24
  N2               41                 34
  N3                3                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V6, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED    53   3
  22Q LOSS WILD-TYPE 132   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     53    3
  22Q LOSS WILD-TYPE  132    7
   clus
vv  22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  0               53                132
  1                3                  7
[1] 2 2
[1] FALSE
D80V7, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED    40 112
  22Q LOSS WILD-TYPE  61 176
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     40  112
  22Q LOSS WILD-TYPE   61  176
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  FEMALE               40                 61
  MALE                112                176
[1] 2 2
[1] FALSE
D80V8, continuous
D80V9, continuous
D80V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  22Q LOSS MUTATED       8                         8   128
  22Q LOSS WILD-TYPE    34                        13   183
D80V11, multiclass
                           clus
vv                          22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  ASIAN                                    8                 34
  BLACK OR AFRICAN AMERICAN                8                 13
  WHITE                                  128                183
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V12, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED     7 134
  22Q LOSS WILD-TYPE   2 218
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      7  134
  22Q LOSS WILD-TYPE    2  218
                        clus
vv                       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    7                  2
  NOT HISPANIC OR LATINO              134                218
[1] 2 2
[1] FALSE

Clustering(81) Variable = XP LOSS MUTATION ANALYSIS
D81V1, survival
                   sevent
clus2                 0   1
  XP LOSS MUTATED    39  26
  XP LOSS WILD-TYPE 191 127
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               65               318 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               26               127 
$`XP LOSS MUTATED`
TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW TCGA-4Z-AA7O TCGA-4Z-AA84 TCGA-BT-A20T 
      103.50       105.70         8.35        16.83        15.12        14.89 
TCGA-BT-A3PH TCGA-BT-A42B TCGA-CF-A27C TCGA-CF-A47X TCGA-CF-A7I0 TCGA-CU-A0YN 
        4.67        17.56         0.69        12.62        12.10        12.92 
TCGA-CU-A3QU TCGA-DK-A1A5 TCGA-DK-A1AB TCGA-DK-A2I6 TCGA-DK-A3IS TCGA-DK-A3IT 
        5.19         2.14        16.70        87.32        50.27        21.30 
TCGA-DK-A3IV TCGA-DK-A6B5 TCGA-DK-AA6L TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6W 
        9.67        41.06        38.24        13.58        12.36         8.65 
TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E7-A3X6 TCGA-E7-A7DU TCGA-FD-A3B4 TCGA-FD-A3B6 
       12.03        43.59        24.66         0.92        16.77        33.04 
TCGA-FD-A3SN TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43Y TCGA-FD-A5BY TCGA-FD-A62N 
       29.16        19.79        12.85        15.58         8.25         2.70 
TCGA-FD-A6TC TCGA-FD-A6TF TCGA-G2-A2EL TCGA-G2-A3IB TCGA-G2-A3VY TCGA-G2-AA3F 
        6.15         2.27        26.93         7.23        17.62        19.46 
TCGA-GC-A4ZW TCGA-GD-A6C6 TCGA-GV-A3JX TCGA-GV-A40G TCGA-HQ-A2OF TCGA-K4-A3WV 
        0.49         2.20        19.10        19.07         3.06        21.24 
TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-AAQO TCGA-LT-A5Z6 TCGA-PQ-A6FI TCGA-S5-A6DX 
        1.74         1.81        11.80        15.58        12.23         1.84 
TCGA-S5-AA26 TCGA-UY-A78P TCGA-UY-A8OD TCGA-XF-A8HF TCGA-XF-A9SZ TCGA-XF-AAML 
        3.75        67.79       112.83        97.12        28.24         7.63 
TCGA-XF-AAMT TCGA-ZF-A9R9 TCGA-ZF-A9RL TCGA-ZF-AA4R TCGA-ZF-AA4U 
        2.96        28.41        82.49        34.06         8.61 

$`XP LOSS WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7Q 
       22.29        11.97        91.63        16.27        44.94        16.77 
TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 
       17.16        34.98        27.62        49.12         0.62        41.75 
TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A0C8 
       51.16        66.54        10.22        47.80        33.83        40.08 
TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX 
        7.33         2.66         6.74        12.39         6.58        13.15 
TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R 
       19.04        32.84        12.16        17.88        19.50         5.06 
TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB 
       14.96         5.06         8.35         8.25        17.16        16.18 
TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F 
       20.48        12.82         9.96        28.70        24.26        28.41 
TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A47S 
        8.98         1.94        23.01         0.46         0.43        10.95 
TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA 
       12.66        12.46        12.10        12.26        13.12        12.00 
TCGA-CF-A8HX TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YO TCGA-CU-A0YR 
       11.34        11.34        11.87        13.08         4.90         7.20 
TCGA-CU-A3KJ TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A6 
        5.46        16.31         1.84        13.58        21.86        66.41 
TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF 
       18.41        19.00       130.88       112.44        16.14        17.62 
TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IK 
       15.62         1.81        10.59         7.79       123.85         2.20 
TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IU TCGA-DK-A3WW 
       13.58         7.82         8.22        17.72        23.21        20.81 
TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW 
       10.55       140.81        48.00        17.98        64.18        41.56 
TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B6 TCGA-DK-AA6P TCGA-DK-AA6S 
       76.60        67.36        15.68        30.67        15.02       166.03 
TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA77 TCGA-E5-A4TZ 
       10.49         7.53        13.64        43.50        10.62        15.35 
TCGA-E5-A4U1 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 
       38.83         0.10         0.49         2.24        16.70        17.39 
TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF 
        0.56         0.66        14.56        13.97        12.99        14.33 
TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A8O7 TCGA-E7-A97P 
        1.22        13.68        14.07        12.95        15.32        14.37 
TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B5 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 
        8.09        32.02         8.94         4.01        12.62        22.52 
TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SO 
       27.98        60.66        24.30        23.41        17.98         5.52 
TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U 
       25.74        46.78        22.98        27.35        14.96        20.91 
TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV 
        3.62        26.73        53.88        11.01        19.33         5.36 
TCGA-FD-A5BX TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62O TCGA-FD-A62P 
        5.69        27.45        18.08        58.92         7.10         6.28 
TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TG 
       13.35        62.86        18.81        12.69        12.36         3.06 
TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE 
        4.31         9.67        10.85        31.07         7.13        10.65 
TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ 
       17.23         8.94         3.25         6.48        61.94        30.61 
TCGA-G2-A2EK TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3C 
       15.95        35.24        33.01        20.12        66.02         6.94 
TCGA-G2-AA3D TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC 
       64.44        21.40         2.24        15.81         4.50        15.91 
TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 
       14.07        17.75        24.92         8.94        13.91         7.73 
TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q 
        2.10         3.12        20.98         7.36        10.92        11.31 
TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 
       11.31         7.63        27.09        20.05         5.62         4.73 
TCGA-GU-AATO TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JZ 
       10.65        32.98         7.00        14.27        21.34        19.82 
TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A6ZA 
       20.28         8.48        10.59        27.35         8.58        22.72 
TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS 
        1.51        19.40        38.60         9.01         8.22        25.02 
TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RI 
        3.45         2.76         9.14        27.68         9.07        11.70 
TCGA-K4-A6MB TCGA-K4-A83P TCGA-LC-A66R TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FN 
       15.42         6.38        15.32        21.07        13.48        16.67 
TCGA-R3-A69X TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M 
       14.24        12.43        31.56        17.62        37.05        22.68 
TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A9PA TCGA-UY-A9PB 
       86.83        76.01        65.75         3.58        35.24        29.56 
TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HD 
       17.82         4.54         1.64        45.04         6.58        97.45 
TCGA-XF-A8HE TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH 
      125.49        15.35         1.87        17.88        48.62        64.80 
TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX 
       79.66         3.22        66.41        12.76        11.90        23.64 
TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 
       21.04        26.27        18.90         2.24        16.27        66.64 
TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAMH 
        2.10        13.74        92.98        10.82       110.60        11.31 
TCGA-XF-AAMJ TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMY 
       54.90        71.57        91.73         8.32         6.77        98.99 
TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN4 
       44.32        56.48        30.94        61.45        86.30        27.06 
TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC 
       75.39        18.81         3.88        18.84         9.63         0.66 
TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 
       11.97        13.64        18.64         7.36        21.11        24.13 
TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE 
       30.28        27.19        21.86        74.56        13.41         3.48 
TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4T 
       52.73        52.60        47.84        20.22         2.89        19.69 
TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA53 
       59.38        60.16        63.02        38.73        35.41        57.90 
TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
       19.40         8.52        47.15        19.17         5.52        10.13 

  XP LOSS MUTATED XP LOSS WILD-TYPE 
             0.49              0.10 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
           112.83            166.03 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
           14.890            16.045 
[1] "0.5 - 112.8 (14.9)" "0.1 - 166.0 (16.0)"
[1] "hr=" "1.1"
D81V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  XP LOSS MUTATED         0       25        20       20
  XP LOSS WILD-TYPE       4       99       107      109
D81V3, multiclass
           clus
vv          XP LOSS MUTATED XP LOSS WILD-TYPE
  STAGE I                 0                 4
  STAGE II               25                99
  STAGE III              20               107
  STAGE IV               20               109
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1+T2  T3  T4
  XP LOSS MUTATED         21  29   9
  XP LOSS WILD-TYPE      100 155  44
D81V4, multiclass
          clus
vv         XP LOSS MUTATED XP LOSS WILD-TYPE
  T0+T1+T2              21               100
  T3                    29               155
  T4                     9                44
[1] 3 2
[1] TRUE
[1] "dimension of 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    40   9  10   1
  XP LOSS WILD-TYPE 184  33  65   7
D81V5, multiclass
    clus
vv   XP LOSS MUTATED XP LOSS WILD-TYPE
  N0              40               184
  N1               9                33
  N2              10                65
  N3               1                 7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D81V6, binary
                   cls
clus                  0   1
  XP LOSS MUTATED    29   2
  XP LOSS WILD-TYPE 156   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED     29    2
  XP LOSS WILD-TYPE  156    8
   clus
vv  XP LOSS MUTATED XP LOSS WILD-TYPE
  0              29               156
  1               2                 8
[1] 2 2
[1] FALSE
D81V7, binary
                   cls
clus                  0   1
  XP LOSS MUTATED    16  51
  XP LOSS WILD-TYPE  85 237
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED     16   51
  XP LOSS WILD-TYPE   85  237
        clus
vv       XP LOSS MUTATED XP LOSS WILD-TYPE
  FEMALE              16                85
  MALE                51               237
[1] 2 2
[1] FALSE
D81V8, continuous
D81V9, continuous
D81V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  XP LOSS MUTATED       7                         5    53
  XP LOSS WILD-TYPE    35                        16   258
D81V11, multiclass
                           clus
vv                          XP LOSS MUTATED XP LOSS WILD-TYPE
  ASIAN                                   7                35
  BLACK OR AFRICAN AMERICAN               5                16
  WHITE                                  53               258
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D81V12, binary
                   cls
clus                  0   1
  XP LOSS MUTATED     2  61
  XP LOSS WILD-TYPE   7 291
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED      2   61
  XP LOSS WILD-TYPE    7  291
                        clus
vv                       XP LOSS MUTATED XP LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                 7
  NOT HISPANIC OR LATINO              61               291
[1] 2 2
[1] FALSE

Clustering(82) Variable = XQ LOSS MUTATION ANALYSIS
D82V1, survival
                   sevent
clus2                 0   1
  XQ LOSS MUTATED    49  27
  XQ LOSS WILD-TYPE 181 126
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               76               307 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               27               126 
$`XQ LOSS MUTATED`
TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW TCGA-4Z-AA7O TCGA-4Z-AA80 TCGA-4Z-AA84 
      103.50       105.70         8.35        16.83         0.62        15.12 
TCGA-BT-A20T TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A42B TCGA-CF-A27C TCGA-CF-A47X 
       14.89        16.18         4.67        17.56         0.69        12.62 
TCGA-CF-A7I0 TCGA-CU-A3QU TCGA-DK-A1A5 TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A2I6 
       12.10         5.19         2.14        16.70       130.88        87.32 
TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IV TCGA-DK-A6B5 TCGA-DK-AA6Q TCGA-DK-AA6T 
       50.27        21.30         9.67        41.06        13.58        12.36 
TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E7-A3X6 TCGA-E7-A7DU 
        8.65        13.64        12.03        43.59        24.66         0.92 
TCGA-E7-A85H TCGA-FD-A3B4 TCGA-FD-A3SN TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A5BY 
       12.95        16.77        29.16        19.79        12.85         8.25 
TCGA-FD-A62N TCGA-FJ-A3Z7 TCGA-FT-A3EE TCGA-G2-A2EL TCGA-G2-A3IB TCGA-G2-AA3B 
        2.70        31.07         3.25        26.93         7.23        66.02 
TCGA-G2-AA3F TCGA-GC-A4ZW TCGA-GD-A6C6 TCGA-GU-A42P TCGA-GV-A3JX TCGA-GV-A3QI 
       19.46         0.49         2.20        10.92        19.10        10.59 
TCGA-GV-A40G TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-K4-A3WV TCGA-K4-A54R TCGA-K4-A5RJ 
       19.07        38.60         3.06        21.24        27.68         1.74 
TCGA-K4-A6FZ TCGA-K4-AAQO TCGA-LT-A5Z6 TCGA-PQ-A6FI TCGA-S5-A6DX TCGA-S5-AA26 
        1.81        11.80        15.58        12.23         1.84         3.75 
TCGA-UY-A78P TCGA-UY-A8OD TCGA-UY-A9PD TCGA-UY-A9PF TCGA-XF-A8HF TCGA-XF-A8HI 
       67.79       112.83        17.82         1.64        97.12        17.88 
TCGA-XF-A9SZ TCGA-XF-AAMG TCGA-XF-AAMT TCGA-XF-AAN7 TCGA-YF-AA3L TCGA-ZF-A9R9 
       28.24       110.60         2.96        18.81        11.97        28.41 
TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-AA4R TCGA-ZF-AA4U 
       82.49        47.84        34.06         8.61 

$`XQ LOSS WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7Q 
       22.29        11.97        91.63        16.27        44.94        16.77 
TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA81 TCGA-4Z-AA82 
       17.16        34.98        27.62        49.12        41.75        51.16 
TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I 
       66.54        10.22        47.80        33.83        40.08         7.33 
TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J 
        2.66         6.74        12.39         6.58        13.15        19.04 
TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U 
       32.84        12.16        17.88        19.50         5.06        14.96 
TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LD TCGA-BT-A3PJ 
        5.06         8.35         8.25        17.16        20.48        12.82 
TCGA-BT-A3PK TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 
        9.96        28.70        24.26        28.41         8.98         1.94 
TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V 
       23.01         0.46         0.43        10.95        12.66        12.46 
TCGA-CF-A47W TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A8HX TCGA-CF-A8HY 
       12.10        12.26        13.12        12.00        11.34        11.34 
TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ 
       11.87        13.08        12.92         4.90         7.20         5.46 
TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 
       16.31         1.84        13.58        21.86        66.41        18.41 
TCGA-DK-A1AA TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX 
       19.00       112.44        16.14        17.62        15.62         1.81 
TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM 
       10.59         7.79       123.85         2.20        13.58         7.82 
TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IU TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY 
        8.22        17.72        23.21        20.81        10.55       140.81 
TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 
       48.00        17.98        64.18        41.56        76.60        67.36 
TCGA-DK-A6B2 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6P TCGA-DK-AA6S TCGA-DK-AA6U 
       15.68        30.67        38.24        15.02       166.03        10.49 
TCGA-DK-AA6X TCGA-DK-AA74 TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3Y1 
        7.53        43.50        10.62        15.35        38.83         0.10 
TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF 
        0.49         2.24        16.70        17.39         0.56         0.66 
TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DV TCGA-E7-A7PW 
       14.56        13.97        12.99        14.33         1.22        13.68 
TCGA-E7-A7XN TCGA-E7-A8O7 TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B5 
       14.07        15.32        14.37         8.09        32.02         8.94 
TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA 
       33.04         4.01        12.62        22.52        27.98        60.66 
TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ 
       24.30        23.41        17.98         5.52        25.74        46.78 
TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A43Y 
       22.98        27.35        14.96        20.91         3.62        15.58 
TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX 
       26.73        53.88        11.01        19.33         5.36         5.69 
TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S 
       27.45        18.08        58.92         7.10         6.28        13.35 
TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF 
       62.86        18.81         6.15        12.69        12.36         2.27 
TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE 
        3.06         4.31         9.67        10.85         7.13        10.65 
TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK 
       17.23         8.94         6.48        61.94        30.61        15.95 
TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3C TCGA-G2-AA3D 
       35.24        33.01        20.12        17.62         6.94        64.44 
TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD 
       21.40         2.24        15.81         4.50        15.91        14.07 
TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP 
       17.75        24.92         8.94        13.91         7.73         2.10 
TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A76B TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 
        3.12        20.98         7.36        11.31        11.31         7.63 
TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATP 
       27.09        20.05         5.62         4.73        10.65        32.98 
TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH 
        7.00        14.27        21.34        19.82        20.28         8.48 
TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A5ND 
       27.35         8.58        22.72         1.51        19.40         9.01 
TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A5RH 
        8.22        25.02         3.45         2.76         9.14         9.07 
TCGA-K4-A5RI TCGA-K4-A6MB TCGA-K4-A83P TCGA-LC-A66R TCGA-LT-A8JT TCGA-MV-A51V 
       11.70        15.42         6.38        15.32        21.07        13.48 
TCGA-PQ-A6FN TCGA-R3-A69X TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L 
       16.67        14.24        12.43        31.56        17.62        37.05 
TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A9PA 
       22.68        86.83        76.01        65.75         3.58        35.24 
TCGA-UY-A9PB TCGA-UY-A9PE TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HE 
       29.56         4.54        45.04         6.58        97.45       125.49 
TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ 
       15.35         1.87        48.62        64.80        79.66         3.22 
TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9T0 
       66.41        12.76        11.90        23.64        21.04        26.27 
TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 
       18.90         2.24        16.27        66.64         2.10        13.74 
TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ 
       92.98        10.82        11.31        54.90         7.63        71.57 
TCGA-XF-AAMR TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN0 
       91.73         8.32         6.77        98.99        44.32        56.48 
TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN8 
       30.94        61.45        86.30        27.06        75.39         3.88 
TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R1 
       18.84         9.63         0.66        13.64        18.64         7.36 
TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9RC 
       21.11        24.13        30.28        27.19        21.86        74.56 
TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RN TCGA-ZF-AA4N 
       13.41         3.48        52.73        52.60        20.22         2.89 
TCGA-ZF-AA4T TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 
       19.69        59.38        60.16        63.02        38.73        35.41 
TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N 
       57.90        19.40         8.52        47.15        19.17         5.52 
TCGA-ZF-AA5P 
       10.13 

  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
             0.49              0.10 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
           130.88            166.03 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
            15.35             15.81 
[1] "0.5 - 130.9 (15.3)" "0.1 - 166.0 (15.8)"
[1] "hr=" "1.1"
D82V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  XQ LOSS MUTATED         0       28        24       24
  XQ LOSS WILD-TYPE       4       96       103      105
D82V3, multiclass
           clus
vv          XQ LOSS MUTATED XQ LOSS WILD-TYPE
  STAGE I                 0                 4
  STAGE II               28                96
  STAGE III              24               103
  STAGE IV               24               105
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1+T2  T3  T4
  XQ LOSS MUTATED         27  34  10
  XQ LOSS WILD-TYPE       94 150  43
D82V4, multiclass
          clus
vv         XQ LOSS MUTATED XQ LOSS WILD-TYPE
  T0+T1+T2              27                94
  T3                    34               150
  T4                    10                43
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  XQ LOSS MUTATED    48  10  13   1
  XQ LOSS WILD-TYPE 176  32  62   7
D82V5, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  N0              48               176
  N1              10                32
  N2              13                62
  N3               1                 7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D82V6, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED    35   1
  XQ LOSS WILD-TYPE 150   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     35    1
  XQ LOSS WILD-TYPE  150    9
   clus
vv  XQ LOSS MUTATED XQ LOSS WILD-TYPE
  0              35               150
  1               1                 9
[1] 2 2
[1] FALSE
D82V7, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED    19  59
  XQ LOSS WILD-TYPE  82 229
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     19   59
  XQ LOSS WILD-TYPE   82  229
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  FEMALE              19                82
  MALE                59               229
[1] 2 2
[1] FALSE
D82V8, continuous
D82V9, continuous
D82V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  XQ LOSS MUTATED       7                         5    62
  XQ LOSS WILD-TYPE    35                        16   249
D82V11, multiclass
                           clus
vv                          XQ LOSS MUTATED XQ LOSS WILD-TYPE
  ASIAN                                   7                35
  BLACK OR AFRICAN AMERICAN               5                16
  WHITE                                  62               249
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D82V12, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED     4  67
  XQ LOSS WILD-TYPE   5 285
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      4   67
  XQ LOSS WILD-TYPE    5  285
                        clus
vv                       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  HISPANIC OR LATINO                   4                 5
  NOT HISPANIC OR LATINO              67               285
[1] 2 2
[1] FALSE
